/* asn2gnbk.c * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information (NCBI) * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government do not place any restriction on its use or reproduction. * We would, however, appreciate having the NCBI and the author cited in * any work or product based on this material * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * =========================================================================== * * File Name: asn2gnbk.c * * Author: Karl Sirotkin, Tom Madden, Tatiana Tatusov, Jonathan Kans * * Version Creation Date: 10/21/98 * * $Revision: 6.329 $ * * File Description: New GenBank flatfile generator - work in progress * * Modifications: * -------------------------------------------------------------------------- * ========================================================================== */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #ifdef WIN_MAC #if __profile__ #include #endif #endif #define ASN2FF_EMBL_MAX 78 #define ASN2FF_GB_MAX 79 #define SEQID_MAX_LEN 41 #define TILDE_IGNORE 0 #define TILDE_TO_SPACES 1 #define TILDE_EXPAND 2 #define TILDE_OLD_EXPAND 3 /* flags set by mode to customize behavior */ typedef struct asn2gbflags { Boolean suppressLocalID; Boolean validateFeats; Boolean ignorePatPubs; Boolean dropShortAA; Boolean avoidLocusColl; Boolean iupacaaOnly; Boolean dropBadCitGens; Boolean noAffilOnUnpub; Boolean dropIllegalQuals; Boolean checkQualSyntax; Boolean needRequiredQuals; Boolean needOrganismQual; Boolean needAtLeastOneRef; Boolean citArtIsoJta; Boolean dropBadDbxref; Boolean useEmblMolType; Boolean hideBankItComment; Boolean checkCDSproductID; Boolean forGbRelease; } Asn2gbFlags, PNTR Asn2gbFlagsPtr; /* internal Asn2gbSect structure has fields on top of Asn2gbSect fields */ typedef struct int_Asn2gbSect { Asn2gbSect asp; SeqPortPtr spp; } IntAsn2gbSect, PNTR IntAsn2gbSectPtr; /* internal asn2gbjob structure has fields on top of Asn2gbJob fields */ typedef struct int_asn2gb_job { Asn2gbJob ajp; FmtType format; Asn2gbFlags flags; Boolean showFarTransl; Boolean transientSeqPort; Boolean masterStyle; Boolean newSourceOrg; ValNodePtr lockedBspList; } IntAsn2gbJob, PNTR IntAsn2gbJobPtr; /* structure for storing working parameters while building asn2gb_job structure */ typedef struct asn2gbwork { IntAsn2gbJobPtr ajp; Uint2 entityID; FmtType format; StlType style; ValNodePtr pubhead; /* for collecting publications */ ValNodePtr srchead; /* for collecting biosources */ /* linked lists of paragraphs, sections, blocks */ ValNodePtr sectionList; ValNodePtr blockList; /* reset for each new section */ /* most recent node of linked lists, for quickly adding next node */ ValNodePtr lastsection; ValNodePtr lastblock; /* reset for each new section */ Int4 currsection; /* section fields needed for populating blocks */ Asn2gbSectPtr asp; BioseqPtr target; BioseqPtr parent; BioseqPtr bsp; SeqLocPtr slp; Uint2 seg; Int4 numsegs; Int4 from; Int4 to; Boolean contig; Boolean showconfeats; Boolean showconsource; Boolean citSubsFirst; Boolean hideGeneFeats; Boolean newLocusLine; Boolean isGPS; Boolean copyGpsCdsUp; Boolean copyGpsGeneDown; Char basename [SEQID_MAX_LEN]; SeqFeatPtr lastsfp; SeqAnnotPtr lastsap; Int4 lastleft; Int4 lastright; Boolean firstfeat; SeqSubmitPtr ssp; Boolean hup; Boolean failed; } Asn2gbWork, PNTR Asn2gbWorkPtr; /* array for assigning biosource and feature data fields to qualifiers */ /* should be allocated to MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR) */ typedef union qualval { CharPtr str; Boolean bool; Int4 num; ValNodePtr vnp; GBQualPtr gbq; OrgModPtr omp; SubSourcePtr ssp; CodeBreakPtr cbp; SeqLocPtr slp; SeqIdPtr sip; tRNAPtr trp; UserObjectPtr uop; } QualVal, PNTR QualValPtr; /* structure passed to individual paragraph format functions */ typedef struct asn2gbformat { IntAsn2gbJobPtr ajp; Asn2gbSectPtr asp; QualValPtr qvp; FmtType format; } Asn2gbFormat, PNTR Asn2gbFormatPtr; /* Seq-hist replacedBy is preformatted into string field, */ /* then comment descriptors, Map location:, and Region:, */ /* then comment features, finally HTGS */ typedef struct comment_block { ASN2GB_BASE_BLOCK Boolean first; } CommentBlock, PNTR CommentBlockPtr; /* internal reference block has fields on top of RefBlock fields */ typedef struct int_ref_block { RefBlock rb; DatePtr date; /* internal sorting use only */ SeqLocPtr loc; /* final location on target bioseq */ CharPtr authstr; /* author string */ Uint2 index; /* index if feature on target bioseq */ Boolean justuids; /* gibb pub with uids and Figure, etc. */ CharPtr fig; /* figure string from equivalent gibb pub */ CharPtr maploc; /* maploc string from equivalent gibb pub */ Boolean poly_a; /* poly_a field from equivalent gibb pub */ } IntRefBlock, PNTR IntRefBlockPtr; /* internal source block has fields on top of BaseBlock fields */ typedef struct int_src_block { BaseBlock bb; Boolean is_descriptor; Boolean is_focus; Boolean is_synthetic; BioSourcePtr biop; Uint4 orghash; Uint4 modhash; Uint4 subhash; Uint4 xrfhash; SeqLocPtr loc; /* final location on target bioseq */ CharPtr taxname; CharPtr comment; OrgModPtr omp; SubSourcePtr ssp; ValNodePtr vnp; Int4 left; Int4 right; } IntSrcBlock, PNTR IntSrcBlockPtr; /* internal feature block has fields on top of FeatBlock fields */ typedef struct int_feat_block { FeatBlock fb; Boolean mapToNuc; Boolean mapToProt; Boolean mapToGen; Boolean mapToMrna; Boolean isCDS; /* set if using IntCdsBlock */ Boolean firstfeat; } IntFeatBlock, PNTR IntFeatBlockPtr; /* internal cds block has fields on top of IntFeatBlock fields */ typedef struct int_cds_block { IntFeatBlock ifb; FeatBlock fb; CharPtr fig; /* figure string from pub */ CharPtr maploc; /* maploc string from pub */ } IntCdsBlock, PNTR IntCdsBlockPtr; /* enumerated qualifier category definitions */ typedef enum { Qual_class_ignore = 0, Qual_class_string, Qual_class_sgml, Qual_class_boolean, Qual_class_int, Qual_class_evidence, Qual_class_valnode, Qual_class_EC_valnode, Qual_class_xtraprds, Qual_class_quote, Qual_class_EC_quote, Qual_class_noquote, Qual_class_label, Qual_class_number, Qual_class_paren, Qual_class_region, Qual_class_replace, Qual_class_consplice, Qual_class_site, Qual_class_L_R_B, Qual_class_rpt, Qual_class_organelle, Qual_class_orgmod, Qual_class_subsource, Qual_class_code_break, Qual_class_anti_codon, Qual_class_codon, Qual_class_method, Qual_class_pubset, Qual_class_db_xref, Qual_class_seq_id, Qual_class_seq_loc, Qual_class_its, Qual_class_sec_str, Qual_class_trna_codons, Qual_class_translation, Qual_class_protnames, Qual_class_illegal, Qual_class_note, Qual_class_rpt_unit, Qual_class_product, Qual_class_model_ev } QualType; /* source 'feature' */ /* some qualifiers will require additional content verification not explicitly indicated by the class type */ typedef enum { SCQUAL_acronym = 1, SCQUAL_anamorph, SCQUAL_authority, SCQUAL_biotype, SCQUAL_biovar, SCQUAL_breed, SCQUAL_cell_line, SCQUAL_cell_type, SCQUAL_chemovar, SCQUAL_chromosome, SCQUAL_citation, SCQUAL_clone, SCQUAL_clone_lib, SCQUAL_common, SCQUAL_common_name, SCQUAL_country, SCQUAL_cultivar, SCQUAL_db_xref, SCQUAL_dev_stage, SCQUAL_dosage, SCQUAL_ecotype, SCQUAL_endogenous_virus_name, SCQUAL_environmental_sample, SCQUAL_extrachrom, SCQUAL_focus, SCQUAL_forma, SCQUAL_forma_specialis, SCQUAL_frequency, SCQUAL_genotype, SCQUAL_germline, SCQUAL_group, SCQUAL_haplotype, SCQUAL_ins_seq_name, SCQUAL_isolate, SCQUAL_isolation_source, SCQUAL_lab_host, SCQUAL_label, SCQUAL_macronuclear, SCQUAL_map, SCQUAL_note, SCQUAL_old_lineage, SCQUAL_old_name, SCQUAL_organism, SCQUAL_organelle, SCQUAL_orgmod_note, SCQUAL_pathovar, SCQUAL_plasmid_name, SCQUAL_plastid_name, SCQUAL_pop_variant, SCQUAL_rearranged, SCQUAL_segment, SCQUAL_seqfeat_note, SCQUAL_sequenced_mol, SCQUAL_serogroup, SCQUAL_serotype, SCQUAL_serovar, SCQUAL_sex, SCQUAL_spec_or_nat_host, SCQUAL_specimen_voucher, SCQUAL_strain, SCQUAL_sub_clone, SCQUAL_sub_group, SCQUAL_sub_species, SCQUAL_sub_strain, SCQUAL_sub_type, SCQUAL_subsource_note, SCQUAL_synonym, SCQUAL_teleomorph, SCQUAL_tissue_lib, SCQUAL_tissue_type, SCQUAL_transgenic, SCQUAL_transposon_name, SCQUAL_type, SCQUAL_unstructured, SCQUAL_usedin, SCQUAL_variety, SCQUAL_zero_orgmod, SCQUAL_one_orgmod, SCQUAL_zero_subsrc, ASN2GNBK_TOTAL_SOURCE } SourceType; /* ordering arrays for qualifiers and note components */ static Uint1 source_qual_order [] = { SCQUAL_organism, SCQUAL_organelle, SCQUAL_strain, SCQUAL_sub_strain, SCQUAL_variety, SCQUAL_serotype, SCQUAL_serovar, SCQUAL_cultivar, SCQUAL_isolate, SCQUAL_isolation_source, SCQUAL_spec_or_nat_host, SCQUAL_sub_species, SCQUAL_specimen_voucher, SCQUAL_db_xref, SCQUAL_chromosome, SCQUAL_map, SCQUAL_clone, SCQUAL_sub_clone, SCQUAL_haplotype, SCQUAL_sex, SCQUAL_cell_line, SCQUAL_cell_type, SCQUAL_tissue_type, SCQUAL_clone_lib, SCQUAL_dev_stage, SCQUAL_frequency, SCQUAL_germline, SCQUAL_rearranged, SCQUAL_transgenic, SCQUAL_environmental_sample, SCQUAL_lab_host, SCQUAL_pop_variant, SCQUAL_tissue_lib, SCQUAL_plasmid_name, SCQUAL_transposon_name, SCQUAL_ins_seq_name, SCQUAL_country, SCQUAL_focus, SCQUAL_note, SCQUAL_sequenced_mol, SCQUAL_label, SCQUAL_usedin, SCQUAL_citation, 0 }; static Uint1 source_desc_note_order [] = { SCQUAL_seqfeat_note, SCQUAL_orgmod_note, SCQUAL_subsource_note, SCQUAL_type, SCQUAL_sub_type, SCQUAL_serogroup, SCQUAL_pathovar, SCQUAL_chemovar, SCQUAL_biovar, SCQUAL_biotype, SCQUAL_group, SCQUAL_sub_group, SCQUAL_common, SCQUAL_acronym, SCQUAL_dosage, SCQUAL_authority, SCQUAL_forma, SCQUAL_forma_specialis, SCQUAL_ecotype, SCQUAL_synonym, SCQUAL_anamorph, SCQUAL_teleomorph, SCQUAL_breed, SCQUAL_genotype, SCQUAL_plastid_name, SCQUAL_segment, SCQUAL_endogenous_virus_name, SCQUAL_common_name, SCQUAL_zero_orgmod, SCQUAL_one_orgmod, SCQUAL_zero_subsrc, /* SCQUAL_old_lineage, */ /* SCQUAL_old_name, */ 0 }; static Uint1 source_feat_note_order [] = { SCQUAL_unstructured, SCQUAL_type, SCQUAL_sub_type, SCQUAL_serogroup, SCQUAL_pathovar, SCQUAL_chemovar, SCQUAL_biovar, SCQUAL_biotype, SCQUAL_group, SCQUAL_sub_group, SCQUAL_common, SCQUAL_acronym, SCQUAL_dosage, SCQUAL_authority, SCQUAL_forma, SCQUAL_forma_specialis, SCQUAL_ecotype, SCQUAL_synonym, SCQUAL_anamorph, SCQUAL_teleomorph, SCQUAL_breed, SCQUAL_genotype, SCQUAL_plastid_name, SCQUAL_segment, SCQUAL_endogenous_virus_name, SCQUAL_seqfeat_note, SCQUAL_orgmod_note, SCQUAL_subsource_note, SCQUAL_common_name, SCQUAL_zero_orgmod, SCQUAL_one_orgmod, SCQUAL_zero_subsrc, /* SCQUAL_old_lineage, */ /* SCQUAL_old_name, */ 0 }; typedef struct sourcequal { CharPtr name; Uint1 qualclass; } SourceQual, PNTR SourceQualPtr; static SourceQual asn2gnbk_source_quals [ASN2GNBK_TOTAL_SOURCE] = { { "", Qual_class_ignore }, { "acronym", Qual_class_orgmod }, { "anamorph", Qual_class_orgmod }, { "authority", Qual_class_orgmod }, { "biotype", Qual_class_orgmod }, { "biovar", Qual_class_orgmod }, { "breed", Qual_class_orgmod }, { "cell_line", Qual_class_subsource }, { "cell_type", Qual_class_subsource }, { "chemovar", Qual_class_orgmod }, { "chromosome", Qual_class_subsource }, { "citation", Qual_class_pubset }, { "clone", Qual_class_subsource }, { "clone_lib", Qual_class_subsource }, { "common", Qual_class_orgmod }, { "common", Qual_class_string }, { "country", Qual_class_subsource }, { "cultivar", Qual_class_orgmod }, { "db_xref", Qual_class_db_xref }, { "dev_stage", Qual_class_subsource }, { "dosage", Qual_class_orgmod }, { "ecotype", Qual_class_orgmod }, { "endogenous_virus", Qual_class_subsource }, { "environmental_sample", Qual_class_subsource }, { "extrachromosomal", Qual_class_boolean }, { "focus", Qual_class_boolean }, { "forma", Qual_class_orgmod }, { "forma_specialis", Qual_class_orgmod }, { "frequency", Qual_class_subsource }, { "genotype", Qual_class_subsource }, { "germline", Qual_class_subsource }, { "group", Qual_class_orgmod }, { "haplotype", Qual_class_subsource }, { "insertion_seq", Qual_class_subsource }, { "isolate", Qual_class_orgmod }, { "isolation_source", Qual_class_subsource }, { "lab_host", Qual_class_subsource }, { "label", Qual_class_label }, { "macronuclear", Qual_class_boolean }, { "map", Qual_class_subsource }, { "note", Qual_class_note }, { "old_lineage", Qual_class_orgmod }, { "old_name", Qual_class_orgmod }, { "organism", Qual_class_string }, { "organelle", Qual_class_organelle }, { "orgmod_note", Qual_class_orgmod }, { "pathovar", Qual_class_orgmod }, { "plasmid", Qual_class_subsource }, { "plastid", Qual_class_subsource }, { "pop_variant", Qual_class_subsource }, { "rearranged", Qual_class_subsource }, { "segment", Qual_class_subsource }, { "seqfeat_note", Qual_class_string }, { "sequenced_mol", Qual_class_quote }, { "serogroup", Qual_class_orgmod }, { "serotype", Qual_class_orgmod }, { "serovar", Qual_class_orgmod }, { "sex", Qual_class_subsource }, { "specific_host", Qual_class_orgmod }, { "specimen_voucher", Qual_class_orgmod }, { "strain", Qual_class_orgmod }, { "sub_clone", Qual_class_subsource }, { "subgroup", Qual_class_orgmod }, { "sub_species", Qual_class_orgmod }, { "sub_strain", Qual_class_orgmod }, { "subtype", Qual_class_orgmod }, { "subsource_note", Qual_class_subsource }, { "synonym", Qual_class_orgmod }, { "teleomorph", Qual_class_orgmod }, { "tissue_lib", Qual_class_subsource }, { "tissue_type", Qual_class_subsource }, { "transgenic", Qual_class_subsource }, { "transposon", Qual_class_subsource }, { "type", Qual_class_orgmod }, { "unstructured", Qual_class_valnode }, { "usedin", Qual_class_quote }, { "variety", Qual_class_orgmod }, { "?", Qual_class_orgmod }, { "?", Qual_class_orgmod }, { "?", Qual_class_subsource }, }; static Int2 subSourceToSourceIdx [30] = { SCQUAL_zero_subsrc, SCQUAL_chromosome, SCQUAL_map, SCQUAL_clone, SCQUAL_sub_clone, SCQUAL_haplotype, SCQUAL_genotype, SCQUAL_sex, SCQUAL_cell_line, SCQUAL_cell_type, SCQUAL_tissue_type, SCQUAL_clone_lib, SCQUAL_dev_stage, SCQUAL_frequency, SCQUAL_germline, SCQUAL_rearranged, SCQUAL_lab_host, SCQUAL_pop_variant, SCQUAL_tissue_lib, SCQUAL_plasmid_name, SCQUAL_transposon_name, SCQUAL_ins_seq_name, SCQUAL_plastid_name, SCQUAL_country, SCQUAL_segment, SCQUAL_endogenous_virus_name, SCQUAL_transgenic, SCQUAL_environmental_sample, SCQUAL_isolation_source, SCQUAL_subsource_note }; typedef enum { FTQUAL_allele = 1, FTQUAL_anticodon, FTQUAL_bound_moiety, FTQUAL_cds_product, FTQUAL_citation, FTQUAL_clone, FTQUAL_coded_by, FTQUAL_codon, FTQUAL_codon_start, FTQUAL_cons_splice, FTQUAL_db_xref, FTQUAL_direction, FTQUAL_EC_number, FTQUAL_evidence, FTQUAL_exception, FTQUAL_exception_note, FTQUAL_figure, FTQUAL_frequency, FTQUAL_function, FTQUAL_gene, FTQUAL_gene_desc, FTQUAL_gene_allele, FTQUAL_gene_map, FTQUAL_gene_syn, FTQUAL_gene_note, FTQUAL_gene_xref, FTQUAL_heterogen, FTQUAL_illegal_qual, FTQUAL_insertion_seq, FTQUAL_label, FTQUAL_map, FTQUAL_maploc, FTQUAL_mod_base, FTQUAL_modelev, FTQUAL_note, FTQUAL_number, FTQUAL_organism, FTQUAL_partial, FTQUAL_PCR_conditions, FTQUAL_phenotype, FTQUAL_product, FTQUAL_product_quals, FTQUAL_prot_activity, FTQUAL_prot_comment, FTQUAL_prot_EC_number, FTQUAL_prot_note, FTQUAL_prot_method, FTQUAL_prot_conflict, FTQUAL_prot_desc, FTQUAL_prot_missing, FTQUAL_prot_name, FTQUAL_prot_names, FTQUAL_protein_id, FTQUAL_pseudo, FTQUAL_region, FTQUAL_region_name, FTQUAL_replace, FTQUAL_rpt_family, FTQUAL_rpt_type, FTQUAL_rpt_unit, FTQUAL_rrna_its, FTQUAL_sec_str_type, FTQUAL_selenocysteine, FTQUAL_seqfeat_note, FTQUAL_site, FTQUAL_site_type, FTQUAL_standard_name, FTQUAL_transcript_id, FTQUAL_transl_except, FTQUAL_transl_table, FTQUAL_translation, FTQUAL_transposon, FTQUAL_trna_aa, FTQUAL_trna_codons, FTQUAL_usedin, FTQUAL_xtra_prod_quals, ASN2GNBK_TOTAL_FEATUR } FtQualType; /* ordering arrays for qualifiers and note components */ static Uint1 feat_qual_order [] = { FTQUAL_partial, FTQUAL_gene, FTQUAL_product, FTQUAL_prot_EC_number, FTQUAL_prot_activity, FTQUAL_standard_name, FTQUAL_coded_by, FTQUAL_prot_name, FTQUAL_region_name, FTQUAL_site_type, FTQUAL_sec_str_type, FTQUAL_heterogen, FTQUAL_note, FTQUAL_citation, FTQUAL_number, FTQUAL_pseudo, FTQUAL_codon_start, FTQUAL_anticodon, FTQUAL_bound_moiety, FTQUAL_clone, FTQUAL_cons_splice, FTQUAL_direction, FTQUAL_function, FTQUAL_evidence, FTQUAL_exception, FTQUAL_frequency, FTQUAL_EC_number, FTQUAL_gene_map, FTQUAL_gene_allele, FTQUAL_allele, FTQUAL_map, FTQUAL_mod_base, FTQUAL_PCR_conditions, FTQUAL_phenotype, FTQUAL_rpt_family, FTQUAL_rpt_type, FTQUAL_rpt_unit, FTQUAL_insertion_seq, FTQUAL_transposon, FTQUAL_usedin, FTQUAL_illegal_qual, FTQUAL_replace, FTQUAL_transl_except, FTQUAL_transl_table, FTQUAL_codon, FTQUAL_organism, FTQUAL_label, FTQUAL_cds_product, FTQUAL_protein_id, FTQUAL_transcript_id, FTQUAL_db_xref, FTQUAL_gene_xref, FTQUAL_translation, 0 }; /* prot_names after seqfeat_note - gi|4210642|emb|AJ005084.1|HBVAJ5084 prot_conflict after prot_desc - gi|61183|emb|V01135.1|PIVM02 figure after prot_desc - gi|400553|gb|S64006.1| seqfeat_note after prot_desc - gi|431713|gb|L20354.1|STVPATPOLB but prot_desc after seqfeat_note - AF252556.1 prot_names after figure - gi|234022|gb|S56149.1|S56149 seqfeat_note after prot_conflict after figure - gi|234046|gb|S51392.1|S51392 prot_method after prot_comment (descriptor) after prot_note after prot_desc region after seqfeat_note - gi|6554164|gb|AF043644.3|AF043644 prot_desc after prot_names - gi|6581069|gb|AF202541.1|AF202541 - cannot do !!! gene_syn after gene_desc - gi|3386543|gb|AF079528.1|AF079528 pseudo after note - gi|6598562|gb|AC006419.3|AC006419 */ static Uint1 feat_note_order [] = { FTQUAL_gene_desc, FTQUAL_gene_syn, FTQUAL_trna_codons, FTQUAL_prot_desc, FTQUAL_prot_note, FTQUAL_prot_comment, FTQUAL_prot_method, FTQUAL_figure, FTQUAL_maploc, FTQUAL_prot_conflict, FTQUAL_prot_missing, FTQUAL_seqfeat_note, FTQUAL_exception_note, FTQUAL_region, FTQUAL_selenocysteine, FTQUAL_prot_names, FTQUAL_site, FTQUAL_rrna_its, FTQUAL_xtra_prod_quals, FTQUAL_modelev, 0 }; typedef struct featurqual { CharPtr name; Uint1 qualclass; } FeaturQual, PNTR FeaturQualPtr; static FeaturQual asn2gnbk_featur_quals [ASN2GNBK_TOTAL_FEATUR] = { { "", Qual_class_ignore }, { "allele", Qual_class_quote }, { "anticodon", Qual_class_anti_codon }, { "bound_moiety", Qual_class_quote }, { "product", Qual_class_string }, { "citation", Qual_class_pubset }, { "clone", Qual_class_quote }, { "coded_by", Qual_class_seq_loc }, { "codon", Qual_class_codon }, { "codon_start", Qual_class_int }, { "cons_splice", Qual_class_consplice }, { "db_xref", Qual_class_db_xref }, { "direction", Qual_class_L_R_B }, { "EC_number", Qual_class_EC_quote }, { "evidence", Qual_class_evidence }, { "exception", Qual_class_string }, { "exception_note", Qual_class_string }, { "figure", Qual_class_string }, { "frequency", Qual_class_quote }, { "function", Qual_class_quote }, { "gene", Qual_class_sgml }, { "gene_desc", Qual_class_string }, { "allele", Qual_class_string }, { "map", Qual_class_string }, { "gene_syn", Qual_class_valnode }, { "gene_note", Qual_class_string }, { "db_xref", Qual_class_db_xref }, { "heterogen", Qual_class_string }, { "illegal", Qual_class_illegal }, { "insertion_seq", Qual_class_quote }, { "label", Qual_class_label }, { "map", Qual_class_quote }, { "maploc", Qual_class_string }, { "mod_base", Qual_class_noquote }, { "model_evidence", Qual_class_model_ev }, { "note", Qual_class_note }, { "number", Qual_class_number }, { "organism", Qual_class_quote }, { "partial", Qual_class_boolean }, { "PCR_conditions", Qual_class_quote }, { "phenotype", Qual_class_quote }, { "product", Qual_class_product }, { "product", Qual_class_quote }, { "function", Qual_class_valnode }, { "prot_comment", Qual_class_string }, { "EC_number", Qual_class_EC_valnode }, { "prot_note", Qual_class_string }, { "prot_method", Qual_class_method }, { "prot_conflict", Qual_class_string }, { "prot_desc", Qual_class_string }, { "prot_missing", Qual_class_string }, { "name", Qual_class_string }, { "prot_names", Qual_class_protnames }, { "protein_id", Qual_class_seq_id }, { "pseudo", Qual_class_boolean }, { "region", Qual_class_region }, { "region_name", Qual_class_string }, { "replace", Qual_class_replace }, { "rpt_family", Qual_class_quote }, { "rpt_type", Qual_class_rpt }, { "rpt_unit", Qual_class_rpt_unit }, { "rrna_its", Qual_class_its }, { "sec_str_type", Qual_class_sec_str }, { "selenocysteine", Qual_class_string }, { "seqfeat_note", Qual_class_string }, { "site", Qual_class_site }, { "site_type", Qual_class_site }, { "standard_name", Qual_class_quote }, { "transcript_id", Qual_class_seq_id }, { "transl_except", Qual_class_code_break }, { "transl_table", Qual_class_int }, { "translation", Qual_class_translation }, { "transposon", Qual_class_quote }, { "trna_aa", Qual_class_ignore }, { "trna_codons", Qual_class_trna_codons }, { "usedin", Qual_class_paren }, { "xtra_products", Qual_class_xtraprds } }; static Boolean AllowedValQual (Uint2 featureKey, FtQualType qualKey); /* ********************************************************************** */ /* utility functions */ /* the val node strings mechanism will be replaced by a more efficient method later */ static CharPtr MergeValNodeStrings ( ValNodePtr list ) { size_t len; CharPtr ptr; CharPtr str; CharPtr tmp; ValNodePtr vnp; if (list == NULL) return NULL; for (vnp = list, len = 0; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; len += StringLen (str); } if (len == 0) return NULL; ptr = MemNew (sizeof (Char) * (len + 2)); if (ptr == NULL) return NULL; for (vnp = list, tmp = ptr; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; tmp = StringMove (tmp, str); } return ptr; } static void AddValNodeString ( ValNodePtr PNTR head, CharPtr prefix, CharPtr string, CharPtr suffix ) { Char buf [256]; CharPtr freeme = NULL; size_t len; CharPtr newstr; CharPtr strptr; len = StringLen (prefix) + StringLen (string) + StringLen (suffix); if (len == 0) return; if (len < sizeof (buf)) { /* if new string fits in stack buffer, no need to allocate */ MemSet ((Pointer) buf, 0, sizeof (buf)); newstr = buf; } else { /* new string bigger than stack buffer, so allocate sufficient string */ newstr = (CharPtr) MemNew (sizeof (Char) * (len + 2)); if (newstr == NULL) return; /* allocated string will be freed at end of function */ freeme = newstr; } strptr = newstr; if (prefix != NULL) { strptr = StringMove (strptr, prefix); } if (string != NULL) { strptr = StringMove (strptr, string); } if (suffix != NULL) { strptr = StringMove (strptr, suffix); } /* currently just makes a valnode list, to be enhanced later */ ValNodeCopyStr (head, 0, newstr); /* if large string was allocated, free it now */ if (freeme != NULL) { MemFree (freeme); } } /* */ /* s_isWholeWordSubstr () -- Determines if a substring that is */ /* contained in another string is a whole */ /* word or phrase -- i.e. is it both */ /* preceded and followed by white space. */ /* */ static Boolean s_isWholeWordSubstr (CharPtr searchStr, CharPtr foundStr, CharPtr subStr) { Char previousChar; Char nextChar; /* Is beginning of substr on a word boundary ? */ if (searchStr != foundStr) { previousChar = *(--foundStr); foundStr++; if (!isspace(previousChar)) return FALSE; } /* Check for case where the substring is found */ /* at the very end of the search string. */ if (StringCmp(foundStr, subStr) == 0) return TRUE; /* Is end of substr on a word boundary -- i.e., is */ /* the next character white space or punctuation? */ nextChar = *(foundStr + StringLen(subStr)); if (isspace(nextChar)) return TRUE; if (ispunct(nextChar)) return TRUE; /* If we made it this far, the substring */ /* is on a whole word boundary. */ return TRUE; } /* s_ValNodeListStrstr () -- Searches a valnode list to see if any */ /* of its String nodes contain the given */ /* string. */ /* */ /* Returns values -- */ /* */ /* 0 : No match found for search string. */ /* N : Search string is a substring of node N */ /* -N : Node N is a substring of the search string */ #define VALNODE_STRING 0 static Int4 s_ValNodeListStrstr (ValNodePtr valNodeList, CharPtr searchString, Boolean wholeWord) { Boolean found = FALSE; ValNodePtr vNode; CharPtr vNodeStr; Int4 nodeNum = 0; CharPtr foundStr; /* Loop through the linked list of nodes, */ /* looking for string nodes to check. */ for (vNode = valNodeList; vNode != NULL; vNode = vNode->next) { nodeNum++; if (vNode->choice == VALNODE_STRING) { vNodeStr = (CharPtr) vNode->data.ptrvalue; /* Is searchstring a substring of the node's string? */ if ((foundStr = StringStr(vNodeStr,searchString)) != NULL) { /* If whole word checking is turned */ /* on make sure that the substring */ /* matches a whole word (or words). */ if ( (wholeWord == TRUE) && (s_isWholeWordSubstr(vNodeStr, foundStr, searchString) == FALSE)) continue; /* Found a substring so break */ found = TRUE; break; } /* Is node string a substring of the search string? */ else if ((foundStr = StringStr(searchString, vNodeStr)) != NULL) { /* If whole word checking is turned */ /* on make sure that the substring */ /* matches a whole word (or words). */ if ( (wholeWord == TRUE) && (s_isWholeWordSubstr(searchString, foundStr, vNodeStr) == FALSE)) continue; /* Found a substring -- save it's number and break */ found = TRUE; nodeNum = -nodeNum; break; } } } /* If we found a node, return it */ if (found == TRUE) return nodeNum; else return 0; } /* s_ValNodeListDelete () - Deletes a given node N from a ValNode list */ /* */ /* NOTE: This is based on NodeListDelete () in ncbimisc.c but */ /* adds the ability to delete the first node by passing in */ /* a pointer to a pointer. */ static Nlm_Boolean s_ValNodeListDelete (ValNodePtr PNTR headPtr, Nlm_Int2 item) { ValNodePtr prev; ValNodePtr deleteNode; CharPtr vNodeStr; CharPtr tempStr; /* Check parameters */ if ((headPtr == NULL) || (*headPtr == NULL) || (item <= 0)) return FALSE; /* Logically delete the node by linking the */ /* previous node to the following node. */ if (item > 1) { prev = NodeListFind (*headPtr, (Nlm_Int2)(item - 1), FALSE); if (prev == NULL) return FALSE; deleteNode = prev->next; if (deleteNode == NULL) return FALSE; prev->next = deleteNode->next; } /* Special case if we're deleting the first */ /* node and have to change the list pointer. */ else { deleteNode = *headPtr; *headPtr = deleteNode->next; /* If there's a following node, it's */ /* prefix needs to be removed. */ if (*headPtr != NULL) { vNodeStr = (CharPtr) (*headPtr)->data.ptrvalue; if (StringNCmp (vNodeStr, "; ", 2) == 0) { tempStr = (CharPtr) MemNew(StringLen(vNodeStr+2)); StringCpy (tempStr, vNodeStr + 2); StringCpy (vNodeStr, tempStr); MemFree(tempStr); } } } /* Physically delete the node */ Nlm_MemFree (deleteNode->data.ptrvalue); Nlm_MemFree (deleteNode); /* Return successfully */ return TRUE; } /* s_AddValNodeString_NoRedund() -- Adds a string to a valnode list, */ /* but first checks to make sure */ /* that it's not redundant. */ static void s_AddValNodeString_NoRedund ( ValNodePtr PNTR head, CharPtr prefix, CharPtr string, CharPtr suffix ) { Int4 isRedund; if (StringNICmp (string, "tRNA-", 5) == 0) isRedund = s_ValNodeListStrstr(*head, string+5,TRUE); else isRedund = s_ValNodeListStrstr(*head, string, TRUE); /* If the new string is a substring of an */ /* already existing string, don't add it. */ if (isRedund > 0) return; /* If a previous string is a substring, */ /* remove it and then add the new. */ /* Temporarily remove 'backward' check else if (isRedund < 0) { s_ValNodeListDelete(head,-isRedund); */ /* If we just deleted the only previous node, */ /* then don't use the "; " prefix. */ /* if (*head == NULL) AddValNodeString (head, NULL, string, suffix); else AddValNodeString (head, prefix, string, suffix); } */ /* If no redundancies, just add the string */ else if (isRedund == 0) AddValNodeString (head, prefix, string, suffix); /* bailing on isRedund < 0 was suppress sfp->comment in gi|7715975|gb|AF203972| */ else AddValNodeString (head, prefix, string, suffix); } /* s_AddPeriodToEnd () -- Adds a '.' to the end of a given string if */ /* there is not already one there. */ /* */ /* Note that this adds one character to the */ /* length of the string, leading to a */ /* memory overrun if space was not previously */ /* allocated for this. */ static void s_AddPeriodToEnd (CharPtr someString) { Int4 len; if (StringHasNoText (someString)) return; len = StringLen (someString); if (len < 1) return; if (someString[len-1] != '.') { someString[len] = '.'; someString[len+1] = '\0'; } } /* s_RemovePeriodFromEnd () -- If the last character in a given */ /* string is a '.', removes it. */ static Boolean s_RemovePeriodFromEnd (CharPtr someString) { Int4 len; if (StringHasNoText (someString)) return FALSE; len = StringLen (someString); if (len < 1) return FALSE; if (someString[len-1] == '.') { someString[len-1] = '\0'; return TRUE; } return FALSE; } /**/ /* isEllipsis () - Determines if a string ends in an ellipses */ /**/ static Boolean IsEllipsis ( CharPtr str ) { size_t len; CharPtr ptr; if (StringHasNoText (str)) return FALSE; len = StringLen (str); if (len < 3) return FALSE; ptr = str + len - 3; return (Boolean) (ptr [0] == '.' && ptr [1] == '.' && ptr [2] == '.'); } /**/ /* s_StringCleanup () - Performs various cosmetic cleanup functions */ /* on a given string. */ /**/ static void s_StringCleanup (CharPtr str) { CharPtr p; CharPtr q; /* Remove junk from string's interior */ p = str; q = str; while (*p) { if (*p == ';' && p [1] == ' ' && p [2] == ';') p += 2; else if (*p == ',' && p [1] == ' ' && p [2] == ';') p += 2; else { *q = *p; p++; q++; } } *q = '\0'; } static Int2 gb_StartPrint ( FmtType format, Int2 gb_init_indent, Int2 gb_cont_indent, CharPtr gb_label, Int2 gb_tab_to, Int2 eb_init_indent, Int2 eb_cont_indent, CharPtr eb_line_prefix, Boolean eb_print_xx ) { Int2 result = 0; if (format == GENBANK_FMT || format == GENPEPT_FMT) { result = ff_StartPrint (gb_init_indent, gb_cont_indent, ASN2FF_GB_MAX, NULL); if (gb_label != NULL) { ff_AddString (gb_label); } if (gb_tab_to > 0) { TabToColumn (gb_tab_to); } } else if (format == EMBL_FMT || format == EMBLPEPT_FMT) { if (eb_print_xx) { PrintXX (); } result = ff_StartPrint (eb_init_indent, eb_cont_indent, ASN2FF_EMBL_MAX, eb_line_prefix); } return result; } /* */ /* s_ReplaceTildesWithSpaces () - Replace all tildes */ /* with spaces in the */ /* given string UNLESS: */ /* */ /* A. The tilde is followed by a number. */ /* OR */ /* B. The tilde is followed by a space and then */ /* a number. */ /* OR */ /* C. The tilde is followed by a left paren and */ /* then a number. */ /* */ static void s_ReplaceTildesWithSpaces (CharPtr someString) { while (*someString != '\0') { if ((*someString == '~') && (!IS_DIGIT(*(someString+1))) && (!((*(someString+1) == ' ') && IS_DIGIT(*(someString+2)))) && (!((*(someString+1) == '(') && IS_DIGIT(*(someString+2))))) *someString = ' '; someString++; } } /* */ /* s_ExpandTildes () - Process tildes according to */ /* the following rules. */ /* */ /* 1) Single tilde replaced by linefeed. */ /* 2) Double tilde replaced by single one. */ /* */ static void s_ExpandTildes (CharPtr someString) { CharPtr startOfString; startOfString = someString; /* Loop through the string checking each character */ while (*someString != '\0') { if (*someString == '~') { /* Handle single tilde */ if (*(someString+1) != '~') *someString = '\n'; /* Handle double tilde */ else { someString++; *someString = '\0'; StringCat(startOfString,someString+1); } } someString++; } } static void gb_AddString ( CharPtr prefix, CharPtr string, CharPtr suffix, Boolean addPeriod, Boolean convertQuotes, Int2 tildeAction ) { Char buf [256]; Char ch; CharPtr convertHere; CharPtr freeme = NULL; size_t len; CharPtr newstr; CharPtr strptr; len = StringLen (prefix) + StringLen (string) + StringLen (suffix); if (len == 0) { if (addPeriod) { ff_AddString ("."); } return; } if (len + 1 < sizeof (buf)) { /* if new string fits in stack buffer, no need to allocate */ MemSet ((Pointer) buf, 0, sizeof (buf)); newstr = buf; } else { /* new string bigger than stack buffer, so allocate sufficient string */ newstr = (CharPtr) MemNew (sizeof (Char) * (len + 3)); if (newstr == NULL) return; /* allocated string will be freed at end of function */ freeme = newstr; } strptr = newstr; if (prefix != NULL) { strptr = StringMove (strptr, prefix); } convertHere = strptr; if (string != NULL) { strptr = StringMove (strptr, string); } /* convertQuotes retains double quotes in the prefix and suffix */ if (convertQuotes) { strptr = convertHere; ch = *strptr; while (ch != '\0') { if (ch == '\"') { *strptr = '\''; } strptr++; ch = *strptr; } } if (suffix != NULL) { strptr = StringMove (strptr, suffix); } /* Trim junk off the end of a string */ /* and replace it with a period. */ if (addPeriod) { for (strptr = newstr + len - 1; strptr > newstr; strptr--) { ch = *strptr; if (ch == ' ' || ch == '\t' || ch == '~' || ch == '.') { *strptr = '\0'; } else { break; } } if (*strptr != '.') { strptr++; *strptr = '.'; strptr++; *strptr = '\0'; } } /* Process tildes in one of 4 possible ways */ switch (tildeAction) { case TILDE_EXPAND : s_ExpandTildes (newstr); ff_AddString (newstr); break; case TILDE_OLD_EXPAND : ff_AddStringWithTildes (newstr); break; case TILDE_TO_SPACES : s_ReplaceTildesWithSpaces (newstr); ff_AddString (newstr); break; case TILDE_IGNORE : default: ff_AddString (newstr); break; } /* if large string was allocated, free it now */ if (freeme != NULL) { MemFree (freeme); } } static CharPtr gb_MergeString ( Boolean call_end_print ) { if (call_end_print) { ff_EndPrint (); } return ff_MergeString (); } static CharPtr asn2gb_PrintDate ( DatePtr dp ) { Char buf [30]; size_t len; if (dp == NULL) return NULL; if (DatePrint (dp, buf)) { if (StringICmp (buf, "Not given") != 0) { len = StringLen (buf); if (len > 0) { if (buf [len - 1] == '\n') { if (buf [len - 2] == '.') { buf [len - 2] = '\0'; } else { buf [len - 1] = '\0'; } } } return StringSave (buf); } } return NULL; } static CharPtr month_names [] = { "JAN", "FEB", "MAR", "APR", "MAY", "JUN", "JUL", "AUG", "SEP", "OCT", "NOV", "DEC", "??" }; static CharPtr DateToGB ( CharPtr buf, DatePtr dp, Boolean citSub ) { Int2 day; Int2 month; Int2 year; if (buf != NULL) { *buf = '\0'; } if (dp == NULL) return NULL; if (dp->data [0] == 0) { StringCpy (buf, dp->str); } else if (dp->data [0] == 1) { year = 1900 + (Int2) dp->data [1]; month = (Int2) dp->data [2]; day = (Int2) dp->data [3]; if (citSub) { if (month < 1 || month > 12) { month = 13; } if (day < 1 || day > 31) { day = 0; } } else { if (month < 1 || month > 12) { month = 1; } if (day < 1 || day > 31) { day = 1; } } if (day < 1) { sprintf (buf, "??-%s-%ld", month_names [month-1], (long) year); } else if (day < 10) { sprintf (buf, "0%ld-%s-%ld", (long) day, month_names [month-1], (long) year); } else { sprintf(buf, "%ld-%s-%ld", (long) day, month_names [month-1], (long) year); } } return buf; } /* ********************************************************************** */ /* format functions allocate printable string for given paragraph */ static CharPtr DefaultFormatBlock ( Asn2gbFormatPtr afp, BaseBlockPtr bbp ) { if (afp == NULL || bbp == NULL) return NULL; /* default format function assumes string pre-allocated by add block function */ return StringSaveNoNull (bbp->string); } /* superset of http://www.ncbi.nlm.nih.gov/collab/db_xref.html and RefSeq db_xrefs */ static CharPtr legalDbXrefs [] = { "PIDe", "PIDd", "PIDg", "PID", "ATCC", "ATCC(in host)", "ATCC(dna)", "BDGP_EST", "BDGP_INS", "CDD", "CK", "COG", "dbEST", "dbSNP", "dbSTS", "ENSEMBL", "ESTLIB", "FANTOM_DB", "FLYBASE", "GDB", "GeneID", "GI", "GO", "InterimID", "LocusID", "MaizeDB", "MGD", "MGI", "MIM", "niaEST", "PIR", "PSEUDO", "RATMAP", "RiceGenes", "REMTREMBL", "RGD", "RZPD", "SGD", "SoyBase", "SPTREMBL", "SWISS-PROT", "taxon", "UniGene", "UniSTS", NULL }; static CharPtr legalRefSeqDbXrefs [] = { "WormBase", NULL }; static CharPtr organellePrefix [] = { NULL, NULL, "Chloroplast ", "Chromoplast ", "Kinetoplast ", "Mitochondrion ", "Plastid ", NULL, NULL, NULL, NULL, NULL, "Cyanelle ", NULL, NULL, "Nucleomorph ", "Apicoplast ", "Leucoplast ", "Proplastid ", NULL }; static CharPtr FormatSourceBlock ( Asn2gbFormatPtr afp, BaseBlockPtr bbp ) { CharPtr acr = NULL; Boolean addPeriod = TRUE; IntAsn2gbJobPtr ajp; CharPtr ana = NULL; BioSourcePtr biop = NULL; CharPtr com = NULL; CharPtr common = NULL; SeqMgrDescContext dcontext; SeqMgrFeatContext fcontext; GBBlockPtr gbp = NULL; Uint1 genome; ValNodePtr head = NULL; CharPtr lineage = NULL; ValNodePtr mod = NULL; OrgModPtr omp = NULL; OrgNamePtr onp; CharPtr organelle = NULL; OrgRefPtr orp; SeqDescrPtr sdp; CharPtr second = NULL; SeqFeatPtr sfp; CharPtr str; CharPtr syn = NULL; CharPtr taxname = NULL; CharPtr tel = NULL; ValNodePtr vnp; if (afp == NULL || bbp == NULL) return NULL; ajp = afp->ajp; if (ajp == NULL) return NULL; if (! StringHasNoText (bbp->string)) return StringSave (bbp->string); if (bbp->itemtype == OBJ_SEQDESC) { sdp = SeqMgrGetDesiredDescriptor (bbp->entityID, NULL, bbp->itemID, 0, NULL, &dcontext); if (sdp != NULL) { if (dcontext.seqdesctype == Seq_descr_source) { biop = (BioSourcePtr) sdp->data.ptrvalue; } else if (dcontext.seqdesctype == Seq_descr_genbank) { gbp = (GBBlockPtr) sdp->data.ptrvalue; } } } else if (bbp->itemtype == OBJ_SEQFEAT) { sfp = SeqMgrGetDesiredFeature (bbp->entityID, NULL, bbp->itemID, 0, NULL, &fcontext); if (sfp != NULL && fcontext.seqfeattype == SEQFEAT_BIOSRC) { biop = (BioSourcePtr) sfp->data.value.ptrvalue; } } if (gbp != NULL) { common = gbp->source; } if (biop != NULL) { genome = biop->genome; if (genome <= 19) { organelle = organellePrefix [genome]; } orp = biop->org; if (orp != NULL) { taxname = orp->taxname; common = orp->common; mod = orp->mod; onp = orp->orgname; if (onp != NULL) { lineage = onp->lineage; omp = onp->mod; if (ajp->newSourceOrg) { for (omp = onp->mod; omp != NULL; omp = omp->next) { switch (omp->subtype) { case ORGMOD_common : com = omp->subname; break; case ORGMOD_acronym : acr = omp->subname; break; case ORGMOD_synonym : syn = omp->subname; break; case ORGMOD_anamorph : ana = omp->subname; break; case ORGMOD_teleomorph : tel = omp->subname; break; default : break; } } } } vnp = orp->syn; if (vnp != NULL) { second = (CharPtr) vnp->data.ptrvalue; } if (StringHasNoText (second)) { second = ana; } if (StringHasNoText (second)) { second = tel; } if (StringHasNoText (second)) { second = common; } if (StringHasNoText (second)) { second = syn; } if (StringHasNoText (second)) { second = acr; } if (StringHasNoText (second)) { second = com; } } } /* If the organelle prefix is already on the */ /* name, don't add it. */ if (StringNCmp (organelle, taxname, StringLen (organelle)) == 0) organelle = ""; if (StringHasNoText (common)) { common = taxname; } if (StringHasNoText (common)) { common = "Unknown."; } if (StringHasNoText (taxname)) { taxname = "Unknown."; } if (StringHasNoText (lineage)) { lineage = "Unclassified."; } if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) { if (ajp->newSourceOrg) { if (! StringHasNoText (organelle)) { AddValNodeString (&head, NULL, common, " "); } AddValNodeString (&head, NULL, taxname, NULL); if (! StringHasNoText (second)) { AddValNodeString (&head, " (", second, ")"); } addPeriod = FALSE; } else { AddValNodeString (&head, NULL, common, NULL); while (mod != NULL) { str = (CharPtr) mod->data.ptrvalue; if (! StringHasNoText (str)) { AddValNodeString (&head, " ", str, NULL); } mod = mod->next; } } str = MergeValNodeStrings (head); gb_StartPrint (afp->format, 0, 12, "SOURCE", 13, 5, 5, "OS", TRUE); gb_AddString (NULL, str, NULL, addPeriod, FALSE, TILDE_TO_SPACES); ValNodeFreeData (head); MemFree (str); } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) { gb_StartPrint (afp->format, 0, 12, "SOURCE", 13, 5, 5, "OS", TRUE); gb_AddString (organelle, taxname, NULL, FALSE, FALSE, TILDE_TO_SPACES); gb_AddString (" (", common, ")", FALSE, FALSE, TILDE_TO_SPACES); } ff_EndPrint(); return gb_MergeString (FALSE); } static CharPtr FormatOrganismBlock ( Asn2gbFormatPtr afp, BaseBlockPtr bbp ) { BioSourcePtr biop = NULL; CharPtr common = NULL; DbtagPtr dbt; SeqMgrDescContext dcontext; SeqMgrFeatContext fcontext; Uint1 genome; CharPtr lineage = NULL; ObjectIdPtr oip; OrgNamePtr onp; CharPtr organelle = NULL; OrgRefPtr orp; SeqDescrPtr sdp; SeqFeatPtr sfp; Int4 taxid = -1; CharPtr taxname = NULL; ValNodePtr vnp; if (afp == NULL || bbp == NULL) return NULL; if (! StringHasNoText (bbp->string)) return StringSave (bbp->string); if (bbp->itemtype == OBJ_SEQDESC) { sdp = SeqMgrGetDesiredDescriptor (bbp->entityID, NULL, bbp->itemID, 0, NULL, &dcontext); if (sdp != NULL && dcontext.seqdesctype == Seq_descr_source) { biop = (BioSourcePtr) sdp->data.ptrvalue; } } else if (bbp->itemtype == OBJ_SEQFEAT) { sfp = SeqMgrGetDesiredFeature (bbp->entityID, NULL, bbp->itemID, 0, NULL, &fcontext); if (sfp != NULL && fcontext.seqfeattype == SEQFEAT_BIOSRC) { biop = (BioSourcePtr) sfp->data.value.ptrvalue; } } if (biop != NULL) { genome = biop->genome; if (genome <= 19) { organelle = organellePrefix [genome]; } orp = biop->org; if (orp != NULL) { taxname = orp->taxname; common = orp->common; onp = orp->orgname; if (onp != NULL) { lineage = onp->lineage; } for (vnp = orp->db; vnp != NULL; vnp = vnp->next) { dbt = (DbtagPtr) vnp->data.ptrvalue; if (dbt == NULL) continue; if (StringCmp (dbt->db, "taxon") == 0) { oip = dbt->tag; if (oip != NULL) { taxid = oip->id; } } } } } /* If the organelle prefix is already on the */ /* name, don't add it. */ if (StringNCmp (organelle, taxname, StringLen (organelle)) == 0) organelle = ""; if (StringHasNoText (common)) { common = taxname; } if (StringHasNoText (common)) { common = "Unknown."; } if (StringHasNoText (taxname)) { taxname = "Unknown."; } if (StringHasNoText (lineage)) { lineage = "Unclassified."; } if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) { gb_StartPrint (afp->format, 2, 12, "ORGANISM", 13, 5, 5, "OC", FALSE); ff_AddString (organelle); if (StringNICmp (taxname, "Unknown", 7) != 0) { www_organism (taxname, taxid); } else { ff_AddString (taxname); } /* gb_AddString (organelle, taxname, NULL, FALSE, FALSE, TILDE_TO_SPACES); */ ff_EndPrint(); gb_StartPrint (afp->format, 12, 12, NULL, 0, 5, 5, "OC", FALSE); gb_AddString (NULL, lineage, NULL, TRUE, FALSE, TILDE_TO_SPACES); ff_EndPrint(); } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) { gb_StartPrint (afp->format, 12, 12, NULL, 0, 5, 5, "OC", FALSE); gb_AddString (NULL, lineage, NULL, TRUE, FALSE, TILDE_TO_SPACES); ff_EndPrint(); } return ff_print_string_mem (gb_MergeString (FALSE)); } /* format references section */ static AuthListPtr GetAuthListPtr ( PubdescPtr pdp, CitSubPtr csp ) { AuthListPtr alp = NULL; CitArtPtr cap; CitBookPtr cbp; CitGenPtr cgp; CitPatPtr cpp; ValNodePtr vnp; if (csp != NULL) { alp = csp->authors; if (alp != NULL) return alp; } if (pdp == NULL) return NULL; for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) { switch (vnp->choice) { case PUB_Gen : cgp = (CitGenPtr) vnp->data.ptrvalue; if (cgp != NULL) { alp = cgp->authors; } break; case PUB_Sub : csp = (CitSubPtr) vnp->data.ptrvalue; if (csp != NULL) { alp = csp->authors; } break; case PUB_Article : cap = (CitArtPtr) vnp->data.ptrvalue; if (cap != NULL) { alp = cap->authors; } break; case PUB_Book : case PUB_Proc : case PUB_Man : cbp = (CitBookPtr) vnp->data.ptrvalue; if (cbp != NULL) { alp = cbp->authors; } break; case PUB_Patent : cpp = (CitPatPtr) vnp->data.ptrvalue; if (cpp != NULL) { alp = cpp->authors; } break; default : break; } if (alp != NULL) return alp; } return NULL; } static CharPtr MakeSingleAuthorString ( FmtType format, CharPtr prefix, CharPtr name, CharPtr initials, CharPtr suffix ) { Char ch; Char dummy [10]; size_t len; CharPtr ptr; CharPtr str; CharPtr tmp; if (name == NULL) return NULL; /* !!! clean up 'et al' as (presumably) last author !!! */ /* !!! temporary to suppress diff !!! */ { if (StringLen (name) <= 6 && (StringNICmp (name, "et al", 5) == 0 || StringNICmp (name, "et,al", 5) == 0)) { if (StringCmp (prefix, " and ") == 0) { prefix = NULL; dummy [0] = ' '; StringNCpy_0 (dummy + 1, name, sizeof (dummy) - 1); name = dummy; } } } /* if (StringLen (name) <= 6 && (StringNICmp (name, "et al", 5) == 0 || StringNICmp (name, "et,al", 5) == 0)) { name = "et al."; if (StringCmp (prefix, " and ") == 0) { prefix = ", "; } } */ len = StringLen (name) + StringLen (initials) + StringLen (suffix) + StringLen (prefix); str = MemNew (sizeof (Char) * (len + 4)); if (str == NULL) return NULL; ptr = str; if (! StringHasNoText (prefix)) { ptr = StringMove (ptr, prefix); } /* initials and suffix to support structured name fields */ tmp = StringMove (ptr, name); if (! StringHasNoText (initials)) { tmp = StringMove (tmp, ","); tmp = StringMove (tmp, initials); } if (! StringHasNoText (suffix)) { tmp = StringMove (tmp, " "); tmp = StringMove (tmp, suffix); } /* if embl, remove commas in individual names, starting after prefix */ if (format == EMBL_FMT || format == EMBLPEPT_FMT) { tmp = ptr; ch = *tmp; while (ch != '\0') { if (ch == ',') { *tmp = ' '; } tmp++; ch = *tmp; } } return str; } static CharPtr GetAuthorsString ( FmtType format, AuthListPtr alp ) { AuthorPtr ap; Int2 count; ValNodePtr head = NULL; ValNodePtr names; ValNodePtr next; NameStdPtr nsp; PersonIdPtr pid; CharPtr prefix = NULL; CharPtr str; ValNodePtr vnp; if (alp == NULL) return NULL; count = 0; if (alp->choice == 1) { for (names = alp->names; names != NULL; names = names->next) { next = names->next; if (next == NULL) { if (format == GENBANK_FMT || format == GENPEPT_FMT) { if (count == 0) { prefix = NULL; } else { prefix = " and "; } } } str = NULL; ap = (AuthorPtr) names->data.ptrvalue; if (ap != NULL) { pid = ap->name; if (pid != NULL) { if (pid->choice == 2) { nsp = (NameStdPtr) pid->data; if (nsp != NULL) { if (! StringHasNoText (nsp->names [0])) { str = MakeSingleAuthorString (format, prefix, nsp->names [0], nsp->names [4], nsp->names [5]); } else if (! StringHasNoText (nsp->names [3])) { str = MakeSingleAuthorString (format, prefix, nsp->names [3], NULL, NULL); } } } else if (pid->choice == 3 || pid->choice == 4) { str = MakeSingleAuthorString (format, prefix, (CharPtr) pid->data, NULL, NULL); } } } if (str != NULL) { ValNodeCopyStr (&head, 0, str); count++; } prefix = ", "; } } else if (alp->choice == 2 || alp->choice == 3) { for (vnp = alp->names; vnp != NULL; vnp = vnp->next) { next = vnp->next; if (next == NULL) { if (format == GENBANK_FMT || format == GENPEPT_FMT) { if (count == 0) { prefix = NULL; } else { prefix = " and "; } } } str = MakeSingleAuthorString (format, prefix, (CharPtr) vnp->data.ptrvalue, NULL, NULL); if (str != NULL) { ValNodeCopyStr (&head, 0, str); count++; } prefix = ", "; } } str = MergeValNodeStrings (head); ValNodeFreeData (head); return str; } /* Strips all spaces in string in following manner. If the function meet several spaces (spaces and tabs) in succession it replaces them with one space. Strips all spaces after '(' and before ')' */ static void StrStripSpaces ( CharPtr str ) { CharPtr new_str; if (str == NULL) return; new_str = str; while (*str != '\0') { *new_str++ = *str; if (*str == ' ' || *str == '\t' || *str == '(') { for (str++; *str == ' ' || *str == '\t'; str++) continue; if (*str == ')' || *str == ',') { new_str--; } } else { str++; } } *new_str = '\0'; } static Boolean AllCaps ( CharPtr p ) { if (p == NULL) return FALSE; for (p++; p != NULL && *p != '\0'; p++) { if (IS_LOWER (*p)) return FALSE; } return TRUE; } static void CleanEquals ( CharPtr p ) { if (p == NULL) return; for (; *p != '\0'; p++) { if (*p == '\"') { *p = '\''; } } } static CharPtr GetPubTitle ( FmtType format, PubdescPtr pdp, CitSubPtr csp ) { CitArtPtr cap; CitBookPtr cbp; CitGenPtr cgp; Char ch; CitPatPtr cpp; MedlineEntryPtr mep; CharPtr ptr; CharPtr title = NULL; ValNodePtr ttl = NULL; ValNodePtr vnp; if (csp != NULL) { if (format == GENBANK_FMT || format == GENPEPT_FMT) { title = "Direct Submission"; return StringSave (title); } else if (format == EMBL_FMT || format == EMBLPEPT_FMT) { return NULL; } } if (pdp == NULL) return NULL; for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) { switch (vnp->choice) { case PUB_Gen : cgp = (CitGenPtr) vnp->data.ptrvalue; if (cgp != NULL) { if (! StringHasNoText (cgp->title)) return StringSave (cgp->title); if (! StringHasNoText (cgp->cit)) { ptr = StringStr (cgp->cit, "Title=\""); if (ptr != NULL) { title = StringSave (ptr + 7); for (ptr = title; *ptr != '\0'; ptr++) { if (*ptr == '"') { *ptr = '\0'; break; } } return title; } } } break; case PUB_Sub : csp = (CitSubPtr) vnp->data.ptrvalue; if (csp != NULL) { if (format == GENBANK_FMT || format == GENPEPT_FMT) { title = "Direct Submission"; return StringSave (title); } else if (format == EMBL_FMT || format == EMBLPEPT_FMT) { return NULL; } } break; case PUB_Medline : mep = (MedlineEntryPtr) vnp->data.ptrvalue; if (mep != NULL) { cap = mep->cit; if (cap != NULL) { ttl = cap->title; } } break; case PUB_Article : cap = (CitArtPtr) vnp->data.ptrvalue; if (cap != NULL) { ttl = cap->title; } break; case PUB_Book : case PUB_Proc : case PUB_Man : cbp = (CitBookPtr) vnp->data.ptrvalue; if (cbp != NULL) { ttl = cbp->title; if (ttl != NULL) { title = (CharPtr) ttl->data.ptrvalue; if (! StringHasNoText (title)) { title = StringSave (title); if (StringLen (title) > 3) { ch = *title; if (IS_LOWER (ch)) { *title = TO_UPPER (ch); } ptr = title; if (AllCaps (ptr)) { for (ptr++; ptr != NULL && *ptr != '\0'; ptr++) { ch = *ptr; *ptr = TO_LOWER (ch); } } } return title; } } } break; case PUB_Patent : cpp = (CitPatPtr) vnp->data.ptrvalue; if (cpp != NULL) { title = cpp->title; if (! StringHasNoText (title)) { return StringSave (title); } } break; default : break; } if (ttl != NULL) { title = (CharPtr) ttl->data.ptrvalue; if (! StringHasNoText (title)) { return StringSave (title); } } } return NULL; } static void CleanPubTitle ( CharPtr title ) { CharPtr p; Boolean remove_it; if (title == NULL) return; CleanEquals (title); for (p = title + StringLen (title) - 1; p > title + 2; p--) { if (*p == ' ') { *p = '\0'; } else if (*p == '.') { remove_it = FALSE; if (p > title + 5) { if (*(p - 1) != '.' || *(p - 2) != '.') { remove_it = TRUE; } } if (remove_it) { *p = '\0'; } break; } else { break; } } } /* !!! GetPubJournal needs to be implemented !!! */ /* medline type page numbering is expanded (e.g., 125-35 -> 125-135, F124-34 -> F124-F134, 12a-c -> 12a-12c). If only one page is given, this is output without a dash. Expanded numbering is validated to ensure that the first number is smaller than or equal to the second and that the first letter is less than or identical to the second (i.e., a < c). If the input is all letters (i.e., roman numerals) this is not validated. Return values: 0 : valid page numbering. -1 : invalid page numbering. */ #define MAX_PAGE_DIGITS 12 static Int2 FixPages ( CharPtr out_pages, CharPtr in_pages ) { Boolean dash=TRUE, first_alpha; Char firstbegin[MAX_PAGE_DIGITS]; Char secondbegin[MAX_PAGE_DIGITS]; Char firstend[MAX_PAGE_DIGITS]; Char secondend[MAX_PAGE_DIGITS]; Char temp[MAX_PAGE_DIGITS]; CharPtr alphabegin, numbegin, alphaend, numend, ptr, in=in_pages; Int2 diff, index, retval=0; Int2 length_nb, length_ab, length_ne, length_ae; Int4 num1=0, num2=0; if (in_pages == NULL) return retval; while (*in != '\0') { /* Check for digits in input*/ if (IS_DIGIT(*in)) break; in++; } if (*in == '\0' || (in != in_pages && *(in-1) == ' ')) { /* if all letters (i.e. roman numerals), put out. */ out_pages = StringCpy(out_pages, in_pages); return retval; } in = in_pages; if (IS_DIGIT(*in)) { /* Do digits come first? */ first_alpha = FALSE; index=0; while (IS_DIGIT(*in) || *in == ' ') { firstbegin[index] = *in; if (*in != ' ') index++; in++; if (*in == '-') break; } firstbegin[index] = '\0'; index=0; if (*in != '-') { /* After digits look for letters. */ while (IS_ALPHA(*in) || *in == ' ') { secondbegin[index] = *in; index++; in++; if (*in == '-') break; } } secondbegin[index] = '\0'; if (*in == '-') /* if dash is not present, note */ in++; else dash=FALSE; index=0; while (IS_DIGIT(*in) || *in == ' ') { /* Look for digits. */ firstend[index] = *in; if (*in != ' ') index++; in++; } firstend[index] = '\0'; index=0; if (*in != '\0') { /* Look for letters again. */ while (IS_ALPHA(*in) || *in == ' ') { secondend[index] = *in; index++; in++; } } secondend[index] = '\0'; } else { /* Do letters come first? */ first_alpha = TRUE; index=0; while (IS_ALPHA(*in) || *in == ' ') { firstbegin[index] = *in; index++; in++; if (*in == '-') break; } firstbegin[index] = '\0'; index=0; if (*in != '-') { /* After letters look for digits. */ while (IS_DIGIT(*in) || *in == ' ') { secondbegin[index] = *in; if (*in != ' ') index++; in++; if (*in == '-') break; } } secondbegin[index] = '\0'; if (*in == '-') /* Note if dash is missing. */ in++; else dash=FALSE; index=0; while (IS_ALPHA(*in) || *in == ' ') { /* Look for letters again. */ firstend[index] = *in; index++; in++; } firstend[index] = '\0'; index=0; if (*in != '\0') { /* Any digits here? */ while (IS_DIGIT(*in) || *in == ' ') { secondend[index] = *in; if (*in != ' ') index++; in++; } } secondend[index] = '\0'; } if (first_alpha) { alphabegin = firstbegin; numbegin = secondbegin; alphaend = firstend; numend = secondend; } else { numbegin = firstbegin; alphabegin = secondbegin; numend = firstend; alphaend = secondend; } length_nb = StringLen(numbegin); length_ab = StringLen(alphabegin); length_ne = StringLen(numend); length_ae = StringLen(alphaend); /* If no dash, but second letters or numbers present, reject. */ if (dash == FALSE) { if (length_ne != 0 || length_ae != 0) retval = -1; } /* Check for situations like "AAA-123" or "222-ABC". */ if (dash == TRUE) { if (length_ne == 0 && length_ab == 0) retval = -1; else if (length_ae == 0 && length_nb == 0) retval = -1; } /* The following expands "F502-512" into "F502-F512" and checks, for entries like "12a-12c" that a > c. "12aa-12ab", "125G-137A", "125-G137" would be rejected. */ if (retval == 0) { if (length_ab > 0) { if (length_ae > 0) { if (StringCmp(alphabegin, alphaend) != 0) { if (length_ab != 1 || length_ae != 1) retval = -1; else if (*alphabegin > *alphaend) retval = -1; } } else { alphaend = alphabegin; length_ae = length_ab; } } else if (length_ae > 0) retval = -1; } /* The following expands "125-37" into "125-137". */ if (retval == 0) { if (length_nb > 0) { if (length_ne > 0) { diff = length_nb - length_ne; if (diff > 0) { index=0; while (numend[index] != '\0') { temp[index+diff] = numend[index]; index++; } temp[index+diff] = numend[index]; for (index=0; index 0) retval = -1; /* Check that the first number is <= the second (expanded) number. */ if (retval == 0) { /* sscanf(numbegin, "%ld", &num_type); num1 = (Int4) num_type; sscanf( numend, "%ld", &num_type); num2 = (Int4) num_type; */ num1 = (Int4) atol(numbegin); num2 = (Int4) atol(numend); if (num2 < num1) retval = -1; } } if (retval == -1) { out_pages = StringCpy(out_pages, in_pages); } else { ptr = out_pages; /* Place expanded and validated page numbers into "out_pages". */ if (first_alpha) { while (*alphabegin != '\0') { *ptr = *alphabegin; alphabegin++; ptr++; } while (*numbegin != '\0') { *ptr = *numbegin; numbegin++; ptr++; } if (dash == TRUE) { *ptr = '-'; ptr++; while (*alphaend != '\0') { *ptr = *alphaend; alphaend++; ptr++; } while (*numend != '\0') { *ptr = *numend; numend++; ptr++; } } *ptr = '\0'; } else { while (*numbegin != '\0') { *ptr = *numbegin; numbegin++; ptr++; } while (*alphabegin != '\0') { *ptr = *alphabegin; alphabegin++; ptr++; } if (dash == TRUE) { *ptr = '-'; ptr++; while (*numend != '\0') { *ptr = *numend; numend++; ptr++; } while (*alphaend != '\0') { *ptr = *alphaend; alphaend++; ptr++; } } *ptr = '\0'; } } return retval; } /* !!! still need to add StripParanthesis equivalent !!! */ static void DoSup ( ValNodePtr PNTR head, CharPtr issue, CharPtr part_sup, CharPtr part_supi ) { size_t len; CharPtr str; CharPtr temp; len = StringLen (issue) + StringLen (part_sup) + StringLen (part_supi) + 25; str = MemNew (sizeof (Char) * len); if (str == NULL) return; temp = str; if (! StringHasNoText (part_sup)) { *temp = ' '; temp++; temp = StringMove (temp, part_sup); } if (StringHasNoText (issue) && StringHasNoText (part_supi)) { ValNodeCopyStr (head, 0, str); MemFree (str); return; } *temp = ' '; temp++; *temp = '('; temp++; if (! StringHasNoText (issue)) { temp = StringMove (temp, issue); } if (! StringHasNoText (part_supi)) { *temp = ' '; temp++; temp = StringMove (temp, part_supi); } *temp = ')'; temp++; ValNodeCopyStr (head, 0, str); MemFree (str); } static CharPtr FormatCitJour ( FmtType format, Boolean citArtIsoJta, CitJourPtr cjp ) { Char buf [256]; DatePtr dp; ValNodePtr head = NULL; ImprintPtr imp; CharPtr issue = NULL; Char pages [128]; CharPtr part_sup = NULL; CharPtr part_supi = NULL; CharPtr rsult = NULL; CharPtr title; ValNodePtr ttl; CharPtr volume; Char year [8]; if (cjp == NULL) return NULL; ttl = cjp->title; if (ttl == NULL) return NULL; /* always use iso_jta title if present */ while (ttl != NULL && ttl->choice != Cit_title_iso_jta) { ttl = ttl->next; } /* release mode requires iso_jta title */ if (ttl == NULL) { if (citArtIsoJta) return NULL; ttl = cjp->title; } imp = cjp->imp; if (imp == NULL) return NULL; dp = imp->date; year [0] = '\0'; if (dp != NULL) { if (dp->data [0] == 1) { if (dp->data [1] != 0) { sprintf (year, " (%ld)", (long) (1900 + dp->data [1])); } } else { StringCpy (year, " ("); StringNCat (year, dp->str, 4); StringCat (year, ")"); } } if (imp->prepub == 1 || imp->prepub == 255) { sprintf (buf, "Unpublished %s", year); return StringSave (buf); } title = (CharPtr) ttl->data.ptrvalue; if (StringLen (title) < 3) return StringSave ("."); ValNodeCopyStr (&head, 0, title); volume = imp->volume; if (format == GENBANK_FMT || format == GENPEPT_FMT) { issue = imp->issue; part_sup = imp->part_sup; part_supi = imp->part_supi; } pages [0] = '\0'; FixPages (pages, imp->pages); if (! StringHasNoText (volume)) { AddValNodeString (&head, " ", volume, NULL); } if ((! StringHasNoText (volume)) || (! StringHasNoText (pages))) { DoSup (&head, issue, part_sup, part_supi); } if (format == GENBANK_FMT || format == GENPEPT_FMT) { if (! StringHasNoText (pages)) { AddValNodeString (&head, ", ", pages, NULL); } } else if (format == EMBL_FMT || format == EMBLPEPT_FMT) { if (! StringHasNoText (pages)) { AddValNodeString (&head, ":", pages, NULL); } else if (imp->prepub == 2 || (StringHasNoText (volume))) { ValNodeCopyStr (&head, 0, " 0:0-0"); } } ValNodeCopyStr (&head, 0, year); if (format == GENBANK_FMT || format == GENPEPT_FMT) { if (imp->prepub == 2) { ValNodeCopyStr (&head, 0, " In press"); } } rsult = MergeValNodeStrings (head); ValNodeFreeData (head); return rsult; } static CharPtr MakeAffilStr ( AffilPtr afp ) { ValNodePtr head = NULL; CharPtr prefix = ""; CharPtr rsult = NULL; if (afp == NULL) return NULL; if (! StringHasNoText (afp->affil)) { ValNodeCopyStr (&head, 0, afp->affil); prefix = ", "; } if (afp->choice == 2) { if (! StringHasNoText (afp->div)) { AddValNodeString (&head, prefix, afp->div, NULL); prefix = ", "; } if (! StringHasNoText (afp->street)) { AddValNodeString (&head, prefix, afp->street, NULL); prefix = ", "; } if (! StringHasNoText (afp->city)) { AddValNodeString (&head, prefix, afp->city, NULL); prefix = ", "; } if (! StringHasNoText (afp->sub)) { AddValNodeString (&head, prefix, afp->sub, NULL); prefix = ", "; } if (! StringHasNoText (afp->country)) { AddValNodeString (&head, prefix, afp->country, NULL); prefix = ", "; } } rsult = MergeValNodeStrings (head); ValNodeFreeData (head); return rsult; } static CharPtr GetAffil ( AffilPtr afp ) { Boolean need_comma=FALSE; CharPtr string=NULL, temp, ptr; Char ch; Int2 aflen=15; if (afp == NULL) return NULL; if (afp) { if (afp -> choice == 1){ if (afp -> affil){ aflen += StringLen(afp -> affil); } }else if (afp -> choice == 2){ aflen += StringLen (afp -> affil) + StringLen (afp -> div) + StringLen (afp -> city) + StringLen (afp -> sub) + StringLen (afp -> street) + StringLen (afp -> country) + StringLen(afp->postal_code); } temp = string = MemNew(aflen); if ( afp -> choice == 1){ if (afp -> affil){ ptr = afp->affil; while ((*temp = *ptr) != '\0') { temp++; ptr++; } } }else if (afp -> choice == 2){ if( afp -> div) { if (need_comma) { *temp = ','; temp++; *temp = ' '; temp++; } ptr = afp->div; while ((*temp = *ptr) != '\0') { temp++; ptr++; } need_comma = TRUE; } if(afp -> affil) { if (need_comma) { *temp = ','; temp++; *temp = ' '; temp++; } ptr = afp->affil; while ((*temp = *ptr) != '\0') { temp++; ptr++; } need_comma = TRUE; } if(afp -> street) { if (need_comma) { *temp = ','; temp++; *temp = ' '; temp++; } ptr = afp->street; while ((*temp = *ptr) != '\0') { temp++; ptr++; } need_comma = TRUE; } if( afp -> city) { if (need_comma) { *temp = ','; temp++; *temp = ' '; temp++; } ptr = afp->city; while ((*temp = *ptr) != '\0') { temp++; ptr++; } need_comma = TRUE; } if( afp -> sub) { if (need_comma) { *temp = ','; temp++; *temp = ' '; temp++; } ptr = afp->sub; while ((*temp = *ptr) != '\0') { temp++; ptr++; } need_comma = TRUE; } if( afp -> postal_code){ *temp = ' '; temp++; ptr = afp->postal_code; while ((*temp = *ptr) != '\0') { temp++; ptr++; } } if( afp -> country){ if (need_comma) { *temp = ','; temp++; *temp = ' '; temp++; } ptr = afp->country; while ((*temp = *ptr) != '\0') { temp++; ptr++; } need_comma = TRUE; } } temp++; *temp = '\0'; } /* convert double quotes to single quotes */ ptr = string; ch = *ptr; while (ch != '\0') { if (ch == '\"') { *ptr = '\''; } ptr++; ch = *ptr; } return string; } static CharPtr FormatCitBookArt ( FmtType format, CitBookPtr cbp ) { AffilPtr afp; AuthListPtr alp; CharPtr book_title = NULL; Char buf [256]; Char ch; DatePtr dp; ValNodePtr head = NULL; ImprintPtr imp; CharPtr issue = NULL; ValNodePtr names = NULL; Char pages [128]; CharPtr part_sup = NULL; CharPtr part_supi = NULL; CharPtr rsult = NULL; CharPtr str; CharPtr title; ValNodePtr ttl; ValNodePtr vnp; CharPtr volume; Char year [8]; if (cbp == NULL) return NULL; ttl = cbp->title; if (ttl == NULL) return NULL; imp = cbp->imp; if (imp == NULL) return NULL; dp = imp->date; year [0] = '\0'; if (dp != NULL) { if (dp->data [0] == 1) { if (dp->data [1] != 0) { sprintf (year, "(%ld)", (long) (1900 + dp->data [1])); } } else { StringCpy (year, "("); StringNCat (year, dp->str, 4); StringCpy (year, ")"); } } if (imp->prepub == 1 || imp->prepub == 255) { sprintf (buf, "Unpublished %s", year); return StringSave (buf); } title = (CharPtr) ttl->data.ptrvalue; if (StringLen (title) < 3) return StringSave ("."); ValNodeCopyStr (&head, 0, "(in) "); alp = cbp->authors; if (alp != NULL) { str = GetAuthorsString (format, alp); if (str != NULL) { ValNodeCopyStr (&head, 0, str); names = alp->names; if (names != NULL) { if (names->next != NULL) { ValNodeCopyStr (&head, 0, " (Eds.);"); } else { ValNodeCopyStr (&head, 0, " (Ed.);"); } } ValNodeCopyStr (&head, 0, "\n"); } MemFree (str); } book_title = StringSaveNoNull (title); vnp = ValNodeAddStr (&head, 0, book_title); if (book_title != NULL) { /* make book title all caps */ title = book_title; ch = *title; while (ch != '\0') { *title = TO_UPPER (ch); title++; ch = *title; } } volume = imp->volume; if (format == GENBANK_FMT || format == GENPEPT_FMT) { issue = imp->issue; part_sup = imp->part_sup; part_supi = imp->part_supi; } pages [0] = '\0'; FixPages (pages, imp->pages); if ((! StringHasNoText (volume)) && (StringCmp (volume, "0") != 0)) { AddValNodeString (&head, ", Vol. ", volume, NULL); DoSup (&head, issue, part_sup, part_supi); } if (! StringHasNoText (pages)) { AddValNodeString (&head, ": ", pages, NULL); } if (book_title != NULL) { ValNodeCopyStr (&head, 0, ";\n"); } afp = imp->pub; if (afp != NULL) { str = MakeAffilStr (afp); if (str != NULL) { ValNodeCopyStr (&head, 0, str); ValNodeCopyStr (&head, 0, " "); MemFree (str); } } AddValNodeString (&head, NULL, year, NULL); if (format == GENBANK_FMT || format == GENPEPT_FMT) { if (imp->prepub == 2) { ValNodeCopyStr (&head, 0, " In press"); } } rsult = MergeValNodeStrings (head); ValNodeFreeData (head); return rsult; } static CharPtr FormatCitBook ( FmtType format, CitBookPtr cbp ) { AffilPtr afp; char year[5]; CharPtr bookTitle=NULL; CharPtr retval = NULL; CharPtr temp; DatePtr dp; ImprintPtr ip; int aflen = 0; CharPtr p; CharPtr affilStr = NULL; /* Check parameters */ if (cbp == NULL) return NULL; if ( cbp -> othertype != 0) return NULL; ip = cbp -> imp; /* Format the year */ dp = ip -> date; year[0] = '\0'; if ( dp -> data[0] == 1) sprintf(year,"%ld",(long) ( 1900+dp -> data[1])); else { StringNCpy( (CharPtr) year, (CharPtr) dp -> str, (size_t) 4); year[4] = '\0'; } /* Get the book title */ if (cbp->title) bookTitle = StringSave(cbp -> title -> data.ptrvalue); /* Get the affiliation length */ if ( ip -> pub){ afp = ip -> pub; aflen = StringLen(afp -> affil)+ 5; if ( afp -> choice == 2){ aflen += 3 + StringLen(afp -> div); aflen += 3 + StringLen(afp -> street); aflen += 3 + StringLen(afp -> city); aflen += 3 + StringLen(afp -> sub); aflen += 3 + StringLen(afp -> country); } } else{ aflen = 22; } if (ip->prepub == 2) aflen += 10; /* Create a Char String big enough to hold */ /* the title, year, and affiliation. */ temp = retval = MemNew( (size_t) (30+StringLen( bookTitle)+StringLen( year) + aflen) ); /* Convert the title to upper case and */ /* add it to the string. */ for ( p = bookTitle; *p; p++) *p = TO_UPPER(*p); temp = StringMove(temp, "Book: "); temp = StringMove(temp, bookTitle); temp = StringMove(temp, "."); /* Add the affiliation to the string */ if ( ip -> pub) { afp = ip -> pub; *temp = ' '; temp++; affilStr = MakeAffilStr(afp); temp = StringMove(temp,affilStr); } /* Add the year to the string */ if (year[0] != '\0') { if (affilStr != NULL) temp = StringMove(temp," ("); else temp = StringMove(temp, "("); temp = StringMove(temp, year); temp = StringMove(temp, ")"); } /* If in press, add note */ if (ip->prepub == 2) temp = StringMove(temp, ", In press"); /* Clean up and return */ if (bookTitle) MemFree(bookTitle); return retval; } static CharPtr FormatThesis ( FmtType format, CitBookPtr cbp ) { AffilPtr afp; Char ch; DatePtr dp; ValNodePtr head = NULL; ImprintPtr imp; CharPtr ptr; CharPtr rsult = NULL; CharPtr str; CharPtr suffix = NULL; Char year [8]; if (cbp == NULL) return NULL; if (cbp->othertype != 2 || cbp->let_type != 3) return NULL; imp = cbp->imp; if (imp == NULL) return NULL; dp = imp->date; year [0] = '\0'; if (dp != NULL) { if (dp->data [0] == 1) { if (dp->data [1] != 0) { sprintf (year, "%ld", (long) (1900 + dp->data [1])); } } else { StringNCpy (year, dp->str, (size_t) 4); year [4] = '\0'; } } AddValNodeString (&head, "Thesis (", year, ")"); if (imp->prepub == 2) { suffix = ", In press"; } str = NULL; afp = imp->pub; if (afp != NULL) { if (afp->choice == 1) { if (StringLen (afp->affil) > 7) { str = StringSave (afp->affil); } } else if (afp->choice == 2) { str = MakeAffilStr (afp); } } if (str != NULL) { /* convert double quotes to single quotes */ ptr = str; ch = *ptr; while (ch != '\0') { if (ch == '\"') { *ptr = '\''; } ptr++; ch = *ptr; } AddValNodeString (&head, " ", str, suffix); MemFree (str); } rsult = MergeValNodeStrings (head); ValNodeFreeData (head); return rsult; } static CharPtr FormatCitArt ( FmtType format, Boolean citArtIsoJta, CitArtPtr cap ) { CitBookPtr cbp; CitJourPtr cjp; CharPtr rsult = NULL; if (cap == NULL) return NULL; switch (cap->from) { case 1 : cjp = (CitJourPtr) cap->fromptr; if (cjp != NULL) { rsult = FormatCitJour (format, citArtIsoJta, cjp); } break; case 2 : cbp = (CitBookPtr) cap->fromptr; if (cbp != NULL) { rsult = FormatCitBookArt (format, cbp); } break; case 3 : cbp = (CitBookPtr) cap->fromptr; if (cbp != NULL) { rsult = FormatCitBookArt (format, cbp); } break; default : break; } return rsult; } static CharPtr FormatCitPat ( FmtType format, CitPatPtr cpp, SeqIdPtr seqidp ) { AffilPtr afp; AuthListPtr alp; Char date [40]; ValNodePtr head = NULL; CharPtr prefix = NULL; CharPtr rsult = NULL; SeqIdPtr sip; CharPtr suffix = NULL; PatentSeqIdPtr psip; Int4 pat_seqid = 0; Char buf[10]; if (cpp == NULL) return NULL; if (format == GENBANK_FMT || format == GENPEPT_FMT) { ValNodeCopyStr (&head, 0, "Patent: "); suffix = " "; } else if (format == EMBL_FMT || format == EMBLPEPT_FMT) { ValNodeCopyStr (&head, 0, "Patent number "); } if (! StringHasNoText (cpp->country)) { AddValNodeString (&head, NULL, cpp->country, suffix); } if (! StringHasNoText (cpp->number)) { ValNodeCopyStr (&head, 0, cpp->number); } else if (! StringHasNoText (cpp->app_number)) { AddValNodeString (&head, "(", cpp->app_number, ")"); } if (! StringHasNoText (cpp->doc_type)) { AddValNodeString (&head, "-", cpp->doc_type, NULL); } /* pat_seqid test */ for (sip = seqidp; sip != NULL; sip = sip->next) { if (sip->choice == SEQID_PATENT) { psip = (PatentSeqIdPtr) sip -> data.ptrvalue; if (psip != NULL) { pat_seqid = psip->seqid; } } } if (pat_seqid > 0) { if (format == EMBL_FMT) { sprintf(buf,"%s%ld%s", "/", (long) pat_seqid, ", "); ValNodeCopyStr (&head, 0, buf); } else { sprintf(buf,"%s%ld ", " ", (long) pat_seqid); ValNodeCopyStr (&head, 0, buf); } } else { ValNodeCopyStr (&head, 0, " "); } /* Date */ date [0] = '\0'; if (cpp->date_issue != NULL) { DateToGB (date, cpp->date_issue, FALSE); } else if (cpp->app_date != NULL) { DateToGB (date, cpp->app_date, FALSE); } if (! StringHasNoText (date)) { ValNodeCopyStr (&head, 0, date); } if (format == GENBANK_FMT || format == GENPEPT_FMT) { ValNodeCopyStr (&head, 0, ";"); } else if (format == EMBL_FMT || format == EMBLPEPT_FMT) { ValNodeCopyStr (&head, 0, "."); } alp = cpp->authors; if (alp != NULL) { afp = alp->affil; if (afp != NULL) { suffix = NULL; if (afp->choice == 2) { suffix = ";"; } /* If and of the affiliation fields are */ /* non-blank, put them on a new line. */ if ((! StringHasNoText (afp->affil)) || (! StringHasNoText (afp->street)) || (! StringHasNoText (afp->div)) || (! StringHasNoText (afp->city)) || (! StringHasNoText (afp->sub)) || (! StringHasNoText (afp->country))) ValNodeCopyStr (&head, 0, "\n"); /* Write out the affiliation fields */ if (! StringHasNoText (afp->affil)) { AddValNodeString (&head, NULL, afp->affil, suffix); prefix = " "; } if (! StringHasNoText (afp->street)) { AddValNodeString (&head, prefix, afp->street, ";"); prefix = " "; } if (! StringHasNoText (afp->div)) { AddValNodeString (&head, prefix, afp->div, ";"); prefix = " "; } if (! StringHasNoText (afp->city)) { AddValNodeString (&head, prefix, afp->city, NULL); prefix = ", "; } if (! StringHasNoText (afp->sub)) { AddValNodeString (&head, prefix, afp->sub, NULL); } if (! StringHasNoText (afp->country)) { AddValNodeString (&head, ";\n", afp->country, ";"); } } } rsult = MergeValNodeStrings (head); ValNodeFreeData (head); /* s_StringCleanup(rsult); */ return rsult; } static CharPtr FormatCitGen ( FmtType format, Boolean dropBadCitGens, Boolean noAffilOnUnpub, CitGenPtr cgp ) { CharPtr affil = NULL; AuthListPtr alp = NULL; Char ch; DatePtr dp; ValNodePtr head = NULL; CharPtr inpress = NULL; CharPtr journal = NULL; Char pages [128]; CharPtr prefix = NULL; CharPtr ptr; CharPtr rsult = NULL; Char year [8]; if (cgp == NULL) return NULL; if (cgp->journal == NULL && StringNICmp (cgp->cit, "unpublished", 11) == 0) { if (noAffilOnUnpub) { return StringSave ("Unpublished"); } alp = cgp->authors; if (alp != NULL) { affil = GetAffil (alp->affil); if (! StringHasNoText (affil)) { rsult = MemNew ((size_t) StringLen (affil) + (size_t) StringLen (cgp->cit) + 15); StringCpy (rsult, "Unpublished "); StringCat (rsult, affil); TrimSpacesAroundString (rsult); return rsult; } } rsult = StringSave (cgp->cit); TrimSpacesAroundString (rsult); return rsult; } year [0] = '\0'; dp = cgp->date; if (dp != NULL) { if (dp->data [0] == 1) { if (dp->data [1] != 0) { sprintf (year, " (%ld)", (long) (1900 + dp->data [1])); } } else { StringCpy (year, " ("); StringNCat (year, dp->str, 4); StringCat (year, ")"); } } pages [0] = '\0'; if (cgp->pages != NULL) { FixPages (pages, cgp->pages); } if (cgp->journal != NULL) { journal = (CharPtr) cgp->journal->data.ptrvalue; } if (cgp->cit != NULL) { ptr = StringStr (cgp->cit, "Journal=\""); if (ptr != NULL) { journal = ptr + 9; } else if (StringNICmp (cgp->cit, "submitted", 8) == 0 || StringNICmp (cgp->cit, "unpublished", 11) == 0 || StringNICmp (cgp->cit, "in press", 8) == 0 || StringNICmp (cgp->cit, "to be published", 15) == 0) { if ((! dropBadCitGens) || journal != NULL) { inpress = cgp->cit; } else { inpress = "Unpublished"; } } else if ((! dropBadCitGens) && journal == NULL) { journal = cgp->cit; } } if (journal != NULL) { journal = StringSave (journal); for (ptr = journal, ch = *ptr; ch != '\0'; ptr++, ch = *ptr) { if (ch == '=' || ch == '\"') { *ptr = '\0'; } } ValNodeAddStr (&head, 0, journal); prefix = " "; } if (! StringHasNoText (inpress)) { AddValNodeString (&head, prefix, inpress, NULL); prefix = " "; } if (! StringHasNoText (cgp->volume)) { AddValNodeString (&head, prefix, cgp->volume, NULL); } if (! StringHasNoText (pages)) { if (format == GENBANK_FMT) { AddValNodeString (&head, ", ", pages, NULL); } else if (format == EMBL_FMT) { AddValNodeString (&head, ":", pages, NULL); } } if (! StringHasNoText (year)) { AddValNodeString (&head, NULL, year, NULL); } rsult = MergeValNodeStrings (head); ValNodeFreeData (head); return rsult; } static CharPtr FormatCitSub ( FmtType format, CitSubPtr csp ) { CharPtr affil; AffilPtr afp; AuthListPtr alp; Char buf [256]; Char date [40]; ValNodePtr head = NULL; CharPtr rsult = NULL; if (csp == NULL) return NULL; date [0] = '\0'; if (csp->date != NULL) { DateToGB (date, csp->date, TRUE); } if (StringHasNoText (date)) { StringCpy (date, "??-???-????"); } sprintf (buf, "Submitted (%s)", date); ValNodeCopyStr (&head, 0, buf); alp = csp->authors; if (alp != NULL) { afp = alp->affil; if (afp != NULL) { affil = GetAffil (afp); if (format == EMBL_FMT || format == EMBLPEPT_FMT) { if (StringNCmp(affil, " to the EMBL/GenBank/DDBJ databases.", 36) != 0) { ValNodeCopyStr (&head, 0, " to the EMBL/GenBank/DDBJ databases.\n"); } else { ValNodeCopyStr (&head, 0, " "); } } else { ValNodeCopyStr (&head, 0, " "); } ValNodeCopyStr (&head, 0, affil); MemFree (affil); } } rsult = MergeValNodeStrings (head); ValNodeFreeData (head); return rsult; } static CharPtr GetPubJournal ( FmtType format, Boolean dropBadCitGens, Boolean noAffilOnUnpub, Boolean citArtIsoJta, PubdescPtr pdp, CitSubPtr csp, SeqIdPtr seqidp ) { CitArtPtr cap; CitBookPtr cbp; CitGenPtr cgp; CitPatPtr cpp; CharPtr journal = NULL; MedlineEntryPtr mep; ValNodePtr vnp; if (csp != NULL) { return FormatCitSub (format, csp); } if (pdp == NULL) return NULL; for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) { switch (vnp->choice) { case PUB_Gen : cgp = (CitGenPtr) vnp->data.ptrvalue; if (cgp != NULL) { if (StringNICmp ("BackBone id_pub", cgp->cit, 15) != 0) { if (cgp->cit == NULL && cgp->journal == NULL && cgp->date == NULL && cgp->serial_number) { break; /* skip just serial number */ } } journal = FormatCitGen (format, dropBadCitGens, noAffilOnUnpub, cgp); } break; case PUB_Sub : csp = (CitSubPtr) vnp->data.ptrvalue; if (csp != NULL) { journal = FormatCitSub (format, csp); } break; case PUB_Medline : mep = (MedlineEntryPtr) vnp->data.ptrvalue; if (mep != NULL) { cap = mep->cit; if (cap != NULL) { journal = FormatCitArt (format, citArtIsoJta, cap); } } break; case PUB_Article : cap = (CitArtPtr) vnp->data.ptrvalue; if (cap != NULL) { journal = FormatCitArt (format, citArtIsoJta, cap); } break; case PUB_Book : case PUB_Proc : cbp = (CitBookPtr) vnp->data.ptrvalue; if (cbp != NULL) { journal = FormatCitBook (format, cbp); } break; case PUB_Man : cbp = (CitBookPtr) vnp->data.ptrvalue; if (cbp != NULL) { journal = FormatThesis (format, cbp); } break; case PUB_Patent : cpp = (CitPatPtr) vnp->data.ptrvalue; if (cpp != NULL) { journal = FormatCitPat (format, cpp, seqidp); } break; default : break; } if (journal != NULL) return journal; } return NULL; } static Int4 GetMuid ( PubdescPtr pdp ) { MedlineEntryPtr mep; ValNodePtr vnp; if (pdp == NULL) return 0; for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) { switch (vnp->choice) { case PUB_Medline : mep = (MedlineEntryPtr) vnp->data.ptrvalue; if (mep != NULL) { return mep->uid; } break; case PUB_Muid : return vnp->data.intvalue; break; default : break; } } return 0; } static Int4 GetPmid ( PubdescPtr pdp ) { MedlineEntryPtr mep; ValNodePtr vnp; if (pdp == NULL) return 0; for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) { switch (vnp->choice) { case PUB_Medline : mep = (MedlineEntryPtr) vnp->data.ptrvalue; if (mep != NULL) { return mep->pmid; } break; case PUB_PMid : return vnp->data.intvalue; break; default : break; } } return 0; } static CharPtr remarksText [] = { "full automatic", "full staff_review", "full staff_entry", "simple staff_review", "simple staff_entry", "simple automatic", "unannotated automatic", "unannotated staff_review", "unannotated staff_entry", NULL }; static CharPtr FormatReferenceBlock ( Asn2gbFormatPtr afp, BaseBlockPtr bbp ) { IntAsn2gbJobPtr ajp; AuthListPtr alp; Asn2gbSectPtr asp; BioseqPtr bsp; Char buf [150]; CitArtPtr cap; CitJourPtr cjp; CitRetractPtr crp; CitSubPtr csp = NULL; SeqMgrDescContext dcontext; SeqMgrFeatContext fcontext; Int4 gibbsq; Int2 i; ImprintPtr imp; IntRefBlockPtr irp; size_t len; SeqLocPtr loc = NULL; Int4 muid; Boolean needsPeriod; SeqLocPtr nextslp; Boolean notFound; ObjMgrDataPtr omdp; PubdescPtr pdp = NULL; Int4 pmid; CharPtr prefix; RefBlockPtr rbp; SubmitBlockPtr sbp; SeqDescrPtr sdp; SeqFeatPtr sfp = NULL; SeqIdPtr sip; SeqLocPtr slp; SeqSubmitPtr ssp; Int4 start; Int4 stop; CharPtr str; CharPtr suffix = NULL; Boolean trailingPeriod; ValNodePtr vnp; if (afp == NULL || bbp == NULL) return NULL; rbp = (RefBlockPtr) bbp; ajp = afp->ajp; if (ajp == NULL) return NULL; asp = afp->asp; if (asp == NULL) return NULL; bsp = asp->bsp; if (bsp == NULL) return NULL; if (! StringHasNoText (rbp->string)) return StringSave (rbp->string); /* could be descriptor, feature, or submit block citation */ if (rbp->itemtype == OBJ_SEQDESC) { sdp = SeqMgrGetDesiredDescriptor (rbp->entityID, NULL, rbp->itemID, 0, NULL, &dcontext); if (sdp != NULL && dcontext.seqdesctype == Seq_descr_pub) { pdp = (PubdescPtr) sdp->data.ptrvalue; } } else if (rbp->itemtype == OBJ_SEQFEAT) { sfp = SeqMgrGetDesiredFeature (rbp->entityID, NULL, rbp->itemID, 0, NULL, &fcontext); if (sfp != NULL && fcontext.seqfeattype == SEQFEAT_PUB) { pdp = (PubdescPtr) sfp->data.value.ptrvalue; } } else if (rbp->itemtype == OBJ_SEQSUB_CIT) { omdp = ObjMgrGetData (rbp->entityID); if (omdp != NULL && omdp->datatype == OBJ_SEQSUB) { ssp = (SeqSubmitPtr) omdp->dataptr; if (ssp != NULL && ssp->datatype == 1) { sbp = ssp->sub; if (sbp != NULL) { csp = sbp->cit; } } } } if (pdp == NULL && csp == NULL) return NULL; /* print serial number */ gb_StartPrint (afp->format, 0, 12, "REFERENCE", 13, 5, 5, "RN", TRUE); if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) { sprintf (buf, "%d", (int) rbp->serial); } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) { sprintf (buf, "[%d]", (int) rbp->serial); } gb_AddString (NULL, buf, NULL, FALSE, FALSE, TILDE_TO_SPACES); /* print base range */ if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) { if (rbp->sites != 3) { TabToColumn (16); } } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) { if (rbp->sites == 0) { ff_EndPrint (); ff_StartPrint (5, 5, ASN2FF_EMBL_MAX, "RP"); } } if (rbp->sites == 1 || rbp->sites == 2) { if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) { gb_AddString (NULL, "(sites)", NULL, FALSE, FALSE, TILDE_TO_SPACES); } ff_EndPrint (); } else if (rbp->sites == 3) { ff_EndPrint (); } else { if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) { TabToColumn (16); if (afp->format == GENBANK_FMT) { gb_AddString (NULL, "(bases ", NULL, FALSE, FALSE, TILDE_TO_SPACES); } else { gb_AddString (NULL, "(residues ", NULL, FALSE, FALSE, TILDE_TO_SPACES); } } irp = (IntRefBlockPtr) rbp; loc = irp->loc; if (loc != NULL) { if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) { suffix = "; "; } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) { suffix = ", "; } slp = SeqLocFindNext (loc, NULL); while (slp != NULL) { nextslp = SeqLocFindNext (loc, slp); start = SeqLocStart (slp) + 1; stop = SeqLocStop (slp) + 1; if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) { sprintf (buf, "%ld to %ld", (long) start, (long) stop); } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) { sprintf (buf, "%ld-%ld", (long) start, (long) stop); } if (nextslp == NULL) { suffix = NULL; } gb_AddString (NULL, buf, suffix, FALSE, FALSE, TILDE_TO_SPACES); slp = nextslp; } } else { /* code still used for ssp->cit */ start = 1; stop = bsp->length; if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) { sprintf (buf, "%ld to %ld", (long) start, (long) stop); } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) { sprintf (buf, "%ld-%ld", (long) start, (long) stop); } gb_AddString (NULL, buf, NULL, FALSE, FALSE, TILDE_TO_SPACES); } if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) { gb_AddString (NULL, ")", NULL, FALSE, FALSE, TILDE_TO_SPACES); } ff_EndPrint (); } /* print author list */ gb_StartPrint (afp->format, 2, 12, "AUTHORS", 13, 5, 5, "RA", FALSE); str = NULL; alp = GetAuthListPtr (pdp, csp); if (alp != NULL) { str = GetAuthorsString (afp->format, alp); TrimSpacesAroundString (str); } if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) { suffix = NULL; trailingPeriod = TRUE; } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) { trailingPeriod = FALSE; len = StringLen (str); if (len > 0 && str [len - 1] != '.') { suffix = ".;"; } else { suffix = ";"; } } gb_AddString (NULL, str, suffix, trailingPeriod, FALSE, TILDE_TO_SPACES); MemFree (str); ff_EndPrint (); /* print title */ str = GetPubTitle (afp->format, pdp, csp); CleanPubTitle (str); StrStripSpaces (str); if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) { prefix = NULL; suffix = NULL; } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) { if (str != NULL) { prefix = "\""; suffix = "\";"; } else { prefix = NULL; suffix = ";"; } } if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) { if (! StringHasNoText (str)) { gb_StartPrint (afp->format, 2, 12, "TITLE", 13, 5, 5, "RT", FALSE); gb_AddString (prefix, str, suffix, FALSE, FALSE, TILDE_TO_SPACES); ff_EndPrint (); } } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) { gb_StartPrint (afp->format, 2, 12, "TITLE", 13, 5, 5, "RT", FALSE); if (! StringHasNoText (str)) { gb_AddString (prefix, str, suffix, FALSE, FALSE, TILDE_TO_SPACES); } else { ff_AddChar (';'); } ff_EndPrint (); } MemFree (str); /* print journal */ gb_StartPrint (afp->format, 2, 12, "JOURNAL", 13, 5, 5, "RL", FALSE); str = GetPubJournal (afp->format, ajp->flags.dropBadCitGens, ajp->flags.noAffilOnUnpub, ajp->flags.citArtIsoJta, pdp, csp, bsp->id); if (str == NULL) { str = StringSave ("Unpublished"); } StrStripSpaces (str); TrimSpacesAroundString (str); if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) { needsPeriod = FALSE; } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) { needsPeriod = TRUE; } gb_AddString (NULL, str, NULL, FALSE, FALSE, TILDE_IGNORE); if (needsPeriod) { gb_AddString (NULL, ".", NULL, FALSE, FALSE, TILDE_TO_SPACES); } MemFree (str); ff_EndPrint (); /* print muid */ muid = GetMuid (pdp); if (muid > 0) { gb_StartPrint (afp->format, 2, 12, "MEDLINE", 13, 5, 5, "RX", FALSE); if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) { www_muid (muid); } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) { sprintf (buf, "MEDLINE; %ld.", (long) muid); gb_AddString (NULL, buf, NULL, FALSE, FALSE, TILDE_TO_SPACES); } ff_EndPrint (); } if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) { pmid = GetPmid (pdp); if (pmid > 0) { gb_StartPrint (afp->format, 3, 12, "PUBMED", 13, 5, 5, "RX", FALSE); www_muid (pmid); ff_EndPrint (); } } if (pdp == NULL) return gb_MergeString (FALSE); /* !!! remainder of fields are only for GenBank !!! */ if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) { prefix = "REMARK"; if (pdp->comment != NULL) { for (i = 0, notFound = TRUE; notFound && remarksText [i] != NULL; i++) { if (StringCmp (pdp->comment, remarksText [i]) == 0) { notFound = FALSE; } } if (notFound) { gb_StartPrint (afp->format, 2, 12, prefix, 13, 5, 5, NULL, FALSE); gb_AddString (NULL, pdp->comment, NULL, FALSE, TRUE, TILDE_EXPAND); ff_EndPrint (); prefix = NULL; } } gibbsq = 0; for (sip = bsp->id; sip != NULL; sip = sip->next) { if (sip->choice == SEQID_GIBBSQ) { gibbsq = sip->data.intvalue; } } csp = NULL; for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) { if (vnp->choice == PUB_Sub) { csp = (CitSubPtr) vnp->data.ptrvalue; } } if (gibbsq > 0 /* && csp == NULL */) { sprintf (buf, "GenBank staff at the National Library of Medicine created this entry [NCBI gibbsq %ld] from the original journal article.", (long) gibbsq); gb_StartPrint (afp->format, 2, 12, prefix, 13, 5, 5, NULL, FALSE); gb_AddString (NULL, buf, NULL, FALSE, FALSE, TILDE_EXPAND); ff_EndPrint (); prefix = NULL; /* gibbsq comment section (fields may be copied from degenerate pubdesc) */ str = pdp->fig; if (StringHasNoText (str)) { str = irp->fig; } if (! StringHasNoText (str)) { sprintf (buf, "This sequence comes from %s", str); gb_StartPrint (afp->format, 2, 12, prefix, 13, 5, 5, NULL, FALSE); gb_AddString (NULL, buf, NULL, TRUE, TRUE, TILDE_EXPAND); ff_EndPrint (); prefix = NULL; } if (pdp->poly_a || irp->poly_a) { gb_StartPrint (afp->format, 2, 12, prefix, 13, 5, 5, NULL, FALSE); gb_AddString (NULL, "Polyadenylate residues occurring in the figure were omitted from the sequence.", NULL, TRUE, TRUE, TILDE_EXPAND); ff_EndPrint (); prefix = NULL; } str = pdp->maploc; if (StringHasNoText (str)) { str = irp->maploc; } if (! StringHasNoText (str)) { sprintf (buf, "Map location: %s", str); gb_StartPrint (afp->format, 2, 12, prefix, 13, 5, 5, NULL, FALSE); gb_AddString (NULL, buf, NULL, TRUE, TRUE, TILDE_EXPAND); ff_EndPrint (); prefix = NULL; } } for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) { if (vnp->choice == PUB_Article) { cap = (CitArtPtr) vnp->data.ptrvalue; if (cap != NULL && cap->from == 1) { cjp = (CitJourPtr) cap->fromptr; if (cjp != NULL) { imp = cjp->imp; if (imp != NULL) { crp = imp->retract; if (crp != NULL && crp->type == 3) { gb_StartPrint (afp->format, 2, 12, prefix, 13, 5, 5, NULL, FALSE); gb_AddString (NULL, "Erratum:", NULL, FALSE, FALSE, TILDE_TO_SPACES); gb_AddString ("[", crp->exp, "]", FALSE, TRUE, TILDE_EXPAND); ff_EndPrint (); prefix = NULL; } } } } } else if (vnp->choice == PUB_Sub) { csp = (CitSubPtr) vnp->data.ptrvalue; if (csp != NULL) { if (! StringHasNoText (csp->descr)) { gb_StartPrint (afp->format, 2, 12, prefix, 13, 5, 5, NULL, FALSE); gb_AddString (NULL, csp->descr, NULL, FALSE, TRUE, TILDE_EXPAND); ff_EndPrint (); prefix = NULL; } } } } } return ff_print_string_mem (gb_MergeString (FALSE)); } static CharPtr FormatCommentBlock ( Asn2gbFormatPtr afp, BaseBlockPtr bbp ) { Boolean add_period; CommentBlockPtr cbp; CharPtr db; DbtagPtr dbt; SeqMgrDescContext dcontext; SeqMgrFeatContext fcontext; size_t len; ObjectIdPtr oip; CharPtr prefix; SeqDescrPtr sdp; SeqFeatPtr sfp; Char sfx [32]; CharPtr str; CharPtr suffix; CharPtr title; if (afp == NULL || bbp == NULL) return NULL; cbp = (CommentBlockPtr) bbp; /* some comments are allocated (along with possible first COMMENT label) */ if (! StringHasNoText (bbp->string)) return StringSave (bbp->string); title = NULL; prefix = NULL; suffix = NULL; add_period = FALSE; sfx [0] = '\0'; if (bbp->itemtype == OBJ_SEQDESC) { /* usually should reference comment, maploc, or region descriptor IDs */ sdp = SeqMgrGetDesiredDescriptor (bbp->entityID, NULL, bbp->itemID, 0, NULL, &dcontext); if (sdp != NULL) { if (dcontext.seqdesctype == Seq_descr_comment) { title = (CharPtr) sdp->data.ptrvalue; } else if (dcontext.seqdesctype == Seq_descr_maploc) { dbt = (DbtagPtr) sdp->data.ptrvalue; if (dbt != NULL) { db = dbt->db; oip = dbt->tag; if (oip != NULL) { if (oip->str != NULL) { title = oip->str; prefix = ("Map location: "); } else if (db != NULL && oip->id != 0) { title = db; prefix = ("Map location: (Database "); sprintf (sfx, "; id # %ld).", (long) oip->id); suffix = sfx; } } } } else if (dcontext.seqdesctype == Seq_descr_region) { title = (CharPtr) sdp->data.ptrvalue; prefix = "Region: "; } } } else if (bbp->itemtype == OBJ_SEQFEAT) { /* also have to deal with comment feature across entire sequence */ sfp = SeqMgrGetDesiredFeature (bbp->entityID, NULL, bbp->itemID, 0, NULL, &fcontext); if (sfp != NULL && fcontext.seqfeattype == SEQFEAT_COMMENT) { title = sfp->comment; } } if (title == NULL) return NULL; if (cbp->first) { gb_StartPrint (afp->format, 0, 12, "COMMENT", 13, 5, 5, "CC", TRUE); } else { gb_StartPrint (afp->format, 0, 12, NULL, 13, 5, 5, "CC", FALSE); } str = StringSave (title); TrimSpacesAndJunkFromEnds (str, TRUE); if (! IsEllipsis (str)) { s_RemovePeriodFromEnd (str); len = StringLen (str); if (len > 0 && str [len - 1] != '.') { add_period = TRUE; } } gb_AddString (prefix, str, suffix, FALSE, TRUE, TILDE_OLD_EXPAND); if (add_period) { gb_AddString (NULL, ".", NULL, FALSE, FALSE, TILDE_TO_SPACES); } MemFree (str); return gb_MergeString (TRUE); } /* format features section */ static Boolean is_real_id ( SeqIdPtr sip, SeqIdPtr this_sip ) { BioseqPtr bsp; if (sip == NULL || this_sip == NULL) return FALSE; if (! SeqIdIn (sip, this_sip)) { bsp = BioseqFind (sip); if (bsp == NULL) return TRUE; /* ??? */ if (bsp->repr == Seq_repr_virtual) return FALSE; } return TRUE; } static Boolean FlatVirtLoc ( BioseqPtr bsp, SeqLocPtr location ) { SeqIntPtr sintp; SeqIdPtr sip; SeqPntPtr spp; if (bsp == NULL || location == NULL) return FALSE; switch (location->choice) { case SEQLOC_WHOLE : sip = (SeqIdPtr) location->data.ptrvalue; if (sip == NULL) return TRUE; if (! is_real_id (sip, bsp->id)) return TRUE; break; case SEQLOC_INT : sintp = (SeqIntPtr) location->data.ptrvalue; if (sintp == NULL) return TRUE; sip = sintp->id; if (sip == NULL) return TRUE; if (! is_real_id (sip, bsp->id)) return TRUE; break; case SEQLOC_PNT : spp = (SeqPntPtr) location->data.ptrvalue; if (spp == NULL) return TRUE; sip = spp->id; if (sip == NULL) return TRUE; if (! is_real_id (sip, bsp->id)) return TRUE; break; default : break; } return FALSE; } static Uint1 order [NUM_SEQID]; static Boolean order_initialized = FALSE; static CharPtr lim_str [5] = { "", ">","<", ">", "<" }; static void FlatLocSeqId ( ValNodePtr PNTR head, SeqIdPtr sip ) { BioseqPtr bsp; Char buf [40]; ObjectIdPtr oip; SeqIdPtr use_id = NULL; Boolean was_lock = FALSE; if (head == NULL || sip == NULL) return; bsp = BioseqFind (sip); if (bsp == NULL) { bsp = BioseqLockById (sip); was_lock = TRUE; } if (bsp != NULL) { use_id = SeqIdSelect (bsp->id, order, NUM_SEQID); } else if (sip->choice == SEQID_GI) { use_id = GetSeqIdForGI (sip->data.intvalue); } if (use_id != NULL) { SeqIdWrite (use_id, buf, PRINTID_TEXTID_ACC_VER, sizeof (buf) - 1); } else if (sip->choice == SEQID_GI) { SeqIdWrite (sip, buf, PRINTID_FASTA_LONG, sizeof (buf) - 1); } if (was_lock) { BioseqUnlock (bsp); } if (StringHasNoText (buf)) { StringCpy (buf, "?00000"); if (use_id != NULL && use_id->choice == SEQID_LOCAL) { oip = (ObjectIdPtr) use_id->data.ptrvalue; if (oip != NULL && (! StringHasNoText (oip->str))) { StringNCpy_0 (buf, oip->str, 13); } } } AddValNodeString (head, NULL, buf, ":"); } static void FlatLocCaret ( ValNodePtr PNTR head, SeqIdPtr sip, SeqIdPtr this_sip, Int4 point, IntFuzzPtr fuzz ) { Char buf [128]; Uint1 index; if (head == NULL) return; if (sip != NULL && (! SeqIdIn (sip, this_sip))) { FlatLocSeqId (head, sip); } buf [0] = '\0'; point++; /* orginal FlatLocHalfCaret was called with point + 1 */ if (fuzz != NULL) { switch (fuzz->choice) { case 1 : sprintf (buf, "(%ld.%ld)..(%ld.%ld)", (long) (point - fuzz->a), (long) point, (long) point, (long) (point + fuzz->a)); break; case 2 : sprintf (buf, "%ld^%ld", (long) (1 + fuzz->b), (long) (1 + fuzz->a)); break; case 3 : sprintf (buf, "%ld^%ld", (long) (point - point * ((double) fuzz->a / 1000.0)), (long) (point + point * ((double) fuzz->a / 1000.0))); break; case 4 : if (fuzz->a == 3) { /* space to right */ sprintf (buf, "%ld^%ld", (long) (point), (long) (point + 1)); } else if (fuzz->a == 4 && point > 1) { /* space to left */ sprintf (buf, "%ld^%ld", (long) (point - 1), (long) point); } else { index = (Uint1) fuzz->a; if (index > 4) { index = 0; } sprintf (buf, "%s%ld", lim_str [index], (long) point); } break; default : sprintf (buf, "%ld", (long) point); break; } } else { sprintf (buf, "%ld", (long) point); } ValNodeCopyStr (head, 0, buf); } static void FlatLocPoint ( ValNodePtr PNTR head, SeqIdPtr sip, SeqIdPtr this_sip, Int4 point, IntFuzzPtr fuzz ) { Char buf [128]; Uint1 index; if (head == NULL) return; if (sip != NULL && (! SeqIdIn (sip, this_sip))) { FlatLocSeqId (head, sip); } buf [0] = '\0'; point++; if (fuzz != NULL) { switch (fuzz->choice) { case 1 : sprintf (buf, "(%ld.%ld)", (long) (point - fuzz->a), (long) (point + fuzz->a)); break; case 2 : sprintf (buf, "(%ld.%ld)", (long) (1 + fuzz->b), (long) (1 + fuzz->a)); break; case 3 : sprintf (buf, "(%ld.%ld)", (long) (point - point * ((double) fuzz->a / 1000.0)), (long) (point + point * ((double) fuzz->a / 1000.0))); break; case 4 : index = (Uint1) fuzz->a; if (index > 4) { index = 0; } sprintf (buf, "%s%ld", lim_str [index], (long) point); break; default : sprintf (buf, "%ld", (long) point); break; } } else { sprintf (buf, "%ld", (long) point); } ValNodeCopyStr (head, 0, buf); } static void FlatLocElement ( ValNodePtr PNTR head, BioseqPtr bsp, SeqLocPtr location ) { Boolean minus_strand = FALSE; SeqBondPtr sbp; SeqIntPtr sintp; SeqIdPtr sip; SeqPntPtr spp; BioseqPtr wholebsp; if (head == NULL || bsp == NULL || location == NULL) return; switch (location->choice) { case SEQLOC_WHOLE : sip = (SeqIdPtr) location->data.ptrvalue; if (sip == NULL) return; wholebsp = BioseqFind (sip); if (wholebsp == NULL) return; if (is_real_id (sip, bsp->id)) { FlatLocPoint (head, sip, bsp->id, 0, NULL); if (bsp->length > 0) { ValNodeCopyStr (head, 0, ".."); FlatLocPoint (head, NULL, bsp->id, bsp->length - 1, NULL); } } break; case SEQLOC_INT : sintp = (SeqIntPtr) location->data.ptrvalue; if (sintp == NULL) return; sip = sintp->id; if (sip == NULL) return; if (is_real_id (sip, bsp->id)) { minus_strand = (Boolean) (sintp->strand == Seq_strand_minus); if (minus_strand) { ValNodeCopyStr (head, 0, "complement("); } FlatLocPoint (head, sip, bsp->id, sintp->from, sintp->if_from); if (sintp->to > 0 && (sintp->to != sintp->from || sintp->if_from != NULL || sintp->if_to != NULL)) { ValNodeCopyStr (head, 0, ".."); FlatLocPoint (head, NULL, bsp->id, sintp->to, sintp->if_to); } if (minus_strand) { ValNodeCopyStr (head, 0, ")"); } } break; case SEQLOC_PNT : spp = (SeqPntPtr) location->data.ptrvalue; if (spp == NULL) return; sip = spp->id; if (sip == NULL) return; if (is_real_id (sip, bsp->id)) { minus_strand = (Boolean) (spp->strand == Seq_strand_minus); if (minus_strand) { ValNodeCopyStr (head, 0, "complement("); } if (spp->fuzz != NULL) { FlatLocCaret (head, sip, bsp->id, spp->point, spp->fuzz); } else { FlatLocPoint (head, sip, bsp->id, spp->point, NULL); } if (minus_strand) { ValNodeCopyStr (head, 0, ")"); } } break; case SEQLOC_BOND : sbp = (SeqBondPtr) location->data.ptrvalue; if (sbp == NULL) return; spp = sbp->a; if (spp == NULL) return; sip = spp->id; if (sip == NULL) return; ValNodeCopyStr (head, 0, "bond("); FlatLocPoint (head, sip, bsp->id, spp->point, spp->fuzz); spp = sbp->b; if (spp != NULL) { ValNodeCopyStr (head, 0, ","); FlatLocPoint (head, NULL, bsp->id, spp->point, spp->fuzz); } ValNodeCopyStr (head, 0, ")"); break; default : /* unexpected internal complex type or unimplemented SEQLOC_FEAT */ return; } } static Boolean FlatNullAhead ( BioseqPtr bsp, ValNodePtr location ) { SeqLocPtr next; if (bsp == NULL || location == NULL) return FALSE; next = location->next; if (next == NULL) return TRUE; if (next->choice == SEQLOC_NULL) return TRUE; if (FlatVirtLoc (bsp, next)) return TRUE; return FALSE; } static void FlatPackedPoint ( ValNodePtr PNTR head, PackSeqPntPtr pspp, BioseqPtr bsp ) { Uint1 dex; if (head == NULL || pspp == NULL || bsp == NULL) return; for (dex = 0; dex < pspp->used; dex++) { FlatLocPoint (head, pspp->id, bsp->id, pspp->pnts [dex], pspp->fuzz); } } static void DoFlatLoc ( ValNodePtr PNTR head, BioseqPtr bsp, SeqLocPtr location, Boolean ok_to_complement ); static void GroupFlatLoc ( ValNodePtr PNTR head, BioseqPtr bsp, SeqLocPtr location, CharPtr prefix, Boolean is_flat_order ) { Boolean found_non_virt = FALSE; SeqIdPtr hold_next; Int2 parens = 1; PackSeqPntPtr pspp; SeqLocPtr slp; Boolean special_mode = FALSE; /* join in order */ if (head == NULL || bsp == NULL || location == NULL) return; /* prefix will have the first parenthesis */ ValNodeCopyStr (head, 0, prefix); for (slp = (SeqLocPtr) location->data.ptrvalue; slp != NULL; slp = slp->next) { if (slp->choice == SEQLOC_NULL || FlatVirtLoc (bsp, slp)) { if (slp != location && slp->next != NULL) { if (special_mode) { special_mode = FALSE; ValNodeCopyStr (head, 0, ")"); parens--; } } continue; } if (found_non_virt && slp->choice != SEQLOC_EMPTY && slp->choice != SEQLOC_NULL) { ValNodeCopyStr (head, 0, ","); } switch (slp->choice) { case SEQLOC_WHOLE : case SEQLOC_PNT : case SEQLOC_BOND : case SEQLOC_FEAT : found_non_virt = TRUE; if (FlatVirtLoc (bsp, slp)) { if (slp != location && slp->next != NULL) { if (special_mode) { special_mode = FALSE; ValNodeCopyStr (head, 0, ")"); parens--; } } } else { FlatLocElement (head, bsp, slp); } break; case SEQLOC_INT : found_non_virt = TRUE; if (is_flat_order && (! FlatNullAhead (bsp, slp))) { special_mode = TRUE; ValNodeCopyStr (head, 0, "join("); parens++; } FlatLocElement (head, bsp, slp); break; case SEQLOC_PACKED_PNT : found_non_virt = TRUE; pspp = (PackSeqPntPtr) slp->data.ptrvalue; if (pspp != NULL) { FlatPackedPoint (head, pspp, bsp); } break; case SEQLOC_PACKED_INT : case SEQLOC_MIX : case SEQLOC_EQUIV : found_non_virt = TRUE; hold_next = slp->next; slp->next = NULL; DoFlatLoc (head, bsp, slp, FALSE); slp->next = hold_next; break; default : break; } } while (parens > 0) { ValNodeCopyStr (head, 0, ")"); parens--; } } static void DoFlatLoc ( ValNodePtr PNTR head, BioseqPtr bsp, SeqLocPtr location, Boolean ok_to_complement ) { Boolean found_null; SeqLocPtr next_loc; PackSeqPntPtr pspp; SeqLocPtr slp; if (head == NULL || bsp == NULL || location == NULL) return; /* deal with complement of entire location */ if (ok_to_complement && SeqLocStrand (location) == Seq_strand_minus) { slp = AsnIoMemCopy ((Pointer) location, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite); if (slp != NULL) { SeqLocRevCmp (slp); ValNodeCopyStr (head, 0, "complement("); DoFlatLoc (head, bsp, slp, FALSE); ValNodeCopyStr (head, 0, ")"); } SeqLocFree (slp); return; } /* handle each location component */ for (slp = location; slp != NULL; slp = slp->next) { if (slp->choice == SEQLOC_NULL || FlatVirtLoc (bsp, slp)) continue; /* print comma between components */ if (slp != location) { ValNodeCopyStr (head, 0, ","); } switch (slp->choice) { case SEQLOC_MIX : case SEQLOC_PACKED_INT : found_null = FALSE; for (next_loc = (SeqLocPtr) slp->data.ptrvalue; next_loc != NULL; next_loc = next_loc->next) { if (next_loc->choice == SEQLOC_NULL || FlatVirtLoc (bsp, next_loc) || LocationHasNullsBetween (slp)) found_null = TRUE; } if (found_null) { GroupFlatLoc (head, bsp, slp, "order(", TRUE); } else { GroupFlatLoc (head, bsp, slp, "join(", FALSE); } break; case SEQLOC_EQUIV : GroupFlatLoc (head, bsp, slp, "one-of(", FALSE); break; case SEQLOC_PACKED_PNT : pspp = (PackSeqPntPtr) slp->data.ptrvalue; if (pspp != NULL) { FlatPackedPoint (head, pspp, bsp); } break; default : FlatLocElement (head, bsp, slp); break; } } } static CharPtr FlatLoc ( BioseqPtr bsp, SeqLocPtr location, Boolean masterStyle ) { ValNodePtr head = NULL; SeqLocPtr loc; Boolean noLeft; Boolean noRight; Uint1 num = 1; CharPtr str; if (bsp == NULL || location == NULL) return NULL; if (! order_initialized) { order [SEQID_GENBANK] = num++; order [SEQID_EMBL] = num++; order [SEQID_DDBJ] = num++; order [SEQID_LOCAL] = num++; order [SEQID_OTHER] = num++; order [SEQID_TPG] = num++; order [SEQID_TPE] = num++; order [SEQID_TPD] = num++; order [SEQID_GIBBSQ] = num++; order [SEQID_GIBBMT] = num++; order [SEQID_PRF] = num++; order [SEQID_PDB] = num++; order [SEQID_PIR] = num++; order [SEQID_SWISSPROT] = num++; order [SEQID_PATENT] = num++; order [SEQID_GI] = num++;; order [SEQID_GENERAL] = num++; order [SEQID_GIIM] = num++; order_initialized = TRUE; } if (masterStyle) { /* map location from parts to segmented bioseq */ CheckSeqLocForPartial (location, &noLeft, &noRight); loc = SeqLocMerge (bsp, location, NULL, FALSE, TRUE, FALSE); if (loc == NULL) { return StringSave ("?"); } FreeAllFuzz (loc); SetSeqLocPartial (loc, noLeft, noRight); DoFlatLoc (&head, bsp, loc, TRUE); SeqLocFree (loc); } else { DoFlatLoc (&head, bsp, location, TRUE); } str = MergeValNodeStrings (head); ValNodeFreeData (head); return str; } static void SubSourceToQualArray ( SubSourcePtr ssp, QualValPtr qvp ) { Int2 idx; Uint1 subtype; if (ssp == NULL || qvp == NULL) return; while (ssp != NULL) { subtype = ssp->subtype; if (subtype == 255) { subtype = 29; } if (subtype < 30) { idx = subSourceToSourceIdx [subtype]; if (idx > 0 && idx < ASN2GNBK_TOTAL_SOURCE) { if (qvp [idx].ssp == NULL) { qvp [idx].ssp = ssp; } } } ssp = ssp->next; } } static Int2 orgModToSourceIdx [35] = { SCQUAL_zero_orgmod, SCQUAL_one_orgmod, SCQUAL_strain, SCQUAL_sub_strain, SCQUAL_type, SCQUAL_sub_type, SCQUAL_variety, SCQUAL_serotype, SCQUAL_serogroup, SCQUAL_serovar, SCQUAL_cultivar, SCQUAL_pathovar, SCQUAL_chemovar, SCQUAL_biovar, SCQUAL_biotype, SCQUAL_group, SCQUAL_sub_group, SCQUAL_isolate, SCQUAL_common, SCQUAL_acronym, SCQUAL_dosage, SCQUAL_spec_or_nat_host, SCQUAL_sub_species, SCQUAL_specimen_voucher, SCQUAL_authority, SCQUAL_forma, SCQUAL_forma_specialis, SCQUAL_ecotype, SCQUAL_synonym, SCQUAL_anamorph, SCQUAL_teleomorph, SCQUAL_breed, SCQUAL_old_lineage, SCQUAL_old_name, SCQUAL_orgmod_note }; static void OrgModToQualArray ( OrgModPtr omp, QualValPtr qvp ) { Int2 idx; Uint1 subtype; if (omp == NULL || qvp == NULL) return; while (omp != NULL) { subtype = omp->subtype; if (subtype == 253) { subtype = 32; } else if (subtype == 254) { subtype = 33; } else if (subtype == 255) { subtype = 34; } if (subtype < 35) { idx = orgModToSourceIdx [subtype]; if (idx > 0 && idx < ASN2GNBK_TOTAL_SOURCE) { if (qvp [idx].omp == NULL) { qvp [idx].omp = omp; } } } omp = omp->next; } } static CharPtr organelleQual [] = { NULL, NULL, "/organelle=\"plastid:chloroplast\"", "/organelle=\"plastid:chromoplast\"", "/organelle=\"mitochondrion:kinetoplast\"", "/organelle=\"mitochondrion\"", "/organelle=\"plastid\"", "/macronuclear", NULL, "/plasmid", "/transposon", "/insertion_seq", "/organelle=\"plastid:cyanelle\"", "/proviral", "/virion", "/organelle=\"nucleomorph\"", "/organelle=\"plastid:apicoplast\"", "/organelle=\"plastid:leucoplast\"", "/organelle=\"plastid:proplastid\"", NULL }; static Boolean StringIsJustQuotes ( CharPtr str ) { Nlm_Uchar ch; /* to use 8bit characters in multibyte languages */ if (str != NULL) { ch = *str; while (ch != '\0') { if (ch > ' ' && ch != '"' && ch != '\'') { return FALSE; } str++; ch = *str; } } return TRUE; } static CharPtr FormatSourceFeatBlock ( Asn2gbFormatPtr afp, BaseBlockPtr bbp ) { Boolean add_period; IntAsn2gbJobPtr ajp; Asn2gbSectPtr asp; BioSourcePtr biop = NULL; BioseqPtr bsp; Char buf [80]; CharPtr common = NULL; DbtagPtr dbt; SeqMgrDescContext dcontext; SeqMgrFeatContext fcontext; ValNodePtr head; Int2 i; Uint1 idx; IntSrcBlockPtr isp; Boolean is_desc = TRUE; Int2 j; Uint1 jdx; Uint1 lastomptype; Uint1 lastssptype; SeqLocPtr location = NULL; CharPtr notestr; Uint1Ptr notetbl = NULL; Boolean okay; ObjectIdPtr oip; OrgModPtr omp; OrgNamePtr onp = NULL; OrgRefPtr orp = NULL; CharPtr prefix; Uint1Ptr qualtbl = NULL; QualValPtr qvp; SeqDescrPtr sdp; SeqFeatPtr sfp = NULL; SubSourcePtr ssp; CharPtr str; CharPtr taxname = NULL; ValNodePtr vnp; CharPtr wwwbuf; if (afp == NULL || bbp == NULL) return NULL; ajp = afp->ajp; if (ajp == NULL) return NULL; asp = afp->asp; if (asp == NULL) return NULL; bsp = asp->bsp; if (bsp == NULL) return NULL; qvp = afp->qvp; if (qvp == NULL) return NULL; if (! StringHasNoText (bbp->string)) return StringSave (bbp->string); isp = (IntSrcBlockPtr) bbp; /* could be descriptor or feature */ if (bbp->itemtype == OBJ_SEQDESC) { sdp = SeqMgrGetDesiredDescriptor (bbp->entityID, NULL, bbp->itemID, 0, NULL, &dcontext); if (sdp != NULL && dcontext.seqdesctype == Seq_descr_source) { biop = (BioSourcePtr) sdp->data.ptrvalue; } } else if (bbp->itemtype == OBJ_SEQFEAT) { sfp = SeqMgrGetDesiredFeature (bbp->entityID, NULL, bbp->itemID, 0, NULL, &fcontext); if (sfp != NULL && fcontext.seqfeattype == SEQFEAT_BIOSRC) { biop = (BioSourcePtr) sfp->data.value.ptrvalue; } is_desc = FALSE; } if (biop == NULL) return NULL; gb_StartPrint (afp->format, 5, 21, NULL, 0, 5, 21, "FT", FALSE); ff_AddString ("source"); TabToColumn (22); location = isp->loc; str = FlatLoc (bsp, location, ajp->masterStyle); if (get_www ()) { wwwbuf = www_featloc (str); ff_AddString (wwwbuf); MemFree (wwwbuf); } else { ff_AddString (str); } MemFree (str); orp = biop->org; if (orp != NULL) { taxname = orp->taxname; /* common = orp->common; */ } if (StringHasNoText (taxname)) { if (ajp->flags.needOrganismQual) { taxname = "unknown"; common = orp->common; #ifdef ASN2GNBK_PRINT_UNKNOWN_ORG } else { taxname = "unknown"; common = orp->common; #endif } } /* populate qualifier table from biosource fields */ qvp [SCQUAL_organism].str = taxname; qvp [SCQUAL_common_name].str = common; if (biop->is_focus) { qvp [SCQUAL_focus].bool = TRUE; } SubSourceToQualArray (biop->subtype, qvp); if (orp != NULL) { onp = orp->orgname; if (onp != NULL) { OrgModToQualArray (onp->mod, qvp); } if (! is_desc) { qvp [SCQUAL_unstructured].vnp = orp->mod; } qvp [SCQUAL_db_xref].vnp = orp->db; } /* organelle currently prints /mitochondrion, /virion, etc. */ qvp [SCQUAL_organelle].num = biop->genome; /* some qualifiers are flags in genome and names in subsource, print once with name */ if (qvp [SCQUAL_ins_seq_name].ssp != NULL && qvp [SCQUAL_organelle].num == GENOME_insertion_seq) { qvp [SCQUAL_organelle].num = 0; } if (qvp [SCQUAL_plasmid_name].ssp != NULL && qvp [SCQUAL_organelle].num == GENOME_plasmid) { qvp [SCQUAL_organelle].num = 0; } /* AF095904.1 if (qvp [SCQUAL_plastid_name].ssp != NULL && qvp [SCQUAL_organelle].num == GENOME_plastid) { qvp [SCQUAL_organelle].num = 0; } */ if (qvp [SCQUAL_transposon_name].ssp != NULL && qvp [SCQUAL_organelle].num == GENOME_transposon) { qvp [SCQUAL_organelle].num = 0; } if (sfp != NULL) { qvp [SCQUAL_seqfeat_note].str = sfp->comment; } /* now print qualifiers from table */ qualtbl = source_qual_order; if (is_desc) { notetbl = source_desc_note_order; } else { notetbl = source_feat_note_order; } for (i = 0, idx = qualtbl [i]; idx != 0; i++, idx = qualtbl [i]) { lastomptype = 0; lastssptype = 0; switch (asn2gnbk_source_quals [idx].qualclass) { case Qual_class_ignore : break; case Qual_class_string : if (! StringHasNoText (qvp [idx].str)) { NewContLine (); sprintf (buf, "/%s=\"", asn2gnbk_source_quals [idx].name); gb_AddString (buf, qvp [idx].str, "\"", FALSE, TRUE, TILDE_TO_SPACES); } break; case Qual_class_boolean : if (qvp [idx].bool) { NewContLine (); sprintf (buf, "/%s", asn2gnbk_source_quals [idx].name); ff_AddString (buf); } break; case Qual_class_organelle : j = (Int2) qvp [idx].num; if (organelleQual [j] != NULL) { NewContLine (); sprintf (buf, "%s", organelleQual [j]); ff_AddString (buf); } break; case Qual_class_orgmod : omp = qvp [idx].omp; if (lastomptype == 0 && omp != NULL) { lastomptype = omp->subtype; } while (omp != NULL && omp->subtype == lastomptype) { if (StringIsJustQuotes (omp->subname)) { NewContLine (); sprintf (buf, "/%s=\"", asn2gnbk_source_quals [idx].name); gb_AddString (buf, NULL, "\"", FALSE, TRUE, TILDE_TO_SPACES); } else if (! StringHasNoText (omp->subname)) { NewContLine (); sprintf (buf, "/%s=\"", asn2gnbk_source_quals [idx].name); gb_AddString (buf, omp->subname, "\"", FALSE, TRUE, TILDE_TO_SPACES); } omp = omp->next; } break; case Qual_class_subsource : ssp = qvp [idx].ssp; if (lastssptype == 0 && ssp != NULL) { lastssptype = ssp->subtype; } while (ssp != NULL && ssp->subtype == lastssptype) { if (ssp->subtype == SUBSRC_germline || ssp->subtype == SUBSRC_rearranged || ssp->subtype == SUBSRC_transgenic || ssp->subtype == SUBSRC_environmental_sample) { NewContLine (); sprintf (buf, "/%s", asn2gnbk_source_quals [idx].name); gb_AddString (buf, NULL, NULL, FALSE, TRUE, TILDE_TO_SPACES); } else if (StringIsJustQuotes (ssp->name)) { NewContLine (); sprintf (buf, "/%s=\"", asn2gnbk_source_quals [idx].name); gb_AddString (buf, NULL, "\"", FALSE, TRUE, TILDE_TO_SPACES); } else if (! StringHasNoText (ssp->name)) { NewContLine (); sprintf (buf, "/%s=\"", asn2gnbk_source_quals [idx].name); gb_AddString (buf, ssp->name, "\"", FALSE, TRUE, TILDE_TO_SPACES); } ssp = ssp->next; } break; case Qual_class_pubset : break; case Qual_class_quote : break; case Qual_class_noquote : break; case Qual_class_label : break; case Qual_class_db_xref : for (vnp = qvp [idx].vnp; vnp != NULL; vnp = vnp->next) { buf [0] = '\0'; dbt = (DbtagPtr) vnp->data.ptrvalue; if (dbt != NULL && (! StringHasNoText (dbt->db))) { oip = dbt->tag; if (oip != NULL) { okay = TRUE; if (ajp->flags.dropBadDbxref) { /* if RELEASE_MODE, drop unknown dbtag */ okay = FALSE; for (j = 0; legalDbXrefs [j] != NULL; j++) { if (StringCmp (dbt->db, legalDbXrefs [j]) == 0) { okay = TRUE; } } } if (okay) { if (! StringHasNoText (oip->str)) { if (StringLen (dbt->db) + StringLen (oip->str) < 80) { sprintf (buf, "%s:%s", dbt->db, oip->str); } } else { sprintf (buf, "%s:%ld", dbt->db, (long) oip->id); } } } } if (! StringHasNoText (buf)) { NewContLine (); ff_AddString ("/db_xref=\""); www_db_xref (buf); ff_AddString ("\""); /* gb_AddString ("/db_xref=\"", buf, "\"", FALSE, TRUE, TILDE_TO_SPACES); */ } } break; case Qual_class_illegal : break; case Qual_class_note : head = NULL; notestr = NULL; prefix = ""; add_period = FALSE; if (biop->genome == 8) { AddValNodeString (&head, "", "extrachromosomal", NULL); prefix = "\n"; } for (j = 0, jdx = notetbl [j]; jdx != 0; j++, jdx = notetbl [j]) { lastomptype = 0; lastssptype = 0; switch (asn2gnbk_source_quals [jdx].qualclass) { case Qual_class_string : if (! StringHasNoText (qvp [jdx].str)) { s_AddValNodeString_NoRedund (&head, prefix, qvp [jdx].str, NULL); add_period = FALSE; prefix = "\n"; } break; case Qual_class_orgmod : omp = qvp [jdx].omp; if (lastomptype == 0 && omp != NULL) { lastomptype = omp->subtype; } while (omp != NULL && omp->subtype == lastomptype) { if (! StringHasNoText (omp->subname)) { if (jdx == SCQUAL_orgmod_note) { sprintf (buf, "%s", prefix); } else { sprintf (buf, "%s%s: ", prefix, asn2gnbk_source_quals [jdx].name); } str = StringSave (omp->subname); add_period = s_RemovePeriodFromEnd (str); if (jdx == SCQUAL_orgmod_note) { s_AddValNodeString_NoRedund (&head, buf, str, NULL); } else { AddValNodeString (&head, buf, str, NULL); } MemFree (str); if (jdx == SCQUAL_orgmod_note) { if (add_period) { prefix = ".\n"; } else { prefix = "\n"; } } else { prefix = "; "; } } omp = omp->next; } break; case Qual_class_subsource : ssp = qvp [jdx].ssp; if (lastssptype == 0 && ssp != NULL) { lastssptype = ssp->subtype; } while (ssp != NULL && ssp->subtype == lastssptype) { if (! StringHasNoText (ssp->name)) { if (jdx == SCQUAL_subsource_note) { sprintf (buf, "%s", prefix); } else { sprintf (buf, "%s%s: ", prefix, asn2gnbk_source_quals [jdx].name); } str = StringSave (ssp->name); add_period = s_RemovePeriodFromEnd (str); if (jdx == SCQUAL_subsource_note) { s_AddValNodeString_NoRedund (&head, buf, str, NULL); } else { AddValNodeString (&head, buf, str, NULL); } MemFree (str); if (jdx == SCQUAL_subsource_note) { if (add_period) { prefix = ".\n"; } else { prefix = "\n"; } } else { prefix = "; "; } } ssp = ssp->next; } break; case Qual_class_valnode : for (vnp = qvp [jdx].vnp; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (! StringHasNoText (str)) { s_AddValNodeString_NoRedund (&head, prefix, str, NULL); add_period = FALSE; prefix = "; "; } } break; default : break; } } if (head != NULL) { NewContLine (); notestr = MergeValNodeStrings (head); if (add_period) { s_AddPeriodToEnd (notestr); } #ifdef ASN2GNBK_STRIP_NOTE_PERIODS if (! IsEllipsis (notestr)) s_RemovePeriodFromEnd (notestr); #endif gb_AddString (NULL, "/note=\"", NULL, FALSE, FALSE, TILDE_IGNORE); if (is_desc) { /* AB055064.1 says TILDE_IGNORE on descriptors */ gb_AddString (NULL, notestr, NULL, FALSE, TRUE, TILDE_IGNORE); } else { /* ASZ93724.1 says TILDE_EXPAND on features */ gb_AddString (NULL, notestr, NULL, FALSE, TRUE, TILDE_EXPAND); } gb_AddString (NULL, "\"", NULL, FALSE, FALSE, TILDE_IGNORE); MemFree (notestr); ValNodeFreeData (head); } break; default : break; } } /* and then deal with the various note types separately (not in order table) */ return ff_print_string_mem (gb_MergeString (TRUE)); } typedef struct qualfeatur { CharPtr name; Uint1 featurclass; } QualFeatur, PNTR QualFeaturPtr; #define NUM_GB_QUALS 25 static QualFeatur qualToFeature [NUM_GB_QUALS] = { { "allele", FTQUAL_allele }, { "bound_moiety", FTQUAL_bound_moiety }, { "clone", FTQUAL_clone }, { "codon", FTQUAL_codon }, { "cons_splice", FTQUAL_cons_splice }, { "direction", FTQUAL_direction }, { "EC_number", FTQUAL_EC_number }, { "frequency", FTQUAL_frequency }, { "function", FTQUAL_function }, { "insertion_seq", FTQUAL_insertion_seq }, { "label", FTQUAL_label }, { "map", FTQUAL_map }, { "mod_base", FTQUAL_mod_base }, { "number", FTQUAL_number }, { "organism", FTQUAL_organism }, { "PCR_conditions", FTQUAL_PCR_conditions }, { "phenotype", FTQUAL_phenotype }, { "product", FTQUAL_product_quals }, { "replace", FTQUAL_replace }, { "rpt_family", FTQUAL_rpt_family }, { "rpt_type", FTQUAL_rpt_type }, { "rpt_unit", FTQUAL_rpt_unit }, { "standard_name", FTQUAL_standard_name }, { "transposon", FTQUAL_transposon }, { "usedin", FTQUAL_usedin } }; static Int2 GbqualToFeaturIndex ( CharPtr qualname ) { Int2 L, R, mid; if (qualname == NULL || *qualname == '\0') return 0; L = 0; R = NUM_GB_QUALS - 1; while (L < R) { mid = (L + R) / 2; if (StringICmp (qualToFeature [mid].name, qualname) < 0) { L = mid + 1; } else { R = mid; } } if (StringICmp (qualToFeature [R].name, qualname) == 0) { return qualToFeature [R].featurclass; } return 0; } #define NUM_ILLEGAL_QUALS 14 static FeaturQual illegalGbqualList [NUM_ILLEGAL_QUALS] = { { "anticodon", Qual_class_noquote }, { "citation", Qual_class_noquote }, { "codon_start", Qual_class_noquote }, { "db_xref", Qual_class_quote }, { "evidence", Qual_class_noquote }, { "exception", Qual_class_quote }, { "gene", Qual_class_quote }, { "note", Qual_class_quote }, { "protein_id", Qual_class_quote }, { "pseudo", Qual_class_noquote }, { "transcript_id", Qual_class_quote }, { "transl_except", Qual_class_noquote }, { "transl_table", Qual_class_noquote }, { "translation", Qual_class_quote }, }; static Int2 IllegalGbqualToClass ( CharPtr qualname ) { Int2 L, R, mid; if (qualname == NULL || *qualname == '\0') return 0; L = 0; R = NUM_ILLEGAL_QUALS - 1; while (L < R) { mid = (L + R) / 2; if (StringICmp (illegalGbqualList [mid].name, qualname) < 0) { L = mid + 1; } else { R = mid; } } if (StringICmp (illegalGbqualList [R].name, qualname) == 0) { return illegalGbqualList [R].qualclass; } return 0; } static CharPtr trnaList [] = { "tRNA-Gap", "tRNA-Ala", "tRNA-Asx", "tRNA-Cys", "tRNA-Asp", "tRNA-Glu", "tRNA-Phe", "tRNA-Gly", "tRNA-His", "tRNA-Ile", "tRNA-Lys", "tRNA-Leu", "tRNA-Met", "tRNA-Asn", "tRNA-Pro", "tRNA-Gln", "tRNA-Arg", "tRNA-Ser", "tRNA-Thr", "tRNA-Sec", "tRNA-Val", "tRNA-Trp", "tRNA-OTHER", "tRNA-Tyr", "tRNA-Glx", NULL }; static CharPtr evidenceText [] = { NULL, "experimental", "not_experimental" }; static CharPtr secStrText [] = { NULL, "helix", "sheet", "turn" }; static CharPtr oops = "?"; static CharPtr SeqCodeNameGet ( SeqCodeTablePtr table, Uint1 residue ) { Uint1 index; if (table != NULL) { index = residue - table->start_at; if (index >= 0 && index < table->num) { return (table->names) [index]; } } return oops; } static CharPtr Get3LetterSymbol ( IntAsn2gbJobPtr ajp, Uint1 seq_code, SeqCodeTablePtr table, Uint1 residue ) { Uint1 code = Seq_code_ncbieaa; Int2 index; Uint1 new_residue; CharPtr ptr; CharPtr retval = NULL; SeqMapTablePtr smtp; SeqCodeTablePtr table_3aa; if (residue == 42) { /* stop codon in NCBIeaa */ retval = "TERM"; return retval; } if (ajp->flags.iupacaaOnly) { code = Seq_code_iupacaa; } else { code = Seq_code_ncbieaa; } if (seq_code != code) { /* if code and seq_code are identical, then smtp is NULL?? */ smtp = SeqMapTableFind (code, seq_code); new_residue = SeqMapTableConvert (smtp, residue); } else { new_residue = residue; } /* The following looks for non-symbols (255) and "Undetermined" (88) */ if ((int) new_residue == 255 || (int) new_residue == 88) { retval = "OTHER"; return retval; } else { ptr = SeqCodeNameGet (table, residue); table_3aa=SeqCodeTableFind (Seq_code_iupacaa3); if (ptr != NULL && table_3aa != NULL) { for (index=0; index < (int) table_3aa->num; index++) { if (StringCmp(ptr, (table_3aa->names) [index]) == 0) { retval = (table_3aa->symbols) [index]; return retval; } } } } retval = "OTHER"; return retval; } static Boolean MatchCit ( ValNodePtr ppr, RefBlockPtr rbp ) { Char buf [121]; size_t len; Int4 uid; ValNodePtr vnp; if (ppr == NULL || rbp == NULL) return FALSE; switch (ppr->choice) { case PUB_Muid : uid = ppr->data.intvalue; if (rbp->muid == uid) return TRUE; break; case PUB_PMid : uid = ppr->data.intvalue; if (rbp->pmid == uid) return TRUE; break; case PUB_Equiv : for (vnp = (ValNodePtr) ppr->data.ptrvalue; vnp != NULL; vnp = vnp->next) { if (MatchCit (vnp, rbp)) return TRUE; } break; default : PubLabelUnique (ppr, buf, sizeof (buf) - 1, OM_LABEL_CONTENT, TRUE); len = StringLen (buf); if (len > 0 && buf [len - 1] == '>') { buf [len - 1] = '\0'; len--; } len = MIN (len, StringLen (rbp->uniquestr)); if (StringNICmp (rbp->uniquestr, buf, len) == 0) return TRUE; break; } return FALSE; } static Int2 MatchRef ( ValNodePtr ppr, RefBlockPtr PNTR rbpp, Int2 numReferences ) { Int2 j; RefBlockPtr rbp; if (ppr == NULL || rbpp == NULL) return 0; for (j = 0; j < numReferences; j++) { rbp = rbpp [j]; if (rbp == NULL) continue; if (MatchCit (ppr, rbp)) return j + 1; } return 0; } /* taken from asn2ff4.c */ static Boolean LookForFuzz (SeqLocPtr head) { Boolean retval=FALSE; IntFuzzPtr ifp; PackSeqPntPtr pspp; SeqIntPtr sip; SeqLocPtr slp; SeqPntPtr spp; if (head == NULL) return retval; slp=NULL; while ((slp = SeqLocFindNext(head, slp)) != NULL) { switch (slp->choice) { case SEQLOC_INT: sip = (SeqIntPtr)(slp->data.ptrvalue); ifp = sip->if_from; if (ifp != NULL) { if (ifp->choice == 4) { if (ifp->a != 0) retval=TRUE; } else retval = TRUE; } ifp = sip->if_to; if (ifp != NULL) { if (ifp->choice == 4) { if (ifp->a != 0) retval=TRUE; } else retval = TRUE; } break; case SEQLOC_PNT: spp = (SeqPntPtr)(slp->data.ptrvalue); ifp = spp->fuzz; if (ifp != NULL) { if (ifp->choice == 4) { if (ifp->a != 0) retval=TRUE; } else retval = TRUE; } break; case SEQLOC_PACKED_PNT: pspp = (PackSeqPntPtr)(slp->data.ptrvalue); ifp = pspp->fuzz; if (ifp != NULL) { if (ifp->choice == 4) { if (ifp->a != 0) retval=TRUE; } else retval = TRUE; } break; default: break; } if (retval == TRUE) break; } return retval; } static CharPtr siteList [] = { NULL, "active", "binding", "cleavage", "inhibit", "modified", "glycosylation", "myristoylation", "mutagenized", "metal-binding", "phosphorylation", "acetylation", "amidation", "methylation", "hydroxylation", "sulfatation", "oxidative-deamination", "pyrrolidone-carboxylic-acid", "gamma-carboxyglutamic-acid", "blocked", "lipid-binding", "np-binding", "DNA binding", "signal-peptide", "transit-peptide", "transmembrane-region", "unclassified" }; static CharPtr conflict_msg = "Protein sequence is in conflict with the conceptual translation"; static CharPtr no_protein_msg = "Coding region translates with internal stops"; /**/ /* s_DisplayQVP () -- Displays the strings in a QVP structure. */ /* This is a debugging function only. */ /**/ static void s_DisplayQVP(QualValPtr qvp, Uint1Ptr notetbl) { Int2 j; Int2 jdx; fprintf(stderr,"\n"); for (j = 0, jdx = notetbl [j]; jdx != 0; j++, jdx = notetbl [j]) { if (((int) qvp[jdx].str != 0x1000000) && ((int) qvp[jdx].str != 0x1) && ((int) qvp[jdx].str != 0xb) && (qvp[jdx].str != NULL)) fprintf(stderr, "%d\t%-25s %s\n", j, asn2gnbk_featur_quals[jdx].name, qvp[jdx].str); else fprintf(stderr, "%d\t%-25s %s\n", j, asn2gnbk_featur_quals[jdx].name, "NULL"); } } static Boolean NotInGeneSyn ( CharPtr str, ValNodePtr gene_syn) { CharPtr syn; ValNodePtr vnp; for (vnp = gene_syn; vnp != NULL; vnp = vnp->next) { syn = (CharPtr) vnp->data.ptrvalue; if (! StringHasNoText (syn)) { if (StringICmp (str, syn) == 0) return FALSE; } } return TRUE; } typedef struct valqualstruc { Uint2 featdef; FtQualType ftqual; } ValQual, PNTR ValQualPtr; /* WARNING - This list MUST be kept sorted in FEATDEF order as the primary key, and within a FEATDEF group sorted by FTQUAL as the secondary key */ static ValQual legalGbqualList [] = { {FEATDEF_GENE , FTQUAL_allele}, {FEATDEF_GENE , FTQUAL_function}, {FEATDEF_GENE , FTQUAL_label}, {FEATDEF_GENE , FTQUAL_map}, {FEATDEF_GENE , FTQUAL_phenotype}, {FEATDEF_GENE , FTQUAL_product}, {FEATDEF_GENE , FTQUAL_standard_name}, {FEATDEF_GENE , FTQUAL_usedin}, {FEATDEF_CDS , FTQUAL_allele}, {FEATDEF_CDS , FTQUAL_codon}, {FEATDEF_CDS , FTQUAL_label}, {FEATDEF_CDS , FTQUAL_map}, {FEATDEF_CDS , FTQUAL_number}, {FEATDEF_CDS , FTQUAL_standard_name}, {FEATDEF_CDS , FTQUAL_usedin}, {FEATDEF_PROT , FTQUAL_product}, {FEATDEF_preRNA , FTQUAL_allele}, {FEATDEF_preRNA , FTQUAL_function}, {FEATDEF_preRNA , FTQUAL_label}, {FEATDEF_preRNA , FTQUAL_map}, {FEATDEF_preRNA , FTQUAL_product}, {FEATDEF_preRNA , FTQUAL_standard_name}, {FEATDEF_preRNA , FTQUAL_usedin}, {FEATDEF_mRNA , FTQUAL_allele}, {FEATDEF_mRNA , FTQUAL_function}, {FEATDEF_mRNA , FTQUAL_label}, {FEATDEF_mRNA , FTQUAL_map}, {FEATDEF_mRNA , FTQUAL_product}, {FEATDEF_mRNA , FTQUAL_standard_name}, {FEATDEF_mRNA , FTQUAL_usedin}, {FEATDEF_tRNA , FTQUAL_function}, {FEATDEF_tRNA , FTQUAL_label}, {FEATDEF_tRNA , FTQUAL_map}, {FEATDEF_tRNA , FTQUAL_product}, {FEATDEF_tRNA , FTQUAL_standard_name}, {FEATDEF_tRNA , FTQUAL_usedin}, {FEATDEF_rRNA , FTQUAL_function}, {FEATDEF_rRNA , FTQUAL_label}, {FEATDEF_rRNA , FTQUAL_map}, {FEATDEF_rRNA , FTQUAL_product}, {FEATDEF_rRNA , FTQUAL_standard_name}, {FEATDEF_rRNA , FTQUAL_usedin}, {FEATDEF_snRNA , FTQUAL_function}, {FEATDEF_snRNA , FTQUAL_label}, {FEATDEF_snRNA , FTQUAL_map}, {FEATDEF_snRNA , FTQUAL_product}, {FEATDEF_snRNA , FTQUAL_standard_name}, {FEATDEF_snRNA , FTQUAL_usedin}, {FEATDEF_scRNA , FTQUAL_function}, {FEATDEF_scRNA , FTQUAL_label}, {FEATDEF_scRNA , FTQUAL_map}, {FEATDEF_scRNA , FTQUAL_product}, {FEATDEF_scRNA , FTQUAL_standard_name}, {FEATDEF_scRNA , FTQUAL_usedin}, {FEATDEF_otherRNA , FTQUAL_function}, {FEATDEF_otherRNA , FTQUAL_label}, {FEATDEF_otherRNA , FTQUAL_map}, {FEATDEF_otherRNA , FTQUAL_product}, {FEATDEF_otherRNA , FTQUAL_standard_name}, {FEATDEF_otherRNA , FTQUAL_usedin}, {FEATDEF_attenuator , FTQUAL_label}, {FEATDEF_attenuator , FTQUAL_map}, {FEATDEF_attenuator , FTQUAL_phenotype}, {FEATDEF_attenuator , FTQUAL_usedin}, {FEATDEF_C_region , FTQUAL_label}, {FEATDEF_C_region , FTQUAL_map}, {FEATDEF_C_region , FTQUAL_product}, {FEATDEF_C_region , FTQUAL_standard_name}, {FEATDEF_C_region , FTQUAL_usedin}, {FEATDEF_CAAT_signal , FTQUAL_label}, {FEATDEF_CAAT_signal , FTQUAL_map}, {FEATDEF_CAAT_signal , FTQUAL_usedin}, {FEATDEF_Imp_CDS , FTQUAL_codon}, {FEATDEF_Imp_CDS , FTQUAL_EC_number}, {FEATDEF_Imp_CDS , FTQUAL_function}, {FEATDEF_Imp_CDS , FTQUAL_label}, {FEATDEF_Imp_CDS , FTQUAL_map}, {FEATDEF_Imp_CDS , FTQUAL_number}, {FEATDEF_Imp_CDS , FTQUAL_product}, {FEATDEF_Imp_CDS , FTQUAL_standard_name}, {FEATDEF_Imp_CDS , FTQUAL_usedin}, {FEATDEF_conflict , FTQUAL_label}, {FEATDEF_conflict , FTQUAL_map}, {FEATDEF_conflict , FTQUAL_replace}, {FEATDEF_conflict , FTQUAL_usedin}, {FEATDEF_D_loop , FTQUAL_label}, {FEATDEF_D_loop , FTQUAL_map}, {FEATDEF_D_loop , FTQUAL_usedin}, {FEATDEF_D_segment , FTQUAL_label}, {FEATDEF_D_segment , FTQUAL_map}, {FEATDEF_D_segment , FTQUAL_product}, {FEATDEF_D_segment , FTQUAL_standard_name}, {FEATDEF_D_segment , FTQUAL_usedin}, {FEATDEF_enhancer , FTQUAL_label}, {FEATDEF_enhancer , FTQUAL_map}, {FEATDEF_enhancer , FTQUAL_standard_name}, {FEATDEF_enhancer , FTQUAL_usedin}, {FEATDEF_exon , FTQUAL_allele}, {FEATDEF_exon , FTQUAL_EC_number}, {FEATDEF_exon , FTQUAL_function}, {FEATDEF_exon , FTQUAL_label}, {FEATDEF_exon , FTQUAL_map}, {FEATDEF_exon , FTQUAL_number}, {FEATDEF_exon , FTQUAL_product}, {FEATDEF_exon , FTQUAL_standard_name}, {FEATDEF_exon , FTQUAL_usedin}, {FEATDEF_GC_signal , FTQUAL_label}, {FEATDEF_GC_signal , FTQUAL_map}, {FEATDEF_GC_signal , FTQUAL_usedin}, {FEATDEF_iDNA , FTQUAL_function}, {FEATDEF_iDNA , FTQUAL_label}, {FEATDEF_iDNA , FTQUAL_map}, {FEATDEF_iDNA , FTQUAL_number}, {FEATDEF_iDNA , FTQUAL_standard_name}, {FEATDEF_iDNA , FTQUAL_usedin}, {FEATDEF_intron , FTQUAL_allele}, {FEATDEF_intron , FTQUAL_cons_splice}, {FEATDEF_intron , FTQUAL_function}, {FEATDEF_intron , FTQUAL_label}, {FEATDEF_intron , FTQUAL_map}, {FEATDEF_intron , FTQUAL_number}, {FEATDEF_intron , FTQUAL_standard_name}, {FEATDEF_intron , FTQUAL_usedin}, {FEATDEF_J_segment , FTQUAL_label}, {FEATDEF_J_segment , FTQUAL_map}, {FEATDEF_J_segment , FTQUAL_product}, {FEATDEF_J_segment , FTQUAL_standard_name}, {FEATDEF_J_segment , FTQUAL_usedin}, {FEATDEF_LTR , FTQUAL_function}, {FEATDEF_LTR , FTQUAL_label}, {FEATDEF_LTR , FTQUAL_map}, {FEATDEF_LTR , FTQUAL_standard_name}, {FEATDEF_LTR , FTQUAL_usedin}, {FEATDEF_mat_peptide , FTQUAL_EC_number}, {FEATDEF_mat_peptide , FTQUAL_function}, {FEATDEF_mat_peptide , FTQUAL_label}, {FEATDEF_mat_peptide , FTQUAL_map}, {FEATDEF_mat_peptide , FTQUAL_product}, {FEATDEF_mat_peptide , FTQUAL_standard_name}, {FEATDEF_mat_peptide , FTQUAL_usedin}, {FEATDEF_misc_binding , FTQUAL_bound_moiety}, {FEATDEF_misc_binding , FTQUAL_function}, {FEATDEF_misc_binding , FTQUAL_label}, {FEATDEF_misc_binding , FTQUAL_map}, {FEATDEF_misc_binding , FTQUAL_usedin}, {FEATDEF_misc_difference , FTQUAL_clone}, {FEATDEF_misc_difference , FTQUAL_label}, {FEATDEF_misc_difference , FTQUAL_map}, {FEATDEF_misc_difference , FTQUAL_phenotype}, {FEATDEF_misc_difference , FTQUAL_replace}, {FEATDEF_misc_difference , FTQUAL_standard_name}, {FEATDEF_misc_difference , FTQUAL_usedin}, {FEATDEF_misc_feature , FTQUAL_function}, {FEATDEF_misc_feature , FTQUAL_label}, {FEATDEF_misc_feature , FTQUAL_map}, {FEATDEF_misc_feature , FTQUAL_number}, {FEATDEF_misc_feature , FTQUAL_phenotype}, {FEATDEF_misc_feature , FTQUAL_product}, {FEATDEF_misc_feature , FTQUAL_standard_name}, {FEATDEF_misc_feature , FTQUAL_usedin}, {FEATDEF_misc_recomb , FTQUAL_label}, {FEATDEF_misc_recomb , FTQUAL_map}, {FEATDEF_misc_recomb , FTQUAL_organism}, {FEATDEF_misc_recomb , FTQUAL_standard_name}, {FEATDEF_misc_recomb , FTQUAL_usedin}, {FEATDEF_misc_signal , FTQUAL_function}, {FEATDEF_misc_signal , FTQUAL_label}, {FEATDEF_misc_signal , FTQUAL_map}, {FEATDEF_misc_signal , FTQUAL_phenotype}, {FEATDEF_misc_signal , FTQUAL_standard_name}, {FEATDEF_misc_signal , FTQUAL_usedin}, {FEATDEF_misc_structure , FTQUAL_function}, {FEATDEF_misc_structure , FTQUAL_label}, {FEATDEF_misc_structure , FTQUAL_map}, {FEATDEF_misc_structure , FTQUAL_standard_name}, {FEATDEF_misc_structure , FTQUAL_usedin}, {FEATDEF_modified_base , FTQUAL_frequency}, {FEATDEF_modified_base , FTQUAL_label}, {FEATDEF_modified_base , FTQUAL_map}, {FEATDEF_modified_base , FTQUAL_mod_base}, {FEATDEF_modified_base , FTQUAL_usedin}, {FEATDEF_N_region , FTQUAL_label}, {FEATDEF_N_region , FTQUAL_map}, {FEATDEF_N_region , FTQUAL_product}, {FEATDEF_N_region , FTQUAL_standard_name}, {FEATDEF_N_region , FTQUAL_usedin}, {FEATDEF_old_sequence , FTQUAL_label}, {FEATDEF_old_sequence , FTQUAL_map}, {FEATDEF_old_sequence , FTQUAL_replace}, {FEATDEF_old_sequence , FTQUAL_usedin}, {FEATDEF_polyA_signal , FTQUAL_label}, {FEATDEF_polyA_signal , FTQUAL_map}, {FEATDEF_polyA_signal , FTQUAL_usedin}, {FEATDEF_polyA_site , FTQUAL_label}, {FEATDEF_polyA_site , FTQUAL_map}, {FEATDEF_polyA_site , FTQUAL_usedin}, {FEATDEF_prim_transcript , FTQUAL_allele}, {FEATDEF_prim_transcript , FTQUAL_function}, {FEATDEF_prim_transcript , FTQUAL_label}, {FEATDEF_prim_transcript , FTQUAL_map}, {FEATDEF_prim_transcript , FTQUAL_standard_name}, {FEATDEF_prim_transcript , FTQUAL_usedin}, {FEATDEF_primer_bind , FTQUAL_label}, {FEATDEF_primer_bind , FTQUAL_map}, {FEATDEF_primer_bind , FTQUAL_PCR_conditions}, {FEATDEF_primer_bind , FTQUAL_standard_name}, {FEATDEF_primer_bind , FTQUAL_usedin}, {FEATDEF_promoter , FTQUAL_function}, {FEATDEF_promoter , FTQUAL_label}, {FEATDEF_promoter , FTQUAL_map}, {FEATDEF_promoter , FTQUAL_phenotype}, {FEATDEF_promoter , FTQUAL_standard_name}, {FEATDEF_promoter , FTQUAL_usedin}, {FEATDEF_protein_bind , FTQUAL_bound_moiety}, {FEATDEF_protein_bind , FTQUAL_function}, {FEATDEF_protein_bind , FTQUAL_label}, {FEATDEF_protein_bind , FTQUAL_map}, {FEATDEF_protein_bind , FTQUAL_standard_name}, {FEATDEF_protein_bind , FTQUAL_usedin}, {FEATDEF_RBS , FTQUAL_label}, {FEATDEF_RBS , FTQUAL_map}, {FEATDEF_RBS , FTQUAL_standard_name}, {FEATDEF_RBS , FTQUAL_usedin}, {FEATDEF_repeat_region , FTQUAL_function}, {FEATDEF_repeat_region , FTQUAL_insertion_seq}, {FEATDEF_repeat_region , FTQUAL_label}, {FEATDEF_repeat_region , FTQUAL_map}, {FEATDEF_repeat_region , FTQUAL_rpt_family}, {FEATDEF_repeat_region , FTQUAL_rpt_type}, {FEATDEF_repeat_region , FTQUAL_rpt_unit}, {FEATDEF_repeat_region , FTQUAL_standard_name}, {FEATDEF_repeat_region , FTQUAL_transposon}, {FEATDEF_repeat_region , FTQUAL_usedin}, {FEATDEF_repeat_unit , FTQUAL_function}, {FEATDEF_repeat_unit , FTQUAL_label}, {FEATDEF_repeat_unit , FTQUAL_map}, {FEATDEF_repeat_unit , FTQUAL_rpt_family}, {FEATDEF_repeat_unit , FTQUAL_rpt_type}, {FEATDEF_repeat_unit , FTQUAL_usedin}, {FEATDEF_rep_origin , FTQUAL_direction}, {FEATDEF_rep_origin , FTQUAL_label}, {FEATDEF_rep_origin , FTQUAL_map}, {FEATDEF_rep_origin , FTQUAL_standard_name}, {FEATDEF_rep_origin , FTQUAL_usedin}, {FEATDEF_S_region , FTQUAL_label}, {FEATDEF_S_region , FTQUAL_map}, {FEATDEF_S_region , FTQUAL_product}, {FEATDEF_S_region , FTQUAL_standard_name}, {FEATDEF_S_region , FTQUAL_usedin}, {FEATDEF_satellite , FTQUAL_label}, {FEATDEF_satellite , FTQUAL_map}, {FEATDEF_satellite , FTQUAL_rpt_family}, {FEATDEF_satellite , FTQUAL_rpt_type}, {FEATDEF_satellite , FTQUAL_rpt_unit}, {FEATDEF_satellite , FTQUAL_standard_name}, {FEATDEF_satellite , FTQUAL_usedin}, {FEATDEF_sig_peptide , FTQUAL_function}, {FEATDEF_sig_peptide , FTQUAL_label}, {FEATDEF_sig_peptide , FTQUAL_map}, {FEATDEF_sig_peptide , FTQUAL_product}, {FEATDEF_sig_peptide , FTQUAL_standard_name}, {FEATDEF_sig_peptide , FTQUAL_usedin}, {FEATDEF_stem_loop , FTQUAL_function}, {FEATDEF_stem_loop , FTQUAL_label}, {FEATDEF_stem_loop , FTQUAL_map}, {FEATDEF_stem_loop , FTQUAL_standard_name}, {FEATDEF_stem_loop , FTQUAL_usedin}, {FEATDEF_STS , FTQUAL_label}, {FEATDEF_STS , FTQUAL_map}, {FEATDEF_STS , FTQUAL_standard_name}, {FEATDEF_STS , FTQUAL_usedin}, {FEATDEF_TATA_signal , FTQUAL_label}, {FEATDEF_TATA_signal , FTQUAL_map}, {FEATDEF_TATA_signal , FTQUAL_usedin}, {FEATDEF_terminator , FTQUAL_label}, {FEATDEF_terminator , FTQUAL_map}, {FEATDEF_terminator , FTQUAL_standard_name}, {FEATDEF_terminator , FTQUAL_usedin}, {FEATDEF_transit_peptide , FTQUAL_function}, {FEATDEF_transit_peptide , FTQUAL_label}, {FEATDEF_transit_peptide , FTQUAL_map}, {FEATDEF_transit_peptide , FTQUAL_product}, {FEATDEF_transit_peptide , FTQUAL_standard_name}, {FEATDEF_transit_peptide , FTQUAL_usedin}, {FEATDEF_unsure , FTQUAL_label}, {FEATDEF_unsure , FTQUAL_map}, {FEATDEF_unsure , FTQUAL_replace}, {FEATDEF_unsure , FTQUAL_usedin}, {FEATDEF_V_region , FTQUAL_label}, {FEATDEF_V_region , FTQUAL_map}, {FEATDEF_V_region , FTQUAL_product}, {FEATDEF_V_region , FTQUAL_standard_name}, {FEATDEF_V_region , FTQUAL_usedin}, {FEATDEF_V_segment , FTQUAL_label}, {FEATDEF_V_segment , FTQUAL_map}, {FEATDEF_V_segment , FTQUAL_product}, {FEATDEF_V_segment , FTQUAL_standard_name}, {FEATDEF_V_segment , FTQUAL_usedin}, {FEATDEF_variation , FTQUAL_allele}, {FEATDEF_variation , FTQUAL_frequency}, {FEATDEF_variation , FTQUAL_label}, {FEATDEF_variation , FTQUAL_map}, {FEATDEF_variation , FTQUAL_phenotype}, {FEATDEF_variation , FTQUAL_product}, {FEATDEF_variation , FTQUAL_replace}, {FEATDEF_variation , FTQUAL_standard_name}, {FEATDEF_variation , FTQUAL_usedin}, {FEATDEF_3clip , FTQUAL_allele}, {FEATDEF_3clip , FTQUAL_function}, {FEATDEF_3clip , FTQUAL_label}, {FEATDEF_3clip , FTQUAL_map}, {FEATDEF_3clip , FTQUAL_standard_name}, {FEATDEF_3clip , FTQUAL_usedin}, {FEATDEF_3UTR , FTQUAL_allele}, {FEATDEF_3UTR , FTQUAL_function}, {FEATDEF_3UTR , FTQUAL_label}, {FEATDEF_3UTR , FTQUAL_map}, {FEATDEF_3UTR , FTQUAL_standard_name}, {FEATDEF_3UTR , FTQUAL_usedin}, {FEATDEF_5clip , FTQUAL_allele}, {FEATDEF_5clip , FTQUAL_function}, {FEATDEF_5clip , FTQUAL_label}, {FEATDEF_5clip , FTQUAL_map}, {FEATDEF_5clip , FTQUAL_standard_name}, {FEATDEF_5clip , FTQUAL_usedin}, {FEATDEF_5UTR , FTQUAL_allele}, {FEATDEF_5UTR , FTQUAL_function}, {FEATDEF_5UTR , FTQUAL_label}, {FEATDEF_5UTR , FTQUAL_map}, {FEATDEF_5UTR , FTQUAL_standard_name}, {FEATDEF_5UTR , FTQUAL_usedin}, {FEATDEF_10_signal , FTQUAL_label}, {FEATDEF_10_signal , FTQUAL_map}, {FEATDEF_10_signal , FTQUAL_standard_name}, {FEATDEF_10_signal , FTQUAL_usedin}, {FEATDEF_35_signal , FTQUAL_label}, {FEATDEF_35_signal , FTQUAL_map}, {FEATDEF_35_signal , FTQUAL_standard_name}, {FEATDEF_35_signal , FTQUAL_usedin}, {FEATDEF_REGION , FTQUAL_function}, {FEATDEF_REGION , FTQUAL_label}, {FEATDEF_REGION , FTQUAL_map}, {FEATDEF_REGION , FTQUAL_number}, {FEATDEF_REGION , FTQUAL_phenotype}, {FEATDEF_REGION , FTQUAL_product}, {FEATDEF_REGION , FTQUAL_standard_name}, {FEATDEF_REGION , FTQUAL_usedin}, {FEATDEF_mat_peptide_aa , FTQUAL_label}, {FEATDEF_mat_peptide_aa , FTQUAL_map}, {FEATDEF_mat_peptide_aa , FTQUAL_product}, {FEATDEF_mat_peptide_aa , FTQUAL_standard_name}, {FEATDEF_mat_peptide_aa , FTQUAL_usedin}, {FEATDEF_sig_peptide_aa , FTQUAL_label}, {FEATDEF_sig_peptide_aa , FTQUAL_map}, {FEATDEF_sig_peptide_aa , FTQUAL_product}, {FEATDEF_sig_peptide_aa , FTQUAL_standard_name}, {FEATDEF_sig_peptide_aa , FTQUAL_usedin}, {FEATDEF_transit_peptide_aa , FTQUAL_label}, {FEATDEF_transit_peptide_aa , FTQUAL_map}, {FEATDEF_transit_peptide_aa , FTQUAL_product}, {FEATDEF_transit_peptide_aa , FTQUAL_standard_name}, {FEATDEF_transit_peptide_aa , FTQUAL_usedin}, {FEATDEF_snoRNA , FTQUAL_function}, {FEATDEF_snoRNA , FTQUAL_label}, {FEATDEF_snoRNA , FTQUAL_map}, {FEATDEF_snoRNA , FTQUAL_product}, {FEATDEF_snoRNA , FTQUAL_standard_name}, {FEATDEF_snoRNA , FTQUAL_usedin} }; /* comparison of ValQual's -- first compare featdef then ftqual */ #define COMPARE_VALQUAL(av,aq,bv,bq) ( ((av)-(bv)) ? ((av)-(bv)) : ((aq)-(bq)) ) /* Returns TRUE if {featureKey, qualKey} exists in legalGbqualList */ static Boolean AllowedValQual (Uint2 featureKey, FtQualType qualKey) { Int2 L, R, mid; L = 0; R = sizeof (legalGbqualList) / sizeof (ValQual) - 1; while (L < R) { mid = (L + R) / 2; if (COMPARE_VALQUAL (legalGbqualList [mid].featdef, legalGbqualList [mid].ftqual, featureKey, qualKey) < 0) L = mid + 1; else R = mid; } if (COMPARE_VALQUAL (legalGbqualList [R].featdef, legalGbqualList [R].ftqual, featureKey, qualKey)) { return 0; } return 1; } static CharPtr validRptString [] = { "tandem", "inverted", "flanking", "terminal", "direct", "dispersed", "other", NULL }; static CharPtr validLRBString [] = { "LEFT", "RIGHT", "BOTH", NULL }; static CharPtr validConsSpliceString [] = { "(5'site:YES, 3'site:YES)", "(5'site:YES, 3'site:NO)", "(5'site:YES, 3'site:ABSENT)", "(5'site:NO, 3'site:YES)", "(5'site:NO, 3'site:NO)", "(5'site:NO, 3'site:ABSENT)", "(5'site:ABSENT, 3'site:YES)", "(5'site:ABSENT, 3'site:NO)", "(5'site:ABSENT, 3'site:ABSENT)", NULL }; static CharPtr validExceptionString [] = { "RNA editing", "reasons given in citation", NULL }; static Boolean StringInStringList (CharPtr testString, CharPtr PNTR stringList) { Int2 i; i = 0; while (stringList [i] != NULL) { if (StringICmp (testString, stringList [i]) == 0) return 1; i++; } return 0; } /* Return values are: 0: no problem - Accession is in proper format -1: Accession did not start with a letter (or two letters) -2: Accession did not contain five numbers (or six numbers after 2 letters) -3: the original Accession number to be validated was NULL -4: the original Accession number is too long (>10) */ static Int2 ValidateAccession ( CharPtr accession ) { Char ch; Int2 numAlpha = 0; Int2 numDigits = 0; Int2 numUndersc = 0; CharPtr str; if (accession == NULL || accession [0] == '\0') return -3; if (StringLen (accession) >= 10) return -4; if (accession [0] < 'A' || accession [0] > 'Z') return -1; str = accession; ch = *str; while (IS_ALPHA (ch)) { numAlpha++; str++; ch = *str; } while (ch == '_') { numUndersc++; str++; ch = *str; } while (IS_DIGIT (ch)) { numDigits++; str++; ch = *str; } if (ch != '\0' && ch != ' ') return -2; if (numUndersc > 1) return -2; if (numUndersc == 0) { if (numAlpha == 1 && numDigits == 5) return 0; if (numAlpha == 2 && numDigits == 6) return 0; if (numAlpha == 3 && numDigits == 5) return 0; } else if (numUndersc == 1) { if (numAlpha != 2 || numDigits != 6) return -2; if (accession [0] == 'N' || accession [0] == 'X') { if (accession [1] == 'M' || accession [1] == 'C' || accession [1] == 'T' || accession [1] == 'P' || accession [1] == 'G' || accession [1] == 'R') { return 0; } } } return -2; } static CharPtr mrnaevtext1 = "Derived by automated computational analysis"; static CharPtr mrnaevtext2 = "using gene prediction method:"; static CharPtr mrnaevtext3 = "Supporting evidence includes similarity to:"; static CharPtr GetStrFormRNAEvidence ( UserObjectPtr uop ) { size_t len; CharPtr method = NULL; Int2 nm = 0; ObjectIdPtr oip; CharPtr str = NULL; Char tmp [20]; UserFieldPtr u, ufp, uu; if (uop == NULL) return NULL; oip = uop->type; if (oip == NULL) return NULL; if (StringCmp (oip->str, "ModelEvidence") != 0) return NULL; for (ufp = uop->data; ufp != NULL; ufp = ufp->next) { oip = ufp->label; if (oip == NULL || ufp->data.ptrvalue == NULL) continue; if (StringCmp (oip->str, "Method") == 0) { method = StringSaveNoNull ((CharPtr) ufp->data.ptrvalue); } if (StringCmp (oip->str, "mRNA") == 0) { for (u = (UserFieldPtr) ufp->data.ptrvalue; u != NULL; u = u->next) { if (u->data.ptrvalue == NULL) continue; for (uu = (UserFieldPtr) u->data.ptrvalue; uu != NULL; uu = uu->next) { oip = uu->label; if (oip == NULL) continue; if (StringCmp (oip->str, "accession") == 0) { nm++; } } } } } len = StringLen (mrnaevtext1) + StringLen (mrnaevtext2) + StringLen (mrnaevtext3) + StringLen (method) + 30; str = (CharPtr) MemNew (len); if (str == NULL) return NULL; if (method != NULL) { sprintf (str, "%s %s %s.", mrnaevtext1, mrnaevtext1, method); } else { sprintf (str, "%s.", mrnaevtext1); } if (nm > 0) { StringCat (str, " "); StringCat (str, mrnaevtext3); if (nm > 1) { sprintf (tmp, " %d mRNAs", (int) nm); } else { sprintf (tmp, " %d mRNA", (int) nm); } StringCat (str, tmp); } return str; } /* FormatFeatureblockQuals should not be called directly, except from FormatFeatureBlock. It performs no input validation. (perhaps it should?) */ static void FormatFeatureBlockQuals ( IntAsn2gbJobPtr ajp, Asn2gbFormatPtr afp, Asn2gbSectPtr asp, BioseqPtr bsp, Uint1 featdeftype, ValNodePtr gene_syn, CharPtr lasttype, SeqLocPtr location, BioseqPtr prod, CharPtr protein_pid_g, QualValPtr qvp, Int4 left, Int4 right, Uint1 strand, SeqFeatPtr sfp, BioseqPtr target, Boolean is_other, Boolean is_gps ) { Boolean add_period; CharPtr ascii; Int2 ascii_len; Boolean at_end = FALSE; Char buf[80]; Choice cbaa; CodeBreakPtr cbp; Char ch; Uint1 choice; Uint1 code = Seq_code_ncbieaa; ValNodePtr dbx; ValNodePtr dbxrefs = NULL; Int4 gi; ValNodePtr head; Boolean hadProtDesc = FALSE; DbtagPtr dbt; Int4 exp_ev; GBQualPtr gbq; Int2 i; Uint1 idx; Boolean isTRNA; Int2 j; Uint1 jdx; Boolean keep; Int4 len; SeqLocPtr newloc; CharPtr notestr; Char numbuf [32]; Int2 numcodons; ObjectIdPtr oip; Boolean okay; Boolean only_digits; ValNodePtr ppr; CharPtr prefix; CharPtr protein_seq = NULL; CharPtr ptr; Uint1 residue; SeqCodeTablePtr sctp; Int4 sec_str; Uint1 seqcode; Char seqid [50]; SeqIntPtr sintp; SeqIdPtr sip; SeqLocPtr slp; Boolean split; SeqPortPtr spp; CharPtr start; CharPtr str; Boolean suppress_period; CharPtr tmp; tRNAPtr trna; UserObjectPtr uop; ValNodePtr vnp; for (i = 0, idx = feat_qual_order [i]; idx != 0; i++, idx = feat_qual_order [i]) { lasttype = NULL; switch (asn2gnbk_featur_quals [idx].qualclass) { case Qual_class_ignore : break; case Qual_class_string : if (! StringHasNoText (qvp [idx].str)) { sprintf (buf, "/%s=\"", asn2gnbk_featur_quals [idx].name); NewContLine (); gb_AddString (buf, qvp [idx].str, "\"", FALSE, TRUE, TILDE_TO_SPACES); } break; case Qual_class_product : if (StringHasNoText (qvp [idx].str) || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, FTQUAL_product)))) break; sprintf (buf, "/%s=\"", asn2gnbk_featur_quals [idx].name); NewContLine (); gb_AddString (buf, qvp [idx].str, "\"", FALSE, TRUE, TILDE_TO_SPACES); break; case Qual_class_sgml : if (! StringHasNoText (qvp [idx].str)) { ascii_len = Sgml2AsciiLen (qvp [idx].str); start = ascii = MemNew ((size_t) (10 + ascii_len)); if (start != NULL) { ascii = Sgml2Ascii (qvp [idx].str, ascii, ascii_len + 1); sprintf (buf, "/%s=\"", asn2gnbk_featur_quals [idx].name); NewContLine (); gb_AddString (buf, start, "\"", FALSE, TRUE, TILDE_TO_SPACES); MemFree (start); } } break; case Qual_class_boolean : if (qvp [idx].bool) { sprintf (buf, "/%s", asn2gnbk_featur_quals [idx].name); NewContLine (); ff_AddString (buf); } break; case Qual_class_int : if (qvp [idx].num > 0) { if (idx == FTQUAL_transl_table) { NewContLine (); sprintf (numbuf, "/%s=", asn2gnbk_featur_quals [idx].name); ff_AddString (numbuf); sprintf (numbuf, "%ld", (long) qvp [idx].num); www_gcode (numbuf); } else { sprintf (numbuf, "/%s=%ld", asn2gnbk_featur_quals [idx].name, (long) qvp [idx].num); NewContLine (); ff_AddString (numbuf); } } break; case Qual_class_evidence : exp_ev = qvp [idx].num; if (exp_ev > 0 && exp_ev <= 2) { sprintf (numbuf, "/%s=%s", asn2gnbk_featur_quals [idx].name, evidenceText [exp_ev]); NewContLine (); ff_AddString (numbuf); } break; case Qual_class_valnode : for (vnp = qvp [idx].vnp; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (str != NULL) { sprintf (buf, "/%s=\"", asn2gnbk_featur_quals [idx].name); NewContLine (); gb_AddString (buf, str, "\"", FALSE, TRUE, TILDE_TO_SPACES); } } break; /* !!! Eric wonders if this EC code works */ case Qual_class_EC_valnode : for (vnp = qvp [idx].vnp; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; okay = TRUE; if (str == NULL) continue; if (ajp->flags.dropIllegalQuals) { tmp = str; while (*tmp != '\0' && *tmp == '\"') tmp++; for (; *tmp != '\0' && *tmp != '\"'; tmp++) { if (!IS_DIGIT(*tmp) && *tmp != '.' && *tmp != '-') { okay = FALSE; } } } if (!okay) continue; sprintf (buf, "/%s=\"", asn2gnbk_featur_quals [idx].name); NewContLine (); gb_AddString (buf, str, "\"", FALSE, TRUE, TILDE_TO_SPACES); } break; case Qual_class_EC_quote : gbq = qvp [idx].gbq; if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break; if (lasttype == NULL) { lasttype = gbq->qual; } while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) { okay = TRUE; if (gbq->val == NULL) { okay = FALSE; } if (ajp->flags.dropIllegalQuals && okay) { tmp = gbq->val; while (*tmp != '\0' && *tmp == '\"') tmp++; for (; *tmp != '\0' && *tmp != '\"'; tmp++) { if (!IS_DIGIT(*tmp) && *tmp != '.' && *tmp != '-') { okay = FALSE; } } } if (StringHasNoText (gbq->val)) { okay = FALSE; } if (okay) { sprintf (buf, "/%s=\"", asn2gnbk_featur_quals [idx].name); NewContLine (); if (StringIsJustQuotes (gbq->val)) { gb_AddString (buf, NULL, "\"", FALSE, TRUE, TILDE_IGNORE); } else { gb_AddString (buf, gbq->val, "\"", FALSE, TRUE, TILDE_TO_SPACES); } } gbq = gbq->next; } break; case Qual_class_quote : gbq = qvp [idx].gbq; if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break; if (lasttype == NULL) { lasttype = gbq->qual; } while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) { if (! StringHasNoText (gbq->val)) { sprintf (buf, "/%s=\"", asn2gnbk_featur_quals [idx].name); NewContLine (); if (StringIsJustQuotes (gbq->val)) { gb_AddString (buf, NULL, "\"", FALSE, TRUE, TILDE_IGNORE); } else { gb_AddString (buf, gbq->val, "\"", FALSE, TRUE, TILDE_TO_SPACES); } } gbq = gbq->next; } break; case Qual_class_noquote : gbq = qvp [idx].gbq; if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break; if (lasttype == NULL) { lasttype = gbq->qual; } while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) { if (! StringHasNoText (gbq->val)) { sprintf (buf, "/%s=", asn2gnbk_featur_quals [idx].name); NewContLine (); gb_AddString (buf, gbq->val, NULL, FALSE, TRUE, TILDE_TO_SPACES); } gbq = gbq->next; } break; case Qual_class_label : gbq = qvp [idx].gbq; if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break; if (lasttype == NULL) { lasttype = gbq->qual; } while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) { if (! StringHasNoText (gbq->val)) { if (ajp->flags.checkQualSyntax) { /* single token, not just numeric */ str = gbq->val; ch = *str; only_digits = TRUE; while (ch != '\0') { if (IS_WHITESP (ch)) break; /* only single token allowed */ if (! IS_DIGIT (ch)) { only_digits = FALSE; } str++; ch = *str; } if (only_digits) break; /* must not be just numeric */ } sprintf (buf, "/%s=", asn2gnbk_featur_quals [idx].name); NewContLine (); gb_AddString (buf, gbq->val, NULL, FALSE, TRUE, TILDE_TO_SPACES); } gbq = gbq->next; } break; case Qual_class_number : gbq = qvp [idx].gbq; if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break; if (ajp->flags.checkQualSyntax) { str = gbq->val; if ( StringHasNoText (str) ) break; while (!IS_WHITESP (*str) && *str != '\0') str++; if (! StringHasNoText (str) ) break; } if (lasttype == NULL) { lasttype = gbq->qual; } while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) { if (! StringHasNoText (gbq->val)) { sprintf (buf, "/%s=", asn2gnbk_featur_quals [idx].name); NewContLine (); gb_AddString (buf, gbq->val, NULL, FALSE, TRUE, TILDE_TO_SPACES); } gbq = gbq->next; } break; case Qual_class_paren : gbq = qvp [idx].gbq; if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break; if (lasttype == NULL) { lasttype = gbq->qual; } while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) { if (! StringHasNoText (gbq->val)) { tmp = StringSave (gbq->val); str = tmp; len = StringLen (str); if (len > 1 && *str == '(' && str [len - 1] == ')' && StringChr (str, ',') != NULL) { str++; while (! StringHasNoText (str)) { ptr = StringChr (str, ','); if (ptr == NULL) { ptr = StringChr (str, ')'); } if (ptr != NULL) { *ptr = '\0'; ptr++; } sprintf (buf, "/%s=", asn2gnbk_featur_quals [idx].name); NewContLine (); gb_AddString (buf, str, NULL, FALSE, TRUE, TILDE_TO_SPACES); str = ptr; } } else { sprintf (buf, "/%s=", asn2gnbk_featur_quals [idx].name); NewContLine (); gb_AddString (buf, str, NULL, FALSE, TRUE, TILDE_TO_SPACES); } MemFree (tmp); } gbq = gbq->next; } break; case Qual_class_rpt : gbq = qvp [idx].gbq; if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break; if (lasttype == NULL) { lasttype = gbq->qual; } while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) { if (! StringHasNoText (gbq->val)) { tmp = StringSave (gbq->val); str = tmp; len = StringLen (str); if (len > 1 && *str == '(' && str [len - 1] == ')' && StringChr (str, ',') != NULL) { str++; while (! StringHasNoText (str)) { ptr = StringChr (str, ','); if (ptr == NULL) { ptr = StringChr (str, ')'); } if (ptr != NULL) { *ptr = '\0'; ptr++; } if ((! ajp->flags.checkQualSyntax) || (StringInStringList (str, validRptString))) { sprintf (buf, "/%s=", asn2gnbk_featur_quals [idx].name); NewContLine (); gb_AddString (buf, str, NULL, FALSE, TRUE, TILDE_TO_SPACES); } str = ptr; } } else { if ((! ajp->flags.checkQualSyntax) || (StringInStringList (str, validRptString))) { sprintf (buf, "/%s=", asn2gnbk_featur_quals [idx].name); NewContLine (); gb_AddString (buf, str, NULL, FALSE, TRUE, TILDE_TO_SPACES); } } MemFree (tmp); } gbq = gbq->next; } break; case Qual_class_rpt_unit : gbq = qvp [idx].gbq; if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break; if (lasttype == NULL) { lasttype = gbq->qual; } if (gbq->val == NULL) break; if (ajp->flags.checkQualSyntax) { /* must be of the form 123..4567 or a single-token label */ Nlm_StrNCpy(buf, gbq->val, sizeof(buf)); TrimSpacesAroundString (buf); /* first check for a alphanumeric token */ str = buf; while (IS_ALPHANUM(*str)) str++; if (*str != '\0') { /* wasn't pure alphanumeric; now check for xxx..yyy */ str = buf; while (IS_DIGIT(*str)) str++; /* xxx */ if (*str == '\0' /* must be something after the xxx */ || StringLen (str) < 3 /* need at least 2 '.'s and a digit*/ || str[0] != '.' || str[1] != '.') break; str+=2; while (IS_DIGIT(*str)) str++; if (*str != '\0') break; /* mustn't be anything after the yyy */ } } str = gbq->val; sprintf (buf, "/%s=", asn2gnbk_featur_quals [idx].name); NewContLine (); gb_AddString (buf, str, NULL, FALSE, TRUE, TILDE_TO_SPACES); break; case Qual_class_replace : gbq = qvp [idx].gbq; if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break; if (lasttype == NULL) { lasttype = gbq->qual; } while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) { if (! StringHasNoText (gbq->val)) { sprintf (buf, "/%s=\"", asn2gnbk_featur_quals [idx].name); NewContLine (); gb_AddString (buf, gbq->val, "\"", FALSE, TRUE, TILDE_TO_SPACES); } else { sprintf (buf, "/%s=\"", asn2gnbk_featur_quals [idx].name); NewContLine (); gb_AddString (buf, NULL, "\"", FALSE, TRUE, TILDE_TO_SPACES); } gbq = gbq->next; } break; case Qual_class_consplice : gbq = qvp [idx].gbq; if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break; if (ajp->flags.checkQualSyntax && (! StringInStringList (gbq->val, validConsSpliceString)) ) { break; } if (lasttype == NULL) { lasttype = gbq->qual; } while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) { if (! StringHasNoText (gbq->val)) { sprintf (buf, "/%s=", asn2gnbk_featur_quals [idx].name); NewContLine (); gb_AddString (buf, gbq->val, NULL, FALSE, TRUE, TILDE_TO_SPACES); } gbq = gbq->next; } break; case Qual_class_site : if (! StringHasNoText (qvp [idx].str)) { NewContLine (); sprintf (buf, "/%s=\"", asn2gnbk_featur_quals [idx].name); gb_AddString (buf, qvp [idx].str, "\"", FALSE, TRUE, TILDE_TO_SPACES); } break; case Qual_class_L_R_B : gbq = qvp [idx].gbq; if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break; if (ajp->flags.checkQualSyntax && (! StringInStringList (gbq->val, validLRBString)) ) { break; } if (lasttype == NULL) { lasttype = gbq->qual; } while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) { if (! StringHasNoText (gbq->val)) { sprintf (buf, "/%s=", asn2gnbk_featur_quals [idx].name); NewContLine (); gb_AddString (buf, gbq->val, NULL, FALSE, TRUE, TILDE_TO_SPACES); } gbq = gbq->next; } break; case Qual_class_sec_str : sec_str = qvp [idx].num; if (sec_str > 0 && sec_str <= 3) { sprintf (numbuf, "/%s=\"%s\"", asn2gnbk_featur_quals [idx].name, secStrText [sec_str]); NewContLine (); ff_AddString (numbuf); } break; case Qual_class_seq_loc : slp = qvp [idx].slp; if (slp != NULL) { sprintf (buf, "/%s=\"", asn2gnbk_featur_quals [idx].name); NewContLine (); str = FlatLoc (target, slp, ajp->masterStyle); gb_AddString (buf, str, "\"", FALSE, TRUE, TILDE_TO_SPACES); MemFree (str); } break; case Qual_class_code_break : cbp = qvp [idx].cbp; seqcode = 0; sctp = NULL; while (cbp != NULL) { cbaa = cbp->aa; switch (cbaa.choice) { case 1 : seqcode = Seq_code_ncbieaa; break; case 2 : seqcode = Seq_code_ncbi8aa; break; case 3 : seqcode = Seq_code_ncbistdaa; break; default : break; } if (seqcode != 0) { sctp = SeqCodeTableFind (seqcode); if (sctp != NULL) { slp = NULL; while ((slp = SeqLocFindNext (cbp->loc, slp)) != NULL) { str = NULL; if (ajp->ajp.slp != NULL) { sip = SeqIdParse ("lcl|dummy"); split = FALSE; newloc = SeqLocCopyRegion (sip, slp, bsp, left, right, strand, &split); SeqIdFree (sip); if (newloc != NULL) { SeqLocReplaceID (newloc, SeqLocId (ajp->ajp.slp)); str = FlatLoc (target, newloc, ajp->masterStyle); SeqLocFree (newloc); } } else { str = FlatLoc (target, slp, ajp->masterStyle); } if (str != NULL) { residue = cbaa.value.intvalue; ptr = Get3LetterSymbol (ajp, seqcode, sctp, residue); if (ptr == NULL) { ptr = "OTHER"; } sprintf (buf, "/transl_except=(pos:%s,aa:%s)", str, ptr); NewContLine (); ff_AddString (buf); } MemFree (str); } } } cbp = cbp->next; } break; case Qual_class_anti_codon : slp = qvp [FTQUAL_anticodon].slp; newloc = NULL; if (ajp->ajp.slp != NULL) { sip = SeqIdParse ("lcl|dummy"); split = FALSE; newloc = SeqLocCopyRegion (sip, slp, bsp, left, right, strand, &split); SeqIdFree (sip); slp = newloc; if (newloc != NULL) { SeqLocReplaceID (newloc, SeqLocId (ajp->ajp.slp)); } } if (slp != NULL && slp->choice == SEQLOC_INT) { sintp = (SeqIntPtr) slp->data.ptrvalue; if (sintp != NULL) { str = qvp [FTQUAL_trna_aa].str; if (! StringHasNoText (str)) { sprintf (buf, "/anticodon=(pos:%ld..%ld,aa:%s)", (long) sintp->from + 1, (long) sintp->to + 1, str); NewContLine (); ff_AddString (buf); } } } if (newloc != NULL) { SeqLocFree (newloc); } break; case Qual_class_codon : gbq = qvp [idx].gbq; if (gbq == NULL || (ajp->flags.dropIllegalQuals && (! AllowedValQual (featdeftype, idx)))) break; if (lasttype == NULL) { lasttype = gbq->qual; } while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) { if (! StringHasNoText (gbq->val)) { sprintf (buf, "/%s=", asn2gnbk_featur_quals [idx].name); NewContLine (); gb_AddString (buf, gbq->val, NULL, FALSE, FALSE, TILDE_TO_SPACES); } gbq = gbq->next; } break; case Qual_class_pubset : vnp = qvp [idx].vnp; if (vnp != NULL && asp->referenceArray != NULL) { for (ppr = vnp->data.ptrvalue; ppr != NULL; ppr = ppr->next) { j = MatchRef (ppr, asp->referenceArray, asp->numReferences); if (j > 0) { sprintf (buf, "%d", (int) j); NewContLine (); gb_AddString ("/citation=[", buf, "]", FALSE, TRUE, TILDE_TO_SPACES); } } } break; case Qual_class_db_xref : for (vnp = qvp [idx].vnp; vnp != NULL; vnp = vnp->next) { buf [0] = '\0'; dbt = (DbtagPtr) vnp->data.ptrvalue; if (dbt != NULL && (! StringHasNoText (dbt->db))) { oip = dbt->tag; if (oip != NULL) { okay = TRUE; if (ajp->flags.dropBadDbxref) { /* if RELEASE_MODE, drop unknown dbtag */ okay = FALSE; for (j = 0; legalDbXrefs [j] != NULL; j++) { if (StringCmp (dbt->db, legalDbXrefs [j]) == 0) { okay = TRUE; } } if (! okay) { if (is_gps || is_other) { for (j = 0; legalRefSeqDbXrefs [j] != NULL; j++) { if (StringCmp (dbt->db, legalRefSeqDbXrefs [j]) == 0) { okay = TRUE; } } } } } if (okay) { if (! StringHasNoText (oip->str)) { if (StringLen (dbt->db) + StringLen (oip->str) < 80) { sprintf (buf, "%s:%s", dbt->db, oip->str); } } else { sprintf (buf, "%s:%ld", dbt->db, (long) oip->id); } } } } if (! StringHasNoText (buf)) { if (StringICmp (buf, protein_pid_g) != 0) { keep = TRUE; for (dbx = dbxrefs; dbx != NULL; dbx = dbx->next) { if (StringICmp ((CharPtr) dbx->data.ptrvalue, buf) == 0) { keep = FALSE; } } if (keep) { NewContLine (); ff_AddString ("/db_xref=\""); www_db_xref (buf); ff_AddString ("\""); /* gb_AddString ("/db_xref=\"", buf, "\"", FALSE, TRUE, TILDE_TO_SPACES); */ ValNodeCopyStr (&dbxrefs, 0, buf); } } } } break; case Qual_class_seq_id : sip = qvp [idx].sip; if (sip != NULL) { /* should always be found above for protein_id or transcript_id prod = BioseqFind (sip); */ if (prod != NULL) { choice = 0; for (sip = prod->id; sip != NULL; sip = sip->next) { if (sip->choice == SEQID_GENBANK || sip->choice == SEQID_EMBL || sip->choice == SEQID_DDBJ || sip->choice == SEQID_OTHER || sip->choice == SEQID_TPG || sip->choice == SEQID_TPE || sip->choice == SEQID_TPD) { choice = sip->choice; if (SeqIdWrite (sip, seqid, PRINTID_TEXTID_ACC_VER, sizeof (seqid)) != NULL) { sprintf (buf, "/%s=\"", asn2gnbk_featur_quals [idx].name); NewContLine (); ff_AddString (buf); www_protein_id (seqid); ff_AddString ("\""); /* gb_AddString (buf, seqid, "\"", FALSE, TRUE, TILDE_TO_SPACES); */ } } } for (sip = prod->id; sip != NULL; sip = sip->next) { if (sip->choice == SEQID_GI) { /* if (choice != 0) { sprintf (seqid, "PID:g%ld", (long) sip->data.intvalue); NewContLine (); gb_AddString ("/db_xref=\"", seqid, "\"", FALSE, TRUE, TILDE_TO_SPACES); } */ if (choice == 0) { sprintf (buf, "/%s=\"", asn2gnbk_featur_quals [idx].name); sprintf (seqid, "%ld", (long) sip->data.intvalue); NewContLine (); ff_AddString (buf); www_protein_id (seqid); ff_AddString ("\""); /* gb_AddString (buf, seqid, "\"", FALSE, TRUE, TILDE_TO_SPACES); */ } sprintf (seqid, "GI:%ld", (long) sip->data.intvalue); NewContLine (); ff_AddString ("/db_xref=\""); www_db_xref (seqid); ff_AddString ("\""); /* gb_AddString ("/db_xref=\"", seqid, "\"", FALSE, TRUE, TILDE_TO_SPACES); */ } else if (sip->choice == SEQID_GENERAL) { dbt = (DbtagPtr) sip->data.ptrvalue; if (dbt != NULL && StringCmp (dbt->db, "PID") == 0) { /* oip = dbt->tag; if (oip != NULL) { if (! StringHasNoText (oip->str)) { sprintf (seqid, "PID:%s", oip->str); NewContLine (); gb_AddString ("/db_xref=\"", seqid, "\"", FALSE, TRUE, TILDE_TO_SPACES); } } */ } } } } else { if (sip->choice == SEQID_GI) { gi = sip->data.intvalue; sip = GetSeqIdForGI (gi); if (sip != NULL && SeqIdWrite (sip, seqid, PRINTID_TEXTID_ACC_VER, sizeof (seqid)) != NULL) { if ((! ajp->flags.dropIllegalQuals) || ValidateAccession (seqid)) { sprintf (buf, "/%s=\"", asn2gnbk_featur_quals [idx].name); NewContLine (); ff_AddString (buf); www_protein_id (seqid); ff_AddString ("\""); /* gb_AddString (buf, seqid, "\"", FALSE, TRUE, TILDE_TO_SPACES); */ } } else if (! ajp->flags.dropIllegalQuals) { sprintf (seqid, "%ld", (long) gi); sprintf (buf, "/%s=\"", asn2gnbk_featur_quals [idx].name); NewContLine (); ff_AddString (buf); www_protein_id (seqid); ff_AddString ("\""); /* gb_AddString (buf, seqid, "\"", FALSE, TRUE, TILDE_TO_SPACES); */ } sprintf (seqid, "GI:%ld", (long) gi); NewContLine (); ff_AddString ("/db_xref=\""); www_db_xref (seqid); ff_AddString ("\""); /* gb_AddString ("/db_xref=\"", seqid, "\"", FALSE, TRUE, TILDE_TO_SPACES); */ } else if (SeqIdWrite (sip, seqid, PRINTID_TEXTID_ACC_VER, sizeof (seqid)) != NULL) { if ((! ajp->flags.dropIllegalQuals) || ValidateAccession (seqid)) { sprintf (buf, "/%s=\"", asn2gnbk_featur_quals [idx].name); NewContLine (); ff_AddString (buf); www_protein_id (seqid); ff_AddString ("\""); /* gb_AddString (buf, seqid, "\"", FALSE, TRUE, TILDE_TO_SPACES); */ } gi = GetGIForSeqId (sip); if (gi > 0) { sprintf (seqid, "GI:%ld", (long) gi); NewContLine (); ff_AddString ("/db_xref=\""); www_db_xref (seqid); ff_AddString ("\""); /* gb_AddString ("/db_xref=\"", seqid, "\"", FALSE, TRUE, TILDE_TO_SPACES); */ } } } } break; case Qual_class_translation : if (qvp [idx].bool) { if (prod != NULL) { len = SeqLocLen (sfp->product); if (len > 0) { if (SeqLocStart (location) == 0 || SeqLocStop (location) == bsp->length - 1) { at_end = TRUE; } str = (CharPtr) MemNew ((size_t) (len + 1) * sizeof (Char)); protein_seq = str; if (ajp->flags.iupacaaOnly) { code = Seq_code_iupacaa; } else { code = Seq_code_ncbieaa; } spp = SeqPortNewByLoc (sfp->product, code); if (spp != NULL) { SeqPortSet_do_virtual (spp, TRUE); while ((residue = SeqPortGetResidue (spp)) != SEQPORT_EOF) { if (! (IS_residue (residue))) continue; if (residue == INVALID_RESIDUE) { residue = (Uint1) 'X'; } *protein_seq = residue; protein_seq++; } if (at_end && StringLen (str) < 0) { str = MemFree (str); } if (! StringHasNoText (str)) { NewContLine (); gb_AddString ("/translation=\"", str, "\"", FALSE, TRUE, TILDE_TO_SPACES); } MemFree (str); } SeqPortFree (spp); } /* } else { bs = ProteinFromCdRegionEx (sfp, TRUE, FALSE); if (bs != NULL) { str = BSMerge (bs, NULL); bs = BSFree (bs); if (str != NULL) { ptr = str; ch = *ptr; while (ch != '\0') { *ptr = TO_UPPER (ch); ptr++; ch = *ptr; } if (! StringHasNoText (str)) { NewContLine (); gb_AddString ("/translation=\"", str, "\"", FALSE, TRUE, TILDE_TO_SPACES); } MemFree (str); } } */ } } break; case Qual_class_illegal : for (vnp = qvp [idx].vnp; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (str != NULL) { NewContLine (); gb_AddString (NULL, str, NULL, FALSE, FALSE, TILDE_TO_SPACES); } } break; case Qual_class_note : head = NULL; notestr = NULL; prefix = NULL; add_period = FALSE; suppress_period = FALSE; lasttype = NULL; isTRNA = TRUE; #ifdef DISPLAY_STRINGS s_DisplayQVP (qvp, feat_note_order); #endif for (j = 0, jdx = feat_note_order [j]; jdx != 0; j++, jdx = feat_note_order [j]) { switch (asn2gnbk_featur_quals [jdx].qualclass) { case Qual_class_string : if (! StringHasNoText (qvp [jdx].str)) { if (jdx == FTQUAL_figure) { if (!IsEllipsis (qvp [jdx].str)) s_RemovePeriodFromEnd (qvp [jdx].str); sprintf (buf, "This sequence comes from %s", qvp [jdx].str); s_AddValNodeString_NoRedund (&head, prefix, buf, NULL); add_period = FALSE; } else if (jdx == FTQUAL_maploc) { if (!IsEllipsis (qvp [jdx].str)) s_RemovePeriodFromEnd (qvp [jdx].str); sprintf (buf, "Map location %s", qvp [jdx].str); s_AddValNodeString_NoRedund (&head, prefix, buf, NULL); add_period = FALSE; } else if (jdx == FTQUAL_seqfeat_note) { str = StringSave (qvp [jdx].str); TrimSpacesAndJunkFromEnds (str, TRUE); if (! IsEllipsis (str)) add_period = s_RemovePeriodFromEnd (str); /* NOTE -- The following function call cleans up some strings (i.e., U34661 & U31565) but should be commented back in only if the problem can't be fixed upstream of here s_StringCleanup(str); */ s_AddValNodeString_NoRedund (&head, prefix, str, NULL); MemFree (str); if (hadProtDesc) { suppress_period = TRUE; } } else if (jdx == FTQUAL_prot_note) { str = StringSave (qvp [jdx].str); TrimSpacesAndJunkFromEnds (str, TRUE); if (! IsEllipsis (str)) s_RemovePeriodFromEnd (str); s_AddValNodeString_NoRedund (&head, prefix, str, NULL); MemFree (str); add_period = FALSE; } else if (jdx == FTQUAL_prot_desc) { str = StringSave (qvp [jdx].str); TrimSpacesAndJunkFromEnds (str, TRUE); if (! IsEllipsis (str)) add_period = s_RemovePeriodFromEnd (str); s_AddValNodeString_NoRedund (&head, prefix, str, NULL); MemFree (str); hadProtDesc = TRUE; /* gi|347886|gb|M96268.1|ECOUBIA */ } else { if (! IsEllipsis (qvp [jdx].str)) s_RemovePeriodFromEnd (qvp [jdx].str); s_AddValNodeString_NoRedund (&head, prefix, qvp [jdx].str, NULL); add_period = FALSE; } prefix = "; "; } break; case Qual_class_method : if (! StringHasNoText (qvp [jdx].str)) { if (head == NULL) { prefix = "Method: "; } else { prefix = "; Method: "; } s_AddValNodeString_NoRedund (&head, prefix, qvp [jdx].str, NULL); prefix = "; "; add_period = FALSE; } break; case Qual_class_valnode : for (vnp = qvp [jdx].vnp; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (! StringHasNoText (str)) { s_AddValNodeString_NoRedund (&head, prefix, str, NULL); prefix = "; "; add_period = FALSE; } } break; case Qual_class_region : if (! StringHasNoText (qvp [jdx].str)) { if (head == NULL) { prefix = "Region: "; } else { prefix = "; Region: "; } #ifdef ASN2GNBK_STRIP_NOTE_PERIODS AddValNodeString (&head, prefix, qvp [jdx].str, NULL); #else s_AddValNodeString_NoRedund (&head, prefix, qvp [jdx].str, NULL); #endif prefix = "; "; add_period = FALSE; } break; case Qual_class_site : if (! StringHasNoText (qvp [jdx].str)) { s_AddValNodeString_NoRedund (&head, prefix, qvp [jdx].str, " site"); add_period = FALSE; prefix = "\n"; } break; case Qual_class_protnames : /* process gene sgml for check against subsequent protein names */ start = NULL; if (! StringHasNoText (qvp [FTQUAL_gene].str)) { ascii_len = Sgml2AsciiLen (qvp [FTQUAL_gene].str); start = ascii = MemNew ((size_t) (10 + ascii_len)); if (start != NULL) { ascii = Sgml2Ascii (qvp [FTQUAL_gene].str, ascii, ascii_len + 1); } } for (vnp = qvp [jdx].vnp; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (! StringHasNoText (str)) { /* case sensitive - gi|4973426|gb|AF148501.1|AF148501 */ /* check with and without sgml conversion */ if (StringCmp (start, str) != 0 && StringCmp (qvp [FTQUAL_gene].str, str) != 0) { if (! StringStr (qvp [FTQUAL_prot_desc].str, str)) { if (NotInGeneSyn (str, gene_syn)) { s_AddValNodeString_NoRedund (&head, prefix, str, NULL); prefix = "; "; add_period = FALSE; } } } } } MemFree (start); break; case Qual_class_xtraprds : gbq = qvp [jdx].gbq; if (lasttype == NULL && gbq != NULL) { lasttype = gbq->qual; } while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) { if (! StringHasNoText (gbq->val)) { if (StringCmp(gbq->val,qvp[FTQUAL_gene].str) != 0 && StringCmp(gbq->val,qvp[FTQUAL_product].str) != 0) { if (!isTRNA || !StringStr (gbq->val, "RNA")) { s_AddValNodeString_NoRedund (&head, prefix, gbq->val, NULL); prefix = "; "; add_period = FALSE; } } } gbq = gbq->next; } break; case Qual_class_its : str = qvp [jdx].str; if (! StringHasNoText (str)) { if (sfp->comment == NULL || StringStr (sfp->comment, str) == NULL) { s_AddValNodeString_NoRedund (&head, prefix, str, NULL); prefix = "; "; add_period = FALSE; } } break; case Qual_class_trna_codons : trna = qvp [jdx].trp; if (trna) { numcodons = ComposeCodonsRecognizedString (trna, numbuf, sizeof (numbuf)); if (numcodons < 1 || StringHasNoText (numbuf)) { } else if (numcodons == 1) { isTRNA = TRUE; sprintf (buf, "codon recognized: %s", numbuf); if (StringStr (qvp [FTQUAL_seqfeat_note].str, buf) == NULL) { s_AddValNodeString_NoRedund (&head, prefix, "codon recognized: ", numbuf); prefix = "; "; } } else { isTRNA = TRUE; s_AddValNodeString_NoRedund (&head, prefix, "codons recognized: ", numbuf); prefix = "; "; add_period = FALSE; } } break; case Qual_class_model_ev : uop = qvp [jdx].uop; if (uop != NULL) { str = GetStrFormRNAEvidence (uop); if (! StringHasNoText (str)) { s_AddValNodeString_NoRedund (&head, prefix, str, NULL); prefix = "; "; add_period = FALSE; } } break; default : break; } } if (head != NULL) { notestr = MergeValNodeStrings (head); NewContLine (); TrimSpacesAroundString (notestr); if (add_period) { if (! suppress_period) { s_AddPeriodToEnd (notestr); } } #ifdef ASN2GNBK_STRIP_NOTE_PERIODS if (! IsEllipsis (notestr)) s_RemovePeriodFromEnd (notestr); #endif gb_AddString (NULL, "/note=\"", NULL, FALSE, FALSE, TILDE_IGNORE); gb_AddString (NULL, notestr, NULL, FALSE, TRUE, TILDE_EXPAND); gb_AddString (NULL, "\"", NULL, FALSE, FALSE, TILDE_IGNORE); MemFree (notestr); ValNodeFreeData (head); } break; default : break; } } ValNodeFreeData (dbxrefs); } static void RecordUserObjectsInQVP ( UserObjectPtr uop, Pointer userdata ) { ObjectIdPtr oip; QualValPtr qvp; if (uop == NULL || userdata == NULL) return; qvp = (QualValPtr) userdata; oip = uop->type; if (oip == NULL) return; if (StringCmp (oip->str, "ModelEvidence") == 0) { qvp [FTQUAL_modelev].uop = uop; } } static CharPtr FormatFeatureBlock ( Asn2gbFormatPtr afp, BaseBlockPtr bbp ) { Uint1 aa; IntAsn2gbJobPtr ajp; Asn2gbSectPtr asp; BioseqPtr bsp; BioseqSetPtr bssp; Char buf [80]; Choice cbaa; CodeBreakPtr cbp; BioseqPtr cdna; SeqFeatPtr cds; Char ch; Uint1 code = Seq_code_ncbieaa; CdRegionPtr crp; SeqMgrDescContext dcontext; SeqMgrFeatContext fcontext; Uint1 featdeftype; Uint1 from; GBQualPtr gbq; SeqMgrFeatContext gcontext; ValNodePtr gcp; SeqFeatPtr gene = NULL; ValNodePtr gene_syn = NULL; Int4 gi = 0; GeneRefPtr grp; IntCdsBlockPtr icp; Uint1 idx; IntFeatBlockPtr ifp; ValNodePtr illegal = NULL; ImpFeatPtr imp = NULL; Boolean is_gps = FALSE; Boolean is_other = FALSE; CharPtr key; CharPtr lasttype; Int4 left = -1; SeqLocPtr loc = NULL; SeqLocPtr location = NULL; SeqLocPtr locforgene = NULL; SeqMgrFeatContext mcontext; MolInfoPtr mip; SeqFeatPtr mrna; SeqLocPtr newloc; Boolean noLeft; Boolean noRight; SeqEntryPtr oldscope; Uint2 partial; SeqMgrFeatContext pcontext; BioseqPtr prod = NULL; SeqFeatPtr prot; Boolean protein = FALSE; Char protein_pid_g [32]; ProtRefPtr prp; Boolean pseudo = FALSE; CharPtr ptr; Int2 qualclass; QualValPtr qvp; Uint1 residue; Int4 right = -1; RnaRefPtr rrp; SeqCodeTablePtr sctp; SeqDescrPtr sdp; SeqEntryPtr sep; Uint1 seqcode; SeqFeatPtr sfp; Uint1 shift; SeqIdPtr sip; Int2 siteidx; SeqMapTablePtr smtp; Boolean split; CharPtr str; Uint1 strand = Seq_strand_unknown; BioseqPtr target; CharPtr tmp; tRNAPtr trna; BioseqPtr unlockme = NULL; ValNodePtr vnp; CharPtr wwwbuf; if (afp == NULL || bbp == NULL) return NULL; asp = afp->asp; if (asp == NULL) return NULL; target = asp->target; bsp = asp->bsp; if (target == NULL || bsp == NULL) return NULL; ajp = afp->ajp; if (ajp == NULL) return NULL; qvp = afp->qvp; if (qvp == NULL) return NULL; protein_pid_g [0] = '\0'; /* all features in this list are known to be valid for the designated mode */ sfp = SeqMgrGetDesiredFeature (bbp->entityID, NULL, bbp->itemID, 0, NULL, &fcontext); if (sfp == NULL) return NULL; /* may need to map location between aa and dna */ ifp = (IntFeatBlockPtr) bbp; if (ifp->mapToNuc) { /* map mat_peptide, etc., to nucleotide coordinates */ sip = SeqLocId (sfp->location); prod = BioseqFind (sip); cds = SeqMgrGetCDSgivenProduct (prod, NULL); CheckSeqLocForPartial (sfp->location, &noLeft, &noRight); location = aaFeatLoc_to_dnaFeatLoc (cds, sfp->location); SetSeqLocPartial (location, noLeft, noRight); locforgene = location; loc = location; } else if (ifp->mapToProt) { /* map CDS to protein product coordinates */ sip = SeqLocId (sfp->product); prod = BioseqFind (sip); cds = SeqMgrGetCDSgivenProduct (prod, NULL); location = dnaLoc_to_aaLoc (cds, sfp->location, TRUE, NULL, FALSE); SetSeqLocPartial (location, FALSE, FALSE); locforgene = sfp->location; loc = location; } else if (ifp->mapToGen) { /* map CDS from cDNA to genomic Bioseq */ cdna = BioseqFindFromSeqLoc (sfp->location); mrna = SeqMgrGetRNAgivenProduct (cdna, &mcontext); CheckSeqLocForPartial (sfp->location, &noLeft, &noRight); location = productLoc_to_locationLoc (mrna, sfp->location); SetSeqLocPartial (location, noLeft, noRight); locforgene = location; loc = location; } else if (ifp->mapToMrna) { /* map gene from genomic to cDNA Bioseq */ sep = SeqMgrGetSeqEntryForData (bsp); location = CreateWholeInterval (sep); SetSeqLocPartial (location, FALSE, FALSE); locforgene = location; loc = location; } else { /* no aa-dna or dna-aa mapping, just use location */ location = sfp->location; locforgene = sfp->location; } if (location == NULL) return NULL; sep = GetTopSeqEntryForEntityID (ajp->ajp.entityID); if (sep == NULL && IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp != NULL && bssp->_class == BioseqseqSet_class_gen_prod_set) { is_gps = TRUE; } } for (sip = bsp->id; sip != NULL; sip = sip->next) { if (sip->choice == SEQID_OTHER) { is_other = TRUE; } else if (sip->choice == SEQID_GI) { gi = (Int4) sip->data.intvalue; } } featdeftype = fcontext.featdeftype; if (featdeftype < FEATDEF_GENE || featdeftype >= FEATDEF_MAX) { featdeftype = FEATDEF_BAD; } key = FindKeyFromFeatDefType (featdeftype, TRUE); if (afp->format == GENPEPT_FMT && ISA_aa (bsp->mol)) { if (featdeftype == FEATDEF_REGION) { key = "Region"; } else if (featdeftype == FEATDEF_SITE) { key = "Site"; } } /* deal with unmappable impfeats */ if (featdeftype == FEATDEF_BAD && fcontext.seqfeattype == SEQFEAT_IMP) { imp = (ImpFeatPtr) sfp->data.value.ptrvalue; if (imp != NULL) { key = imp->key; } } gb_StartPrint (afp->format, 5, 21, NULL, 0, 5, 21, "FT", ifp->firstfeat); if (ajp->ajp.slp != NULL) { ff_AddString (key); } else { www_featkey (key, gi, fcontext.entityID, fcontext.itemID); } TabToColumn (22); if (imp == NULL || StringHasNoText (imp->loc)) { if (ajp->ajp.slp != NULL) { sip = SeqIdParse ("lcl|dummy"); left = GetOffsetInBioseq (ajp->ajp.slp, bsp, SEQLOC_LEFT_END); right = GetOffsetInBioseq (ajp->ajp.slp, bsp, SEQLOC_RIGHT_END); strand = SeqLocStrand (ajp->ajp.slp); split = FALSE; newloc = SeqLocCopyRegion (sip, location, bsp, left, right, strand, &split); SeqIdFree (sip); if (newloc == NULL) return NULL; SeqLocReplaceID (newloc, SeqLocId (ajp->ajp.slp)); str = FlatLoc (target, newloc, ajp->masterStyle); SeqLocFree (newloc); } else { str = FlatLoc (target, location, ajp->masterStyle); } } else { str = StringSave (imp->loc); } if (get_www ()) { wwwbuf = www_featloc (str); ff_AddString (wwwbuf); MemFree (wwwbuf); } else { ff_AddString (str); } MemFree (str); /* populate qualifier table from feature fields */ /* if (sfp->partial == TRUE) sfp->partial = FlatAnnotPartial(sfp, use_product); */ if (sfp->partial) { partial = SeqLocPartialCheck (location); if (partial == SLP_COMPLETE /* || partial > SLP_OTHER */ ) { qvp [FTQUAL_partial].bool = TRUE; } if (LookForFuzz (location)) { qvp [FTQUAL_partial].bool = FALSE; } if (imp != NULL) { if (StringChr (imp->loc, '<') != NULL || StringChr (imp->loc, '>') != NULL) { qvp [FTQUAL_partial].bool = FALSE; } } /* a few features cannot show /partial in RELEASE_MODE - later no features will */ if (ajp->flags.checkQualSyntax) { switch (featdeftype) { case FEATDEF_conflict: case FEATDEF_mutation: case FEATDEF_N_region: case FEATDEF_polyA_site: qvp [FTQUAL_partial].bool = FALSE; break; default: break; } } } if (ifp->mapToProt) { qvp [FTQUAL_partial].bool = FALSE; } if (sfp->pseudo) { pseudo = TRUE; } if (fcontext.seqfeattype == SEQFEAT_GENE) { grp = (GeneRefPtr) sfp->data.value.ptrvalue; if (grp != NULL) { if (! StringHasNoText (grp->locus)) { qvp [FTQUAL_gene].str = grp->locus; qvp [FTQUAL_gene_desc].str = grp->desc; qvp [FTQUAL_gene_syn].vnp = grp->syn; } else if (! StringHasNoText (grp->desc)) { qvp [FTQUAL_gene].str = grp->desc; qvp [FTQUAL_gene_syn].vnp = grp->syn; } else if (grp->syn != NULL) { vnp = grp->syn; qvp [FTQUAL_gene].str = (CharPtr) vnp->data.ptrvalue; vnp = vnp->next; qvp [FTQUAL_gene_syn].vnp = vnp; } qvp [FTQUAL_gene_map].str = grp->maploc; qvp [FTQUAL_gene_allele].str = grp->allele; qvp [FTQUAL_gene_xref].vnp = grp->db; if (grp->pseudo) { pseudo = TRUE; } } } else { grp = SeqMgrGetGeneXref (sfp); if (grp != NULL) { qvp [FTQUAL_gene_xref].vnp = grp->db; } if (grp == NULL) { sep = GetTopSeqEntryForEntityID (ajp->ajp.entityID); oldscope = SeqEntrySetScope (sep); gene = SeqMgrGetOverlappingGene (locforgene, &gcontext); SeqEntrySetScope (oldscope); if (gene != NULL) { qvp [FTQUAL_gene_note].str = gene->comment; grp = (GeneRefPtr) gene->data.value.ptrvalue; if (gene->pseudo) { pseudo = TRUE; } qvp [FTQUAL_gene_xref].vnp = grp->db; } } if (grp != NULL && grp->pseudo) { pseudo = TRUE; } if (grp != NULL && (! SeqMgrGeneIsSuppressed (grp)) && (fcontext.featdeftype != FEATDEF_repeat_region || gene == NULL)) { if (! StringHasNoText (grp->locus)) { qvp [FTQUAL_gene].str = grp->locus; gene_syn = grp->syn; } else if (! StringHasNoText (grp->desc)) { qvp [FTQUAL_gene].str = grp->desc; gene_syn = grp->syn; } else if (grp->syn != NULL) { vnp = grp->syn; qvp [FTQUAL_gene].str = (CharPtr) vnp->data.ptrvalue; vnp = vnp->next; gene_syn = vnp; } } if (fcontext.seqfeattype != SEQFEAT_CDREGION && fcontext.seqfeattype != SEQFEAT_RNA) { qvp [FTQUAL_gene_xref].vnp = NULL; } /* specific fields set here */ switch (fcontext.seqfeattype) { case SEQFEAT_CDREGION : if (! ifp->mapToProt) { crp = (CdRegionPtr) sfp->data.value.ptrvalue; if (crp != NULL) { qvp [FTQUAL_codon_start].num = crp->frame; if (qvp [FTQUAL_codon_start].num == 0) { qvp [FTQUAL_codon_start].num = 1; } qvp [FTQUAL_transl_except].cbp = crp->code_break; for (cbp = crp->code_break; cbp != NULL; cbp = cbp->next) { seqcode = 0; sctp = NULL; cbaa = cbp->aa; switch (cbaa.choice) { case 1 : seqcode = Seq_code_ncbieaa; break; case 2 : seqcode = Seq_code_ncbi8aa; break; case 3 : seqcode = Seq_code_ncbistdaa; break; default : break; } if (seqcode != 0) { sctp = SeqCodeTableFind (seqcode); if (sctp != NULL) { residue = cbaa.value.intvalue; if (residue != 42) { if (seqcode != Seq_code_ncbieaa) { smtp = SeqMapTableFind (seqcode, Seq_code_ncbieaa); residue = SeqMapTableConvert (smtp, residue); } if (residue == 'U') { qvp [FTQUAL_selenocysteine].str = "selenocysteine"; } } } } } gcp = crp->genetic_code; if (gcp != NULL) { for (vnp = gcp->data.ptrvalue; vnp != NULL; vnp = vnp->next) { if (vnp->choice == 2 && vnp->data.intvalue != 0) { qvp [FTQUAL_transl_table].num = vnp->data.intvalue; } } /* suppress table 1 */ if (qvp [FTQUAL_transl_table].num == 1) { qvp [FTQUAL_transl_table].num = 0; } } if (sfp->product != NULL && SeqLocLen (sfp->product) != 0) { protein = TRUE; } if (crp->conflict && (protein || (! sfp->excpt))) { if (protein) { qvp [FTQUAL_prot_conflict].str = conflict_msg; } else { /* qvp [FTQUAL_prot_missing].str = no_protein_msg; */ } } } prp = SeqMgrGetProtXref (sfp); if (prp == NULL) { sip = SeqLocId (sfp->product); qvp [FTQUAL_protein_id].sip = sip; sep = GetTopSeqEntryForEntityID (ajp->ajp.entityID); /* by default only show /translation if product bioseq is within entity */ oldscope = SeqEntrySetScope (sep); prod = BioseqFind (sip); SeqEntrySetScope (oldscope); if (prod == NULL && ajp->showFarTransl) { /* but flag can override and force far /translation */ prod = BioseqLockById (sip); unlockme = prod; } if (prod != NULL) { for (sip = prod->id; sip != NULL; sip = sip->next) { if (sip->choice == SEQID_GI) { sprintf (protein_pid_g, "PID:g%ld", (long) sip->data.intvalue); } } sdp = SeqMgrGetNextDescriptor (prod, NULL, Seq_descr_comment, &dcontext); if (sdp != NULL && dcontext.level == 0) { if (! StringHasNoText ((CharPtr) sdp->data.ptrvalue)) { qvp [FTQUAL_prot_comment].str = (CharPtr) sdp->data.ptrvalue; } } sdp = SeqMgrGetNextDescriptor (prod, NULL, Seq_descr_molinfo, &dcontext); if (sdp != NULL && dcontext.level == 0) { mip = (MolInfoPtr) sdp->data.ptrvalue; if (mip != NULL && mip->tech > 1 && mip->tech != MI_TECH_concept_trans && mip->tech != MI_TECH_concept_trans_a) { str = StringForSeqTech (mip->tech); if (! StringHasNoText (str)) { qvp [FTQUAL_prot_method].str = str; } } } prot = SeqMgrGetBestProteinFeature (prod, &pcontext); if (prot != NULL) { prp = (ProtRefPtr) prot->data.value.ptrvalue; if (prp != NULL && prp->processed < 2) { qvp [FTQUAL_prot_note].str = prot->comment; } } } } if (prp != NULL) { vnp = prp->name; if (vnp != NULL && (! StringHasNoText ((CharPtr) vnp->data.ptrvalue))) { qvp [FTQUAL_cds_product].str = (CharPtr) vnp->data.ptrvalue; vnp = vnp->next; qvp [FTQUAL_prot_names].vnp = vnp; } qvp [FTQUAL_prot_desc].str = prp->desc; qvp [FTQUAL_prot_activity].vnp = prp->activity; qvp [FTQUAL_prot_EC_number].vnp = prp->ec; } if (! pseudo) { if (prod != NULL) { qvp [FTQUAL_translation].bool = TRUE; } } if (ifp->isCDS) { icp = (IntCdsBlockPtr) ifp; qvp [FTQUAL_figure].str = icp->fig; qvp [FTQUAL_maploc].str = icp->maploc; } } else { qvp [FTQUAL_coded_by].slp = sfp->location; crp = (CdRegionPtr) sfp->data.value.ptrvalue; if (crp != NULL) { gcp = crp->genetic_code; if (gcp != NULL) { for (vnp = gcp->data.ptrvalue; vnp != NULL; vnp = vnp->next) { if (vnp->choice == 2 && vnp->data.intvalue != 0) { qvp [FTQUAL_transl_table].num = vnp->data.intvalue; } } /* suppress table 1 */ if (qvp [FTQUAL_transl_table].num == 1) { qvp [FTQUAL_transl_table].num = 0; } } } } break; case SEQFEAT_PROT : prp = (ProtRefPtr) sfp->data.value.ptrvalue; if (prp != NULL) { vnp = prp->name; if (vnp != NULL && (! StringHasNoText ((CharPtr) vnp->data.ptrvalue))) { qvp [FTQUAL_product].str = (CharPtr) vnp->data.ptrvalue; vnp = vnp->next; qvp [FTQUAL_prot_names].vnp = vnp; } if (afp->format != GENPEPT_FMT) { qvp [FTQUAL_prot_desc].str = prp->desc; } else { qvp [FTQUAL_prot_name].str = prp->desc; } if (afp->format != GENPEPT_FMT || prp->processed != 2) { qvp [FTQUAL_prot_activity].vnp = prp->activity; } qvp [FTQUAL_prot_EC_number].vnp = prp->ec; } break; case SEQFEAT_RNA : rrp = (RnaRefPtr) sfp->data.value.ptrvalue; if (rrp != NULL) { if (rrp->pseudo) { pseudo = TRUE; } if (rrp->type == 2) { sip = SeqLocId (sfp->product); if (sip != NULL) { /* currently for RefSeq records only, not in GenBank release */ if (is_other) { qvp [FTQUAL_transcript_id].sip = sip; } prod = BioseqFind (sip); } } if (rrp->type == 3) { if (rrp->ext.choice == 1) { /* amino acid could not be parsed into structured form */ if (! ajp->flags.dropIllegalQuals) { str = (CharPtr) rrp->ext.value.ptrvalue; qvp [FTQUAL_product].str = str; } else { qvp [FTQUAL_product].str = "tRNA-OTHER"; } } else if (rrp->ext.choice == 2) { trna = (tRNAPtr) rrp->ext.value.ptrvalue; if (trna != NULL) { aa = 0; if (trna->aatype == 2) { aa = trna->aa; } else { from = 0; switch (trna->aatype) { case 0 : from = 0; break; case 1 : from = Seq_code_iupacaa; break; case 2 : from = Seq_code_ncbieaa; break; case 3 : from = Seq_code_ncbi8aa; break; case 4 : from = Seq_code_ncbistdaa; break; default: break; } if (ajp->flags.iupacaaOnly) { code = Seq_code_iupacaa; } else { code = Seq_code_ncbieaa; } smtp = SeqMapTableFind (code, from); if (smtp != NULL) { aa = SeqMapTableConvert (smtp, trna->aa); if (aa == 255 && from == Seq_code_iupacaa && trna->aa == 'U') { aa = 'U'; } } } if (ajp->flags.iupacaaOnly) { smtp = SeqMapTableFind (Seq_code_iupacaa, Seq_code_ncbieaa); if (smtp != NULL) { aa = SeqMapTableConvert (smtp, trna->aa); } else { aa = 'X'; } } if (aa > 0 && aa != 255) { if (aa <= 74) { shift = 0; } else if (aa > 79) { shift = 2; } else { shift = 1; } idx = aa - (64 + shift); if (idx > 0 && idx < 25) { str = trnaList [idx]; qvp [FTQUAL_product].str = str; if (StringNICmp (str, "tRNA-", 5) == 0) { qvp [FTQUAL_trna_aa].str = str + 5; } } } qvp [FTQUAL_anticodon].slp = trna->anticodon; qvp [FTQUAL_trna_codons].trp = trna; } } } else { if (rrp->ext.choice == 1) { str = (CharPtr) rrp->ext.value.ptrvalue; qvp [FTQUAL_product].str = str; /* if (rrp->type == 255 && (! StringHasNoText (str))) { if (StringICmp (str, "internal transcribed spacer 1") == 0 || StringICmp (str, "internal transcribed spacer ITS1") == 0 || StringICmp (str, "ITS1") == 0) { qvp [FTQUAL_rrna_its].str = "ITS1"; } else if (StringICmp (str, "internal transcribed spacer 2") == 0 || StringICmp (str, "internal transcribed spacer ITS2") == 0 || StringICmp (str, "ITS2") == 0) { qvp [FTQUAL_rrna_its].str = "ITS2"; } else if (StringICmp (str, "internal transcribed spacer 3") == 0 || StringICmp (str, "internal transcribed spacer ITS3") == 0 || StringICmp (str, "ITS3") == 0) { qvp [FTQUAL_rrna_its].str = "ITS3"; } } */ } } } break; case SEQFEAT_REGION : if (afp->format == GENPEPT_FMT && featdeftype == FEATDEF_REGION && ISA_aa (bsp->mol)) { qvp [FTQUAL_region_name].str = (CharPtr) sfp->data.value.ptrvalue; } else { qvp [FTQUAL_region].str = (CharPtr) sfp->data.value.ptrvalue; } break; case SEQFEAT_COMMENT : break; case SEQFEAT_SITE : siteidx = (Int2) sfp->data.value.intvalue; if (siteidx == 255) { siteidx = 26; } if (siteidx > 0 && siteidx < 27) { if (afp->format == GENPEPT_FMT && ISA_aa (bsp->mol)) { qvp [FTQUAL_site_type].str = siteList [siteidx]; } else { qvp [FTQUAL_site].str = siteList [siteidx]; } } break; case SEQFEAT_PSEC_STR : qvp [FTQUAL_sec_str_type].num = sfp->data.value.intvalue; break; case SEQFEAT_HET : qvp [FTQUAL_heterogen].str = (CharPtr) sfp->data.value.ptrvalue; break; default : break; } } /* common fields set here */ VisitUserObjectsInUop (sfp->ext, (Pointer) qvp, RecordUserObjectsInQVP); if (fcontext.featdeftype == FEATDEF_repeat_region) { pseudo = FALSE; } qvp [FTQUAL_seqfeat_note].str = sfp->comment; qvp [FTQUAL_pseudo].bool = pseudo; /* if RELEASE_MODE, check list of features that can have /pseudo */ if (ajp->flags.dropIllegalQuals && pseudo && (fcontext.seqfeattype == SEQFEAT_RNA || fcontext.seqfeattype == SEQFEAT_IMP) ) { switch (featdeftype) { case FEATDEF_allele: case FEATDEF_attenuator: case FEATDEF_CAAT_signal: case FEATDEF_conflict: case FEATDEF_D_loop: case FEATDEF_enhancer: case FEATDEF_GC_signal: case FEATDEF_iDNA: case FEATDEF_intron: case FEATDEF_LTR: case FEATDEF_misc_binding: case FEATDEF_misc_difference: case FEATDEF_misc_recomb: case FEATDEF_misc_RNA: case FEATDEF_misc_signal: case FEATDEF_misc_structure: case FEATDEF_modified_base: case FEATDEF_mutation: case FEATDEF_old_sequence: case FEATDEF_polyA_signal: case FEATDEF_polyA_site: case FEATDEF_precursor_RNA: case FEATDEF_prim_transcript: case FEATDEF_primer_bind: case FEATDEF_protein_bind: case FEATDEF_RBS: case FEATDEF_repeat_region: case FEATDEF_repeat_unit: case FEATDEF_rep_origin: case FEATDEF_satellite: case FEATDEF_stem_loop: case FEATDEF_STS: case FEATDEF_TATA_signal: case FEATDEF_terminator: case FEATDEF_unsure: case FEATDEF_variation: case FEATDEF_3clip: case FEATDEF_3UTR: case FEATDEF_5clip: case FEATDEF_5UTR: qvp [FTQUAL_pseudo].bool = FALSE; break; default: break; } } if (afp->format != GENPEPT_FMT) { qvp [FTQUAL_evidence].num = sfp->exp_ev; } /* exception currently legal only on CDS */ if ((! ajp->flags.dropIllegalQuals) || fcontext.seqfeattype == SEQFEAT_CDREGION) { qvp [FTQUAL_exception].str = sfp->except_text; if (sfp->excpt && qvp [FTQUAL_exception].str == NULL) { if (qvp [FTQUAL_seqfeat_note].str != NULL) { if (ajp->flags.dropIllegalQuals && (! StringInStringList (qvp [FTQUAL_seqfeat_note].str, validExceptionString))) { /* !!! if ajp->flags.dropIllegalQuals, check CDS list to avoid losing note !!! */ qvp [FTQUAL_exception].str = NULL; } else { /* if no /exception text, use text in comment, remove from /note */ qvp [FTQUAL_exception].str = qvp [FTQUAL_seqfeat_note].str; qvp [FTQUAL_seqfeat_note].str = NULL; } } else { qvp [FTQUAL_exception].str = "No explanation supplied"; } /* !!! if ajp->flags.dropIllegalQuals, check CDS list here as well !!! */ if (ajp->flags.dropIllegalQuals && (! StringInStringList (qvp [FTQUAL_seqfeat_note].str, validExceptionString)) ) { qvp [FTQUAL_exception].str = NULL; } } if (ajp->flags.dropIllegalQuals && (! StringInStringList (qvp [FTQUAL_exception].str, validExceptionString))) { qvp [FTQUAL_exception_note].str = qvp [FTQUAL_exception].str; qvp [FTQUAL_exception].str = NULL; } } else { qvp [FTQUAL_exception_note].str = sfp->except_text; } if (StringHasNoText (qvp [FTQUAL_exception].str)) { qvp [FTQUAL_exception].str = NULL; } if (StringHasNoText (qvp [FTQUAL_exception_note].str)) { qvp [FTQUAL_exception_note].str = NULL; } qvp [FTQUAL_db_xref].vnp = sfp->dbxref; qvp [FTQUAL_citation].vnp = sfp->cit; /* /product same as sfp->comment will suppress /note */ if (! StringHasNoText (qvp [FTQUAL_product].str) && StringICmp (sfp->comment, qvp [FTQUAL_product].str) == 0) { qvp [FTQUAL_seqfeat_note].str = NULL; } /* case sensitive AJ011317.1 */ if (! StringHasNoText (qvp [FTQUAL_cds_product].str) && StringCmp (sfp->comment, qvp [FTQUAL_cds_product].str) == 0) { qvp [FTQUAL_seqfeat_note].str = NULL; } /* /gene same as sfp->comment will suppress /note */ /* case sensitive -gi|6572973|gb|AF195052.1|AF195052 */ if (! StringHasNoText (qvp [FTQUAL_gene].str) && StringCmp (sfp->comment, qvp [FTQUAL_gene].str) == 0) { qvp [FTQUAL_seqfeat_note].str = NULL; } /* gene /note same as sfp->comment will suppress /note - U92435.1 says do not do this */ /* if (! StringHasNoText (qvp [FTQUAL_gene_note].str) && StringICmp (sfp->comment, qvp [FTQUAL_gene_note].str) == 0) { qvp [FTQUAL_seqfeat_note].str = NULL; } */ /* if site sfp->comment contains site name, suppress site in /note */ if (! StringHasNoText (qvp [FTQUAL_site].str) && StringStr (sfp->comment, qvp [FTQUAL_site].str) != NULL) { qvp [FTQUAL_site].str = NULL; } /* /EC_number same as sfp->comment will suppress /note */ for (vnp = qvp [FTQUAL_prot_EC_number].vnp; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if ((! StringHasNoText (str)) && StringICmp (sfp->comment, str) == 0) { qvp [FTQUAL_seqfeat_note].str = NULL; } } /* now go through gbqual list */ for (gbq = sfp->qual; gbq != NULL; gbq = gbq->next) { idx = GbqualToFeaturIndex (gbq->qual); if (idx > 0 && idx < ASN2GNBK_TOTAL_FEATUR) { if (qvp [idx].gbq == NULL) { if (idx == FTQUAL_product_quals) { if (qvp [FTQUAL_product].str == NULL) { qvp [FTQUAL_product].str = gbq->val; } else if (qvp [FTQUAL_xtra_prod_quals].gbq == NULL) { /* chain will include remaining product gbquals */ qvp [FTQUAL_xtra_prod_quals].gbq = gbq; } } else { qvp [idx].gbq = gbq; } } } else if (idx == 0) { qualclass = IllegalGbqualToClass (gbq->qual); if (qualclass == 0) { qualclass = Qual_class_quote; } tmp = StringSave (gbq->val); if (tmp != NULL) { str = MemNew (sizeof (Char) * (StringLen (gbq->val) + StringLen (tmp) + 10)); if (str != NULL) { if (qualclass == Qual_class_quote) { if (StringIsJustQuotes (tmp)) { sprintf (buf, "/%s", gbq->qual); } else { ptr = tmp; ch = *ptr; while (ch != '\0') { if (ch == '"') { *ptr = '\''; } ptr++; ch = *ptr; } sprintf (str, "/%s=\"%s\"", gbq->qual, tmp); } ValNodeCopyStr (&illegal, 0, str); } else if (qualclass == Qual_class_noquote || qualclass == Qual_class_label) { if (StringIsJustQuotes (tmp)) { sprintf (str, "/%s", gbq->qual); } else { sprintf (str, "/%s=%s", gbq->qual, tmp); } ValNodeCopyStr (&illegal, 0, str); } MemFree (str); } MemFree (tmp); } } } /* illegal qualifiers are copied and formatted in valnode chain */ if (! ajp->flags.dropIllegalQuals) { qvp [FTQUAL_illegal_qual].vnp = illegal; } /* remove protein description that equals the gene name, case sensitive */ if (StringCmp (qvp [FTQUAL_gene].str, qvp [FTQUAL_prot_desc].str) == 0) { qvp [FTQUAL_prot_desc].str = NULL; } /* remove protein description that equals the cds product, case sensitive */ if (StringCmp (qvp [FTQUAL_cds_product].str, qvp [FTQUAL_prot_desc].str) == 0) { qvp [FTQUAL_prot_desc].str = NULL; } /* remove comment contained in prot_desc - gi|4530123|gb|AF071539.1|AF071539 */ if (StringStr (qvp [FTQUAL_prot_desc].str, qvp [FTQUAL_seqfeat_note].str) != NULL) { qvp [FTQUAL_seqfeat_note].str = NULL; } /* remove protein description that equals the standard name */ if (qvp [FTQUAL_standard_name].gbq != NULL && qvp [FTQUAL_prot_desc].str != NULL) { gbq = qvp [FTQUAL_standard_name].gbq; lasttype = gbq->qual; while (gbq != NULL && StringICmp (gbq->qual, lasttype) == 0) { if (StringICmp (gbq->val, qvp [FTQUAL_prot_desc].str) == 0) { qvp [FTQUAL_prot_desc].str = NULL; } gbq = gbq->next; } } /* remove protein description that equals a gene synonym - case insensitive AF109216.1 */ for (vnp = gene_syn; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if ((! StringHasNoText (str)) && StringCmp (str, qvp [FTQUAL_prot_desc].str) == 0) { qvp [FTQUAL_prot_desc].str = NULL; } } /* remove comment that equals a gene synonym */ if (afp->format != GENPEPT_FMT && (! ifp->mapToProt)) { for (vnp = gene_syn; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if ((! StringHasNoText (str)) && StringICmp (str, qvp [FTQUAL_seqfeat_note].str) == 0) { qvp [FTQUAL_seqfeat_note].str = NULL; } } } /* remove protein comment descriptor that equals the protein note */ if (StringCmp (qvp [FTQUAL_prot_note].str, qvp [FTQUAL_prot_comment].str) == 0) { qvp [FTQUAL_prot_comment].str = NULL; } /* suppress cds comment if a subset of protein note - AF002218.1 */ if (StringStr (qvp [FTQUAL_prot_note].str, qvp [FTQUAL_seqfeat_note].str) != NULL) { qvp [FTQUAL_seqfeat_note].str = NULL; } /* suppress selenocysteine note if already in comment */ if (StringStr (sfp->comment, "selenocysteine") != NULL) { qvp [FTQUAL_selenocysteine].str = NULL; } /* now print qualifiers from table */ #ifdef DISPLAY_STRINGS s_DisplayQVP(qvp, feat_note_order); #endif /* Strip duplicate notes */ if ((StringCmp(qvp[FTQUAL_product].str, qvp[FTQUAL_seqfeat_note].str) == 0)) { qvp[FTQUAL_seqfeat_note].str = NULL; } if ((qvp[FTQUAL_standard_name].gbq != NULL) && (qvp[FTQUAL_standard_name].gbq->val != NULL)) { if ((StringCmp(qvp[FTQUAL_seqfeat_note].str, qvp[FTQUAL_standard_name].gbq->val) == 0)) { qvp[FTQUAL_seqfeat_note].str = NULL; } } /* Display strings for debugging purposes */ #ifdef DISPLAY_STRINGS s_DisplayQVP(qvp, feat_qual_order); #endif /* Build the flat file */ FormatFeatureBlockQuals (ajp, afp, asp, bsp, featdeftype, gene_syn, lasttype, location, prod, protein_pid_g, qvp, left, right, strand, sfp, target, is_other, is_gps); /* ??? and then deal with the various note types separately (not in order table) ??? */ /* free aa-dna or dna-aa mapped location */ SeqLocFree (loc); ValNodeFreeData (illegal); BioseqUnlock (unlockme); return ff_print_string_mem (gb_MergeString (TRUE)); } static CharPtr FormatBasecountBlock ( Asn2gbFormatPtr afp, BaseBlockPtr bbp ) { IntAsn2gbJobPtr ajp; Asn2gbSectPtr asp; Int4 base_count [5]; BioseqPtr bsp; Char buf [80]; Byte bases [400]; Uint1 code = Seq_code_iupacna; Int2 ctr; Int2 i; Int4 len; Uint1 residue; SeqPortPtr spp = NULL; Int4 total = 0; if (afp == NULL || bbp == NULL) return NULL; ajp = afp->ajp; if (ajp == NULL) return NULL; asp = afp->asp; if (asp == NULL) return NULL; bsp = (asp->bsp); if (bsp == NULL) return NULL; /* after first formatting, result is cached into bbp->string */ if (! StringHasNoText (bbp->string)) return StringSave (bbp->string); for (i = 0; i < 5; i++) { base_count [i] = 0; } if (ISA_aa (bsp->mol)) { code = Seq_code_ncbieaa; } if (ajp->ajp.slp != NULL) { spp = SeqPortNewByLoc (ajp->ajp.slp, code); len = SeqLocLen (ajp->ajp.slp); } else { spp = SeqPortNew (bsp, 0, -1, 0, code); len = bsp->length; } if (spp == NULL) return NULL; if (bsp->repr == Seq_repr_delta || bsp->repr == Seq_repr_virtual) { SeqPortSet_do_virtual (spp, TRUE); } /* use SeqPortRead rather than SeqPortGetResidue for faster performance */ ctr = SeqPortRead (spp, bases, sizeof (bases)); i = 0; residue = (Uint1) bases [i]; while (residue != SEQPORT_EOF) { if (IS_residue (residue)) { total++; switch (residue) { case 'A' : (base_count [0])++; break; case 'C' : (base_count [1])++; break; case 'G' : (base_count [2])++; break; case 'T' : (base_count [3])++; break; default : (base_count [4])++; break; } } i++; if (i >= ctr) { i = 0; ctr = SeqPortRead (spp, bases, sizeof (bases)); if (ctr < 0) { bases [0] = -ctr; } else if (ctr < 1) { bases [0] = SEQPORT_EOF; } } residue = (Uint1) bases [i]; } SeqPortFree (spp); if (afp->format == GENBANK_FMT || afp->format == GENPEPT_FMT) { if (base_count [4] == 0) { sprintf (buf, "%7ld a%7ld c%7ld g%7ld t", (long) base_count [0], (long) base_count [1], (long) base_count [2], (long) base_count [3]); } else { sprintf (buf, "%7ld a%7ld c%7ld g%7ld t%7ld others", (long) base_count [0], (long) base_count [1], (long) base_count [2], (long) base_count [3], (long) base_count [4]); } } else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) { sprintf (buf, "Sequence %ld BP; %ld A; %ld C; %ld G; %ld T; %ld other;", (long) len, (long) base_count [0], (long) base_count [1], (long) base_count [2], (long) base_count [3], (long) base_count [4]); PrintXX (); } gb_StartPrint (afp->format, 0, 0, "BASE COUNT", 13, 5, 5, "SQ", FALSE); gb_AddString (NULL, buf, NULL, FALSE, FALSE, TILDE_TO_SPACES); return gb_MergeString (TRUE); } static void PrintSeqLine ( FmtType format, CharPtr buf, Int4 start, Int4 stop ) { Char pos [16]; #ifdef WIN_MAC /* !!! To eliminate spurious diffs when comparing with Sequin exported GenBank format on Mac !!! */ { size_t len; len = StringLen (buf); if (len > 0 && buf [len - 1] == ' ') { buf [len - 1] = '\0'; } } #endif if (format == GENBANK_FMT || format == GENPEPT_FMT) { sprintf (pos, "%9ld", (long) (start + 1)); ff_StartPrint (0, 0, ASN2FF_GB_MAX, NULL); gb_AddString (NULL, pos, NULL, FALSE, FALSE, TILDE_TO_SPACES); TabToColumn (11); gb_AddString (NULL, buf, NULL, FALSE, FALSE, TILDE_TO_SPACES); ff_EndPrint(); } else if (format == EMBL_FMT || format == EMBLPEPT_FMT) { sprintf (pos, "%8ld", (long) (stop)); ff_StartPrint (5, 5, 0, NULL); gb_AddString (NULL, buf, NULL, FALSE, FALSE, TILDE_TO_SPACES); TabToColumn (73); gb_AddString (NULL, pos, NULL, FALSE, FALSE, TILDE_TO_SPACES); ff_EndPrint(); } } static CharPtr FormatSequenceBlock ( Asn2gbFormatPtr afp, BaseBlockPtr bbp ) { IntAsn2gbJobPtr ajp; Asn2gbSectPtr asp; Byte bases [400]; Int2 blk; BioseqPtr bsp; Char buf [80]; Int2 cnt; Uint1 code = Seq_code_iupacna; Int2 count; Int2 ctr; Int2 i; IntAsn2gbSectPtr iasp; Boolean is_na; Int2 lin; Int4 pos; Uint1 residue; SeqBlockPtr sbp; SeqPortPtr spp; Int4 start; Int4 stop; if (afp == NULL || bbp == NULL) return NULL; sbp = (SeqBlockPtr) bbp; ajp = afp->ajp; if (ajp == NULL) return NULL; asp = afp->asp; if (asp == NULL) return NULL; iasp = (IntAsn2gbSectPtr) asp; bsp = (asp->bsp); if (bsp == NULL) return NULL; spp = iasp->spp; if (spp == NULL) { /* if first time, create SeqPort for this section */ if (ISA_aa (bsp->mol)) { if (ajp->flags.iupacaaOnly) { code = Seq_code_iupacaa; } else { code = Seq_code_ncbieaa; } } if (ajp->ajp.slp != NULL) { spp = SeqPortNewByLoc (ajp->ajp.slp, code); } else { spp = SeqPortNew (bsp, 0, -1, 0, code); } if (spp == NULL) return NULL; if (bsp->repr == Seq_repr_delta || bsp->repr == Seq_repr_virtual) { SeqPortSet_do_virtual (spp, TRUE); } iasp->spp = spp; } start = sbp->start; stop = sbp->stop; if (start != spp->curpos) { SeqPortSeek (spp, start, SEEK_SET); } pos = start; count = 0; cnt = 0; blk = 0; lin = 0; is_na = ISA_na (bsp->mol); ctr = (Int2) MIN ((Int4) (stop - pos), (Int4) sizeof (bases)); ctr = SeqPortRead (spp, bases, ctr); i = 0; if (ctr < 0) { residue = -ctr; } else if (ctr < 1) { residue = SEQPORT_EOF; } else { residue = (Uint1) bases [i]; } while (pos < stop && residue != SEQPORT_EOF) { if (residue == INVALID_RESIDUE) { if (is_na) { residue = 'N'; } else { residue = 'X'; } } if (IS_residue (residue)) { buf [count] = (Char) (TO_LOWER (residue)); count++; cnt++; pos++; blk++; lin++; if (lin >= 60) { buf [count] = '\0'; PrintSeqLine (afp->format, buf, start, start + cnt); count = 0; cnt = 0; blk = 0; lin = 0; start += 60; } else if (blk >= 10) { buf [count] = ' '; count++; blk = 0; } } i++; if (i >= ctr) { i = 0; ctr = (Int2) MIN ((Int4) (stop - pos), (Int4) sizeof (bases)); ctr = SeqPortRead (spp, bases, ctr); if (ctr < 0) { bases [0] = -ctr; } else if (ctr < 1) { bases [0] = SEQPORT_EOF; } } residue = (Uint1) bases [i]; } buf [count] = '\0'; if (count > 0) { PrintSeqLine (afp->format, buf, start, start + cnt); } if (ajp->transientSeqPort) { iasp->spp = SeqPortFree (iasp->spp); } return gb_MergeString (FALSE); } static Uint1 fasta_order [NUM_SEQID] = { 33, /* 0 = not set */ 20, /* 1 = local Object-id */ 15, /* 2 = gibbsq */ 16, /* 3 = gibbmt */ 30, /* 4 = giim Giimport-id */ 10, /* 5 = genbank */ 10, /* 6 = embl */ 10, /* 7 = pir */ 10, /* 8 = swissprot */ 15, /* 9 = patent */ 20, /* 10 = other TextSeqId */ 20, /* 11 = general Dbtag */ 255, /* 12 = gi */ 10, /* 13 = ddbj */ 10, /* 14 = prf */ 12, /* 15 = pdb */ 10, /* 16 = tpg */ 10, /* 17 = tpe */ 10 /* 18 = tpd */ }; static void PrintGenome (SeqLocPtr slp_head, CharPtr prefix) { Char buf[14], val[166]; Boolean first = TRUE; SeqLocPtr slp; Int4 from, to, start, stop; SeqIdPtr sid, newid; BioseqPtr bsp = NULL; SeqEntryPtr sep = NULL; Int2 p1=0, p2=0; #ifdef ENABLE_ENTREZ SeqLocPtr sslp; Int4 beg, end, lcur, lprev; Int4 uid; Boolean is_network; #endif for (slp = slp_head; slp; slp = slp->next) { from = to = 0; sid = SeqLocId(slp); if (slp->choice == SEQLOC_INT || slp->choice == SEQLOC_WHOLE) { start = from = SeqLocStart(slp); stop = to = SeqLocStop(slp); } else if (slp->choice == SEQLOC_NULL){ sprintf(val, ",%s", "gap()"); ff_AddString(val); continue; } else { continue; } if (sid == NULL) { continue; } if (sid->choice == SEQID_GI) { newid = GetSeqIdForGI(sid->data.intvalue); } else if (sid->choice == SEQID_GENERAL) { #ifdef ENABLE_ENTREZ if ((uid = GetUniGeneIDForSeqId(sid)) != 0) { vn.choice = SEQID_GI; vn.data.intvalue = uid; vn.next = NULL; bsp = BioseqLockById (&vn); } if (bsp && (bsp->seq_ext_type == 1 || bsp->seq_ext_type)) { lcur = lprev = 0; for (sslp = slp_head; sslp; sslp = sslp->next) { lprev = lcur; lcur += SeqLocLen(sslp); beg = SeqLocStart(sslp); end = SeqLocStop(sslp); sid = SeqLocId(sslp); if (from > lcur || to < lprev) { continue; } if (from > lprev) { /* first */ start = beg + from - lprev; } else { start = beg; /* middle */ } if (to > lcur) { /* middle */ stop = end; } else { stop = beg + to - lprev; } if (first) { first = FALSE; } else { ff_AddChar(','); } if (sid->choice == SEQID_GI) { newid = GetSeqIdForGI(sid->data.intvalue); if (newid == NULL) { newid = sid; } } else { newid = sid; } SeqIdWrite(SeqIdSelect(newid, fasta_order, NUM_SEQID), buf, PRINTID_TEXTID_ACC_VER, 13); if (SeqLocStrand(slp) == Seq_strand_minus) { ff_AddString("complement("); } ff_AddString(buf); if (SeqLocStrand(slp) == Seq_strand_minus) { sprintf(val,":%ld..%ld)",(long) start+1, (long) stop+1 ); } else { sprintf(val,":%ld..%ld",(long) start+1, (long) stop+1 ); } ff_AddString(val); p1 += StringLen(val); p2 += StringLen(val); } continue; } newid = sid; #else newid = sid; #endif } else { newid = sid; } if (prefix != NULL) { ff_AddString (prefix); } if (first) { first = FALSE; } else { ff_AddChar(','); } SeqIdWrite(SeqIdSelect(newid, fasta_order, NUM_SEQID), buf, PRINTID_TEXTID_ACC_VER, 13); ff_AddString( buf); if (SeqLocStrand(slp) == Seq_strand_minus) { sprintf(val,":%ld..%ld)",(long) start+1, (long) stop+1 ); } else { sprintf(val,":%ld..%ld",(long) start+1, (long) stop+1 ); } ff_AddString(val); p1 += StringLen(val); p2 += StringLen(val); } } static CharPtr FormatContigBlock ( Asn2gbFormatPtr afp, BaseBlockPtr bbp ) { Asn2gbSectPtr asp; BioseqPtr bsp; DeltaSeqPtr dsp; SeqLitPtr litp; CharPtr prefix = NULL; SeqLocPtr slp_head = NULL; Char val [20]; if (afp == NULL || bbp == NULL) return NULL; asp = afp->asp; if (asp == NULL) return NULL; bsp = (asp->bsp); if (bsp == NULL) return NULL; ff_StartPrint (0, 12, ASN2FF_GB_MAX, NULL); ff_AddString ("CONTIG"); TabToColumn (13); ff_AddString("join("); if (bsp->seq_ext_type == 1) { slp_head = (SeqLocPtr) bsp->seq_ext; PrintGenome (slp_head, prefix); } else if (bsp->seq_ext_type == 4) { for (dsp = (DeltaSeqPtr) bsp->seq_ext; dsp; dsp=dsp->next) { if (dsp->choice == 1) { slp_head = (SeqLocPtr) dsp->data.ptrvalue; PrintGenome (slp_head, prefix); } else { litp = (SeqLitPtr) dsp->data.ptrvalue; if (litp != NULL) { if (litp->seq_data != NULL) { if (litp->length == 0) { sprintf (val, "gap(%ld)", (long) litp->length); ff_AddString (val); } else { /* don't know what to do here */ } } else { sprintf (val, ",gap(%ld)", (long) litp->length); ff_AddString (val); } } } prefix = ","; } } ff_AddChar (')'); ff_EndPrint (); return gb_MergeString (FALSE); } /* ********************************************************************** */ /* functions to record sections or blocks in linked lists */ static Asn2gbSectPtr Asn2gbAddSection ( Asn2gbWorkPtr awp ) { Asn2gbSectPtr asp; ValNodePtr vnp; if (awp == NULL) return NULL; asp = (Asn2gbSectPtr) MemNew (sizeof (IntAsn2gbSect)); if (asp == NULL) return NULL; vnp = ValNodeAddPointer (&(awp->lastsection), 0, asp); if (vnp == NULL) return asp; awp->lastsection = vnp; if (awp->sectionList == NULL) { awp->sectionList = vnp; } return asp; } static BaseBlockPtr Asn2gbAddBlock ( Asn2gbWorkPtr awp, BlockType blocktype, size_t size ) { BaseBlockPtr bbp; ValNodePtr vnp; if (awp == NULL || size < 1) return NULL; bbp = (BaseBlockPtr) MemNew (size); if (bbp == NULL) return NULL; bbp->blocktype = blocktype; bbp->section = awp->currsection; vnp = ValNodeAddPointer (&(awp->lastblock), 0, bbp); if (vnp == NULL) return bbp; awp->lastblock = vnp; if (awp->blockList == NULL) { awp->blockList = vnp; } return bbp; } /* ********************************************************************** */ /* add functions allocate specific blocks, populate with paragraph print info */ static CharPtr strd [4] = { " ", "ss-", "ds-", "ms-" }; static CharPtr gnbk_mol [14] = { " ", "DNA ", "RNA ", "mRNA", "rRNA", "tRNA", "uRNA", "scRNA", " AA ", "DNA ", "DNA ", "RNA ", "snoRNA", "RNA " }; /* EMBL_FMT in RELEASE_MODE or ENTREZ_MODE, otherwise use gnbk_mol */ static CharPtr embl_mol [14] = { "xxx", "DNA", "RNA", "RNA", "RNA", "RNA", "RNA", "RNA", "AA ", "DNA", "DNA", "RNA", "RNA", "RNA" }; static CharPtr embl_divs [18] = { "FUN", "INV", "MAM", "ORG", "PHG", "PLN", "PRI", "PRO", "ROD" "SYN", "UNA", "VRL", "VRT", "PAT", "EST", "STS", "HUM", "HTC" }; static DatePtr GetBestDate ( DatePtr a, DatePtr b ) { Int2 status; if (a == NULL) return b; if (b == NULL) return a; status = DateMatch (a, b, FALSE); if (status == 1) return a; return b; } /*--------------------------------------------------------*/ /* */ /* s_IsSeperatorNeeded() */ /* */ /*--------------------------------------------------------*/ static Boolean s_IsSeperatorNeeded(CharPtr baseString, Int4 baseLength, Int2 suffixLength) { Char lastChar; Char nextToLastChar; lastChar = baseString[baseLength - 1]; nextToLastChar = baseString[baseLength - 2]; /* This first check put here to emulate what may be a */ /* bug in the original code (in CheckLocusLength() ) */ /* which adds an 'S' segment seperator only if it */ /* DOES make the string longer than the max. */ if (baseLength + suffixLength < 10) return FALSE; /* If the last character is not a digit */ /* then don't use a seperator. */ if (!IS_DIGIT(lastChar)) return FALSE; /* If the last two characters are a non-digit */ /* followed by a '0', then don't use seperator. */ if ((lastChar == '0') && (!IS_DIGIT(nextToLastChar))) return FALSE; /* If we made it to here, use a seperator */ return TRUE; } /*--------------------------------------------------------*/ /* */ /* s_LocusAddSuffix() - */ /* */ /*--------------------------------------------------------*/ static Boolean s_LocusAddSuffix (CharPtr locus, Asn2gbWorkPtr awp) { size_t buflen; Char ch; Char segCountStr[6]; Int2 segCountStrLen; Char segSuffix[5]; buflen = StringLen (locus); /* If there's one or less segments, */ /* no suffix is needed. */ if (awp->numsegs <= 1) return FALSE; /* If the basestring has one or less */ /* characters, no suffix is needed. */ if (buflen <=1) return FALSE; /* Add the suffix */ ch = locus[buflen-1]; sprintf(segCountStr,"%d",awp->numsegs); segCountStrLen = StringLen(segCountStr); segSuffix[0] = '\0'; if (s_IsSeperatorNeeded(locus,buflen,segCountStrLen) == TRUE) sprintf(segSuffix,"S%0*d",segCountStrLen,awp->seg); else sprintf(segSuffix,"%0*d",segCountStrLen,awp->seg); StringCat(locus,segSuffix); /* Return successfully */ return TRUE; } /*--------------------------------------------------------*/ /* */ /* s_LocusAdjustLength() - */ /* */ /*--------------------------------------------------------*/ static Boolean s_LocusAdjustLength(CharPtr locus, Int2 maxLength) { Int2 trimCount; Int2 buflen; CharPtr buftmp; buftmp = MemNew(maxLength + 1); buflen = StringLen (locus); if (buflen <= maxLength) return FALSE; /* If the sequence id is an NCBI locus of the */ /* form HSU00001, then make sure that if */ /* there is trimming the HS gets trimmed off */ /* as a unit, never just the 'H'. */ trimCount = buflen - maxLength; if (trimCount == 1) if (IS_ALPHA(locus[0]) != 0 && IS_ALPHA(locus[1]) != 0 && IS_ALPHA(locus[2]) != 0 && IS_DIGIT(locus[3]) != 0 && IS_DIGIT(locus[4]) != 0 && IS_DIGIT(locus[5]) != 0 && IS_DIGIT(locus[6]) != 0 && IS_DIGIT(locus[7]) != 0 && locus[8] == 'S' && locus[9] == '\0') trimCount++; /* Left truncate the sequence id */ StringCpy(buftmp, &locus[trimCount]); StringCpy(locus, buftmp); MemFree(buftmp); return TRUE; } /*--------------------------------------------------------*/ /* */ /* AddLocusBlock() - */ /* */ /*--------------------------------------------------------*/ static DatePtr GetBestDateForBsp ( BioseqPtr bsp ) { DatePtr best_date = NULL; SeqMgrDescContext dcontext; DatePtr dp; EMBLBlockPtr ebp; GBBlockPtr gbp; PdbBlockPtr pdp; PdbRepPtr prp; SeqDescrPtr sdp; SPBlockPtr spp; if (bsp == NULL) return NULL; dp = NULL; sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_update_date, &dcontext); if (sdp != NULL) { dp = (DatePtr) sdp->data.ptrvalue; best_date = GetBestDate (dp, best_date); } /* !!! temporarily also look at genbank block entry date !!! */ sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_genbank, &dcontext); if (sdp != NULL) { gbp = (GBBlockPtr) sdp->data.ptrvalue; if (gbp != NULL) { dp = gbp->entry_date; best_date = GetBestDate (dp, best_date); } } /* more complicated code for dates from various objects goes here */ sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_embl, &dcontext); if (sdp != NULL) { ebp = (EMBLBlockPtr) sdp->data.ptrvalue; if (ebp != NULL) { dp = ebp->creation_date; best_date = GetBestDate (dp, best_date); dp = ebp->update_date; best_date = GetBestDate (dp, best_date); } } sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_sp, &dcontext); if (sdp != NULL) { spp = (SPBlockPtr) sdp->data.ptrvalue; if (spp != NULL) { dp = spp->created; if (dp != NULL && dp->data [0] == 1) { best_date = GetBestDate (dp, best_date); } dp = spp->sequpd; if (dp != NULL && dp->data [0] == 1) { best_date = GetBestDate (dp, best_date); } dp = spp->annotupd; if (dp != NULL && dp->data [0] == 1) { best_date = GetBestDate (dp, best_date); } } } sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_pdb, &dcontext); if (sdp != NULL) { pdp = (PdbBlockPtr) sdp->data.ptrvalue; if (pdp != NULL) { dp = pdp->deposition; if (dp != NULL && dp->data [0] == 1) { best_date = GetBestDate (dp, best_date); } prp = pdp->replace; if (prp != NULL) { dp = prp->date; if (dp != NULL && dp->data[0] == 1) { best_date = GetBestDate (dp, best_date); } } } } sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_create_date, &dcontext); if (sdp != NULL) { dp = (DatePtr) sdp->data.ptrvalue; if (dp != NULL) { best_date = GetBestDate (dp, best_date); } } return best_date; } static Boolean SegHasParts ( BioseqPtr bsp ) { BioseqSetPtr bssp; SeqEntryPtr sep; if (bsp == NULL || bsp->repr != Seq_repr_seg) return FALSE; sep = bsp->seqentry; if (sep == NULL) return FALSE; sep = sep->next; if (sep == NULL || (! IS_Bioseq_set (sep))) return FALSE; bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp != NULL && bssp->_class == BioseqseqSet_class_parts) return TRUE; return FALSE; } static Boolean DeltaLitOnly ( BioseqPtr bsp ) { ValNodePtr vnp; if (bsp == NULL || bsp->repr != Seq_repr_delta) return FALSE; for (vnp = (ValNodePtr)(bsp->seq_ext); vnp != NULL; vnp = vnp->next) { if (vnp->choice == 1) return FALSE; } return TRUE; } static void AddLocusBlock ( Asn2gbWorkPtr awp ) { IntAsn2gbJobPtr ajp; BaseBlockPtr bbp; DatePtr best_date = NULL; BioSourcePtr biop; Int2 bmol = 0; BioseqPtr bsp; SeqFeatPtr cds; Char date [40]; SeqMgrDescContext dcontext; Char div [10]; BioseqPtr dna; CharPtr ebmol; EMBLBlockPtr ebp; SeqMgrFeatContext fcontext; GBBlockPtr gbp; Boolean genome_view; Int2 imol = 0; Int2 istrand; Char len [15]; Int4 length; Char locus [41]; MolInfoPtr mip; Char mol [30]; OrgNamePtr onp; Uint1 origin; OrgRefPtr orp; BioseqPtr parent; SeqDescrPtr sdp; SeqFeatPtr sfp; SeqIdPtr sip; Uint1 tech; Uint1 topology; if (awp == NULL) return; ajp = awp->ajp; if (ajp == NULL) return; bsp = awp->bsp; if (bsp == NULL) return; bbp = Asn2gbAddBlock (awp, LOCUS_BLOCK, sizeof (BaseBlock)); if (bbp == NULL) return; mol [0] = '\0'; len [0] = '\0'; div [0] = '\0'; date [0] = '\0'; genome_view = FALSE; if (bsp->repr == Seq_repr_seg && (! SegHasParts (bsp))) { genome_view = TRUE; } if (bsp->repr == Seq_repr_delta && (! DeltaLitOnly (bsp))) { genome_view = TRUE; } /* locus id */ sip = NULL; for (sip = bsp->id; sip != NULL; sip = sip->next) { if (sip->choice == SEQID_GENBANK || sip->choice == SEQID_EMBL || sip->choice == SEQID_DDBJ || sip->choice == SEQID_OTHER) break; if (sip->choice == SEQID_PIR || sip->choice == SEQID_SWISSPROT || sip->choice == SEQID_PRF || sip->choice == SEQID_PDB) break; if (sip->choice == SEQID_TPG || sip->choice == SEQID_TPE || sip->choice == SEQID_TPD) break; } if (sip == NULL) { sip = SeqIdFindBest (bsp->id, SEQID_GENBANK); } if (genome_view) { SeqIdWrite (sip, locus, PRINTID_TEXTID_ACCESSION, sizeof (locus) - 1); } else { SeqIdWrite (sip, locus, PRINTID_TEXTID_LOCUS, sizeof (locus) - 1); } /* more complicated code to get parent locus, if segmented, goes here */ if (awp->slp != NULL) { length = SeqLocLen (awp->slp); } else { length = bsp->length; } mip = NULL; tech = MI_TECH_standard; origin = 0; bmol = bsp->mol; if (bmol > Seq_mol_aa) { bmol = 0; } istrand = bsp->strand; if (istrand > Seq_strand_both) { istrand = Seq_strand_unknown; } sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext); if (sdp != NULL) { bbp->entityID = dcontext.entityID; bbp->itemID = dcontext.itemID; bbp->itemtype = OBJ_SEQDESC; mip = (MolInfoPtr) sdp->data.ptrvalue; if (mip != NULL) { if (mip->biomol <= MOLECULE_TYPE_TRANSCRIBED_RNA) { imol = (Int2) mip->biomol; } tech = mip->tech; } } /* check inst.mol if mol-type is not-set or genomic */ if (imol <= MOLECULE_TYPE_GENOMIC) { if (bmol == Seq_mol_aa) { imol = MOLECULE_TYPE_PEPTIDE; } else if (bmol == Seq_mol_na) { imol = 0; } else if (bmol == Seq_mol_rna) { imol = 2; } } /* if ds-DNA don't show ds */ if (bmol == Seq_mol_dna && istrand == Seq_strand_minus) { istrand = Seq_strand_unknown; } /* ss=any RNA don't show ss */ if (bmol > Seq_mol_rna && istrand == Seq_strand_plus) { istrand = Seq_strand_unknown; } topology = bsp->topology; if (awp->slp != NULL) { topology = TOPOLOGY_LINEAR; } /* length, topology, and molecule type */ if (awp->format == GENBANK_FMT) { if (awp->newLocusLine) { sprintf (len, "%ld bp", (long) length); sprintf (mol, "%s%-4s", strd [istrand], gnbk_mol [imol]); } else { if (topology == TOPOLOGY_CIRCULAR) { sprintf (len, "%7ld bp", (long) length); sprintf (mol, "%s%-4s circular", strd [istrand], gnbk_mol [imol]); } else { sprintf (len, "%7ld bp", (long) length); sprintf (mol, "%s%-4s ", strd [istrand], gnbk_mol [imol]); } } } else if (awp->format == GENPEPT_FMT) { if (awp->newLocusLine) { sprintf (len, "%ld aa", (long) length); } else { sprintf (len, "%7ld aa", (long) length); } } else if (awp->format == EMBL_FMT) { if (imol < MOLECULE_TYPE_PEPTIDE) { if (ajp->flags.useEmblMolType) { ebmol = embl_mol [imol]; } else { ebmol = gnbk_mol [imol]; } if (topology == TOPOLOGY_CIRCULAR) { sprintf (mol, "circular %s", ebmol); sprintf (len, "%ld BP.", (long) length); } else { sprintf (mol, "%s", ebmol); sprintf (len, "%ld BP.", (long) length); } } } /* division */ biop = NULL; sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext); if (sdp != NULL) { biop = (BioSourcePtr) sdp->data.ptrvalue; } else { sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_BIOSRC, 0, &fcontext); if (sfp != NULL) { biop = (BioSourcePtr) sfp->data.value.ptrvalue; } else if (ISA_aa (bsp->mol)) { /* if protein with no sources, get sources applicable to DNA location of CDS */ cds = SeqMgrGetCDSgivenProduct (bsp, &fcontext); if (cds != NULL) { sfp = SeqMgrGetOverlappingSource (cds->location, &fcontext); if (sfp != NULL) { biop = (BioSourcePtr) sfp->data.value.ptrvalue; } else { dna = BioseqFindFromSeqLoc (cds->location); if (dna != NULL) { sdp = SeqMgrGetNextDescriptor (dna, NULL, Seq_descr_source, &dcontext); if (sdp != NULL) { biop = (BioSourcePtr) sdp->data.ptrvalue; } } } } } } if (biop != NULL) { origin = biop->origin; orp = biop->org; if (orp != NULL) { onp = orp->orgname; if (onp != NULL) { StringNCpy_0 (div, onp->div, sizeof (div)); } } } switch (tech) { case MI_TECH_est : StringCpy (div, "EST"); break; case MI_TECH_sts : StringCpy (div, "STS"); break; case MI_TECH_survey : StringCpy (div, "GSS"); break; case MI_TECH_htgs_0 : case MI_TECH_htgs_1 : case MI_TECH_htgs_2 : StringCpy (div, "HTG"); break; case MI_TECH_htc : StringCpy (div, "HTC"); break; default : break; } if (origin == 5) { StringCpy (div, "SYN"); } sip = SeqIdFindBest (bsp->id, SEQID_PATENT); if (sip != NULL && sip->choice == SEQID_PATENT) { StringCpy (div, "PAT"); } /* more complicated code for division, if necessary, goes here */ sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_genbank, &dcontext); while (sdp != NULL) { gbp = (GBBlockPtr) sdp->data.ptrvalue; if (gbp != NULL) { if (StringHasNoText (div) && gbp->div != NULL) { StringCpy (div, gbp->div); } else if (StringCmp(gbp->div, "PAT") == 0 || StringCmp(gbp->div, "SYN") == 0 ) { StringCpy (div, gbp->div); } } sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_genbank, &dcontext); } if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) { sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_embl, &dcontext); if (sdp != NULL) { ebp = (EMBLBlockPtr) sdp->data.ptrvalue; if (ebp != NULL) { if (ebp->div == 255) { if (mip == NULL) { StringCpy (div, "HUM"); } } else if (ebp->div < 18) { StringCpy (div, embl_divs [ebp->div]); } } } if (StringHasNoText (div)) { StringCpy (div, "UNA"); } } /* empty division field if unable to find anything */ if (StringHasNoText (div)) { StringCpy (div, " "); } /* contig style (old genome_view flag) forces CON division */ if (awp->contig) { StringCpy (div, "CON"); } if (genome_view) { StringCpy (div, "CON"); } /* date */ best_date = GetBestDateForBsp (bsp); if (best_date == NULL) { /* if bsp is product of CDS or mRNA feature, get date from sfp->location bsp */ sfp = NULL; if (ISA_na (bsp->mol)) { sfp = SeqMgrGetRNAgivenProduct (bsp, NULL); } else if (ISA_aa (bsp->mol)) { sfp = SeqMgrGetCDSgivenProduct (bsp, NULL); } if (sfp != NULL) { parent = BioseqFindFromSeqLoc (sfp->location); if (parent != NULL) { best_date = GetBestDateForBsp (parent); } } } /* convert best date */ if (best_date != NULL) { DateToGB (date, best_date, FALSE); } if (StringHasNoText (date)) { StringCpy (date, "01-JAN-1900"); } if (awp->format == GENBANK_FMT || awp->format == GENPEPT_FMT) { /* Create the proper locus name */ parent = awp->parent; if (parent->repr == Seq_repr_seg) { if (! StringHasNoText (awp->basename)) { StringCpy (locus, awp->basename); s_LocusAddSuffix (locus, awp); } } /* Print the "LOCUS_NEW" line, if requested */ if (awp->newLocusLine) { ff_StartPrint (0, 0, ASN2FF_GB_MAX, NULL); ff_AddString ("LOCUS"); TabToColumn (13); parent = awp->parent; if (parent->repr == Seq_repr_seg) s_LocusAdjustLength (locus,16); ff_AddString (locus); TabToColumn (44 - StringLen (len)); ff_AddString (len); TabToColumn (45); ff_AddString (mol); TabToColumn (56); if (topology == TOPOLOGY_CIRCULAR) { ff_AddString ("circular"); } else { ff_AddString ("linear "); } TabToColumn (65); ff_AddString (div); TabToColumn (69); ff_AddString (date); } /* Else print the "LOCUS" line */ else { ff_StartPrint (0, 0, ASN2FF_GB_MAX, NULL); ff_AddString ("LOCUS"); TabToColumn (13); if (parent->repr == Seq_repr_seg) s_LocusAdjustLength (locus,10); ff_AddString (locus); TabToColumn (33 - StringLen (len)); ff_AddString (len); TabToColumn (34); ff_AddString (mol); TabToColumn (53); ff_AddString (div); TabToColumn (63); ff_AddString (date); } } else if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) { ff_StartPrint (5, 0, ASN2FF_EMBL_MAX, "ID"); ff_AddString (locus); TabToColumn (16); if (awp->hup) { ff_AddString (" confidential; "); } else { ff_AddString (" standard; "); } ff_AddString (mol); ff_AddString ("; "); /* conditional code to make div "UNA" goes here */ ff_AddString (div); ff_AddString ("; "); ff_AddString (len); } bbp->string = gb_MergeString (TRUE); } static void AddDeflineBlock ( Asn2gbWorkPtr awp ) { BaseBlockPtr bbp; BioseqPtr bsp; CharPtr buf; size_t buflen = 1001; SeqMgrDescContext dcontext; ItemInfo ii; MolInfoPtr mip; SeqDescrPtr sdp; Uint1 tech; if (awp == NULL) return; bsp = awp->bsp; if (bsp == NULL) return; bbp = Asn2gbAddBlock (awp, DEFLINE_BLOCK, sizeof (BaseBlock)); if (bbp == NULL) return; tech = 0; sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext); if (sdp != NULL) { mip = (MolInfoPtr) sdp->data.ptrvalue; if (mip != NULL) { tech = mip->tech; } } buf = MemNew (sizeof (Char) * (buflen + 1)); MemSet ((Pointer) (&ii), 0, sizeof (ItemInfo)); /* create default defline */ if (buf != NULL && CreateDefLine (&ii, bsp, buf, buflen, tech, NULL, NULL)) { bbp->entityID = ii.entityID; bbp->itemID = ii.itemID; bbp->itemtype = ii.itemtype; gb_StartPrint (awp->format, 0, 12, "DEFINITION", 13, 5, 5, "DE", TRUE); gb_AddString (NULL, buf, NULL, TRUE, TRUE, TILDE_IGNORE); bbp->string = gb_MergeString (TRUE); } MemFree (buf); } /* !!! this definitely needs more work to support all classes, use proper SeqId !!! */ static void AddAccessionBlock ( Asn2gbWorkPtr awp ) { SeqIdPtr accn = NULL; IntAsn2gbJobPtr ajp; BaseBlockPtr bbp; BioseqPtr bsp; Char buf [41]; SeqMgrDescContext dcontext; EMBLBlockPtr ebp; ValNodePtr extra_access; CharPtr flatloc; GBBlockPtr gbp; SeqIdPtr gi = NULL; ValNodePtr head = NULL; SeqIdPtr lcl = NULL; SeqDescrPtr sdp; CharPtr separator; SeqIdPtr sip; CharPtr str; ValNodePtr vnp; CharPtr xtra; if (awp == NULL) return; ajp = awp->ajp; if (ajp == NULL) return; bsp = awp->bsp; if (bsp == NULL) return; for (sip = bsp->id; sip != NULL; sip = sip->next) { switch (sip->choice) { case SEQID_GI : gi = sip; break; case SEQID_GENBANK : case SEQID_EMBL : case SEQID_DDBJ : case SEQID_OTHER : accn = sip; break; case SEQID_PIR : case SEQID_SWISSPROT : case SEQID_PRF : case SEQID_PDB : accn = sip; break; case SEQID_TPG : case SEQID_TPE : case SEQID_TPD : accn = sip; break; case SEQID_LOCAL : lcl = sip; break; default : break; } } sip = NULL; if (accn != NULL) { sip = accn; } else if (lcl != NULL) { sip = lcl; } else if (gi != NULL) { sip = gi; } if (sip == NULL) return; SeqIdWrite (sip, buf, PRINTID_TEXTID_ACC_ONLY, sizeof (buf)); bbp = Asn2gbAddBlock (awp, ACCESSION_BLOCK, sizeof (BaseBlock)); if (bbp == NULL) return; gb_StartPrint (awp->format, 0, 12, "ACCESSION", 13, 5, 5, "AC", TRUE); if (awp->hup && accn != NULL) { gb_AddString (NULL, ";", NULL, FALSE, FALSE, TILDE_TO_SPACES); } else if (ajp->ajp.slp != NULL) { flatloc = FlatLoc (bsp, ajp->ajp.slp, ajp->masterStyle); gb_AddString (buf, " REGION: ", flatloc, FALSE, FALSE, TILDE_TO_SPACES); MemFree (flatloc); } else { gb_AddString (NULL, buf, NULL, FALSE, FALSE, TILDE_TO_SPACES); } if (awp->format == GENBANK_FMT || awp->format == GENPEPT_FMT) { separator = " "; } else if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) { separator = ";"; } if (ajp->ajp.slp == NULL) { sdp = SeqMgrGetNextDescriptor (bsp, NULL, 0, &dcontext); while (sdp != NULL) { extra_access = NULL; switch (dcontext.seqdesctype) { case Seq_descr_genbank : gbp = (GBBlockPtr) sdp->data.ptrvalue; if (gbp != NULL) { extra_access = gbp->extra_accessions; } break; case Seq_descr_embl : ebp = (EMBLBlockPtr) sdp->data.ptrvalue; if (ebp != NULL) { extra_access = ebp->extra_acc; } break; default : break; } if (extra_access != NULL) { bbp->entityID = dcontext.entityID; bbp->itemID = dcontext.itemID; bbp->itemtype = OBJ_SEQDESC; } for (vnp = extra_access; vnp != NULL; vnp = vnp->next) { xtra = (CharPtr) vnp->data.ptrvalue; if (ValidateAccession (xtra) == 0) { ValNodeCopyStr (&head, 0, separator); ValNodeCopyStr (&head, 0, xtra); } } sdp = SeqMgrGetNextDescriptor (bsp, sdp, 0, &dcontext); } } str = MergeValNodeStrings (head); gb_AddString (NULL, str, NULL, FALSE, FALSE, TILDE_TO_SPACES); MemFree (str); ValNodeFreeData (head); bbp->string = gb_MergeString (TRUE); } static void AddVersionBlock ( Asn2gbWorkPtr awp ) { SeqIdPtr accn = NULL; BaseBlockPtr bbp; BioseqPtr bsp; Char buf [41]; Int4 gi = -1; SeqIdPtr sip; Char version [64]; if (awp == NULL) return; bsp = awp->bsp; if (bsp == NULL) return; for (sip = bsp->id; sip != NULL; sip = sip->next) { switch (sip->choice) { case SEQID_GI : gi = sip->data.intvalue; break; case SEQID_GENBANK : case SEQID_EMBL : case SEQID_DDBJ : case SEQID_OTHER : accn = sip; break; case SEQID_PIR : case SEQID_SWISSPROT : case SEQID_PRF : case SEQID_PDB : accn = sip; break; case SEQID_TPG : case SEQID_TPE : case SEQID_TPD : accn = sip; break; default : break; } } /* if (gi < 1 && accn == NULL) return; */ if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) { if (gi < 1) return; } bbp = Asn2gbAddBlock (awp, VERSION_BLOCK, sizeof (BaseBlock)); if (bbp == NULL) return; /* no longer displaying NID */ /* if (gi > 0) { sprintf (version, "g%ld", (long) gi); gb_StartPrint (awp->format, needInitBuff, 0, 12, "NID", 13, 5, 5, "NI", TRUE); needInitBuff = FALSE; gb_AddString (NULL, version, NULL, FALSE, FALSE, TILDE_TO_SPACES); ff_EndPrint(); needEndPrint = FALSE; } */ version [0] = '\0'; if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) { sprintf (version, "g%ld", (long) gi); gb_StartPrint (awp->format, 0, 12, "VERSION", 13, 5, 5, "NI", TRUE); gb_AddString (NULL, version, NULL, FALSE, FALSE, TILDE_TO_SPACES); ff_EndPrint(); bbp->string = gb_MergeString (FALSE); return; } if (accn != NULL) { buf [0] = '\0'; SeqIdWrite (accn, buf, PRINTID_TEXTID_ACC_VER, sizeof (buf) - 1); if (gi > 0) { sprintf (version, "%s GI:%ld", buf, (long) gi); } else { sprintf (version, "%s", buf); } gb_StartPrint (awp->format, 0, 12, "VERSION", 13, 5, 5, "SV", TRUE); gb_AddString (NULL, version, NULL, FALSE, FALSE, TILDE_TO_SPACES); ff_EndPrint(); } else if (gi > 0) { gb_StartPrint (awp->format, 0, 0, "VERSION", 13, 5, 5, "SV", TRUE); sprintf (version, " GI:%ld", (long) gi); gb_AddString (NULL, version, NULL, FALSE, FALSE, TILDE_TO_SPACES); ff_EndPrint(); } else { gb_StartPrint (awp->format, 0, 0, "VERSION", 0, 5, 5, "SV", TRUE); ff_EndPrint(); } bbp->string = gb_MergeString (FALSE); } /* only displaying PID in GenPept format */ static void AddPidBlock (Asn2gbWorkPtr awp) { BaseBlockPtr bbp; BioseqPtr bsp; Int4 gi = -1; SeqIdPtr sip; Char version [64]; if (awp == NULL) return; bsp = awp->bsp; if (bsp == NULL) return; for (sip = bsp->id; sip != NULL; sip = sip->next) { switch (sip->choice) { case SEQID_GI : gi = sip->data.intvalue; break; default : break; } } if (gi < 1) return; bbp = Asn2gbAddBlock (awp, PID_BLOCK, sizeof (BaseBlock)); if (bbp == NULL) return; gb_StartPrint (awp->format, 0, 12, "PID", 13, 5, 5, NULL, TRUE); sprintf (version, "g%ld", (long) gi); gb_AddString (NULL, version, NULL, FALSE, FALSE, TILDE_TO_SPACES); ff_EndPrint(); bbp->string = gb_MergeString (FALSE); } static Uint1 dbsource_fasta_order [NUM_SEQID] = { 33, /* 0 = not set */ 20, /* 1 = local Object-id */ 15, /* 2 = gibbsq */ 16, /* 3 = gibbmt */ 30, /* 4 = giim Giimport-id */ 10, /* 5 = genbank */ 10, /* 6 = embl */ 10, /* 7 = pir */ 10, /* 8 = swissprot */ 15, /* 9 = patent */ 18, /* 10 = other TextSeqId */ 20, /* 11 = general Dbtag */ 31, /* 12 = gi */ 10, /* 13 = ddbj */ 10, /* 14 = prf */ 12, /* 15 = pdb */ 10, /* 16 = tpg */ 10, /* 17 = tpe */ 10 /* 18 = tpd */ }; static void AddToUniqueSipList ( ValNodePtr PNTR list, SeqIdPtr sip ) { ValNodePtr vnp; if (list == NULL || sip == NULL) return; for (vnp = *list; vnp != NULL; vnp = vnp->next) { if (SeqIdMatch (sip, (SeqIdPtr) vnp->data.ptrvalue)) return; } ValNodeAddPointer (list, 0, (Pointer) sip); } static Boolean WriteDbsourceID ( SeqIdPtr sip, CharPtr str ) { DbtagPtr db; CharPtr dt; Int4 gi; ObjectIdPtr oip; CharPtr pfx; PDBSeqIdPtr psip = NULL; CharPtr prefix; Boolean rsult = FALSE; CharPtr sfx; CharPtr suffix; Char tmp [32]; TextSeqIdPtr tsip = NULL; if (sip == NULL || str == NULL) return FALSE; *str = '\0'; switch (sip->choice) { case SEQID_LOCAL : oip = (ObjectIdPtr) sip->data.ptrvalue; if (oip == NULL) return FALSE; if (! StringHasNoText (oip->str)) { StringCat (str, oip->str); return TRUE; } else if (oip->id > 0) { sprintf (tmp, "%ld", (long) oip->id); StringCat (str, tmp); return TRUE; } return FALSE; case SEQID_GI : gi = (Int4) sip->data.intvalue; if (gi == 0) return FALSE; sprintf (tmp, "gi: %ld", (long) gi); StringCat (str, tmp); return TRUE; case SEQID_GENERAL : db = (DbtagPtr) sip->data.ptrvalue; if (db == NULL) return FALSE; /* !!! still need to implement this !!! */ return FALSE; case SEQID_GENBANK : case SEQID_EMBL : case SEQID_DDBJ : case SEQID_OTHER : case SEQID_PIR : case SEQID_SWISSPROT : case SEQID_PRF : tsip = (TextSeqIdPtr) sip->data.ptrvalue; if (tsip == NULL) return FALSE; break; case SEQID_PDB : psip = (PDBSeqIdPtr) sip->data.ptrvalue; if (psip == NULL) return FALSE; break; default : break; } prefix = " "; suffix = NULL; switch (sip->choice) { case SEQID_EMBL : StringCat (str, "embl "); suffix = ","; break; case SEQID_OTHER : StringCat (str, "REFSEQ: "); break; case SEQID_SWISSPROT : StringCat (str, "swissprot: "); suffix = ","; break; case SEQID_PIR : StringCat (str, "pir: "); break; case SEQID_PRF : StringCat (str, "prf: "); break; case SEQID_PDB : StringCat (str, "pdb: "); suffix = ","; break; default : break; } pfx = NULL; sfx = NULL; if (tsip != NULL) { if (! StringHasNoText (tsip->name)) { StringCat (str, sfx); StringCat (str, pfx); StringCat (str, "locus "); StringCat (str, tsip->name); sfx = suffix; pfx = prefix; rsult = TRUE; } if (! StringHasNoText (tsip->accession)) { StringCat (str, sfx); StringCat (str, pfx); StringCat (str, "accession "); StringCat (str, tsip->accession); sfx = suffix; pfx = prefix; rsult = TRUE; } if (tsip->version > 0) { sprintf (tmp, ".%d", (int) tsip->version); StringCat (str, tmp); sfx = suffix; pfx = prefix; } if (! StringHasNoText (tsip->release)) { StringCat (str, pfx); StringCat (str, "release "); StringCat (str, tsip->release); sfx = suffix; pfx = prefix; } if (sip->choice == SEQID_SWISSPROT || sip->choice == SEQID_PIR || sip->choice == SEQID_PRF) { StringCat (str, ";"); } return rsult; } if (psip != NULL) { if (! StringHasNoText (psip->mol)) { StringCat (str, "molecule "); StringCat (str, psip->mol); sfx = suffix; pfx = prefix; rsult = TRUE; } if (psip->chain > 0) { StringCat (str, sfx); StringCat (str, pfx); sprintf (tmp, "chain %d", (int) psip->chain); StringCat (str, tmp); sfx = suffix; pfx = prefix; rsult = TRUE; } if (psip->rel != NULL) { StringCat (str, sfx); StringCat (str, pfx); StringCat (str, "release "); dt = asn2gb_PrintDate (psip->rel); StringCat (str, dt); MemFree (dt); sfx = suffix; pfx = prefix; rsult = TRUE; } StringCat (str, ";"); return rsult; } return rsult; } static void AddSPBlock ( BioseqPtr bsp ) { CharPtr acc; DbtagPtr db; SeqMgrDescContext dcontext; Boolean first; ObjectIdPtr oip; SeqDescrPtr sdp; SeqIdPtr sid; SPBlockPtr spb; CharPtr string; TextSeqIdPtr tid; ValNodePtr vnp; if (bsp == NULL) return; sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_sp, &dcontext); if (sdp == NULL) return; spb = (SPBlockPtr) sdp->data.ptrvalue; if (spb == NULL) return; NewContLine (); if (spb->_class == 1) { ff_AddString ("class: standard."); NewContLine (); } else if (spb->_class == 2) { ff_AddString ("class: preliminary."); NewContLine (); } if (spb->extra_acc) { ff_AddString("extra accessions:"); for (vnp = spb->extra_acc; vnp != NULL; vnp = vnp->next) { ff_AddString ((CharPtr) vnp->data.ptrvalue); ff_AddString (","); } } if (spb->imeth) { ff_AddString ("seq starts with Met"); } if (spb->plasnm != NULL) { ff_AddString("plasmid:"); for (vnp = spb->plasnm; vnp != NULL; vnp = vnp->next) { ff_AddString ((CharPtr) vnp->data.ptrvalue); ff_AddString (","); } } if (spb->created) { string = PrintDate (spb->created); ff_AddString ("created: "); ff_AddString (string); MemFree (string); } if (spb->sequpd) { string = PrintDate (spb->sequpd); ff_AddString ("sequence updated: "); ff_AddString (string); MemFree (string); } if (spb->annotupd) { string = PrintDate (spb->annotupd); ff_AddString ("annotation updated: "); ff_AddString (string); MemFree (string); } if (spb->seqref) { ff_AddString ("xrefs: "); first = TRUE; for (sid = spb->seqref; sid != NULL; sid = sid->next) { acc = NULL; if (first == FALSE) { ff_AddString (", "); } first = FALSE; if (sid->choice == SEQID_GI) { ff_AddString ("gi: "); acc = (CharPtr) MemNew (10); sprintf (acc, "%ld", (long) sid->data.intvalue); } else { tid = (TextSeqIdPtr) sid->data.ptrvalue; if (tid != NULL) { acc = tid->accession; } } if (acc != NULL) { switch (sid->choice) { case SEQID_GENBANK: ff_AddString ("genbank accession "); break; case SEQID_EMBL: ff_AddString ("embl accession "); break; case SEQID_PIR: ff_AddString ("pir locus "); break; case SEQID_SWISSPROT: ff_AddString ("swissprot accession "); break; case SEQID_DDBJ: ff_AddString ("ddbj accession "); break; case SEQID_PRF: ff_AddString ("prf accession "); break; case SEQID_GI: ff_AddString ("gi: "); break; case SEQID_TPG: ff_AddString ("genbank third party accession "); break; case SEQID_TPE: ff_AddString ("embl third party accession "); break; case SEQID_TPD: ff_AddString ("ddbj third party accession "); break; default: acc = NULL; break; } ff_AddString (acc); } } } first = TRUE; for (vnp = spb->dbref; vnp != NULL; vnp = vnp->next) { db = (DbtagPtr) vnp->data.ptrvalue; if (db == NULL) continue; oip = db->tag; if (oip == NULL) continue; if (first) { NewContLine (); ff_AddString ("xrefs (non-sequence databases): "); first = FALSE; } else { ff_AddString (", "); } ff_AddString (db->db); if (oip->str != NULL) { ff_AddString (" "); ff_AddString (oip->str); } else if (oip->id > 0) { ff_AddString (" "); ff_AddInteger ("%ld", (long) oip->id); } } } static void AddPIRBlock ( BioseqPtr bsp ) { CharPtr acc; SeqMgrDescContext dcontext; Boolean first; CharPtr prefix = NULL; SeqDescrPtr sdp; SeqIdPtr sid; PirBlockPtr pbp; TextSeqIdPtr tid; if (bsp == NULL) return; sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_pir, &dcontext); if (sdp == NULL) return; pbp = (PirBlockPtr) sdp->data.ptrvalue; if (pbp == NULL) return; if (pbp->host != NULL) { NewContLine (); gb_AddString ("host:", pbp->host, NULL, FALSE, TRUE, TILDE_IGNORE); prefix = ";"; } if (pbp->source != NULL) { ff_AddString (prefix); NewContLine (); gb_AddString ("source: ", pbp->source, NULL, FALSE, TRUE, TILDE_IGNORE); prefix = ";"; } if (pbp->summary != NULL) { ff_AddString (prefix); NewContLine (); gb_AddString ("summary: ", pbp->summary, NULL, FALSE, TRUE, TILDE_IGNORE); prefix = ";"; } if (pbp->genetic != NULL) { ff_AddString (prefix); NewContLine (); gb_AddString ("genetic: ", pbp->genetic, NULL, FALSE, TRUE, TILDE_IGNORE); prefix = ";"; } if (pbp->includes != NULL) { ff_AddString (prefix); NewContLine (); gb_AddString ("includes: ", pbp->includes, NULL, FALSE, TRUE, TILDE_IGNORE); prefix = ";"; } if (pbp->placement != NULL) { ff_AddString (prefix); NewContLine (); gb_AddString ("placement: ", pbp->placement, NULL, FALSE, TRUE, TILDE_IGNORE); prefix = ";"; } if (pbp->superfamily != NULL) { ff_AddString (prefix); NewContLine (); gb_AddString ("superfamily: ", pbp->superfamily, NULL, FALSE, TRUE, TILDE_IGNORE); prefix = ";"; } if (pbp->cross_reference != NULL) { ff_AddString (prefix); NewContLine (); gb_AddString ("xref: ", pbp->cross_reference, NULL, FALSE, TRUE, TILDE_IGNORE); prefix = ";"; } if (pbp->date != NULL) { ff_AddString (prefix); NewContLine (); gb_AddString ("PIR dates: ", pbp->date, NULL, FALSE, TRUE, TILDE_IGNORE); prefix = ";"; } if (pbp->had_punct) { ff_AddString (prefix); NewContLine (); ff_AddString ("punctuation in sequence"); prefix = ";"; } if (pbp->seqref) { ff_AddString (prefix); NewContLine (); ff_AddString ("xrefs: "); first = TRUE; for (sid = pbp->seqref; sid != NULL; sid = sid->next) { acc = NULL; if (first == FALSE) { ff_AddString (", "); } first = FALSE; if (sid->choice == SEQID_GI) { ff_AddString ("gi: "); acc = (CharPtr) MemNew (10); sprintf (acc, "%ld", (long) sid->data.intvalue); } else { tid = (TextSeqIdPtr) sid->data.ptrvalue; if (tid != NULL) { acc = tid->accession; } } if (acc != NULL) { switch (sid->choice) { case SEQID_GENBANK: ff_AddString ("genbank "); break; case SEQID_EMBL: ff_AddString ("embl "); break; case SEQID_PIR: ff_AddString ("pir "); break; case SEQID_SWISSPROT: ff_AddString ("swissprot "); break; case SEQID_DDBJ: ff_AddString ("ddbj "); break; case SEQID_PRF: ff_AddString ("prf "); break; case SEQID_GI: ff_AddString ("gi: "); break; default: acc = NULL; break; } ff_AddString (acc); } } } ff_AddString ("."); } static void AddPRFBlock ( BioseqPtr bsp ) { SeqMgrDescContext dcontext; PrfExtSrcPtr extra; CharPtr prefix = NULL; SeqDescrPtr sdp; PrfBlockPtr prf; if (bsp == NULL) return; sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_prf, &dcontext); if (sdp == NULL) return; prf = (PrfBlockPtr) sdp->data.ptrvalue; if (prf == NULL) return; extra = prf->extra_src; if (extra != NULL) { if (extra->host != NULL) { NewContLine (); gb_AddString ("host:", extra->host, NULL, FALSE, TRUE, TILDE_IGNORE); prefix = ";"; } if (extra->part != NULL) { ff_AddString (prefix); NewContLine (); gb_AddString ("part: ", extra->part, NULL, FALSE, TRUE, TILDE_IGNORE); prefix = ";"; } if (extra->state != NULL) { ff_AddString (prefix); NewContLine (); gb_AddString ("state: ", extra->state, NULL, FALSE, TRUE, TILDE_IGNORE); prefix = ";"; } if (extra->strain != NULL) { ff_AddString (prefix); NewContLine (); gb_AddString ("strain: ", extra->strain, NULL, FALSE, TRUE, TILDE_IGNORE); prefix = ";"; } if (extra->taxon != NULL) { ff_AddString (prefix); NewContLine (); gb_AddString ("taxonomy: ", extra->taxon, NULL, FALSE, TRUE, TILDE_IGNORE); prefix = ";"; } ff_AddString ("."); } } static void AddPDBBlock ( BioseqPtr bsp ) { SeqMgrDescContext dcontext; CharPtr dt; CharPtr prefix = NULL; SeqDescrPtr sdp; PdbBlockPtr pdb; PdbRepPtr replace; CharPtr str; ValNodePtr vnp; if (bsp == NULL) return; sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_pdb, &dcontext); if (sdp == NULL) return; pdb = (PdbBlockPtr) sdp->data.ptrvalue; if (pdb == NULL) return; if (pdb->deposition != NULL) { NewContLine (); dt = asn2gb_PrintDate (pdb->deposition); gb_AddString ("deposition: ", dt, NULL, FALSE, TRUE, TILDE_IGNORE); MemFree (dt); prefix = ";"; } if (pdb->pdbclass != NULL) { ff_AddString (prefix); NewContLine (); gb_AddString ("class: ", pdb->pdbclass, NULL, FALSE, TRUE, TILDE_IGNORE); prefix = ";"; } if (pdb->source != NULL) { ff_AddString (prefix); NewContLine (); gb_AddString (NULL, "source: ", NULL, FALSE, TRUE, TILDE_IGNORE); prefix = NULL; for (vnp = pdb->source; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (str)) continue; gb_AddString (prefix, str, NULL, FALSE, TRUE, TILDE_IGNORE); prefix = ", "; } prefix = ";"; } if (pdb->exp_method != NULL) { ff_AddString (prefix); NewContLine (); gb_AddString ("Non X-ray method: ", pdb->exp_method, NULL, FALSE, TRUE, TILDE_IGNORE); prefix = ";"; } replace = pdb->replace; if (replace != NULL) { if (replace->ids != NULL) { ff_AddString (prefix); NewContLine (); gb_AddString (NULL, "ids replaced: ", NULL, FALSE, TRUE, TILDE_IGNORE); prefix = NULL; for (vnp = replace->ids; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (str)) continue; gb_AddString (prefix, str, NULL, FALSE, TRUE, TILDE_IGNORE); prefix = ", "; } prefix = ";"; } if (replace->date != NULL) { ff_AddString (prefix); NewContLine (); dt = asn2gb_PrintDate (replace->date); gb_AddString ("replacement date: ", dt, NULL, FALSE, TRUE, TILDE_IGNORE); MemFree (dt); prefix = ";"; } } ff_AddString ("."); } static void AddDbsourceBlock ( Asn2gbWorkPtr awp ) { BaseBlockPtr bbp; BioseqPtr bsp; SeqFeatPtr cds; DbtagPtr db; Boolean first = TRUE; SeqIdPtr id; ValNodePtr list = NULL; BioseqPtr nuc; SeqIdPtr sip; SeqLocPtr slp; Char str [256]; Boolean unknown = TRUE; ValNodePtr vnp; if (awp == NULL) return; bsp = awp->bsp; if (bsp == NULL) return; bbp = Asn2gbAddBlock (awp, DBSOURCE_BLOCK, sizeof (BaseBlock)); if (bbp == NULL) return; gb_StartPrint (awp->format, 0, 12, "DBSOURCE", 13, 5, 5, NULL, TRUE); sip = SeqIdSelect (bsp->id, dbsource_fasta_order, NUM_SEQID); if (sip != NULL) { switch (sip->choice) { case SEQID_PIR : case SEQID_SWISSPROT : case SEQID_PRF : case SEQID_PDB : if (WriteDbsourceID (sip, str)) { www_dbsource (str, TRUE, sip->choice); unknown = FALSE; } break; case SEQID_GENERAL : db = sip->data.ptrvalue; if (db == NULL) { break; } if (StringNCmp (db->db, "PIDe", 4) != 0 && StringNCmp (db->db, "PIDd", 4) != 0 && StringNCmp (db->db, "PID", 3) != 0) { break; } /* if (ChoicePID) found, continue on to next set of cases */ case SEQID_EMBL : case SEQID_GENBANK : case SEQID_DDBJ : case SEQID_GIBBSQ : case SEQID_GIBBMT : case SEQID_OTHER : case SEQID_TPG : case SEQID_TPE : case SEQID_TPD : case SEQID_GI : case SEQID_GIIM : cds = SeqMgrGetCDSgivenProduct (bsp, NULL); if (cds != NULL) { nuc = BioseqFindFromSeqLoc (cds->location); if (nuc != NULL) { slp = SeqLocFindNext (cds->location, NULL); while (slp != NULL) { sip = SeqLocId (slp); AddToUniqueSipList (&list, sip); slp = SeqLocFindNext (cds->location, slp); } for (vnp = list; vnp != NULL; vnp = vnp->next) { id = (SeqIdPtr) vnp->data.ptrvalue; nuc = BioseqFindCore (id); sip = NULL; if (nuc != NULL) { sip = SeqIdSelect (nuc->id, dbsource_fasta_order, NUM_SEQID); } else if (id != NULL && id->choice == SEQID_GI) { sip = GetSeqIdForGI (id->data.intvalue); } if (sip == NULL) { sip = id; } if (sip != NULL) { if (WriteDbsourceID (sip, str)) { if (! first) { NewContLine (); TabToColumn (13); } www_dbsource (str, TRUE, sip->choice); first = FALSE; unknown = FALSE; } } } ValNodeFree (list); } } else { if (WriteDbsourceID (sip, str)) { www_dbsource (str, TRUE, sip->choice); unknown = FALSE; } } break; default : break; } switch (sip->choice) { case SEQID_PIR : AddPIRBlock (bsp); break; case SEQID_SWISSPROT : AddSPBlock (bsp); break; case SEQID_PRF : AddPRFBlock (bsp); break; case SEQID_PDB : AddPDBBlock (bsp); break; default : break; } } if (unknown) { gb_AddString (NULL, "UNKNOWN", NULL, FALSE, FALSE, TILDE_TO_SPACES); } ff_EndPrint(); bbp->string = ff_print_string_mem (gb_MergeString (FALSE)); } static void AddDateBlock ( Asn2gbWorkPtr awp ) { BaseBlockPtr bbp; BioseqPtr bsp; Char date [40]; SeqMgrDescContext dcontext; DatePtr dp; SeqDescrPtr sdp; if (awp == NULL) return; bsp = awp->bsp; if (bsp == NULL) return; bbp = Asn2gbAddBlock (awp, DATE_BLOCK, sizeof (BaseBlock)); if (bbp == NULL) return; date [0] = '\0'; dp = NULL; sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_create_date, &dcontext); if (sdp != NULL) { dp = (DatePtr) sdp->data.ptrvalue; } if (dp != NULL) { DateToGB (date, dp, FALSE); } if (StringHasNoText (date)) { StringCpy (date, "01-JAN-1900"); } PrintXX (); ff_StartPrint (5, 5, ASN2FF_EMBL_MAX, "DT"); ff_AddString (date); bbp->string = gb_MergeString (TRUE); bbp = Asn2gbAddBlock (awp, DATE_BLOCK, sizeof (BaseBlock)); if (bbp == NULL) return; sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_update_date, &dcontext); if (sdp != NULL) { dp = (DatePtr) sdp->data.ptrvalue; } if (dp != NULL) { DateToGB (date, dp, FALSE); } ff_StartPrint (5, 5, ASN2FF_EMBL_MAX, "DT"); ff_AddString (date); bbp->string = gb_MergeString (TRUE); } #define TOTAL_ESTKW 11 #define TOTAL_STSKW 5 #define TOTAL_GSSKW 2 static CharPtr EST_kw_array[ TOTAL_ESTKW] = { "EST", "EST PROTO((expressed sequence tag)", "expressed sequence tag", "EST (expressed sequence tag)", "EST(expressed sequence tag)", "partial cDNA sequence", "transcribed sequence fragment", "TSR", "putatively transcribed partial sequence", "UK putts" }; static CharPtr GSS_kw_array [TOTAL_GSSKW] = { "GSS", "trapped exon" }; static CharPtr STS_kw_array[TOTAL_STSKW] = { "STS", "STS(sequence tagged site)", "STS (sequence tagged site)", "STS sequence", "sequence tagged site" }; static Int2 MatchArrayString ( CharPtr array_string [], Int2 totalstr, CharPtr text ) { Int2 i; for (i = 0; i < totalstr && text != NULL; i++) { if (StringCmp (array_string [i], text) == 0) { return (i); } } return (-1); } static Boolean CheckSpecialKeyword ( Boolean is_est, Boolean is_sts, Boolean is_gss, CharPtr kwd ) { if (kwd == NULL) return FALSE; if (is_est) { if (MatchArrayString (STS_kw_array, TOTAL_STSKW, kwd) != -1) return FALSE; if (MatchArrayString (GSS_kw_array, TOTAL_GSSKW, kwd) != -1) return FALSE; } if (is_sts) { if (MatchArrayString (EST_kw_array, TOTAL_ESTKW, kwd) != -1) return FALSE; if (MatchArrayString (GSS_kw_array, TOTAL_GSSKW, kwd) != -1) return FALSE; } if (is_gss) { if (MatchArrayString (STS_kw_array, TOTAL_STSKW, kwd) != -1) return FALSE; if (MatchArrayString (EST_kw_array, TOTAL_ESTKW, kwd) != -1) return FALSE; } return TRUE; } static Boolean KeywordAlreadyInList ( ValNodePtr head, CharPtr kwd ) { ValNodePtr vnp; for (vnp = head; vnp != NULL; vnp = vnp->next) { if (StringICmp ((CharPtr) vnp->data.ptrvalue, kwd) == 0) return TRUE; } return FALSE; } static void AddKeywordsBlock ( Asn2gbWorkPtr awp ) { BaseBlockPtr bbp; BioseqPtr bsp; SeqMgrDescContext dcontext; EMBLBlockPtr ebp; GBBlockPtr gbp; ValNodePtr head = NULL; Boolean is_est = FALSE; Boolean is_gss = FALSE; Boolean is_sts = FALSE; ValNodePtr keywords; CharPtr kwd; MolInfoPtr mip; PirBlockPtr pir; PrfBlockPtr prf; SeqDescrPtr sdp; SeqIdPtr sip; SPBlockPtr sp; CharPtr str; ValNodePtr vnp; if (awp == NULL) return; bsp = awp->bsp; if (bsp == NULL) return; bbp = (BaseBlockPtr) Asn2gbAddBlock (awp, KEYWORDS_BLOCK, sizeof (BaseBlock)); if (bbp == NULL) return; for (sip = bsp->id; sip != NULL; sip = sip->next) { if (sip->choice == SEQID_TPG || sip->choice == SEQID_TPE || sip->choice == SEQID_TPD) { ValNodeCopyStr (&head, 0, "THIRD PARTY ANNOTATION"); } } sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext); if (sdp != NULL) { bbp->entityID = dcontext.entityID; bbp->itemID = dcontext.itemID; bbp->itemtype = OBJ_SEQDESC; mip = (MolInfoPtr) sdp->data.ptrvalue; if (mip != NULL) { switch (mip->tech) { case MI_TECH_htgs_1 : ValNodeCopyStr (&head, 0, "HTG; HTGS_PHASE1"); break; case MI_TECH_htgs_2 : ValNodeCopyStr (&head, 0, "HTG; HTGS_PHASE2"); break; case MI_TECH_htgs_3 : ValNodeCopyStr (&head, 0, "HTG"); break; case MI_TECH_est : is_est = TRUE; ValNodeCopyStr (&head, 0, "EST"); break; case MI_TECH_sts : is_sts = TRUE; ValNodeCopyStr (&head, 0, "STS"); break; case MI_TECH_survey : is_gss = TRUE; ValNodeCopyStr (&head, 0, "GSS"); break; case MI_TECH_fli_cdna : ValNodeCopyStr (&head, 0, "FLI_CDNA"); break; case MI_TECH_htgs_0 : ValNodeCopyStr (&head, 0, "HTG; HTGS_PHASE0"); break; case MI_TECH_htc : ValNodeCopyStr (&head, 0, "HTC"); break; default : break; } } } sdp = SeqMgrGetNextDescriptor (bsp, NULL, 0, &dcontext); while (sdp != NULL) { keywords = NULL; switch (dcontext.seqdesctype) { case Seq_descr_genbank : gbp = (GBBlockPtr) sdp->data.ptrvalue; if (gbp != NULL) { keywords = gbp->keywords; } break; case Seq_descr_embl : ebp = (EMBLBlockPtr) sdp->data.ptrvalue; if (ebp != NULL) { keywords = ebp->keywords; } break; case Seq_descr_pir : pir = (PirBlockPtr) sdp->data.ptrvalue; if (pir != NULL) { keywords = pir->keywords; } break; case Seq_descr_prf : prf = (PrfBlockPtr) sdp->data.ptrvalue; if (prf != NULL) { keywords = prf->keywords; } break; case Seq_descr_sp : sp = (SPBlockPtr) sdp->data.ptrvalue; if (sp != NULL) { keywords = sp->keywords; } break; default : break; } if (keywords != NULL) { bbp->entityID = dcontext.entityID; bbp->itemID = dcontext.itemID; bbp->itemtype = OBJ_SEQDESC; } for (vnp = keywords; vnp != NULL; vnp = vnp->next) { kwd = (CharPtr) vnp->data.ptrvalue; if (CheckSpecialKeyword (is_est, is_sts, is_gss, kwd)) { if (! KeywordAlreadyInList (head, kwd)) { if (head != NULL) { ValNodeCopyStr (&head, 0, "; "); } ValNodeCopyStr (&head, 0, kwd); } } } sdp = SeqMgrGetNextDescriptor (bsp, sdp, 0, &dcontext); } gb_StartPrint (awp->format, 0, 12, "KEYWORDS", 13, 5, 5, "KW", TRUE); str = MergeValNodeStrings (head); /* if no keywords were found, period will still be added by this call */ gb_AddString (NULL, str, NULL, TRUE, FALSE, TILDE_TO_SPACES); MemFree (str); ValNodeFreeData (head); bbp->string = gb_MergeString (TRUE); } static void AddSegmentBlock ( Asn2gbWorkPtr awp ) { BaseBlockPtr bbp; Char buf [32]; if (awp == NULL) return; if (awp->seg < 1 || awp->numsegs < 1) return; bbp = Asn2gbAddBlock (awp, SEGMENT_BLOCK, sizeof (BaseBlock)); if (bbp == NULL) return; sprintf (buf, "%d of %ld", (int) awp->seg, (long) awp->numsegs); gb_StartPrint (awp->format, 0, 12, "SEGMENT", 13, 5, 5, "XX", FALSE); gb_AddString (NULL, buf, NULL, FALSE, TRUE, TILDE_TO_SPACES); bbp->string = gb_MergeString (TRUE); } static void AddSourceBlock ( Asn2gbWorkPtr awp ) { BaseBlockPtr bbp; BioseqPtr bsp; SeqMgrDescContext dcontext; SeqMgrFeatContext fcontext; GBBlockPtr gbp; SeqDescrPtr sdp; SeqFeatPtr sfp; if (awp == NULL) return; bsp = awp->bsp; if (bsp == NULL) return; bbp = Asn2gbAddBlock (awp, SOURCE_BLOCK, sizeof (BaseBlock)); if (bbp == NULL) return; sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_genbank, &dcontext); if (sdp != NULL) { gbp = (GBBlockPtr) sdp->data.ptrvalue; if (gbp != NULL && (! StringHasNoText (gbp->source))) { bbp->entityID = dcontext.entityID; bbp->itemID = dcontext.itemID; bbp->itemtype = OBJ_SEQDESC; return; } } sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext); if (sdp != NULL) { bbp->entityID = dcontext.entityID; bbp->itemID = dcontext.itemID; bbp->itemtype = OBJ_SEQDESC; } else { sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_BIOSRC, 0, &fcontext); if (sfp != NULL) { bbp->entityID = fcontext.entityID; bbp->itemID = fcontext.itemID; bbp->itemtype = OBJ_SEQFEAT; } } } static void AddOrganismBlock ( Asn2gbWorkPtr awp ) { BaseBlockPtr bbp; BioseqPtr bsp; SeqFeatPtr cds; SeqMgrDescContext dcontext; BioseqPtr dna; SeqMgrFeatContext fcontext; SeqDescrPtr sdp; SeqFeatPtr sfp; if (awp == NULL) return; bsp = awp->bsp; if (bsp == NULL) return; bbp = Asn2gbAddBlock (awp, ORGANISM_BLOCK, sizeof (BaseBlock)); if (bbp == NULL) return; sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext); if (sdp != NULL) { bbp->entityID = dcontext.entityID; bbp->itemID = dcontext.itemID; bbp->itemtype = OBJ_SEQDESC; } else { sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_BIOSRC, 0, &fcontext); if (sfp != NULL) { bbp->entityID = fcontext.entityID; bbp->itemID = fcontext.itemID; bbp->itemtype = OBJ_SEQFEAT; } else if (ISA_aa (bsp->mol)) { /* if protein with no sources, get sources applicable to DNA location of CDS */ cds = SeqMgrGetCDSgivenProduct (bsp, &fcontext); if (cds != NULL) { sfp = SeqMgrGetOverlappingSource (cds->location, &fcontext); if (sfp != NULL) { bbp->entityID = fcontext.entityID; bbp->itemID = fcontext.itemID; bbp->itemtype = OBJ_SEQFEAT; } else { dna = BioseqFindFromSeqLoc (cds->location); if (dna != NULL) { sdp = SeqMgrGetNextDescriptor (dna, NULL, Seq_descr_source, &dcontext); if (sdp != NULL) { bbp->entityID = dcontext.entityID; bbp->itemID = dcontext.itemID; bbp->itemtype = OBJ_SEQDESC; } } } } } } } static RefBlockPtr AddPub ( Asn2gbWorkPtr awp, ValNodePtr PNTR head, PubdescPtr pdp ) { Char buf [121]; CitArtPtr cap; CitBookPtr cbp; CitGenPtr cgp; CitJourPtr cjp; CitPatPtr cpp; CitSubPtr csp; DatePtr dp = NULL; Boolean justuids = TRUE; ImprintPtr imp = NULL; IntRefBlockPtr irp; RefBlockPtr rbp; ValNodePtr vnp; if (awp == NULL || head == NULL || pdp == NULL) return NULL; rbp = (RefBlockPtr) MemNew (sizeof (IntRefBlock)); if (rbp == NULL) return NULL; rbp->blocktype = REFERENCE_BLOCK; rbp->section = awp->currsection; rbp->serial = INT2_MAX; for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) { switch (vnp->choice) { case PUB_Gen : /* may be unpublished, or may be serial number of swiss-prot reference */ cgp = (CitGenPtr) vnp->data.ptrvalue; if (cgp != NULL) { if (StringNICmp ("BackBone id_pub", cgp->cit, 15) != 0) { rbp->category = REF_CAT_UNP; dp = cgp->date; if (cgp->serial_number > 0) { rbp->serial = cgp->serial_number; } if (cgp->cit != NULL) { if (StringNICmp ("unpublished", cgp->cit, 11) != 0 && StringNICmp ("submitted", cgp->cit, 8) != 0 && StringNICmp ("to be published", cgp->cit, 15) != 0 && StringNICmp ("in press", cgp->cit, 8) != 0 && StringStr (cgp->cit, "Journal") == NULL) { if (cgp->serial_number == 0) { MemFree (rbp); return NULL; } } } else if (cgp->journal == NULL || cgp->date == NULL) { if (cgp->serial_number == 0) { MemFree (rbp); return NULL; } } } } break; case PUB_Sub : rbp->category = REF_CAT_SUB; csp = (CitSubPtr) vnp->data.ptrvalue; if (csp != NULL) { imp = csp->imp; if (imp != NULL) { dp = imp->date; } if (csp->date != NULL) { dp = csp->date; } } break; case PUB_Article: cap = (CitArtPtr) vnp->data.ptrvalue; if (cap != NULL) { switch (cap->from) { case 1: cjp = (CitJourPtr) cap->fromptr; if (cjp != NULL) { imp = (ImprintPtr) cjp->imp; if (imp != NULL) { dp = imp->date; } } break; case 2: cbp = (CitBookPtr) cap->fromptr; if (cbp != NULL) { imp = (ImprintPtr) cbp->imp; if (imp != NULL) { dp = imp->date; } } break; case 3: cbp = (CitBookPtr) cap->fromptr; if (cbp != NULL) { imp = (ImprintPtr) cbp->imp; if (imp != NULL) { dp = imp->date; } } break; default: break; } } break; case PUB_Book: cbp = (CitBookPtr) vnp->data.ptrvalue; if (cbp != NULL) { imp = (ImprintPtr) cbp->imp; if (imp != NULL) { dp = imp->date; } } break; case PUB_Proc: cbp = (CitBookPtr) vnp->data.ptrvalue; if (cbp != NULL) { imp = (ImprintPtr) cbp->imp; if (imp != NULL) { dp = imp->date; } } break; case PUB_Patent : rbp->category = REF_CAT_PUB; cpp = (CitPatPtr) vnp->data.ptrvalue; if (cpp != NULL) { if (cpp->date_issue != NULL) { dp = (DatePtr) cpp->date_issue; } else if (cpp->app_date != NULL) { dp = (DatePtr) cpp->app_date; } } break; case PUB_Man: cbp = (CitBookPtr) vnp->data.ptrvalue; if (cbp != NULL) { imp = (ImprintPtr) cbp->imp; if (imp != NULL) { dp = imp->date; } } break; case PUB_Muid : rbp->muid = vnp->data.intvalue; rbp->category = REF_CAT_PUB; break; case PUB_PMid : rbp->pmid = vnp->data.intvalue; rbp->category = REF_CAT_PUB; break; default : break; } if (vnp->choice != PUB_Muid && vnp->choice != PUB_PMid) { justuids = FALSE; } } /* check for submitted vs. in-press */ if (imp != NULL) { rbp->category = REF_CAT_PUB; switch (imp->prepub) { case 1 : rbp->category = REF_CAT_UNP; break; case 2 : rbp->category = REF_CAT_PUB; break; default : break; } } /* check for sites reftype */ if (pdp->reftype != 0) { rbp->sites = pdp->reftype; } if (rbp->muid == 0 && rbp->pmid == 0) { vnp = pdp->pub; /* skip over just serial number */ if (vnp != NULL && vnp->choice == PUB_Gen && vnp->next != NULL) { cgp = (CitGenPtr) vnp->data.ptrvalue; if (cgp != NULL) { if (StringNICmp ("BackBone id_pub", cgp->cit, 15) != 0) { if (cgp->cit == NULL && cgp->journal == NULL && cgp->date == NULL && cgp->serial_number) { vnp = vnp->next; } } } } if (PubLabelUnique (vnp, buf, sizeof (buf) - 1, OM_LABEL_CONTENT, TRUE) > 0) { rbp->uniquestr = StringSaveNoNull (buf); } } irp = (IntRefBlockPtr) rbp; irp->date = DateDup (dp); irp->justuids = justuids; /* if (justuids) { */ irp->fig = StringSaveNoNull (pdp->fig); irp->maploc = StringSaveNoNull (pdp->maploc); irp->poly_a = pdp->poly_a; /* } */ /* if not rejected by now, link in */ ValNodeAddPointer (head, 0, rbp); return rbp; } static int LIBCALLBACK SortReferences ( VoidPtr ptr1, VoidPtr ptr2, Boolean serialFirst ) { int compare; IntRefBlockPtr irp1; IntRefBlockPtr irp2; RefBlockPtr rbp1; RefBlockPtr rbp2; Int2 status; ValNodePtr vnp1; ValNodePtr vnp2; if (ptr1 == NULL || ptr2 == NULL) return 0; vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 == NULL || vnp2 == NULL) return 0; rbp1 = (RefBlockPtr) vnp1->data.ptrvalue; rbp2 = (RefBlockPtr) vnp2->data.ptrvalue; if (rbp1 == NULL || rbp2 == NULL) return 0; if (serialFirst) { if (rbp1->serial > rbp2->serial) { return 1; } else if (rbp1->serial < rbp2->serial) { return -1; } } /* usual first sort by published, unpublished, and cit-subs */ if (rbp1->category > rbp2->category) { return 1; } else if (rbp1->category < rbp2->category) { return -1; } /* within class, sort by date, older publications first */ irp1 = (IntRefBlockPtr) rbp1; irp2 = (IntRefBlockPtr) rbp2; status = DateMatch (irp1->date, irp2->date, FALSE); if (status == 1 || status == -1) return status; /* if dates (e.g., years) match, try to distinguish by uids */ if (rbp1->pmid != 0 && rbp2->pmid != 0) { if (rbp1->pmid > rbp2->pmid) { return 1; } else if (rbp1->pmid < rbp2->pmid) { return -1; } } if (rbp1->muid != 0 && rbp2->muid != 0) { if (rbp1->muid > rbp2->muid) { return 1; } else if (rbp1->muid < rbp2->muid) { return -1; } } /* if same uid, one with just uids goes last to be excised but remembered */ if ((rbp1->pmid != 0 && rbp2->pmid != 0) || (rbp1->muid != 0 && rbp2->muid != 0)) { if (irp1->justuids && (! irp2->justuids)) { return 1; } else if ((! irp1->justuids) && irp2->justuids) { return -1; } } /* put sites after pubs that refer to all or a range of bases */ if (rbp1->sites > 0) { return 1; } else if (rbp2->sites > 0) { return -1; } /* for publication features, sort in explore index order */ if (irp1->index > irp2->index) { return 1; } else if (irp1->index < irp2->index) { return -1; } /* next use author string */ if (irp1->authstr != NULL && irp2->authstr != NULL) { compare = StringICmp (irp1->authstr, irp2->authstr); if (compare > 0) { return 1; } else if (compare < 0) { return -1; } } /* use unique label string to determine sort order */ if (rbp1->uniquestr != NULL && rbp2->uniquestr != NULL) { compare = StringICmp (rbp1->uniquestr, rbp2->uniquestr); if (compare > 0) { return 1; } else if (compare < 0) { return -1; } } /* last resort for equivalent publication descriptors, sort in itemID order */ if (rbp1->itemtype == OBJ_SEQDESC && rbp2->itemtype == OBJ_SEQDESC) { if (rbp1->itemID > rbp2->itemID) { return 1; } else if (rbp1->itemID < rbp2->itemID) { return -1; } } if (! serialFirst) { if (rbp1->serial > rbp2->serial) { return 1; } else if (rbp1->serial < rbp2->serial) { return -1; } } return 0; } static int LIBCALLBACK SortReferencesA ( VoidPtr ptr1, VoidPtr ptr2 ) { return SortReferences (ptr1, ptr2, FALSE); } static int LIBCALLBACK SortReferencesB ( VoidPtr ptr1, VoidPtr ptr2 ) { return SortReferences (ptr1, ptr2, TRUE); } static void GetRefsOnBioseq ( Asn2gbWorkPtr awp, BioseqPtr target, BioseqPtr bsp, Int4 from, Int4 to ) { AuthListPtr alp; SeqMgrDescContext dcontext; SeqMgrFeatContext fcontext; Int2 idx; IntRefBlockPtr irp; Int4Ptr ivals; Int2 numivals; Boolean okay; PubdescPtr pdp; RefBlockPtr rbp; SeqDescrPtr sdp; SeqFeatPtr sfp; SeqInt sint; Int4 start; Int4 stop; ValNode vn; ValNodePtr vnp; if (awp == NULL || target == NULL || bsp == NULL) return; /* full length loc for descriptors */ sint.from = 0; sint.to = bsp->length - 1; sint.strand = Seq_strand_plus; sint.id = SeqIdStripLocus (SeqIdDup (SeqIdFindBest (bsp->id, 0))); sint.if_from = NULL; sint.if_to = NULL; vn.choice = SEQLOC_INT; vn.data.ptrvalue = (Pointer) &sint; vn.next = NULL; sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_pub, &dcontext); while (sdp != NULL) { /* check if descriptor on part already added on segmented bioseq */ okay = TRUE; for (vnp = awp->pubhead; vnp != NULL && okay; vnp = vnp->next) { rbp = (RefBlockPtr) vnp->data.ptrvalue; if (rbp != NULL) { if (rbp->entityID == dcontext.entityID && rbp->itemID == dcontext.itemID && rbp->itemtype == OBJ_SEQDESC) { okay = FALSE; } } } if (okay) { pdp = (PubdescPtr) sdp->data.ptrvalue; rbp = AddPub (awp, &(awp->pubhead), pdp); if (rbp != NULL) { rbp->entityID = dcontext.entityID; rbp->itemID = dcontext.itemID; rbp->itemtype = OBJ_SEQDESC; irp = (IntRefBlockPtr) rbp; irp->loc = SeqLocMerge (target, &vn, NULL, FALSE, TRUE, FALSE); alp = GetAuthListPtr (pdp, NULL); if (alp != NULL) { irp->authstr = GetAuthorsString (awp->format, alp); } irp->index = 0; } } sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_pub, &dcontext); } SeqIdFree (sint.id); /* features are indexed on parent if segmented */ bsp = awp->parent; sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_PUB, 0, &fcontext); while (sfp != NULL) { ivals = fcontext.ivals; numivals = fcontext.numivals; if (ivals != NULL && numivals > 0) { idx = (numivals - 1) * 2; start = ivals [idx]; stop = ivals [idx + 1]; if (stop >= from && stop <= to) { /* start = ivals [0] + 1; stop = ivals [idx + 1] + 1; */ pdp = (PubdescPtr) sfp->data.value.ptrvalue; rbp = AddPub (awp, &(awp->pubhead), pdp); if (rbp != NULL) { rbp->entityID = fcontext.entityID; rbp->itemID = fcontext.itemID; rbp->itemtype = OBJ_SEQFEAT; irp = (IntRefBlockPtr) rbp; irp->loc = SeqLocMerge (target, sfp->location, NULL, FALSE, TRUE, FALSE); alp = GetAuthListPtr (pdp, NULL); if (alp != NULL) { irp->authstr = GetAuthorsString (awp->format, alp); } irp->index = fcontext.index; } } } sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_PUB, 0, &fcontext); } } static Boolean LIBCALLBACK GetRefsOnSeg ( SeqLocPtr slp, SeqMgrSegmentContextPtr context ) { Asn2gbWorkPtr awp; BioseqPtr bsp = NULL; Uint2 entityID; Int4 from; SeqLocPtr loc; SeqIdPtr sip; Int4 to; if (slp == NULL || context == NULL) return FALSE; awp = (Asn2gbWorkPtr) context->userdata; from = context->cumOffset; to = from + context->to - context->from; sip = SeqLocId (slp); if (sip == NULL) { loc = SeqLocFindNext (slp, NULL); if (loc != NULL) { sip = SeqLocId (loc); } } if (sip == NULL) return TRUE; /* may remote fetch genome component if not already in memory */ bsp = BioseqLockById (sip); if (bsp == NULL) return TRUE; entityID = ObjMgrGetEntityIDForPointer (bsp); if (entityID != awp->entityID) { /* if segment not packaged in record, may need to feature index it */ if (SeqMgrFeaturesAreIndexed (entityID) == 0) { SeqMgrIndexFeatures (entityID, NULL); } /* collect features indexed on the remote bioseq */ from = 0; to = bsp->length - 1; } GetRefsOnBioseq (awp, awp->target, bsp, from, to); BioseqUnlock (bsp); return TRUE; } static Boolean AddReferenceBlock ( Asn2gbWorkPtr awp ) { IntAsn2gbJobPtr ajp; AuthListPtr alp; Asn2gbSectPtr asp; BioseqPtr bsp; SeqFeatPtr cds; Boolean combine; SeqMgrFeatContext context; CitSubPtr csp; BioseqPtr dna; Boolean excise; ValNodePtr head = NULL; Int2 i; IntRefBlockPtr irp; IntRefBlockPtr lastirp; RefBlockPtr lastrbp; ValNodePtr next; Int2 numReferences; ValNodePtr PNTR prev; RefBlockPtr rbp; RefBlockPtr PNTR referenceArray; SubmitBlockPtr sbp; SeqLocPtr slp; BioseqPtr target; ValNodePtr vnp; if (awp == NULL) return FALSE; ajp = awp->ajp; if (ajp == NULL) return FALSE; asp = awp->asp; if (asp == NULL) return FALSE; bsp = awp->bsp; if (bsp == NULL) return FALSE; /* collect publications on bioseq */ awp->pubhead = NULL; GetRefsOnBioseq (awp, bsp, bsp, awp->from, awp->to); target = bsp; if (bsp->repr == Seq_repr_seg) { /* collect publications on remote segments in MASTER_STYLE */ SeqMgrExploreSegments (bsp, (Pointer) awp, GetRefsOnSeg); target = awp->target; } if (awp->pubhead == NULL && ISA_aa (bsp->mol)) { /* if protein with no pubs, get pubs applicable to DNA location of CDS */ cds = SeqMgrGetCDSgivenProduct (bsp, &context); if (cds != NULL) { dna = BioseqFindFromSeqLoc (cds->location); if (dna != NULL) { GetRefsOnBioseq (awp, dna, dna, context.left, context.right); target = dna; } } } head = awp->pubhead; awp->pubhead = NULL; if (head == NULL && awp->ssp == NULL) return FALSE; /* sort by pub/unpub/sites/sub, then date, finally existing serial */ head = SortValNode (head, SortReferencesA); if (awp->ssp != NULL) { /* add seq-submit citation */ rbp = (RefBlockPtr) MemNew (sizeof (IntRefBlock)); if (rbp != NULL) { irp = (IntRefBlockPtr) rbp; rbp->blocktype = REFERENCE_BLOCK; rbp->section = awp->currsection; rbp->serial = INT2_MAX; rbp->category = REF_CAT_SUB; rbp->entityID = ajp->ajp.entityID; rbp->itemID = 1; rbp->itemtype = OBJ_SEQSUB_CIT; sbp = awp->ssp->sub; if (sbp != NULL) { csp = sbp->cit; if (csp != NULL) { alp = GetAuthListPtr (NULL, csp); if (alp != NULL) { irp->authstr = GetAuthorsString (awp->format, alp); } } } if (awp->citSubsFirst) { /* for DDBJ, add seq-submit citation to beginning of list */ vnp = ValNodeNew (NULL); if (vnp != NULL) { vnp->choice = 0; vnp->data.ptrvalue = (VoidPtr) rbp; vnp->next = head; head = vnp; } } else { /* for GENBANK and EMBL add seq-submit citation to end of list */ ValNodeAddPointer (&head, 0, rbp); } } } /* unique references, excise duplicates from list */ prev = &(head); vnp = head; lastrbp = NULL; while (vnp != NULL) { excise = FALSE; combine = TRUE; next = vnp->next; rbp = (RefBlockPtr) vnp->data.ptrvalue; if (lastrbp != NULL) { lastirp = (IntRefBlockPtr) lastrbp; if (rbp != NULL) { irp = (IntRefBlockPtr) rbp; if (lastrbp->pmid != 0 && rbp->pmid != 0) { if (lastrbp->pmid == rbp->pmid) { excise = TRUE; } } else if (lastrbp->muid != 0 && rbp->muid != 0) { if (lastrbp->muid == rbp->muid) { excise = TRUE; } } else if (lastrbp->uniquestr != NULL && rbp->uniquestr != NULL) { if (StringICmp (lastrbp->uniquestr, rbp->uniquestr) == 0) { if (SeqLocCompare (irp->loc, lastirp->loc) == SLC_A_EQ_B) { if (StringICmp (irp->authstr, lastirp->authstr) == 0) { /* L76496.1 - removing duplicate submission pubs */ excise = TRUE; } } } } } } if (rbp != NULL) { irp = (IntRefBlockPtr) rbp; if (irp->justuids) { /* do not allow justuids reference to appear by itself - S79174.1 */ excise = TRUE; /* justuids should still combine, even if no authors - S67070.1 */ } else if (StringHasNoText (irp->authstr)) { /* do not allow no author reference to appear by itself - U07000.1 */ excise = TRUE; combine = FALSE; } } if (excise) { *prev = vnp->next; vnp->next = NULL; /* combine locations of duplicate references */ irp = (IntRefBlockPtr) rbp; lastirp = (IntRefBlockPtr) lastrbp; if (combine) { if (lastirp != NULL) { slp = SeqLocMerge (target, lastirp->loc, irp->loc, FALSE, TRUE, FALSE); lastirp->loc = SeqLocFree (lastirp->loc); lastirp->loc = slp; } if (irp != NULL && lastirp != NULL) { if ((rbp->muid == lastrbp->muid && rbp->muid != 0) || (rbp->pmid == lastrbp->pmid && rbp->pmid != 0)) { if (lastirp->fig == NULL) { lastirp->fig = StringSaveNoNull (irp->fig); } if (lastirp->maploc == NULL) { lastirp->maploc = StringSaveNoNull (irp->maploc); } lastirp->poly_a = irp->poly_a; } } } /* and remove duplicate reference */ MemFree (rbp->uniquestr); DateFree (irp->date); SeqLocFree (irp->loc); MemFree (irp->authstr); MemFree (irp->fig); MemFree (irp->maploc); MemFree (rbp); ValNodeFree (vnp); } else { prev = &(vnp->next); lastrbp = rbp; } vnp = next; } /* resort by existing serial, then pub/unpub/sites/sub, then date */ head = SortValNode (head, SortReferencesB); if (head == NULL) return FALSE; /* assign serial numbers */ for (vnp = head, i = 1; vnp != NULL; vnp = vnp->next, i++) { rbp = (RefBlockPtr) vnp->data.ptrvalue; if (rbp != NULL) { rbp->serial = i; } } /* allocate reference array for this section */ numReferences = i - 1; asp->numReferences = numReferences; if (numReferences > 0) { referenceArray = (RefBlockPtr PNTR) MemNew (sizeof (RefBlockPtr) * (numReferences + 1)); asp->referenceArray = referenceArray; if (referenceArray != NULL) { /* fill in reference array */ for (vnp = head, i = 0; vnp != NULL && i < numReferences; vnp = vnp->next, i++) { referenceArray [i] = (RefBlockPtr) vnp->data.ptrvalue; } } } /* finally link into blocks for current section */ ValNodeLink (&(awp->lastblock), head); vnp = awp->lastblock; if (vnp == NULL) return FALSE; while (vnp->next != NULL) { vnp = vnp->next; } awp->lastblock = vnp; if (awp->blockList == NULL) { awp->blockList = vnp; } return TRUE; } static void AddHistCommentString ( CharPtr prefix, CharPtr suffix, DatePtr dp, SeqIdPtr ids ) { Char buf [256]; ValNodePtr head = NULL; SeqIdPtr sip; CharPtr str; CharPtr strd; if (dp == NULL || ids == NULL || prefix == NULL || suffix == NULL) return; strd = asn2gb_PrintDate (dp); if (strd == NULL) { strd = StringSave ("?"); } sprintf (buf, "%s %s %s", prefix, strd, suffix); ValNodeCopyStr (&head, 0, buf); MemFree (strd); for (sip = ids; sip != NULL; sip = sip->next) { if (sip->choice == SEQID_GI) { sprintf (buf, " gi:%ld", (long) sip->data.intvalue); ValNodeCopyStr (&head, 0, buf); } } str = MergeValNodeStrings (head); gb_AddString (NULL, str, NULL, TRUE, FALSE, TILDE_EXPAND); MemFree (str); ValNodeFreeData (head); } static void AddHTGSCommentString ( BioseqPtr bsp, MolInfoPtr mip ) { CharPtr buf = NULL; Char buffer [256]; Int4 buflen = 0; DeltaSeqPtr dsp; ValNodePtr head = NULL; Int4 num_s = 0; Int4 num_g = 0; CharPtr str; if (bsp == NULL || mip == NULL || mip->tech < 2) return; if (bsp->repr == Seq_repr_delta) { for (dsp = (DeltaSeqPtr) bsp->seq_ext, buflen = 0; dsp != NULL; dsp = dsp->next) { buflen += 80; } if (buflen > 0) { buf = MemNew ((size_t) (buflen + 1)); if (buf == NULL) return; CountGapsInDeltaSeq (bsp, &num_s, &num_g, NULL, NULL, buf, buflen); } } if (mip->tech == MI_TECH_htgs_0) { if (num_s > 0) { sprintf (buffer, "* NOTE: This record contains %ld individual~", (long) (num_s - num_g)); ValNodeCopyStr (&head, 0, buffer); ValNodeCopyStr (&head, 0, "* sequencing reads that have not been assembled into~"); ValNodeCopyStr (&head, 0, "* contigs. Runs of N are used to separate the reads~"); ValNodeCopyStr (&head, 0, "* and the order in which they appear is completely~"); ValNodeCopyStr (&head, 0, "* arbitrary. Low-pass sequence sampling is useful for~"); ValNodeCopyStr (&head, 0, "* identifying clones that may be gene-rich and allows~"); ValNodeCopyStr (&head, 0, "* overlap relationships among clones to be deduced.~"); ValNodeCopyStr (&head, 0, "* However, it should not be assumed that this clone~"); ValNodeCopyStr (&head, 0, "* will be sequenced to completion. In the event that~"); ValNodeCopyStr (&head, 0, "* the record is updated, the accession number will~"); ValNodeCopyStr (&head, 0, "* be preserved."); } ValNodeCopyStr (&head, 0, "~"); ValNodeCopyStr (&head, 0, buf); } else if (mip->tech == MI_TECH_htgs_1) { ValNodeCopyStr (&head, 0, "* NOTE: This is a \"working draft\" sequence."); if (num_s > 0) { sprintf (buffer, " It currently~* consists of %ld contigs. The true order of the pieces~", (long) (num_s - num_g)); ValNodeCopyStr (&head, 0, buffer); ValNodeCopyStr (&head, 0, "* is not known and their order in this sequence record is~"); ValNodeCopyStr (&head, 0, "* arbitrary. Gaps between the contigs are represented as~"); ValNodeCopyStr (&head, 0, "* runs of N, but the exact sizes of the gaps are unknown."); } ValNodeCopyStr (&head, 0, "~* This record will be updated with the finished sequence~"); ValNodeCopyStr (&head, 0, "* as soon as it is available and the accession number will~"); ValNodeCopyStr (&head, 0, "* be preserved."); ValNodeCopyStr (&head, 0, "~"); ValNodeCopyStr (&head, 0, buf); } else if (mip->tech == MI_TECH_htgs_2) { ValNodeCopyStr (&head, 0, "* NOTE: This is a \"working draft\" sequence."); if (num_s > 0) { sprintf (buffer, " It currently~* consists of %ld contigs. Gaps between the contigs~", (long) (num_s - num_g)); ValNodeCopyStr (&head, 0, buffer); ValNodeCopyStr (&head, 0, "* are represented as runs of N. The order of the pieces~"); ValNodeCopyStr (&head, 0, "* is believed to be correct as given, however the sizes~"); ValNodeCopyStr (&head, 0, "* of the gaps between them are based on estimates that have~"); ValNodeCopyStr (&head, 0, "* provided by the submittor."); } ValNodeCopyStr (&head, 0, "~* This sequence will be replaced~"); ValNodeCopyStr (&head, 0, "* by the finished sequence as soon as it is available and~"); ValNodeCopyStr (&head, 0, "* the accession number will be preserved."); ValNodeCopyStr (&head, 0, "~"); ValNodeCopyStr (&head, 0, buf); } else if ((str = StringForSeqTech (mip->tech)) != NULL) { sprintf (buffer, "Method: %s.", str); ValNodeCopyStr (&head, 0, buffer); } MemFree (buf); str = MergeValNodeStrings (head); gb_AddString (NULL, str, NULL, TRUE, TRUE, TILDE_EXPAND); MemFree (str); ValNodeFreeData (head); } static CharPtr GetMolInfoCommentString ( BioseqPtr bsp, MolInfoPtr mip ) { Boolean is_aa; CharPtr str = NULL; if (bsp == NULL || mip == NULL) return NULL; is_aa = ISA_aa (bsp->mol); switch (mip->completeness) { case 1 : str = "COMPLETENESS: full length"; break; case 2 : str = "COMPLETENESS: not full length"; break; case 3 : if (is_aa) { str = "COMPLETENESS: incomplete on the amino end"; } else { str = "COMPLETENESS: incomplete on the 5' end"; } break; case 4 : if (is_aa) { str = "COMPLETENESS: incomplete on the carboxy end"; } else { str = "COMPLETENESS: incomplete on the 3' end"; } break; case 5 : str = "COMPLETENESS: incomplete on both ends"; break; case 6 : if (is_aa) { str = "COMPLETENESS: complete on the amino end"; } else { str = "COMPLETENESS: complete on the 5' end"; } break; case 7 : if (is_aa) { str = "COMPLETENESS: complete on the carboxy end"; } else { str = "COMPLETENESS: complete on the 3' end"; } break; default : str = "COMPLETENESS: unknown"; break; } return str; } static CharPtr GetStrForBankit ( UserObjectPtr uop ) { CharPtr bic = NULL, uvc = NULL, ptr; ObjectIdPtr oip; UserFieldPtr ufp; if (uop == NULL) return NULL; if ((oip = uop->type) == NULL) return NULL; if (StringCmp (oip->str, "Submission") != 0) return NULL; for (ufp = uop->data; ufp != NULL; ufp = ufp->next) { oip = ufp->label; if (StringCmp(oip->str, "UniVecComment") == 0) { uvc = ufp->data.ptrvalue; } else if (StringCmp(oip->str, "AdditionalComment") == 0) { bic = ufp->data.ptrvalue; } } if (uvc == NULL || bic == NULL) return NULL; ptr = (CharPtr) MemNew (StringLen (uvc) + StringLen (bic) + 45); if (uvc != NULL && bic != NULL) { sprintf (ptr, "Vector Explanation: %s~Bankit Comment: %s", uvc, bic); } else if (uvc != NULL) { sprintf (ptr, "Vector Explanation: %s", uvc); } else if (bic != NULL) { sprintf (ptr, "Bankit Comment: %s", bic); } return ptr; } static CharPtr reftxt0 = "The reference sequence was derived from "; static CharPtr reftxt1 = "PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. "; static CharPtr reftxt2 = "PREDICTED REFSEQ: The mRNA record is supported by experimental evidence; however, the coding sequence is predicted. "; static CharPtr reftxt3 = "VALIDATED REFSEQ: This record has undergone preliminary review of the sequence, but has not yet been subject to final NCBI review. "; static CharPtr reftxt4 = "REVIEWED REFSEQ: This record has been curated by "; static CharPtr GetStrForRefTrack ( UserObjectPtr uop ) { CharPtr curator = NULL, ptr = NULL, st; ObjectIdPtr oip; UserFieldPtr ufp, tmp, u, urf = NULL; Int2 i = 0; Char p [41]; Int2 review = 0,len; if (uop == NULL) return NULL; if ((oip = uop->type) == NULL) return NULL; if (StringCmp (oip->str, "RefGeneTracking") != 0) return NULL; len = StringLen (reftxt0); for (ufp = uop->data; ufp != NULL; ufp = ufp->next) { oip = ufp->label; if (StringCmp(oip->str, "Assembly") == 0) { urf = ufp; } if (StringCmp (oip->str, "Status") == 0) { st = (CharPtr) ufp->data.ptrvalue; if (StringCmp (st, "Provisional") == 0) { review = 1; } else if (StringCmp (st, "Predicted") == 0) { review = 2; } else if (StringCmp (st, "Validated") == 0) { review = 3; } else if (StringCmp (st, "Reviewed") == 0) { review = 4; } } else if (StringCmp (oip->str, "Collaborator") == 0) { st = (CharPtr) ufp->data.ptrvalue; if (! StringHasNoText (st)) { curator = st; } } } if (urf && urf->choice == 11) { for (tmp = urf->data.ptrvalue; tmp != NULL; tmp = tmp->next) { i++; } if (review == 1) { ptr = (CharPtr) MemNew ( StringLen (reftxt1) + len + 18*i + 1); StringCpy (ptr, reftxt1); } else if (review == 2) { ptr = (CharPtr) MemNew ( StringLen (reftxt2) + len + 18*i + 1); StringCpy (ptr, reftxt2); } else if (review == 3) { ptr = (CharPtr) MemNew ( StringLen (reftxt3) + len + 18*i + 1); StringCpy (ptr, reftxt3); } else if (review == 4) { if (curator == NULL) { curator = "NCBI staff"; } ptr = (CharPtr) MemNew ( StringLen (reftxt4) + StringLen (curator) + len + 18*i + 1); StringCpy (ptr, reftxt4); StringCat (ptr, curator); StringCat (ptr, ". "); } else { ptr = (CharPtr) MemNew ( StringLen ("REFSEQ: ") + len + 18*i + 1); StringCpy (ptr, "REFSEQ: "); } if (i > 0) { StringCat (ptr, reftxt0); } for (tmp = urf->data.ptrvalue; tmp != NULL; tmp = tmp->next) { for (u = tmp->data.ptrvalue; u != NULL; u = u->next) { oip = u->label; if (StringCmp (oip->str, "accession") == 0) break; } if (u != NULL && tmp->next) { sprintf (p, "%s, ", u->data.ptrvalue); } else { sprintf (p, "%s.~~", u->data.ptrvalue); } StringCat (ptr, p); } } return ptr; } static CharPtr reftxt5 = "GENOME ANNOTATION REFSEQ: This model reference sequence was predicted from NCBI contig"; static CharPtr reftxt6 = "by automated computational analysis"; static CharPtr reftxt7 = "using gene prediction method:"; static CharPtr reftxt8 = "~Also see:~ Documentation of NCBI's Annotation Process~ Evidence Viewer - alignments supporting this model"; static CharPtr GetAnnotationComment ( BioseqPtr bsp ) { SeqMgrDescContext dcontext; CharPtr method = NULL; CharPtr name = NULL; ObjectIdPtr oip; SeqDescrPtr sdp; CharPtr str = NULL; UserFieldPtr ufp; UserObjectPtr uop; sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &dcontext); while (sdp != NULL) { uop = (UserObjectPtr) sdp->data.ptrvalue; if (uop != NULL) { oip = uop->type; if (oip != NULL) { if (StringCmp(oip->str, "ModelEvidence") == 0) { for (ufp = uop->data; ufp != NULL; ufp = ufp->next) { oip = ufp->label; if (oip == NULL) continue; if (StringCmp(oip->str, "Contig Name") == 0) { name = (CharPtr) ufp->data.ptrvalue; } else if (StringCmp(oip->str, "Method") == 0) { method = (CharPtr) ufp->data.ptrvalue; } } } } } sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &dcontext); } if (name == NULL || method == NULL) return NULL; str = MemNew (StringLen (reftxt5) + StringLen (reftxt6) + StringLen (reftxt7) + StringLen (reftxt8) + StringLen (name) + StringLen (method) + 10); if (str == NULL) return NULL; if (method != NULL) { sprintf (str, "%s %s %s %s %s.%s", reftxt5, name, reftxt6, reftxt7, method, reftxt8); } else { sprintf (str, "%s %s %s.%s", reftxt5, name, reftxt6, reftxt8); } return str; } static CharPtr reftxt9 = "GENOME ANNOTATION REFSEQ: NCBI contigs are derived from assembled genomic sequence data. They may include both draft and finished sequence."; static CharPtr tpaString = "THIRD PARTY ANNOTATION DATABASE: This entry contains annotation of previously submitted data."; static void AddCommentBlock ( Asn2gbWorkPtr awp ) { IntAsn2gbJobPtr ajp; BioseqPtr bsp; Char buf [128]; CommentBlockPtr cbp = NULL; Boolean didRefTrack = FALSE; DbtagPtr dbt; SeqMgrDescContext dcontext; SeqMgrFeatContext fcontext; Boolean first = TRUE; CommentBlockPtr gsdbcbp = NULL; Int4 gsdbid = 0; SeqHistPtr hist; Boolean is_other = FALSE; MolInfoPtr mip; BioseqPtr parent; SeqDescrPtr sdp; SeqFeatPtr sfp; SeqIdPtr sip; CharPtr str; TextSeqIdPtr tsip; UserObjectPtr uop; if (awp == NULL) return; ajp = awp->ajp; if (ajp == NULL) return; bsp = awp->bsp; if (bsp == NULL) return; for (sip = bsp->id; sip != NULL; sip = sip->next) { if (sip->choice == SEQID_OTHER) { tsip = (TextSeqIdPtr) sip->data.ptrvalue; if (tsip != NULL) { is_other = TRUE; if (StringNCmp(tsip->accession, "NT", 2) == 0) { cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock)); if (cbp != NULL) { cbp->first = first; first = FALSE; if (cbp->first) { gb_StartPrint (awp->format, 0, 12, "COMMENT", 13, 5, 5, "CC", TRUE); } else { gb_StartPrint (awp->format, 0, 12, NULL, 13, 5, 5, "CC", FALSE); } gb_AddString (NULL, reftxt9, NULL, TRUE, FALSE, TILDE_EXPAND); cbp->string = gb_MergeString (TRUE); } } else if (StringNCmp(tsip->accession, "XP_", 3) == 0 || StringNCmp(tsip->accession, "XM_", 3) == 0) { str = GetAnnotationComment (bsp); if (str != NULL) { cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock)); if (cbp != NULL) { cbp->first = first; first = FALSE; if (cbp->first) { gb_StartPrint (awp->format, 0, 12, "COMMENT", 13, 5, 5, "CC", TRUE); } else { gb_StartPrint (awp->format, 0, 12, NULL, 13, 5, 5, "CC", FALSE); } gb_AddString (NULL, str, NULL, TRUE, FALSE, TILDE_EXPAND); cbp->string = gb_MergeString (TRUE); } } } } } else if (sip->choice == SEQID_TPG || sip->choice == SEQID_TPE || sip->choice == SEQID_TPD) { cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock)); if (cbp != NULL) { cbp->first = first; first = FALSE; if (cbp->first) { gb_StartPrint (awp->format, 0, 12, "COMMENT", 13, 5, 5, "CC", TRUE); } else { gb_StartPrint (awp->format, 0, 12, NULL, 13, 5, 5, "CC", FALSE); } gb_AddString (NULL, tpaString, NULL, TRUE, FALSE, TILDE_EXPAND); cbp->string = gb_MergeString (TRUE); } } else if (sip->choice == SEQID_GENERAL) { dbt = (DbtagPtr) sip->data.ptrvalue; /* show GSDB sequence identifier */ if (dbt != NULL && StringCmp (dbt->db, "GSDB") == 0 && dbt->tag != NULL) { gsdbcbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock)); if (gsdbcbp != NULL) { gsdbcbp->first = first; /* string will be created after we know if there are additional comments */ gsdbid = dbt->tag->id; first = FALSE; } } } } /* RefSeq results in allocated comment string */ sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &dcontext); while (sdp != NULL) { uop = (UserObjectPtr) sdp->data.ptrvalue; if (uop != NULL) { if (! ajp->flags.hideBankItComment) { str = GetStrForBankit (uop); if (str != NULL) { cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock)); if (cbp != NULL) { cbp->entityID = dcontext.entityID; cbp->itemID = dcontext.itemID; cbp->itemtype = OBJ_SEQDESC; cbp->first = first; first = FALSE; if (cbp->first) { gb_StartPrint (awp->format, 0, 12, "COMMENT", 13, 5, 5, "CC", TRUE); } else { gb_StartPrint (awp->format, 0, 12, NULL, 13, 5, 5, "CC", FALSE); } gb_AddString (NULL, str, NULL, TRUE, FALSE, TILDE_EXPAND); cbp->string = gb_MergeString (TRUE); } MemFree (str); } } if (! didRefTrack) { str = GetStrForRefTrack (uop); if (str != NULL) { cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock)); if (cbp != NULL) { cbp->entityID = dcontext.entityID; cbp->itemID = dcontext.itemID; cbp->itemtype = OBJ_SEQDESC; cbp->first = first; first = FALSE; if (cbp->first) { gb_StartPrint (awp->format, 0, 12, "COMMENT", 13, 5, 5, "CC", TRUE); } else { gb_StartPrint (awp->format, 0, 12, NULL, 13, 5, 5, "CC", FALSE); } gb_AddString (NULL, str, NULL, TRUE, FALSE, TILDE_EXPAND); cbp->string = gb_MergeString (TRUE); } MemFree (str); didRefTrack = TRUE; } } } sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &dcontext); } /* Seq-hist results in allocated comment string */ hist = bsp->hist; if (hist != NULL) { if (hist->replaced_by_ids != NULL && hist->replaced_by_date != NULL) { cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock)); if (cbp != NULL) { cbp->first = first; first = FALSE; if (cbp->first) { gb_StartPrint (awp->format, 0, 12, "COMMENT", 13, 5, 5, "CC", TRUE); } else { gb_StartPrint (awp->format, 0, 12, NULL, 13, 5, 5, "CC", FALSE); } AddHistCommentString ("[WARNING] On", "this sequence was replaced by a newer version", hist->replaced_by_date, hist->replaced_by_ids); cbp->string = gb_MergeString (TRUE); } } if (hist->replace_ids != NULL && hist->replace_date != NULL) { cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock)); if (cbp != NULL) { cbp->first = first; first = FALSE; if (cbp->first) { gb_StartPrint (awp->format, 0, 12, "COMMENT", 13, 5, 5, "CC", TRUE); } else { gb_StartPrint (awp->format, 0, 12, NULL, 13, 5, 5, "CC", FALSE); } AddHistCommentString ("On", "this sequence version replaced", hist->replace_date, hist->replace_ids); cbp->string = gb_MergeString (TRUE); } } } /* just save IDs for comment, maploc, and region descriptors */ sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_comment, &dcontext); while (sdp != NULL) { if (sdp->data.ptrvalue != NULL) { cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock)); if (cbp != NULL) { cbp->entityID = dcontext.entityID; cbp->itemID = dcontext.itemID; cbp->itemtype = OBJ_SEQDESC; cbp->first = first; first = FALSE; } } sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_comment, &dcontext); } sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_maploc, &dcontext); while (sdp != NULL) { cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock)); if (cbp != NULL) { cbp->entityID = dcontext.entityID; cbp->itemID = dcontext.itemID; cbp->itemtype = OBJ_SEQDESC; cbp->first = first; first = FALSE; } sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_maploc, &dcontext); } sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_region, &dcontext); while (sdp != NULL) { if (sdp->data.ptrvalue != NULL) { cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock)); if (cbp != NULL) { cbp->entityID = dcontext.entityID; cbp->itemID = dcontext.itemID; cbp->itemtype = OBJ_SEQDESC; cbp->first = first; first = FALSE; } } sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_region, &dcontext); } /* HTGS results in allocated comment string */ sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext); if (sdp != NULL) { mip = (MolInfoPtr) sdp->data.ptrvalue; if (mip != NULL) { if (mip->completeness != 0 && is_other) { str = GetMolInfoCommentString (bsp, mip); if (str != NULL) { cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock)); if (cbp != NULL) { cbp->entityID = dcontext.entityID; cbp->itemID = dcontext.itemID; cbp->itemtype = OBJ_SEQDESC; cbp->first = first; first = FALSE; if (cbp->first) { gb_StartPrint (awp->format, 0, 12, "COMMENT", 13, 5, 5, "CC", TRUE); } else { gb_StartPrint (awp->format, 0, 12, NULL, 13, 5, 5, "CC", FALSE); } gb_AddString (NULL, str, NULL, TRUE, FALSE, TILDE_EXPAND); cbp->string = gb_MergeString (TRUE); } } } if (mip->tech == MI_TECH_htgs_0 || mip->tech == MI_TECH_htgs_1 || mip->tech == MI_TECH_htgs_2) { cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock)); if (cbp != NULL) { /* cbp->entityID = dcontext.entityID; cbp->itemID = dcontext.itemID; cbp->itemtype = OBJ_SEQDESC; */ cbp->first = first; first = FALSE; if (cbp->first) { gb_StartPrint (awp->format, 0, 12, "COMMENT", 13, 5, 5, "CC", TRUE); } else { gb_StartPrint (awp->format, 0, 12, NULL, 13, 5, 5, "CC", FALSE); } AddHTGSCommentString (bsp, mip); cbp->string = gb_MergeString (TRUE); } } else { str = StringForSeqTech (mip->tech); if (! StringHasNoText (str)) { cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock)); if (cbp != NULL) { /* cbp->entityID = dcontext.entityID; cbp->itemID = dcontext.itemID; cbp->itemtype = OBJ_SEQDESC; */ cbp->first = first; first = FALSE; if (cbp->first) { gb_StartPrint (awp->format, 0, 12, "COMMENT", 13, 5, 5, "CC", TRUE); } else { gb_StartPrint (awp->format, 0, 12, NULL, 13, 5, 5, "CC", FALSE); } gb_AddString ("Method: ", str, NULL, TRUE, FALSE, TILDE_EXPAND); cbp->string = gb_MergeString (TRUE); } } } } } /* add comment features that are full length on appropriate segment */ parent = awp->parent; if (parent == NULL) return; sfp = SeqMgrGetNextFeature (parent, NULL, SEQFEAT_COMMENT, 0, &fcontext); while (sfp != NULL) { if (fcontext.left == awp->from && fcontext.right == awp->to) { cbp = (CommentBlockPtr) Asn2gbAddBlock (awp, COMMENT_BLOCK, sizeof (CommentBlock)); if (cbp != NULL) { cbp->entityID = fcontext.entityID; cbp->itemID = fcontext.itemID; cbp->itemtype = OBJ_SEQFEAT; cbp->first = first; first = FALSE; } } sfp = SeqMgrGetNextFeature (parent, sfp, SEQFEAT_COMMENT, 0, &fcontext); } if (gsdbcbp != NULL) { /* if there were no subsequent comments, do not add period after GSDB id */ if (cbp == NULL) { sprintf (buf, "GSDB:S:%ld", (long) gsdbid); } else { sprintf (buf, "GSDB:S:%ld.", (long) gsdbid); } if (gsdbcbp->first) { gb_StartPrint (awp->format, 0, 12, "COMMENT", 13, 5, 5, "CC", TRUE); } else { gb_StartPrint (awp->format, 0, 12, NULL, 13, 5, 5, "CC", FALSE); } /* CheckEndPunctuation, ConvertDoubleQuotes, and ExpandTildes already taken into account */ ff_AddString (buf); gsdbcbp->string = gb_MergeString (TRUE); } } static void AddFeatHeaderBlock ( Asn2gbWorkPtr awp ) { BaseBlockPtr bbp; if (awp == NULL) return; bbp = Asn2gbAddBlock (awp, FEATHEADER_BLOCK, sizeof (BaseBlock)); if (bbp == NULL) return; if (awp->format == FTABLE_FMT) return; gb_StartPrint (awp->format, 0, 12, "FEATURES", 22, 5, 0, "FH", TRUE); if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) { ff_AddString ("Key"); TabToColumn (22); } gb_AddString (NULL, "Location/Qualifiers", NULL, FALSE, FALSE, TILDE_TO_SPACES); if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) { NewContLine(); } bbp->string = gb_MergeString (TRUE); } static Uint2 ComputeSourceHash ( CharPtr key, Uint2 start ) { Uint4 h; Uint2 M; Uint2 S; if (key == NULL) return start; M = 101; /* prime key */ S = 256; /* size of alphabet */ for (h = start; *key != '\0'; key++) { h = (S * h + *key) % M; } return (Uint2) h; } static BaseBlockPtr AddSource ( Asn2gbWorkPtr awp, ValNodePtr PNTR head, BioSourcePtr biop, CharPtr comment ) { BaseBlockPtr bbp; DbtagPtr dbt; Uint2 hash; Int2 idx; IntSrcBlockPtr isp; ObjectIdPtr oip; OrgModPtr omp; OrgNamePtr onp; OrgRefPtr orp; SubSourcePtr ssp; CharPtr str; Uint1 subtype; Char tmp [16]; ValNodePtr vnp; if (awp == NULL || head == NULL || biop == NULL) return NULL; bbp = (BaseBlockPtr) MemNew (sizeof (IntSrcBlock)); if (bbp == NULL) return NULL; bbp->blocktype = SOURCEFEAT_BLOCK; bbp->section = awp->currsection; ValNodeAddPointer (head, 0, bbp); isp = (IntSrcBlockPtr) bbp; isp->biop = biop; isp->is_focus = biop->is_focus; if (biop->origin == 5) { isp->is_synthetic = TRUE; } orp = biop->org; if (orp == NULL) return bbp; isp->orghash = ComputeSourceHash (orp->taxname, 0); isp->taxname = orp->taxname; hash = 0; onp = orp->orgname; if (onp != NULL) { if (StringICmp (onp->div, "SYN") == 0) { isp->is_synthetic = TRUE; } isp->omp = onp->mod; for (omp = onp->mod; omp != NULL; omp = omp->next) { subtype = omp->subtype; if (subtype == 254) { subtype = 24; } else if (subtype == 255) { subtype = 25; } if (subtype < 35) { idx = orgModToSourceIdx [subtype]; if (idx > 0 && idx < ASN2GNBK_TOTAL_SOURCE) { str = asn2gnbk_source_quals [idx].name; hash = ComputeSourceHash (str, hash); hash = ComputeSourceHash (omp->subname, hash); } } } } if (comment != NULL) { hash = ComputeSourceHash ("note", hash); hash = ComputeSourceHash (comment, hash); } isp->modhash = hash; hash = 0; for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next) { subtype = ssp->subtype; if (subtype == 255) { subtype = 29; } if (subtype < 30) { idx = subSourceToSourceIdx [subtype]; if (idx > 0 && idx < ASN2GNBK_TOTAL_SOURCE) { str = asn2gnbk_source_quals [idx].name; hash = ComputeSourceHash (str, hash); hash = ComputeSourceHash (ssp->name, hash); } } } isp->subhash = hash; isp->ssp = biop->subtype; hash = 0; for (vnp = orp->db; vnp != NULL; vnp = vnp->next) { dbt = (DbtagPtr) vnp->data.ptrvalue; if (dbt != NULL) { hash = ComputeSourceHash (dbt->db, hash); oip = dbt->tag; if (oip != NULL) { if (oip->str != NULL) { hash = ComputeSourceHash (oip->str, hash); } else { sprintf (tmp, "%ld", (long) oip->id); hash = ComputeSourceHash (tmp, hash); } } } } isp->xrfhash = hash; isp->vnp = orp->db; return bbp; } static int LIBCALLBACK SortSourcesByHash ( VoidPtr ptr1, VoidPtr ptr2 ) { Uint4 diff; IntSrcBlockPtr isp1; IntSrcBlockPtr isp2; ValNodePtr vnp1; ValNodePtr vnp2; if (ptr1 == NULL || ptr2 == NULL) return 0; vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 == NULL || vnp2 == NULL) return 0; isp1 = (IntSrcBlockPtr) vnp1->data.ptrvalue; isp2 = (IntSrcBlockPtr) vnp2->data.ptrvalue; if (isp1 == NULL || isp2 == NULL) return 0; if (isp1->is_focus && (! isp2->is_focus)) return -1; if (isp2->is_focus && (! isp1->is_focus)) return 1; diff = isp1->orghash - isp2->orghash; if (diff > 0) return -1; if (diff < 0) return 1; diff = isp1->xrfhash - isp2->xrfhash; if (diff > 0) return -1; if (diff < 0) return 1; /* sort so that sources with modifiers come first */ diff = isp1->modhash - isp2->modhash; if (diff > 0) return -1; if (diff < 0) return 1; diff = isp1->subhash - isp2->subhash; if (diff > 0) return -1; if (diff < 0) return 1; /* if all hashes are equal, descriptor comes first */ if (isp1->is_descriptor && (! isp2->is_descriptor)) { return -1; } else if (isp2->is_descriptor && (! isp1->is_descriptor)) { return 1; } return 0; } static int LIBCALLBACK SortSourcesByPos ( VoidPtr ptr1, VoidPtr ptr2 ) { IntSrcBlockPtr isp1; IntSrcBlockPtr isp2; ValNodePtr vnp1; ValNodePtr vnp2; if (ptr1 == NULL || ptr2 == NULL) return 0; vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 == NULL || vnp2 == NULL) return 0; isp1 = (IntSrcBlockPtr) vnp1->data.ptrvalue; isp2 = (IntSrcBlockPtr) vnp2->data.ptrvalue; if (isp1 == NULL || isp2 == NULL) return 0; /* descriptor always goes first */ if (isp1->is_descriptor && (! isp2->is_descriptor)) { return -1; } else if (isp2->is_descriptor && (! isp1->is_descriptor)) { return 1; } /* feature with smallest left extreme is first */ if (isp1->left > isp2->left) { return 1; } else if (isp1->left < isp2->left) { return -1; } /* if same left extreme, shortest source feature is first just for flatfile */ if (isp1->right > isp2->right) { return 1; } else if (isp1->right < isp2->right) { return -1; } return 0; } /* */ /* s_isFuzzyLoc () -- Determines is a location has fuzzy coordinates */ /* */ static Boolean s_isFuzzyLoc ( SeqLocPtr pLocation ) { SeqIntPtr pIntLocation; if (pLocation == NULL) return FALSE; if (pLocation->choice != SEQLOC_INT) return FALSE; if (pLocation->data.ptrvalue == NULL) return FALSE; pIntLocation = (SeqIntPtr) pLocation->data.ptrvalue; if ((pIntLocation->if_from != NULL) && (pIntLocation->if_from->choice == 2)) return TRUE; if ((pIntLocation->if_to != NULL) && (pIntLocation->if_to->choice == 2)) return TRUE; return FALSE; } static void GetSourcesOnBioseq ( Asn2gbWorkPtr awp, BioseqPtr target, BioseqPtr bsp, Int4 from, Int4 to ) { BaseBlockPtr bbp; BioSourcePtr biop; SeqMgrDescContext dcontext; SeqMgrFeatContext fcontext; Boolean hasNulls; Boolean loop = FALSE; Int2 idx; IntSrcBlockPtr isp; Int4Ptr ivals; Boolean noLeft; Boolean noRight; Int2 numivals; Boolean okay; SeqDescrPtr sdp; SeqFeatPtr sfp; SeqInt sint; SeqIdPtr sip; Int4 start; Int4 stop; ValNode vn; ValNodePtr vnp; if (awp == NULL || target == NULL || bsp == NULL) return; /* full length loc for descriptors */ sint.from = 0; sint.to = bsp->length - 1; sint.strand = Seq_strand_plus; sint.id = SeqIdStripLocus (SeqIdDup (SeqIdFindBest (bsp->id, 0))); sint.if_from = NULL; sint.if_to = NULL; vn.choice = SEQLOC_INT; vn.data.ptrvalue = (Pointer) &sint; vn.next = NULL; /* if SWISS-PROT, may have multiple source descriptors */ if (ISA_aa (bsp->mol)) { for (sip = bsp->id; sip != NULL; sip = sip->next) { if (sip->choice == SEQID_SWISSPROT) { loop = TRUE; } } } sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext); while (sdp != NULL) { /* check if descriptor on part already added on segmented bioseq */ okay = TRUE; for (vnp = awp->srchead; vnp != NULL && okay; vnp = vnp->next) { bbp = (BaseBlockPtr) vnp->data.ptrvalue; if (bbp != NULL) { if (bbp->entityID == dcontext.entityID && bbp->itemID == dcontext.itemID && bbp->itemtype == OBJ_SEQDESC) { okay = FALSE; } } } if (okay) { biop = (BioSourcePtr) sdp->data.ptrvalue; bbp = AddSource (awp, &(awp->srchead), biop, NULL); if (bbp != NULL) { bbp->entityID = dcontext.entityID; bbp->itemID = dcontext.itemID; bbp->itemtype = OBJ_SEQDESC; isp = (IntSrcBlockPtr) bbp; isp->loc = SeqLocMerge (target, &vn, NULL, FALSE, TRUE, FALSE); isp->left = 0; isp->right = bsp->length - 1; isp->is_descriptor = TRUE; } } /* if SWISS-PROT, loop through multiple source descriptors */ if (loop) { sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_source, &dcontext); } else { sdp = NULL; } } SeqIdFree (sint.id); if ((! awp->contig) || awp->showconsource) { /* features are indexed on parent if segmented */ bsp = awp->parent; sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_BIOSRC, 0, &fcontext); while (sfp != NULL) { ivals = fcontext.ivals; numivals = fcontext.numivals; if (ivals != NULL && numivals > 0) { idx = (numivals - 1) * 2; start = ivals [idx]; stop = ivals [idx + 1]; if (stop >= from && stop <= to) { biop = (BioSourcePtr) sfp->data.value.ptrvalue; bbp = AddSource (awp, &(awp->srchead), biop, sfp->comment); if (bbp != NULL) { bbp->entityID = fcontext.entityID; bbp->itemID = fcontext.itemID; bbp->itemtype = OBJ_SEQFEAT; isp = (IntSrcBlockPtr) bbp; if (sfp->location != NULL && sfp->location->choice == SEQLOC_PNT) { isp->loc = AsnIoMemCopy ((Pointer) sfp->location, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite); } else if (s_isFuzzyLoc (sfp->location)) { isp->loc = AsnIoMemCopy ((Pointer) sfp->location, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite); } else if (SeqLocId(sfp->location) == NULL) { isp->loc = AsnIoMemCopy ((Pointer) sfp->location, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite); } else { CheckSeqLocForPartial (sfp->location, &noLeft, &noRight); hasNulls = LocationHasNullsBetween (sfp->location); isp->loc = SeqLocMerge (target, sfp->location, NULL, FALSE, TRUE, hasNulls); SetSeqLocPartial (isp->loc, noLeft, noRight); } isp->left = fcontext.left; isp->right = fcontext.right; isp->comment = sfp->comment; } } } sfp = SeqMgrGetNextFeature (bsp, sfp, SEQFEAT_BIOSRC, 0, &fcontext); } } } static Boolean LIBCALLBACK GetSourcesOnSeg ( SeqLocPtr slp, SeqMgrSegmentContextPtr context ) { Asn2gbWorkPtr awp; BioseqPtr bsp = NULL; Uint2 entityID; Int4 from; SeqLocPtr loc; SeqIdPtr sip; Int4 to; if (slp == NULL || context == NULL) return FALSE; awp = (Asn2gbWorkPtr) context->userdata; from = context->cumOffset; to = from + context->to - context->from; sip = SeqLocId (slp); if (sip == NULL) { loc = SeqLocFindNext (slp, NULL); if (loc != NULL) { sip = SeqLocId (loc); } } if (sip == NULL) return TRUE; /* may remote fetch genome component if not already in memory */ bsp = BioseqLockById (sip); if (bsp == NULL) return TRUE; entityID = ObjMgrGetEntityIDForPointer (bsp); if (entityID != awp->entityID) { /* if segment not packaged in record, may need to feature index it */ if (SeqMgrFeaturesAreIndexed (entityID) == 0) { SeqMgrIndexFeatures (entityID, NULL); } /* collect features indexed on the remote bioseq */ from = 0; to = bsp->length - 1; } GetSourcesOnBioseq (awp, awp->target, bsp, from, to); BioseqUnlock (bsp); return TRUE; } /* isIdenticalSource() -- Checks to see if two sources are identical */ /* by comparing the actual values in the */ /* fields. This only gets called if the two */ /* sources hashed the same -- it's a double- */ /* check since two non-identical things will */ /* occassionally hash to the same value. */ static Boolean isIdenticalSource (IntSrcBlockPtr isp1, IntSrcBlockPtr isp2) { OrgModPtr omp1; OrgModPtr omp2; SubSourcePtr ssp1; SubSourcePtr ssp2; ValNodePtr vnp1; ValNodePtr vnp2; ObjectIdPtr oip1; ObjectIdPtr oip2; DbtagPtr dbt1; DbtagPtr dbt2; if (isp1->is_focus != isp2->is_focus) return FALSE; /* Compare the taxonomy names */ if (StringICmp(isp1->taxname,isp2->taxname) != 0) return FALSE; /* Compare the comment */ if (StringICmp(isp1->comment,isp2->comment) != 0) return FALSE; /* Compare the org mods */ omp1 = isp1->omp; omp2 = isp2->omp; while (omp1 != NULL && omp2 != NULL) { if (omp1->subtype != omp2->subtype) return FALSE; if (StringICmp (omp1->subname, omp2->subname) != 0) return FALSE; omp1 = omp1->next; omp2 = omp2->next; } if (omp1 != NULL || omp2 != NULL) return FALSE; /* Compare the subtypes */ ssp1 = isp1->ssp; ssp2 = isp2->ssp; while (ssp1 != NULL && ssp2 != NULL) { if (ssp1->subtype != ssp2->subtype) return FALSE; if (StringICmp(ssp1->name,ssp2->name) != 0) return FALSE; ssp1 = ssp1->next; ssp2 = ssp2->next; } if (ssp1 != NULL || ssp2 != NULL) return FALSE; /* Compare the DB tags */ vnp1 = isp1->vnp; vnp2 = isp2->vnp; while (vnp1 != NULL && vnp2 != NULL) { dbt1 = (DbtagPtr) vnp1->data.ptrvalue; dbt2 = (DbtagPtr) vnp2->data.ptrvalue; if ((dbt1 != NULL) && (dbt2 != NULL)) { if (dbt1->db != dbt2->db) return FALSE; oip1 = dbt1->tag; oip2 = dbt2->tag; if ((oip1 != NULL) && (oip2 != NULL)) { if (oip1->str != NULL) { if (StringICmp(oip1->str, oip2->str) != 0) return FALSE; } else { if (oip1->id != oip2->id) return FALSE; } } else if (oip1 != NULL) return FALSE; else if (oip2 != NULL) return FALSE; } else if (dbt1 != NULL) return FALSE; else if (dbt2 != NULL) return FALSE; vnp1 = vnp1->next; vnp2 = vnp2->next; } if (vnp1 != NULL || vnp2 != NULL) return FALSE; /* If it passed all checks, then they */ /* are the same, so return true. */ return TRUE; } static void AddSourceFeatBlock ( Asn2gbWorkPtr awp ) { IntAsn2gbJobPtr ajp; BaseBlockPtr bbp; BioseqPtr bsp; SeqFeatPtr cds; SeqMgrFeatContext context; BioseqPtr dna; SeqLocPtr duploc; Boolean excise; ValNodePtr head = NULL; IntSrcBlockPtr isp; IntSrcBlockPtr lastisp; IntSrcBlockPtr descrIsp; ValNodePtr next; ValNodePtr PNTR prev; SeqInt sint; SeqLocPtr slp; CharPtr str; BioseqPtr target; ValNode vn; ValNodePtr vnp; CharPtr wwwbuf; Boolean descHasFocus = FALSE; if (awp == NULL) return; ajp = awp->ajp; if (ajp == NULL) return; bsp = awp->bsp; if (bsp == NULL) return; /* collect biosources on bioseq */ awp->srchead = NULL; GetSourcesOnBioseq (awp, bsp, bsp, awp->from, awp->to); target = bsp; if (bsp->repr == Seq_repr_seg) { /* collect biosources on remote segments in MASTER_STYLE */ SeqMgrExploreSegments (bsp, (Pointer) awp, GetSourcesOnSeg); target = awp->target; } if (awp->srchead == NULL && ISA_aa (bsp->mol)) { /* if protein with no sources, get sources applicable to DNA location of CDS */ cds = SeqMgrGetCDSgivenProduct (bsp, &context); if (cds != NULL) { dna = BioseqFindFromSeqLoc (cds->location); if (dna != NULL) { GetSourcesOnBioseq (awp, dna, dna, context.left, context.right); target = dna; } } } head = awp->srchead; awp->srchead = NULL; if (head == NULL) { sint.from = 0; sint.to = bsp->length - 1; sint.strand = Seq_strand_plus; sint.id = SeqIdStripLocus (SeqIdDup (SeqIdFindBest (bsp->id, 0))); sint.if_from = NULL; sint.if_to = NULL; vn.choice = SEQLOC_INT; vn.data.ptrvalue = (Pointer) &sint; vn.next = NULL; gb_StartPrint (awp->format, 5, 21, NULL, 0, 5, 21, "FT", FALSE); ff_AddString ("source"); TabToColumn (22); str = FlatLoc (bsp, &vn, (Boolean) (awp->style == MASTER_STYLE)); if (get_www ()) { wwwbuf = www_featloc (str); ff_AddString (wwwbuf); MemFree (wwwbuf); } else { ff_AddString (str); } MemFree (str); if (ajp->flags.needOrganismQual) { NewContLine (); gb_AddString ("/organism=\"", "unknown", "\"", FALSE, TRUE, TILDE_TO_SPACES); #ifdef ASN2GNBK_PRINT_UNKNOWN_ORG } else { NewContLine (); gb_AddString ("/organism=\"", "unknown", "\"", FALSE, TRUE, TILDE_TO_SPACES); #endif } str = ff_print_string_mem (gb_MergeString (TRUE)); bbp = (BaseBlockPtr) Asn2gbAddBlock (awp, SOURCEFEAT_BLOCK, sizeof (IntSrcBlock)); if (bbp != NULL) { bbp->section = awp->currsection; bbp->string = str; } return; } /* sort by hash values */ head = SortValNode (head, SortSourcesByHash); /* unique sources, excise duplicates from list */ prev = &(head); vnp = head; lastisp = NULL; while (vnp != NULL) { excise = FALSE; next = vnp->next; isp = (IntSrcBlockPtr) vnp->data.ptrvalue; if (isp->is_descriptor && isp->is_focus) descHasFocus = TRUE; if (lastisp != NULL) { if (isp != NULL) { if (lastisp->is_focus == isp->is_focus && lastisp->orghash == isp->orghash && lastisp->xrfhash == isp->xrfhash) { /* check for identical modifiers */ if (lastisp->modhash == isp->modhash && lastisp->subhash == isp->subhash) { excise = isIdenticalSource (isp, lastisp); /* or modifiers only in lastisp (e.g., on part bioseq) */ } else if (isp->modhash == 0 && isp->subhash == 0) { excise = isIdenticalSource (isp, lastisp); } } } } if (excise) { *prev = vnp->next; vnp->next = NULL; /* combine locations of duplicate sources */ if (lastisp != NULL) { slp = SeqLocMerge (target, lastisp->loc, isp->loc, FALSE, TRUE, FALSE); lastisp->loc = SeqLocFree (lastisp->loc); lastisp->loc = slp; lastisp->left = MIN (lastisp->left,isp->left); lastisp->right = MAX (lastisp->right, isp->right); } /* and remove duplicate source */ SeqLocFree (isp->loc); MemFree (isp); ValNodeFree (vnp); } else { prev = &(vnp->next); lastisp = isp; } vnp = next; } /* Sort again, by location this time */ head = SortValNode (head, SortSourcesByPos); /* If the descriptor has a focus, then subtract */ /* out all the other source locations. */ descrIsp = (IntSrcBlockPtr) head->data.ptrvalue; /* Sorted 1st by now */ if ((descHasFocus) && (! descrIsp->is_synthetic)) { vnp = head; duploc = AsnIoMemCopy ((Pointer) descrIsp->loc, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite); vnp = vnp->next; while (vnp != NULL) { isp = (IntSrcBlockPtr) vnp->data.ptrvalue; if (SeqLocAinB (descrIsp->loc, isp->loc) >= 0) { vnp = NULL; /* break the chain */ descrIsp->loc = SeqLocFree (descrIsp->loc); descrIsp->loc = duploc; duploc = NULL; } else { SeqLocSubtract (descrIsp->loc, isp->loc); vnp = vnp->next; } } descrIsp->left = SeqLocStart (descrIsp->loc); descrIsp->right = SeqLocStop (descrIsp->loc); SeqLocFree (duploc); } /* finally link into blocks for current section */ ValNodeLink (&(awp->lastblock), head); vnp = awp->lastblock; if (vnp == NULL) return; while (vnp->next != NULL) { vnp = vnp->next; } awp->lastblock = vnp; if (awp->blockList == NULL) { awp->blockList = vnp; } } static void GetFeatsOnCdsProduct ( SeqFeatPtr sfp, BioseqPtr bsp, Asn2gbWorkPtr awp ) { FeatBlockPtr fbp; IntFeatBlockPtr ifp; Int4 lastleft; Int4 lastright; SeqAnnotPtr lastsap; SeqFeatPtr lastsfp; SeqMgrFeatContext pcontext; SeqFeatPtr prt; Boolean suppress; if (sfp == NULL || awp == NULL) return; if (bsp == NULL || (! ISA_aa (bsp->mol))) return; /* explore mat_peptides, sites, etc. */ lastsfp = NULL; lastsap = NULL; lastleft = 0; lastright = 0; prt = SeqMgrGetNextFeature (bsp, NULL, 0, 0, &pcontext); while (prt != NULL) { if (pcontext.featdeftype == FEATDEF_REGION || pcontext.featdeftype == FEATDEF_SITE || pcontext.featdeftype == FEATDEF_mat_peptide_aa || pcontext.featdeftype == FEATDEF_sig_peptide_aa || pcontext.featdeftype == FEATDEF_transit_peptide_aa) { if (pcontext.dnaStop >= awp->from && pcontext.dnaStop <= awp->to) { /* suppress duplicate features (on protein) */ suppress = FALSE; if (lastsfp != NULL && lastsap != NULL) { if (lastsfp->idx.subtype == prt->idx.subtype && lastleft == pcontext.left && lastright == pcontext.right) { if (lastsap == pcontext.sap || (lastsap->desc == NULL && pcontext.sap->desc == NULL)) { if (AsnIoMemComp (lastsfp, prt, (AsnWriteFunc) SeqFeatAsnWrite)) { suppress = TRUE; } } } } if (! suppress) { fbp = (FeatBlockPtr) Asn2gbAddBlock (awp, FEATURE_BLOCK, sizeof (IntFeatBlock)); if (fbp != NULL) { fbp->entityID = pcontext.entityID; fbp->itemID = pcontext.itemID; fbp->itemtype = OBJ_SEQFEAT; fbp->featdeftype = pcontext.featdeftype; ifp = (IntFeatBlockPtr) fbp; ifp->mapToNuc = TRUE; ifp->mapToProt = FALSE; ifp->mapToGen = FALSE; ifp->mapToMrna = FALSE; ifp->firstfeat = awp->firstfeat; awp->firstfeat = FALSE; } } lastsfp = prt; lastsap = pcontext.sap; lastleft = pcontext.left; lastright = pcontext.right; } } prt = SeqMgrGetNextFeature (bsp, prt, 0, 0, &pcontext); } } static Boolean NotEMBL ( BioseqPtr bsp ) { SeqIdPtr sip; if (bsp == NULL) return TRUE; for (sip = bsp->id; sip != NULL; sip = sip->next) { if (sip->choice == SEQID_EMBL) return FALSE; } return TRUE; } static Boolean LIBCALLBACK GetFeatsOnBioseq ( SeqFeatPtr sfp, SeqMgrFeatContextPtr fcontext ) { IntAsn2gbJobPtr ajp; Asn2gbSectPtr asp; Asn2gbWorkPtr awp; BioseqPtr bsp; SeqFeatPtr cds; SeqMgrFeatContext cdscontext; SeqMgrDescContext dcontext; FeatBlockPtr fbp; SeqLocPtr firstslp; GBQualPtr gbq; SeqFeatPtr gene; GeneRefPtr grp; Boolean juststop = FALSE; IntCdsBlockPtr icp; Int2 idx; IntFeatBlockPtr ifp; Int4Ptr ivals; Int2 j; SeqAnnotPtr lastsap; SeqFeatPtr lastsfp; SeqLocPtr lastslp; Int2 numivals; Boolean okay; SeqEntryPtr oldscope; BioseqPtr parent; Boolean partial5; Boolean partial3; ValNodePtr ppr; PubdescPtr pdp; Boolean pseudo = FALSE; SeqDescrPtr sdp; SeqEntryPtr sep; SeqIdPtr sip; SeqLocPtr slp; Int4 start; Int4 stop; ValNodePtr vnp; if (sfp == NULL || fcontext == NULL) return FALSE; awp = (Asn2gbWorkPtr) fcontext->userdata; if (awp == NULL) return FALSE; ajp = awp->ajp; if (ajp == NULL) return FALSE; asp = awp->asp; if (asp == NULL) return FALSE; bsp = asp->bsp; if (bsp == NULL) return FALSE; if (fcontext->featdeftype == FEATDEF_PUB || fcontext->featdeftype == FEATDEF_NON_STD_RESIDUE || fcontext->featdeftype == FEATDEF_BIOSRC || fcontext->featdeftype == FEATDEF_RSITE || fcontext->featdeftype == FEATDEF_SEQ) return TRUE; if (ajp->flags.validateFeats && (fcontext->featdeftype == FEATDEF_BAD || fcontext->featdeftype == FEATDEF_virion)) { return TRUE; } if (ISA_na (bsp->mol) && fcontext->featdeftype == FEATDEF_HET) return TRUE; /* DDBJ does not want to show gene features */ if (fcontext->seqfeattype == SEQFEAT_GENE && awp->hideGeneFeats) return TRUE; /* suppress comment features that are full length */ if (fcontext->seqfeattype == SEQFEAT_COMMENT && fcontext->left == awp->from && fcontext->right == awp->to) return TRUE; ivals = fcontext->ivals; numivals = fcontext->numivals; /* check to see if last interval is on this awp->from - awp->to range */ if (ivals != NULL && numivals > 0) { idx = (numivals - 1) * 2; start = ivals [idx]; stop = ivals [idx + 1]; if (stop < awp->from || stop > awp->to) { /* may need to map sig_peptide on a different segment */ if (fcontext->seqfeattype == SEQFEAT_CDREGION) { sip = SeqLocId (sfp->product); bsp = BioseqFind (sip); GetFeatsOnCdsProduct (sfp, bsp, awp); } return TRUE; } else if (fcontext->farloc && NotEMBL (awp->bsp)) { /* last interval may not have been mapped to bioseq if far */ firstslp = NULL; lastslp = NULL; slp = SeqLocFindNext (sfp->location, NULL); while (slp != NULL) { if (slp->choice != SEQLOC_NULL) { lastslp = slp; if (firstslp == NULL) { firstslp = slp; } } slp = SeqLocFindNext (sfp->location, slp); } /* !!! EMBL may have different desired behavior on where to map !!! */ if (firstslp != NULL && SeqLocStrand (firstslp) == Seq_strand_minus) { slp = firstslp; } else { slp = lastslp; } if (slp != NULL) { sip = SeqLocId (slp); if (sip != NULL) { bsp = BioseqFindCore (sip); if (bsp == NULL || (bsp != awp->parent && bsp != awp->bsp)) { return TRUE; } } } } } /* suppress duplicate features (on nucleotide) */ lastsfp = awp->lastsfp; lastsap = awp->lastsap; if (lastsfp != NULL && lastsap != NULL) { if (lastsfp->idx.subtype == sfp->idx.subtype && awp->lastleft == fcontext->left && awp->lastright == fcontext->right) { if (lastsap == fcontext->sap || (lastsap->desc == NULL && fcontext->sap->desc == NULL)) { if (AsnIoMemComp (lastsfp, sfp, (AsnWriteFunc) SeqFeatAsnWrite)) { return TRUE; } } } } /* if RELEASE_MODE, verify that features have all mandatory qualifiers */ if (ajp->flags.needRequiredQuals) { okay = FALSE; switch (fcontext->featdeftype) { case FEATDEF_CDS: if (ajp->flags.checkCDSproductID) { /* non-pseudo CDS must have /product */ if (sfp->pseudo) { pseudo = TRUE; } grp = SeqMgrGetGeneXref (sfp); if (grp == NULL) { sep = GetTopSeqEntryForEntityID (ajp->ajp.entityID); oldscope = SeqEntrySetScope (sep); gene = SeqMgrGetOverlappingGene (sfp->location, NULL); SeqEntrySetScope (oldscope); if (gene != NULL) { grp = (GeneRefPtr) gene->data.value.ptrvalue; if (gene->pseudo) { pseudo = TRUE; } } } if (grp != NULL && grp->pseudo) { pseudo = TRUE; } if (sfp->location != NULL) { if (CheckSeqLocForPartial (sfp->location, &partial5, &partial3)) { if (partial5 && (! partial3)) { if (SeqLocLen (sfp->location) <= 5) { juststop = TRUE; } } } } if (pseudo || juststop) { okay = TRUE; } else if (sfp->product != NULL) { sip = SeqLocId (sfp->product); if (sip != NULL && sip->choice == SEQID_GI && sip->data.intvalue > 0) { okay = TRUE; } } } else { okay = TRUE; } break; case FEATDEF_conflict: /* conflict requires a publication printable on the segment */ vnp = sfp->cit; if (vnp != NULL && asp->referenceArray != NULL) { for (ppr = vnp->data.ptrvalue; ppr != NULL; ppr = ppr->next) { j = MatchRef (ppr, asp->referenceArray, asp->numReferences); if (j > 0) { okay = TRUE; break; } } } break; case FEATDEF_GENE: /* gene requires /gene */ grp = (GeneRefPtr) sfp->data.value.ptrvalue; if (grp != NULL) { if (! StringHasNoText (grp->locus)) { okay = TRUE; } else if (! StringHasNoText (grp->desc)) { okay = TRUE; } else { vnp = grp->syn; if (vnp != NULL) { if (! StringHasNoText (vnp->data.ptrvalue)) { okay = TRUE; } } } } break; case FEATDEF_protein_bind: case FEATDEF_misc_binding: /* protein_bind or misc_binding require FTQUAL_bound_moiety */ gbq = sfp->qual; while (gbq != NULL) { if (StringICmp (gbq->qual, "bound_moiety") == 0 && (! StringHasNoText (gbq->val))) { okay = TRUE; break; } gbq = gbq->next; } break; case FEATDEF_modified_base: /* modified_base requires FTQUAL_mod_base */ gbq = sfp->qual; while (gbq != NULL) { if (StringICmp (gbq->qual, "mod_base") == 0 && (! StringHasNoText (gbq->val))) { okay = TRUE; break; } gbq = gbq->next; } break; default: if (fcontext->featdeftype >= FEATDEF_GENE && fcontext->featdeftype < FEATDEF_MAX) { okay = TRUE; } break; } if (okay == FALSE) return TRUE; } awp->lastsfp = sfp; awp->lastsap = fcontext->sap; awp->lastleft = fcontext->left; awp->lastright = fcontext->right; if (fcontext->seqfeattype == SEQFEAT_CDREGION) { fbp = (FeatBlockPtr) Asn2gbAddBlock (awp, FEATURE_BLOCK, sizeof (IntCdsBlock)); } else { fbp = (FeatBlockPtr) Asn2gbAddBlock (awp, FEATURE_BLOCK, sizeof (IntFeatBlock)); } if (fbp == NULL) return TRUE; fbp->entityID = fcontext->entityID; fbp->itemID = fcontext->itemID; fbp->itemtype = OBJ_SEQFEAT; fbp->featdeftype = fcontext->featdeftype; ifp = (IntFeatBlockPtr) fbp; ifp->mapToNuc = FALSE; ifp->mapToProt = FALSE; ifp->mapToGen = FALSE; ifp->mapToMrna = FALSE; ifp->firstfeat = awp->firstfeat; awp->firstfeat = FALSE; /* optionally map CDS from cDNA onto genomic */ if (awp->isGPS && ISA_na (bsp->mol) && awp->copyGpsCdsUp && fcontext->featdeftype == FEATDEF_mRNA) { sip = SeqLocId (sfp->product); bsp = BioseqFind (sip); if (bsp != NULL && ISA_na (bsp->mol)) { cds = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_CDREGION, 0, &cdscontext); if (cds != NULL) { fbp = (FeatBlockPtr) Asn2gbAddBlock (awp, FEATURE_BLOCK, sizeof (IntCdsBlock)); if (fbp != NULL) { fbp->entityID = cdscontext.entityID; fbp->itemID = cdscontext.itemID; fbp->itemtype = OBJ_SEQFEAT; fbp->featdeftype = cdscontext.featdeftype; ifp = (IntFeatBlockPtr) fbp; ifp->mapToNuc = FALSE; ifp->mapToProt = FALSE; ifp->mapToGen = TRUE; ifp->mapToMrna = FALSE; ifp->firstfeat = awp->firstfeat; awp->firstfeat = FALSE; } } } } if (fcontext->seqfeattype != SEQFEAT_CDREGION) return TRUE; /* if CDS, collect more information from product protein bioseq - may be part */ sip = SeqLocId (sfp->product); bsp = BioseqFind (sip); if (bsp == NULL || (! ISA_aa (bsp->mol))) return TRUE; ifp->isCDS = TRUE; icp = (IntCdsBlockPtr) ifp; /* first explore pubs to pick up figure and maploc */ sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_pub, &dcontext); while (sdp != NULL) { pdp = (PubdescPtr) sdp->data.ptrvalue; if (pdp != NULL) { if (icp->fig == NULL) { icp->fig = StringSaveNoNull (pdp->fig); } if (icp->maploc == NULL) { icp->maploc = StringSaveNoNull (pdp->maploc); } } sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_pub, &dcontext); } /* product may be segmented part, and remaining features are indexed on parent */ parent = SeqMgrGetParentOfPart (bsp, NULL); if (parent != NULL) { bsp = parent; } /* then explore mat_peptides, sites, etc. */ GetFeatsOnCdsProduct (sfp, bsp, awp); return TRUE; } static Boolean LIBCALLBACK GetFeatsOnSeg ( SeqLocPtr slp, SeqMgrSegmentContextPtr context ) { Asn2gbWorkPtr awp; BioseqPtr bsp = NULL; Uint2 entityID; Int4 from; SeqLocPtr loc; SeqIdPtr sip; Int4 to; if (slp == NULL || context == NULL) return FALSE; awp = (Asn2gbWorkPtr) context->userdata; from = awp->from; to = awp->from; sip = SeqLocId (slp); if (sip == NULL) { loc = SeqLocFindNext (slp, NULL); if (loc != NULL) { sip = SeqLocId (loc); } } if (sip == NULL) return TRUE; /* may remote fetch genome component if not already in memory */ bsp = BioseqLockById (sip); if (bsp == NULL) return TRUE; entityID = ObjMgrGetEntityIDForPointer (bsp); if (entityID != awp->entityID) { /* if segment not packaged in record, may need to feature index it */ if (SeqMgrFeaturesAreIndexed (entityID) == 0) { SeqMgrIndexFeatures (entityID, NULL); } /* collect features indexed on the remote bioseq */ awp->from = 0; awp->to = bsp->length - 1; } awp->lastsfp = NULL; awp->lastsap = NULL; awp->lastleft = 0; awp->lastright = 0; SeqMgrExploreFeatures (bsp, (Pointer) awp, GetFeatsOnBioseq, awp->slp, NULL, NULL); /* restore original from and to */ awp->from = from; awp->to = to; BioseqUnlock (bsp); return TRUE; } static void AddFeatureBlock ( Asn2gbWorkPtr awp ) { BioseqPtr bsp; SeqFeatPtr cds; SeqMgrDescContext dcontext; SeqMgrFeatContext fcontext; FeatBlockPtr fbp; SeqFeatPtr gene; IntFeatBlockPtr ifp; MolInfoPtr mip; SeqFeatPtr mrna; SeqDescrPtr sdp; if (awp == NULL) return; bsp = awp->parent; if (bsp == NULL) return; awp->lastsfp = NULL; awp->lastsap = NULL; awp->lastleft = 0; awp->lastright = 0; /* optionally map gene from genomic onto cDNA */ if (awp->isGPS && ISA_na (bsp->mol) && awp->copyGpsGeneDown) { sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &dcontext); if (sdp != NULL && sdp->choice == Seq_descr_molinfo) { mip = (MolInfoPtr) sdp->data.ptrvalue; if (mip != NULL) { if (mip->biomol == MOLECULE_TYPE_MRNA) { mrna = SeqMgrGetRNAgivenProduct (bsp, NULL); if (mrna != NULL) { gene = SeqMgrGetOverlappingGene (mrna->location, &fcontext); if (gene != NULL && gene->data.choice == SEQFEAT_GENE) { fbp = (FeatBlockPtr) Asn2gbAddBlock (awp, FEATURE_BLOCK, sizeof (IntCdsBlock)); if (fbp != NULL) { fbp->entityID = fcontext.entityID; fbp->itemID = fcontext.itemID; fbp->itemtype = OBJ_SEQFEAT; fbp->featdeftype = fcontext.featdeftype; ifp = (IntFeatBlockPtr) fbp; ifp->mapToNuc = FALSE; ifp->mapToProt = FALSE; ifp->mapToGen = FALSE; ifp->mapToMrna = TRUE; ifp->isCDS = TRUE; ifp->firstfeat = awp->firstfeat; awp->firstfeat = FALSE; } } } } } } } SeqMgrExploreFeatures (bsp, (Pointer) awp, GetFeatsOnBioseq, awp->slp, NULL, NULL); if (awp->format == GENPEPT_FMT && ISA_aa (bsp->mol)) { cds = SeqMgrGetCDSgivenProduct (bsp, &fcontext); if (cds != NULL && cds->data.choice == SEQFEAT_CDREGION) { fbp = (FeatBlockPtr) Asn2gbAddBlock (awp, FEATURE_BLOCK, sizeof (IntCdsBlock)); if (fbp != NULL) { fbp->entityID = fcontext.entityID; fbp->itemID = fcontext.itemID; fbp->itemtype = OBJ_SEQFEAT; fbp->featdeftype = fcontext.featdeftype; ifp = (IntFeatBlockPtr) fbp; ifp->mapToNuc = FALSE; ifp->mapToProt = TRUE; ifp->mapToGen = FALSE; ifp->mapToMrna = FALSE; ifp->isCDS = TRUE; ifp->firstfeat = awp->firstfeat; awp->firstfeat = FALSE; } } } if (bsp->repr == Seq_repr_seg) { /* collect features on remote segments in MASTER_STYLE */ SeqMgrExploreSegments (bsp, (Pointer) awp, GetFeatsOnSeg); } } static void AddBasecountBlock ( Asn2gbWorkPtr awp ) { BaseBlockPtr bbp; if (awp == NULL) return; bbp = Asn2gbAddBlock (awp, BASECOUNT_BLOCK, sizeof (BaseBlock)); } static void AddOriginBlock ( Asn2gbWorkPtr awp ) { BaseBlockPtr bbp; BioseqPtr bsp; Char buf [67]; SeqMgrDescContext dcontext; GBBlockPtr gbp; SeqDescrPtr sdp; if (awp == NULL) return; bsp = awp->bsp; if (bsp == NULL) return; if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) return; bbp = Asn2gbAddBlock (awp, ORIGIN_BLOCK, sizeof (BaseBlock)); if (bbp == NULL) return; if (awp->format == GENBANK_FMT || awp->format == GENPEPT_FMT) { buf [0] = '\0'; sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_genbank, &dcontext); if (sdp != NULL) { gbp = (GBBlockPtr) sdp->data.ptrvalue; if (gbp != NULL && (! StringHasNoText (gbp->origin))) { StringNCpy_0 (buf, gbp->origin, sizeof (buf)); bbp->entityID = dcontext.entityID; bbp->itemID = dcontext.itemID; bbp->itemtype = OBJ_SEQDESC; } } ff_StartPrint (0, 12, ASN2FF_GB_MAX, NULL); ff_AddString ("ORIGIN"); #ifndef WIN_MAC /* !!! To eliminate spurious diffs when comparing with Sequin exported GenBank format on Mac !!! */ TabToColumn (13); #endif if (! StringHasNoText (buf)) { #ifdef WIN_MAC TabToColumn (13); #endif gb_AddString (NULL, buf, NULL, TRUE, FALSE, TILDE_TO_SPACES); } } bbp->string = gb_MergeString (TRUE); } #define BASES_PER_BLOCK 1200 static void AddSequenceBlock ( Asn2gbWorkPtr awp ) { BioseqPtr bsp; Int4 len; SeqBlockPtr sbp; Int4 start; Int4 stop; if (awp == NULL) return; bsp = awp->bsp; if (bsp == NULL) return; if (awp->slp != NULL) { len = SeqLocLen (awp->slp); } else { len = bsp->length; } /* populate individual sequence blocks for given range */ for (start = 0; start < len; start += BASES_PER_BLOCK) { sbp = (SeqBlockPtr) Asn2gbAddBlock (awp, SEQUENCE_BLOCK, sizeof (SeqBlock)); if (sbp == NULL) continue; sbp->entityID = bsp->idx.entityID; sbp->itemID = bsp->idx.itemID; sbp->itemtype = OBJ_BIOSEQ; stop = start + BASES_PER_BLOCK; if (stop >= len) { stop = len; } sbp->start = start; sbp->stop = stop; } } static void AddContigBlock ( Asn2gbWorkPtr awp ) { BaseBlockPtr bbp; if (awp == NULL) return; bbp = Asn2gbAddBlock (awp, CONTIG_BLOCK, sizeof (BaseBlock)); } static void AddSlashBlock ( Asn2gbWorkPtr awp ) { BaseBlockPtr bbp; if (awp == NULL) return; bbp = Asn2gbAddBlock (awp, SLASH_BLOCK, sizeof (BaseBlock)); if (bbp == NULL) return; gb_StartPrint (awp->format, 0, 0, NULL, 0, 0, 0, NULL, FALSE); gb_AddString (NULL, "//", NULL, FALSE, FALSE, TILDE_IGNORE); bbp->string = gb_MergeString (TRUE); } /*--------------------------------------------------------*/ /* */ /* s_LocusGetBaseName() - */ /* */ /*--------------------------------------------------------*/ static Boolean s_LocusGetBaseName (BioseqPtr parent, BioseqPtr segment, CharPtr baseName) { Char parentName[SEQID_MAX_LEN]; Char segName[SEQID_MAX_LEN]; SeqIdPtr sip; TextSeqIdPtr tsip; Char prefix[5]; Char bufTmp[SEQID_MAX_LEN]; Int2 deleteChars; Int2 newLength; Int2 i; Int2 segNameLen; /* Get the parent Sequence ID */ parentName [0] = '\0'; sip = NULL; for (sip = parent->id; sip != NULL; sip = sip->next) { if (sip->choice == SEQID_GENBANK || sip->choice == SEQID_EMBL || sip->choice == SEQID_DDBJ) break; if (sip->choice == SEQID_TPG || sip->choice == SEQID_TPE || sip->choice == SEQID_TPD) break; } if (sip != NULL) { tsip = (TextSeqIdPtr) sip->data.ptrvalue; if (tsip != NULL && (! StringHasNoText (tsip->name))) { StringNCpy_0 (parentName, tsip->name, sizeof (parentName)); } } if (StringHasNoText (parentName)) { StringNCpy_0 (parentName, baseName, sizeof (parentName)); } /* Get segment id */ segName [0] = '\0'; segNameLen = 0; sip = NULL; for (sip = segment->id; sip != NULL; sip = sip->next) { if (sip->choice == SEQID_GENBANK || sip->choice == SEQID_EMBL || sip->choice == SEQID_DDBJ) break; if (sip->choice == SEQID_TPG || sip->choice == SEQID_TPE || sip->choice == SEQID_TPD) break; } if (sip != NULL) { tsip = (TextSeqIdPtr) sip->data.ptrvalue; if (tsip != NULL && (! StringHasNoText (tsip->name))) { StringNCpy_0 (segName, tsip->name, sizeof (segName)); segNameLen = StringLen(segName); } } /* If there's no "SEG_" prefix, then */ /* just use the parent ID. */ StringNCpy_0 (prefix,parentName,sizeof (prefix)); prefix[4] = '\0'; if (StringCmp(prefix,"SEG_") != 0) { StringCpy(baseName,parentName); return FALSE; } /* Otherwise, eliminate the "SEG_" ... */ StringCpy(bufTmp, &parentName[4]); StringCpy(parentName,bufTmp); /* ... And calculate a base name */ if (segNameLen > 0 && (segName[segNameLen-1] == '1') && (StringLen(parentName) == segNameLen) && (parentName[segNameLen-1] == segName[segNameLen-1])) { deleteChars = 1; for (i = segNameLen-2; i >= 0; i--) if (parentName[i] == '0') deleteChars++; else break; newLength = segNameLen - deleteChars; StringNCpy (parentName,segName,newLength); /* not StringNCpy_0 */ parentName[newLength] = '\0'; } /* Return the base name in the basename parameter */ StringCpy(baseName,parentName); return TRUE; } /* ********************************************************************** */ /* DoOneSection builds a single report for one bioseq or segment */ static void DoOneSection ( BioseqPtr target, BioseqPtr parent, BioseqPtr bsp, SeqLocPtr slp, Uint2 seg, Int4 from, Int4 to, Boolean contig, Asn2gbWorkPtr awp ) { IntAsn2gbJobPtr ajp; Asn2gbSectPtr asp; SeqMgrBioseqContext bcontext; BaseBlockPtr PNTR blockArray; Boolean hasRefs; Int4 i; IntAsn2gbSectPtr iasp; Int4 numBlocks; Int4 numsegs = 0; SeqIdPtr sip; ValNodePtr vnp; if (target == NULL || parent == NULL || bsp == NULL || awp == NULL) return; ajp = awp->ajp; if (ajp == NULL) return; if (ajp->flags.suppressLocalID) { sip = SeqIdSelect (bsp->id, fasta_order, NUM_SEQID); if (sip == NULL || sip->choice == SEQID_LOCAL) return; } if (seg == 0) { awp->basename[0] = '\0'; } else if (seg == 1) { s_LocusGetBaseName (parent, bsp, awp->basename); } asp = Asn2gbAddSection (awp); if (asp == NULL) return; if (SeqMgrGetBioseqContext (parent, &bcontext)) { numsegs = bcontext.numsegs; } /* set working data fields */ awp->asp = asp; awp->target = target; awp->parent = parent; awp->bsp = bsp; awp->slp = slp; awp->seg = seg; awp->numsegs = numsegs; awp->from = from; awp->to = to; awp->contig = contig; awp->firstfeat = TRUE; /* initialize empty blockList for this section */ awp->blockList = NULL; awp->lastblock = NULL; /* and store section data into section fields */ asp->target = target; asp->bsp = bsp; asp->slp = slp; asp->seg = seg; asp->numsegs = numsegs; asp->from = from; asp->to = to; iasp = (IntAsn2gbSectPtr) asp; iasp->spp = NULL; asp->blockArray = NULL; asp->numBlocks = 0; /* start exploring and populating paragraphs */ if (awp->format == FTABLE_FMT) { AddFeatHeaderBlock (awp); AddFeatureBlock (awp); } else { AddLocusBlock (awp); if (awp->format == GENBANK_FMT || awp->format == GENPEPT_FMT) { AddDeflineBlock (awp); AddAccessionBlock (awp); if (ISA_aa (bsp->mol)) { AddPidBlock (awp); } AddVersionBlock (awp); if (ISA_aa (bsp->mol)) { AddDbsourceBlock (awp); } } else if (awp->format == EMBL_FMT || awp->format == EMBLPEPT_FMT) { AddAccessionBlock (awp); if (ISA_na (bsp->mol)) { AddVersionBlock (awp); } if (ISA_aa (bsp->mol)) { /* AddPidBlock (awp); */ /* AddDbsourceBlock (awp); */ } AddDateBlock (awp); AddDeflineBlock (awp); } AddKeywordsBlock (awp); if (awp->format == GENBANK_FMT || awp->format == GENPEPT_FMT) { AddSegmentBlock (awp); } AddSourceBlock (awp); AddOrganismBlock (awp); /* !!! RELEASE_MODE should check return value of AddReferenceBlock !!! */ hasRefs = AddReferenceBlock (awp); if (! hasRefs) { if (ajp->flags.needAtLeastOneRef) { awp->failed = TRUE; } } AddCommentBlock (awp); AddFeatHeaderBlock (awp); AddSourceFeatBlock (awp); if (contig) { if (awp->showconfeats) { AddFeatureBlock (awp); } AddContigBlock (awp); } else { AddFeatureBlock (awp); if (ISA_na (bsp->mol)) { AddBasecountBlock (awp); } AddOriginBlock (awp); AddSequenceBlock (awp); } AddSlashBlock (awp); } /* allocate block array for this section */ numBlocks = ValNodeLen (awp->blockList); asp->numBlocks = numBlocks; if (numBlocks > 0) { blockArray = (BaseBlockPtr PNTR) MemNew (sizeof (BaseBlockPtr) * (numBlocks + 1)); asp->blockArray = blockArray; if (blockArray != NULL) { for (vnp = awp->blockList, i = 0; vnp != NULL; vnp = vnp->next, i++) { blockArray [i] = (BaseBlockPtr) vnp->data.ptrvalue; } } } /* free blockList, but leave data, now pointed to by blockArray elements */ awp->blockList = ValNodeFree (awp->blockList); awp->lastblock = NULL; (awp->currsection)++; } /* the following functions handle various kinds of input, all calling DoOneSection once for each component that gets its own report */ static Boolean LIBCALLBACK Asn2Seg ( SeqLocPtr slp, SeqMgrSegmentContextPtr context ) { Asn2gbWorkPtr awp; BioseqPtr bsp = NULL; Uint2 entityID; Int4 from; SeqLocPtr loc; BioseqPtr parent; SeqIdPtr sip; Int4 to; if (slp == NULL || context == NULL) return FALSE; awp = (Asn2gbWorkPtr) context->userdata; parent = context->parent; from = context->cumOffset; to = from + context->to - context->from; sip = SeqLocId (slp); if (sip == NULL) { loc = SeqLocFindNext (slp, NULL); if (loc != NULL) { sip = SeqLocId (loc); } } if (sip == NULL) return TRUE; /* may remote fetch genome component if not already in memory */ bsp = BioseqLockById (sip); if (bsp == NULL) return TRUE; entityID = ObjMgrGetEntityIDForPointer (bsp); if (entityID != awp->entityID) { /* if segment not packaged in record, may need to feature index it */ if (SeqMgrFeaturesAreIndexed (entityID) == 0) { SeqMgrIndexFeatures (entityID, NULL); } /* collect features indexed on the remote bioseq */ parent = bsp; from = 0; to = bsp->length - 1; } DoOneSection (bsp, parent, bsp, /* slp */ NULL, context->index, from, to, FALSE, awp); BioseqUnlock (bsp); return TRUE; } static void DoOneBioseq ( BioseqPtr bsp, Pointer userdata ) { IntAsn2gbJobPtr ajp; Asn2gbWorkPtr awp; SeqMgrSegmentContext context; Boolean contig = FALSE; Int4 from; BioseqPtr parent; Boolean segmented = FALSE; Int4 to; if (bsp == NULL) return; awp = (Asn2gbWorkPtr) userdata; if (awp == NULL) return; ajp = awp->ajp; if (ajp == NULL) return; /* return if molecule not right for format */ if (ISA_na (bsp->mol)) { if (ajp->format == GENPEPT_FMT || ajp->format == EMBLPEPT_FMT) return; } else if (ISA_aa (bsp->mol)) { if (ajp->format == GENBANK_FMT || ajp->format == EMBL_FMT) return; } if (awp->style == SEGMENTED_STYLE) { segmented = TRUE; } if (awp->style == CONTIG_STYLE) { contig = TRUE; } if (bsp->repr == Seq_repr_seg && awp->style == NORMAL_STYLE) { /* if bsp followed by parts set, then do not default to contig style */ if (SegHasParts (bsp)) { segmented = TRUE; contig = FALSE; } else { segmented = FALSE; contig = TRUE; } } if (bsp->repr == Seq_repr_delta && awp->style == NORMAL_STYLE) { if (! DeltaLitOnly (bsp)) { contig = TRUE; } } if (bsp->repr == Seq_repr_seg) { /* this is a segmented bioseq */ if (segmented) { /* show all segments individually */ SeqMgrExploreSegments (bsp, (Pointer) awp, Asn2Seg); } else { /* show as single bioseq */ parent = bsp; from = 0; to = bsp->length - 1; DoOneSection (parent, parent, bsp, ajp->ajp.slp, 0, from, to, contig, awp); } } else if (bsp->repr == Seq_repr_raw || bsp->repr == Seq_repr_const || bsp->repr == Seq_repr_delta || bsp->repr == Seq_repr_virtual) { parent = SeqMgrGetParentOfPart (bsp, &context); if (parent != NULL) { /* this is a part of an indexed segmented bioseq */ from = context.cumOffset; to = from + context.to - context.from; } else { /* this is a regular non-segmented bioseq */ parent = bsp; from = 0; to = bsp->length - 1; } DoOneSection (parent, parent, bsp, ajp->ajp.slp, 0, from, to, contig, awp); } } static void DoBioseqSetList ( SeqEntryPtr seq_set, Asn2gbWorkPtr awp ) { BioseqSetPtr bssp; SeqEntryPtr sep; if (seq_set == NULL || awp == NULL) return; /* iterate rather than recurse unless multiple nested sets > nuc-prot */ for (sep = seq_set; sep != NULL; sep = sep->next) { if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp == NULL) continue; if (bssp->_class == BioseqseqSet_class_genbank || bssp->_class == BioseqseqSet_class_mut_set || bssp->_class == BioseqseqSet_class_pop_set || bssp->_class == BioseqseqSet_class_phy_set || bssp->_class == BioseqseqSet_class_eco_set || bssp->_class == BioseqseqSet_class_gen_prod_set) { /* if popset within genbank set, for example, recurse */ DoBioseqSetList (bssp->seq_set, awp); return; } } /* at most nuc-prot set, so do main bioseqs that fit the format */ VisitSequencesInSep (sep, (Pointer) awp, VISIT_MAINS, DoOneBioseq); } } static void DoOneBioseqSet ( SeqEntryPtr sep, Asn2gbWorkPtr awp ) { BioseqSetPtr bssp; if (sep == NULL || awp == NULL) return; if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp == NULL) return; if (bssp->_class == BioseqseqSet_class_genbank || bssp->_class == BioseqseqSet_class_mut_set || bssp->_class == BioseqseqSet_class_pop_set || bssp->_class == BioseqseqSet_class_phy_set || bssp->_class == BioseqseqSet_class_eco_set || bssp->_class == BioseqseqSet_class_gen_prod_set) { /* this is a pop/phy/mut/eco set, catenate separate reports */ DoBioseqSetList (bssp->seq_set, awp); return; } } /* at most nuc-prot set, so do main bioseqs that fit the format */ VisitSequencesInSep (sep, (Pointer) awp, VISIT_MAINS, DoOneBioseq); } /* ********************************************************************** */ /* public functions */ static int LIBCALLBACK SortParagraphByIDProc ( VoidPtr vp1, VoidPtr vp2 ) { BaseBlockPtr bbp1, bbp2; if (vp1 == NULL || vp2 == NULL) return 0; bbp1 = *((BaseBlockPtr PNTR) vp1); bbp2 = *((BaseBlockPtr PNTR) vp2); if (bbp1 == NULL || bbp2 == NULL) return 0; if (bbp1->entityID > bbp2->entityID) return 1; if (bbp1->entityID < bbp2->entityID) return -1; if (bbp1->itemtype > bbp2->itemtype) return 1; if (bbp1->itemtype < bbp2->itemtype) return -1; if (bbp1->itemID > bbp2->itemID) return 1; if (bbp1->itemID < bbp2->itemID) return -1; if (bbp1->paragraph > bbp2->paragraph) return 1; if (bbp1->paragraph < bbp2->paragraph) return -1; return 0; } typedef struct modeflags { Boolean flags [19]; } ModeFlags, PNTR ModeFlagsPtr; static ModeFlags flagTable [] = { /* RELEASE_MODE */ {TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE}, /* ENTREZ_MODE */ {FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE}, /* SEQUIN_MODE */ {FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE}, /* DUMP_MODE */ {FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE} }; static void SetFlagsFromMode ( IntAsn2gbJobPtr ajp, ModType mode ) { BoolPtr bp; ModeFlagsPtr mfp; if (ajp == NULL) return; if (! (mode >= RELEASE_MODE && mode <= DUMP_MODE)) { mode = DUMP_MODE; } mfp = &(flagTable [(int) (mode - 1)]); bp = &(mfp->flags [0]); ajp->flags.suppressLocalID = *(bp++); ajp->flags.validateFeats = *(bp++); ajp->flags.ignorePatPubs = *(bp++); ajp->flags.dropShortAA = *(bp++); ajp->flags.avoidLocusColl = *(bp++); ajp->flags.iupacaaOnly = *(bp++); ajp->flags.dropBadCitGens = *(bp++); ajp->flags.noAffilOnUnpub = *(bp++); ajp->flags.dropIllegalQuals = *(bp++); ajp->flags.checkQualSyntax = *(bp++); ajp->flags.needRequiredQuals = *(bp++); ajp->flags.needOrganismQual = *(bp++); ajp->flags.needAtLeastOneRef = *(bp++); ajp->flags.citArtIsoJta = *(bp++); ajp->flags.dropBadDbxref = *(bp++); ajp->flags.useEmblMolType = *(bp++); ajp->flags.hideBankItComment = *(bp++); ajp->flags.checkCDSproductID = *(bp++); ajp->flags.forGbRelease = *(bp++); } NLM_EXTERN Asn2gbJobPtr asn2gnbk_setup ( BioseqPtr bsp, BioseqSetPtr bssp, SeqLocPtr slp, FmtType format, ModType mode, StlType style, FlgType flags ) { IntAsn2gbJobPtr ajp = NULL; Asn2gbSectPtr asp; Asn2gbWork aw; BaseBlockPtr bbp; BaseBlockPtr PNTR blockArray; Uint2 entityID = 0; Int4 i; Int4 j; Int4 k; Boolean lockFarComp; Boolean lockFarLocs; Boolean lockFarProd; Int4 numBlocks; Int4 numSections; ObjMgrDataPtr omdp; BaseBlockPtr PNTR paragraphArray; BaseBlockPtr PNTR paragraphByIDs; Int4 numParagraphs; Asn2gbSectPtr PNTR sectionArray; SubmitBlockPtr sbp; SeqEntryPtr sep; SeqIntPtr sintp; SeqSubmitPtr ssp; BioseqSetPtr topbssp; ValNodePtr vnp; if (slp != NULL) { bsp = BioseqFindFromSeqLoc (slp); if (bsp == NULL) return NULL; /* if location is whole, generate normal bioseq report */ if (slp->choice == SEQLOC_WHOLE) { slp = NULL; } else if (slp->choice == SEQLOC_INT) { sintp = (SeqIntPtr) slp->data.ptrvalue; if (sintp != NULL && sintp->from == 0 && sintp->to == bsp->length - 1) { slp = NULL; } } } if (bsp != NULL) { bssp = NULL; entityID = ObjMgrGetEntityIDForPointer (bsp); } else if (bssp != NULL) { entityID = ObjMgrGetEntityIDForPointer (bssp); } if (entityID == 0) return NULL; if (SeqMgrFeaturesAreIndexed (entityID) == 0) { SeqMgrIndexFeatures (entityID, NULL); } ajp = (IntAsn2gbJobPtr) MemNew (sizeof (IntAsn2gbJob)); if (ajp == NULL) return NULL; init_buff (); asn2ff_set_output (NULL, "\n"); ajp->ajp.entityID = entityID; ajp->ajp.bsp = bsp; ajp->ajp.bssp = bssp; if (slp != NULL) { ajp->ajp.slp = AsnIoMemCopy ((Pointer) slp, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite); } else { ajp->ajp.slp = NULL; } ajp->format = format; SetFlagsFromMode (ajp, mode); ajp->showFarTransl = (Boolean) ((flags & SHOW_FAR_TRANSLATION) != 0); ajp->transientSeqPort = (Boolean) ((flags & FREE_SEQPORT_EACH_TIME) != 0); ajp->masterStyle = (Boolean) (style == MASTER_STYLE); if (format == GENBANK_FMT || format == GENPEPT_FMT) { ajp->newSourceOrg = (Boolean) ((flags & USE_NEW_SOURCE_ORG) != 0); } lockFarComp = (Boolean) ((flags & LOCK_FAR_COMPONENTS) != 0); lockFarLocs = (Boolean) ((flags & LOCK_FAR_LOCATIONS) != 0); lockFarProd = (Boolean) ((flags & LOCK_FAR_PRODUCTS) != 0); if (lockFarComp || lockFarLocs || lockFarProd) { /* lock all bioseqs in advance, including remote genome components */ sep = GetTopSeqEntryForEntityID (entityID); ajp->lockedBspList = LockFarComponentsEx (sep, lockFarComp, lockFarLocs, lockFarProd); } MemSet ((Pointer) (&aw), 0, sizeof (Asn2gbWork)); aw.ajp = ajp; aw.entityID = entityID; aw.sectionList = NULL; aw.lastsection = NULL; aw.currsection = 0; aw.showconfeats = (Boolean) ((flags & SHOW_CONTIG_FEATURES) != 0); aw.showconsource = (Boolean) ((flags & SHOW_CONTIG_SOURCES) != 0); aw.newLocusLine = (Boolean) ((flags & USE_OLD_LOCUS_LINE) == 0); aw.isGPS = FALSE; sep = GetTopSeqEntryForEntityID (entityID); if (sep != NULL && IS_Bioseq_set (sep)) { topbssp = (BioseqSetPtr) sep->data.ptrvalue; if (topbssp != NULL && topbssp->_class == BioseqseqSet_class_gen_prod_set) { aw.isGPS = TRUE; aw.copyGpsCdsUp = (Boolean) ((flags & COPY_GPS_CDS_UP) != 0); aw.copyGpsGeneDown = (Boolean) ((flags & COPY_GPS_GENE_DOWN) != 0); } } if ((Boolean) (flags & DDJB_VARIANT_FORMAT) != 0) { aw.citSubsFirst = TRUE; aw.hideGeneFeats = TRUE; ajp->newSourceOrg = FALSE; } aw.format = format; aw.style = style; aw.hup = FALSE; aw.ssp = NULL; aw.failed = FALSE; omdp = ObjMgrGetData (entityID); if (omdp != NULL && omdp->datatype == OBJ_SEQSUB) { ssp = (SeqSubmitPtr) omdp->dataptr; if (ssp != NULL && ssp->datatype == 1) { aw.ssp = ssp; sbp = ssp->sub; if (sbp != NULL) { aw.hup = sbp->hup; } } } if (bssp != NULL) { /* handle all components of a pop/phy/mut/eco set */ sep = SeqMgrGetSeqEntryForData (bssp); DoOneBioseqSet (sep, &aw); } else { /* handle single bioseq, which may be segmented or a local part */ DoOneBioseq (bsp, &aw); } /* check for failure to populate anything */ if (ajp->flags.needAtLeastOneRef && aw.failed) return asn2gnbk_cleanup ((Asn2gbJobPtr) ajp); numSections = ValNodeLen (aw.sectionList); ajp->ajp.numSections = numSections; if (numSections == 0) return asn2gnbk_cleanup ((Asn2gbJobPtr) ajp); /* allocate section array for this job */ sectionArray = (Asn2gbSectPtr PNTR) MemNew (sizeof (Asn2gbSectPtr) * (numSections + 1)); ajp->ajp.sectionArray = sectionArray; if (sectionArray == NULL) return asn2gnbk_cleanup ((Asn2gbJobPtr) ajp); /* fill in section and paragraph arrays */ numParagraphs = 0; for (vnp = aw.sectionList, i = 0; vnp != NULL && i < numSections; vnp = vnp->next, i++) { asp = (Asn2gbSectPtr) vnp->data.ptrvalue; sectionArray [i] = asp; if (asp != NULL) { numParagraphs += asp->numBlocks; } } /* allocate paragraph array pointing to all blocks in all sections */ ajp->ajp.numParagraphs = numParagraphs; if (numParagraphs == 0) return asn2gnbk_cleanup ((Asn2gbJobPtr) ajp); paragraphArray = (BaseBlockPtr PNTR) MemNew (sizeof (BaseBlockPtr) * (numParagraphs + 1)); ajp->ajp.paragraphArray = paragraphArray; paragraphByIDs = (BaseBlockPtr PNTR) MemNew (sizeof (BaseBlockPtr) * (numParagraphs + 1)); ajp->ajp.paragraphByIDs = paragraphByIDs; if (paragraphArray == NULL || paragraphByIDs == NULL) return asn2gnbk_cleanup ((Asn2gbJobPtr) ajp); k = 0; for (i = 0; i < numSections; i++) { asp = sectionArray [i]; if (asp != NULL) { numBlocks = asp->numBlocks; blockArray = asp->blockArray; if (blockArray != NULL) { for (j = 0; j < numBlocks; j++) { bbp = blockArray [j]; paragraphArray [k] = bbp; paragraphByIDs [k] = bbp; bbp->paragraph = k; k++; } } } } /* sort paragraphByIDs array by entityID/itemtype/itemID/paragraph */ HeapSort (paragraphByIDs, (size_t) numParagraphs, sizeof (BaseBlockPtr), SortParagraphByIDProc); /* free sectionList, but leave data, now pointed to by sectionArray elements */ ValNodeFree (aw.sectionList); return (Asn2gbJobPtr) ajp; } typedef CharPtr (*FormatProc) (Asn2gbFormatPtr afp, BaseBlockPtr bbp); static FormatProc asn2gnbk_fmt_functions [22] = { NULL, DefaultFormatBlock, DefaultFormatBlock, DefaultFormatBlock, DefaultFormatBlock, DefaultFormatBlock, DefaultFormatBlock, DefaultFormatBlock, DefaultFormatBlock, DefaultFormatBlock, FormatSourceBlock, FormatOrganismBlock, FormatReferenceBlock, FormatCommentBlock, DefaultFormatBlock, FormatSourceFeatBlock, FormatFeatureBlock, FormatBasecountBlock, DefaultFormatBlock, FormatSequenceBlock, FormatContigBlock, DefaultFormatBlock }; static void PrintFtableIntervals ( ValNodePtr PNTR head, BioseqPtr target, SeqLocPtr location, CharPtr label ) { SeqLocPtr slp; Int4 start; Int4 stop; Char str [64]; if (head == NULL || target == NULL || location == NULL || label == NULL) return; slp = SeqLocFindNext (location, NULL); if (slp == NULL) return; start = GetOffsetInBioseq (slp, target, SEQLOC_START) + 1; stop = GetOffsetInBioseq (slp, target, SEQLOC_STOP) + 1; sprintf (str, "%ld\t%ld\t%s\n", (long) start, (long) stop, label); ValNodeCopyStr (head, 0, str); while ((slp = SeqLocFindNext (location, slp)) != NULL) { start = GetOffsetInBioseq (slp, target, SEQLOC_START) + 1; stop = GetOffsetInBioseq (slp, target, SEQLOC_STOP) + 1; if (start != 0 && stop != 0) { sprintf (str, "%ld\t%ld\n", (long) start, (long) stop); ValNodeCopyStr (head, 0, str); } } } static void PrintFtableLocAndQuals ( IntAsn2gbJobPtr ajp, ValNodePtr PNTR head, BioseqPtr target, SeqFeatPtr sfp, SeqMgrFeatContextPtr context ) { DbtagPtr dbt; GBQualPtr gbq; GeneRefPtr grp; CharPtr label; ObjectIdPtr oip; BioseqPtr prod; SeqFeatPtr prot; ProtRefPtr prp; RnaRefPtr rrp; SeqIdPtr sip; Char str [256]; Char tmp [300]; tRNAPtr trna; ValNodePtr vnp; if (head == NULL || target == NULL || sfp == NULL || context == NULL) return; label = (CharPtr) FeatDefTypeLabel (sfp); if (StringCmp (label, "Gene") == 0) { label = "gene"; } if (StringHasNoText (label)) { label = "???"; } PrintFtableIntervals (head, target, sfp->location, label); switch (context->seqfeattype) { case SEQFEAT_GENE : grp = (GeneRefPtr) sfp->data.value.ptrvalue; if (grp != NULL) { StringNCpy_0 (str, (CharPtr) grp->locus, sizeof (str)); if (! StringHasNoText (str)) { sprintf (tmp, "\t\t\tgene\t%s\n", str); ValNodeCopyStr (head, 0, tmp); } for (vnp = grp->syn; vnp != NULL; vnp = vnp->next) { StringNCpy_0 (str, (CharPtr) vnp->data.ptrvalue, sizeof (str)); if (! StringHasNoText (str)) { sprintf (tmp, "\t\t\tgene_syn\t%s\n", str); ValNodeCopyStr (head, 0, tmp); } } } break; case SEQFEAT_CDREGION : prod = BioseqFind (SeqLocId (sfp->product)); prot = SeqMgrGetBestProteinFeature (prod, NULL); if (prot != NULL) { prp = (ProtRefPtr) prot->data.value.ptrvalue; if (prp != NULL) { if (prp->name != NULL) { for (vnp = prp->name; vnp != NULL; vnp = vnp->next) { StringNCpy_0 (str, (CharPtr) vnp->data.ptrvalue, sizeof (str)); if (! StringHasNoText (str)) { sprintf (tmp, "\t\t\tproduct\t%s\n", str); ValNodeCopyStr (head, 0, tmp); } } } if (prp->desc != NULL) { StringNCpy_0 (str, prp->desc, sizeof (str)); if (! StringHasNoText (str)) { sprintf (tmp, "\t\t\tprot_desc\t%s\n", str); ValNodeCopyStr (head, 0, tmp); } } for (vnp = prp->activity; vnp != NULL; vnp = vnp->next) { StringNCpy_0 (str, (CharPtr) vnp->data.ptrvalue, sizeof (str)); if (! StringHasNoText (str)) { sprintf (tmp, "\t\t\tfunction\t%s\n", str); ValNodeCopyStr (head, 0, tmp); } } for (vnp = prp->ec; vnp != NULL; vnp = vnp->next) { StringNCpy_0 (str, (CharPtr) vnp->data.ptrvalue, sizeof (str)); if (! StringHasNoText (str)) { sprintf (tmp, "\t\t\tEC_number\t%s\n", str); ValNodeCopyStr (head, 0, tmp); } } } } if (prod != NULL) { for (sip = prod->id; sip != NULL; sip = sip->next) { if (sip->choice == SEQID_GENBANK || sip->choice == SEQID_EMBL || sip->choice == SEQID_DDBJ || sip->choice == SEQID_OTHER || sip->choice == SEQID_TPG || sip->choice == SEQID_TPE || sip->choice == SEQID_TPD) { if (SeqIdWrite (sip, str, PRINTID_TEXTID_ACC_VER, sizeof (str)) != NULL) { sprintf (tmp, "\t\t\tprotein_id\t%s\n", str); ValNodeCopyStr (head, 0, tmp); } } else if (sip->choice == SEQID_LOCAL && (! ajp->flags.suppressLocalID)) { if (SeqIdWrite (sip, str, PRINTID_TEXTID_ACC_VER, sizeof (str)) != NULL) { sprintf (tmp, "\t\t\tprotein_id\tlcl|%s\n", str); ValNodeCopyStr (head, 0, tmp); } } } } break; case SEQFEAT_RNA : rrp = (RnaRefPtr) sfp->data.value.ptrvalue; if (rrp != NULL) { switch (rrp->ext.choice) { case 1 : StringNCpy_0 (str, (CharPtr) rrp->ext.value.ptrvalue, sizeof (str)); if (! StringHasNoText (str)) { sprintf (tmp, "\t\t\tproduct\t%s\n", str); ValNodeCopyStr (head, 0, tmp); } break; case 2 : trna = rrp->ext.value.ptrvalue; if (trna != NULL) { FeatDefLabel (sfp, str, sizeof (str) - 1, OM_LABEL_CONTENT); if (! StringHasNoText (str)) { sprintf (tmp, "\t\t\tproduct\t%s\n", str); ValNodeCopyStr (head, 0, tmp); } } break; default : break; } } break; default : break; } if (! StringHasNoText (sfp->comment)) { ValNodeCopyStr (head, 0, "\t\t\tnote\t"); ValNodeCopyStr (head, 0, sfp->comment); ValNodeCopyStr (head, 0, "\n"); } for (gbq = sfp->qual; gbq != NULL; gbq = gbq->next) { if (! StringHasNoText (gbq->qual)) { if (! StringHasNoText (gbq->val)) { sprintf (tmp, "\t\t\t%s\t%s\n", gbq->qual, gbq->val); ValNodeCopyStr (head, 0, tmp); } } } for (vnp = sfp->dbxref; vnp != NULL; vnp = vnp->next) { dbt = (DbtagPtr) vnp->data.ptrvalue; if (dbt != NULL) { if (! StringHasNoText (dbt->db)) { oip = dbt->tag; if (oip->str != NULL && (! StringHasNoText (oip->str))) { sprintf (tmp, "\t\t\tdb_xref\t%s:%s\n", dbt->db, oip->str); ValNodeCopyStr (head, 0, tmp); } else { sprintf (tmp, "\t\t\tdb_xref\t%s:%ld\n", dbt->db, (long) oip->id); ValNodeCopyStr (head, 0, tmp); } } } } } NLM_EXTERN CharPtr asn2gnbk_format ( Asn2gbJobPtr ajp, Int4 paragraph ) { Asn2gbFormat af; Asn2gbSectPtr asp; BaseBlockPtr bbp; BlockType blocktype; SeqMgrFeatContext fcontext; FormatProc fmt; ValNodePtr head; IntAsn2gbJobPtr iajp; Char id [42]; size_t max; QualValPtr qv; Int4 section; SeqFeatPtr sfp; SeqIdPtr sip; CharPtr str = NULL; BioseqPtr target; Char tmp [53]; /* qv must hold MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR) */ iajp = (IntAsn2gbJobPtr) ajp; if (iajp == NULL || ajp->sectionArray == NULL || ajp->paragraphArray == NULL) return NULL; if (paragraph < 0 || paragraph >= ajp->numParagraphs) return NULL; bbp = ajp->paragraphArray [paragraph]; if (bbp == NULL) return NULL; section = bbp->section; if (section < 0 || section >= ajp->numSections) return NULL; asp = ajp->sectionArray [section]; if (asp == NULL) return NULL; blocktype = bbp->blocktype; if (blocktype < LOCUS_BLOCK || blocktype > SLASH_BLOCK) return NULL; max = (size_t) (MAX (ASN2GNBK_TOTAL_SOURCE, ASN2GNBK_TOTAL_FEATUR)); qv = MemNew (sizeof (QualVal) * (max + 5)); if (qv == NULL) return NULL; af.ajp = (IntAsn2gbJobPtr) ajp; af.asp = asp; af.qvp = qv; af.format = iajp->format; if (iajp->format != FTABLE_FMT) { fmt = asn2gnbk_fmt_functions [(int) blocktype]; if (fmt == NULL) return NULL; str = fmt (&af, bbp); } else { target = asp->target; if (target != NULL) { if (blocktype == FEATHEADER_BLOCK) { sip = SeqIdFindBest (target->id, 0); SeqIdWrite (sip, id, PRINTID_FASTA_LONG, sizeof (id) - 1); if (! StringHasNoText (id)) { sprintf (tmp, ">Feature %s\n", id); str = StringSave (tmp); } } else if (blocktype == FEATURE_BLOCK) { sfp = SeqMgrGetDesiredFeature (bbp->entityID, NULL, bbp->itemID, 0, NULL, &fcontext); if (sfp != NULL) { head = NULL; PrintFtableLocAndQuals (af.ajp, &head, target, sfp, &fcontext); str = MergeValNodeStrings (head); ValNodeFreeData (head); } } } } if (str == NULL) { str = StringSave ("???\n"); } MemFree (qv); return str; } NLM_EXTERN Asn2gbJobPtr asn2gnbk_cleanup ( Asn2gbJobPtr ajp ) { Asn2gbSectPtr asp; BaseBlockPtr bbp; BaseBlockPtr PNTR blockArray; Int4 i; IntAsn2gbJobPtr iajp; IntAsn2gbSectPtr iasp; IntCdsBlockPtr icp; IntFeatBlockPtr ifp; IntRefBlockPtr irp; Int4 j; Int4 numBlocks; Int4 numSections; RefBlockPtr rrp; Asn2gbSectPtr PNTR sectionArray; iajp = (IntAsn2gbJobPtr) ajp; if (iajp == NULL) return NULL; SeqLocFree (iajp->ajp.slp); numSections = ajp->numSections; sectionArray = ajp->sectionArray; if (sectionArray != NULL) { for (i = 0; i < numSections; i++) { asp = sectionArray [i]; if (asp != NULL) { iasp = (IntAsn2gbSectPtr) asp; numBlocks = asp->numBlocks; blockArray = asp->blockArray; if (blockArray != NULL) { for (j = 0; j < numBlocks; j++) { bbp = blockArray [j]; if (bbp != NULL) { MemFree (bbp->string); if (bbp->blocktype == REFERENCE_BLOCK) { rrp = (RefBlockPtr) bbp; MemFree (rrp->uniquestr); irp = (IntRefBlockPtr) rrp; DateFree (irp->date); SeqLocFree (irp->loc); MemFree (irp->authstr); MemFree (irp->fig); MemFree (irp->maploc); } else if (bbp->blocktype == FEATURE_BLOCK) { ifp = (IntFeatBlockPtr) bbp; if (ifp->isCDS) { icp = (IntCdsBlockPtr) ifp; MemFree (icp->fig); MemFree (icp->maploc); } } MemFree (bbp); } } } MemFree (asp->blockArray); MemFree (asp->referenceArray); SeqPortFree (iasp->spp); } } } MemFree (ajp->sectionArray); MemFree (ajp->paragraphArray); MemFree (ajp->paragraphByIDs); if (iajp->lockedBspList != NULL) { UnlockFarComponents (iajp->lockedBspList); } free_buff (); MemFree (iajp); return NULL; } NLM_EXTERN Boolean SeqEntryToGnbk ( SeqEntryPtr sep, SeqLocPtr slp, FmtType format, ModType mode, StlType style, FlgType flags, FILE *fp ) { Asn2gbJobPtr ajp; BioseqPtr bsp = NULL; BioseqSetPtr bssp = NULL; Int4 i; Boolean is_html; Int4 numParagraphs; CharPtr str; #ifdef WIN_MAC #if __profile__ ValNodePtr bsplist = NULL; Uint2 entityID; Boolean lockFarComp; Boolean lockFarLocs; Boolean lockFarProd; #endif #endif if (fp == NULL) return FALSE; if (sep == NULL && slp == NULL) return FALSE; if (sep != NULL) { if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; } } #ifdef WIN_MAC #if __profile__ /* this allows profiling of just the formatter, without feature indexing, on the Mac */ if (sep != NULL) { entityID = ObjMgrGetEntityIDForPointer (sep->data.ptrvalue); if (SeqMgrFeaturesAreIndexed (entityID) == 0) { SeqMgrIndexFeatures (entityID, NULL); } } lockFarComp = (Boolean) ((flags & LOCK_FAR_COMPONENTS) != 0); lockFarLocs = (Boolean) ((flags & LOCK_FAR_LOCATIONS) != 0); lockFarProd = (Boolean) ((flags & LOCK_FAR_PRODUCTS) != 0); if (lockFarComp || lockFarLocs || lockFarProd) { flags = flags ^ (LOCK_FAR_COMPONENTS | LOCK_FAR_LOCATIONS | LOCK_FAR_PRODUCTS); bsplist = LockFarComponentsEx (sep, lockFarComp, lockFarLocs, lockFarProd); } ProfilerSetStatus (TRUE); #endif #endif is_html = (Boolean) ((flags & CREATE_HTML_FLATFILE) != 0); if (is_html) { init_www (); } ajp = asn2gnbk_setup (bsp, bssp, slp, format, mode, style, flags); if (ajp != NULL) { if (is_html) { head_www (fp, sep); } numParagraphs = ajp->numParagraphs; for (i = 0; i < numParagraphs; i++) { str = asn2gnbk_format (ajp, i); if (str != NULL) { fprintf (fp, "%s", str); } else { fprintf (fp, "?\n"); } MemFree (str); } asn2gnbk_cleanup (ajp); if (is_html) { tail_www (fp); } } if (is_html) { fini_www (); } #ifdef WIN_MAC #if __profile__ ProfilerSetStatus (FALSE); UnlockFarComponents (bsplist); #endif #endif return TRUE; } NLM_EXTERN Boolean BioseqToGnbk ( BioseqPtr bsp, SeqLocPtr slp, FmtType format, ModType mode, StlType style, FlgType flags, FILE *fp ) { SeqEntryPtr sep = NULL; if (bsp == NULL && slp == NULL) return FALSE; if (bsp != NULL) { sep = SeqMgrGetSeqEntryForData (bsp); } return SeqEntryToGnbk (sep, slp, format, mode, style, flags, fp); }