/* asn2ffg.h * =========================================================================== * * 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: asn2ffg.h * * Author: Karl Sirotkin, Tom Madden, Tatiana Tatusov * * Version Creation Date: 7/15/95 * * $Revision: 6.17 $ * $Revision: 6.17 $ * * File Description: * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * ========================================================================== */ /************************************* * * $Log: asn2ffg.h,v $ * Revision 6.17 2001/12/05 18:14:05 cavanaug * Changes for new LOCUS line format * * Revision 6.16 2000/06/05 17:51:41 tatiana * increase size of feature arrays to Int4 * * Revision 6.15 2000/04/03 23:33:36 tatiana * added showSeqLoc for GenBank region view * * Revision 6.14 2000/03/20 23:38:39 aleksey * Finally submitted the changes which have been made by serge bazhin * and been kept in my local directory. * * These changes allow to establish user callback functions * in 'Asn2ffJobPtr' structure which are called within * 'SeqEntryToFlatAjp' function call. * The new members are: * user_data - pointer to a user context for passing data * ajp_count_index - user defined function * ajp_print_data - user defined function * ajp_print_index - user defined function * * Revision 6.13 2000/02/09 19:34:38 kans * added forgbrel flag to Asn2ffJobPtr, currently used to suppress PUBMED line, which was not formally announced in release notes * * Revision 6.12 1999/11/05 14:54:04 tatiana * EMBL_PREFNUM increased to 5 * * Revision 6.11 1999/10/27 20:57:07 tatiana * bankit added to ajp * * Revision 6.10 1999/09/23 18:06:04 tatiana * contig_view added to ajp * * Revision 6.9 1999/04/02 16:33:15 tatiana * added LinkStr struct and ByteStorePtr to ajp * * Revision 6.8 1999/03/11 19:04:31 tatiana * version added * * Revision 6.7 1998/11/10 15:12:59 bazhin * Macro NUM_OF_ESTIMATES and static array of integers "line_estimate" * moved out to "asn2ff1.c". * * Revision 6.6 1998/09/24 17:46:00 kans * fixed GetDBXrefFromGene problem (TT) * * Revision 6.5 1998/07/14 17:59:06 kans * added useSeqMgrIndexes to OrganizeFeatPtr and Asn2ffJobPtr * * Revision 6.4 1998/03/09 21:41:03 tatiana * accession length increased to 60 * * Revision 6.3 1998/02/12 15:48:26 tatiana * EMBL_PREFNUM increased to 4 * * Revision 6.2 1998/01/13 21:10:50 tatiana * added Biosrclist to organizefeat struct * * Revision 6.0 1997/08/25 18:05:13 madden * Revision changed to 6.0 * * Revision 5.16 1997/07/23 18:35:51 tatiana * SeqIdPtr id_print added to Asn2ffJob structure * * Revision 5.14 1997/04/25 19:26:03 tatiana * #define EMBL_PREFNUM 1 added * * Revision 5.13 1997/03/13 15:42:47 tatiana * *** empty log message *** * * Revision 5.12 1997/01/27 18:33:51 tatiana * hup added to ajp * * Revision 5.11 1996/12/17 22:45:55 tatiana * added Boolean feat_free to SortStruct * * Revision 5.8 1996/10/25 22:22:44 tatiana * defline added to GBEntry * * Revision 5.7 1996/09/03 19:54:01 tatiana * extra_loc added * * Revision 5.6 1996/08/05 13:54:56 tatiana * orgname added to ajp struct * * Revision 5.4 1996/07/30 13:37:37 tatiana * 'show_gene' added to asn2ffJob * * Revision 5.3 1996/07/23 22:32:50 tatiana * added format to orf struct * * Revision 5.2 1996/07/02 18:06:20 tatiana * *** empty log message *** * * Revision 5.2 1996/07/02 18:06:20 tatiana * *** empty log message *** * * Revision 5.1 1996/06/11 15:24:59 tatiana * add embl ni to GBEntry struct * * Revision 4.13 1996/05/16 20:56:46 tatiana * source_info added to GBEntry structure * * Revision 4.12 1996/04/29 18:54:26 tatiana * multiple comments * * Revision 4.11 1996/04/12 03:41:44 tatiana * added Booleans to GBEntry * * Revision 4.10 1996/04/09 14:03:50 tatiana * DescrStructPtr and comms added to GBEntry * * Revision 4.9 1996/03/20 00:00:20 tatiana * add activity to GeneStruct * * Revision 4.8 1996/03/04 17:11:20 ostell * added support for ignore_top features * * Revision 4.7 1996/02/28 04:53:06 ostell * changes to support segmented master seeuquences * * Revision 4.6 1996/02/18 21:17:17 tatiana * number of pubs, feats and seqblocks added to GBEntry structure * * Revision 4.5 1996/02/15 15:57:11 tatiana * SortStruct changed for sorting within one entity * * Revision 4.4 1996/01/29 22:44:00 tatiana * genome_view added to Asn2ffJobPtr * * Revision 4.2 1995/12/13 16:35:02 tatiana * itemID etc. added to FFPrintArray structure * * Revision 1.1 1995/07/17 19:24:04 kans * Initial revision * * **************************************/ #ifndef _ASN2FFG_ #define _ASN2FFG_ #include #include #include #include #include #include #include #define LINKS 20 #define EMBL_AC "AFVXYZ" /* patent is "A" */ /* dbEST = "F" */ #define EMBL_PREFNUM 5 /* embl two-letter prefix {XX} see asn2ff4.c is_embl()*/ #define FF_REGULAR 0 #define FF_TOP_COMPLETE 1 #define FF_TOP_CONTIG 2 typedef struct _link_str { CharPtr line; struct _link_str PNTR next; } LinkStr, PNTR LinkStrPtr; typedef struct genestruct { ValNodePtr gene; ValNodePtr product; ValNodePtr standard_name; CharPtr PNTR map; /* only map[0] is used why we need PNTR? */ ValNodePtr ECNum; ValNodePtr activity; Int2 map_size, map_index; /* map_size is always 1 */ Boolean pseudo; GeneRefPtr grp; } GeneStruct, PNTR GeneStructPtr; typedef struct notestruct { CharPtr PNTR note; Uint1 PNTR note_alloc; CharPtr PNTR note_annot; Int2 note_size, note_index; } NoteStruct, PNTR NoteStructPtr; typedef struct sortstruct { BioseqPtr bsp; BioseqPtr seg_bsp; SeqFeatPtr sfp; /* would be NULL if gather tempload == TRUE */ SeqLocPtr slp; /*for converted locations, free if not NULL!*/ Uint2 entityID, itemID, itemtype; Int4 hash; Boolean dup; SeqLocPtr PNTR extra_loc; Int2 extra_loc_cnt; Boolean feat_free; Boolean tempload; GeneStructPtr gsp; /* information on Genes */ NoteStructPtr nsp; /* information on Notes. */ } SortStruct, PNTR SortStructPtr; typedef struct descrstruct { ValNodePtr vnp; Uint2 entityID, itemID, itemtype; struct descrstruct PNTR next; } DescrStruct, PNTR DescrStructPtr; typedef struct comstruct { CharPtr string; Boolean gsdb_id; Uint2 entityID, itemID, itemtype; struct comstruct PNTR next; } ComStruct, PNTR ComStructPtr; typedef struct organizeprot { SortStructPtr list; Int2 size; } OrganizeProt, PNTR OrganizeProtPtr; typedef struct organizefeat { Boolean embl_feat; BioseqPtr bsp; BioseqPtr seg_bsp; Int4 sfpListsize; Int4 sortListsize; SortStructPtr List; /* ptr's to "generic" features */ Int2 sfpCommsize; /* Number of comment features */ Int2 sortCommsize; /* Number of sorted comment features */ SortStructPtr Commlist; Int4 sfpGenesize; /* Number of gene features */ Int4 sortGenesize; /* Number of sorted gene features */ SortStructPtr Genelist; Int4 sfpOrgsize; /* Number of Organism features. */ Int4 sortOrgsize; /* Number of sorted Organism features. */ SortStructPtr Orglist; Int4 sfpSitesize; /* Number of ImpFeat's with key "Site-ref" */ Int4 sortSitesize; /* Number of sorted ImpFeat's with key "Site-ref" */ SortStructPtr Siteslist; Int4 sfpSourcesize; /* Number of ImpFeat's with key "source" */ Int4 sortSourcesize; /* Number of sorted ImpFeat's with key "source" */ SortStructPtr Sourcelist; Int4 sfpXrefsize; /* Number of Seq's that go out as xref's */ SortStructPtr Xreflist; Uint2 oldID; /* is used to sort within entity */ NoteStructPtr source_notes; /* Note for source feature */ Uint1 format; /* needed for ProtRef convertion */ Boolean show_gene; /* needed temporarely for 'gene' feature */ BioseqPtr lock_bsp; Boolean non_strict; Int2 biosrcsize; /* Number of sorted ImpFeat's with key "source" */ SortStructPtr Biosrclist; Boolean useSeqMgrIndexes; /* new style indexing to eliminate nested gathers */ Boolean showSeqLoc; /* GenBank view for a region, skip truncated check */ } OrganizeFeat, PNTR OrganizeFeatPtr; /***************************************************************************** * * GBEntry * structure with info for a single GenBank record * *****************************************************************************/ typedef struct gbentry { BioseqPtr bsp; /* the Bioseq for this record */ Uint2 entityID, itemID, itemtype; Char date[12]; CharPtr create_date; CharPtr update_date; CharPtr embl_rel; Int2 embl_ver; Int4 gi; CharPtr ni; CharPtr base_cnt_line; Boolean xref_present; Char div[4]; /* division */ Char locus[25]; /* locus */ Char accession[60]; /* primary accession */ Int2 num_seg; /* segment number if segmented */ Int4 length; /* length of entry */ SeqPortPtr spp; /* seqport on entry */ OrganizeFeatPtr feat; /* temporary struct with features */ ValNodePtr Pub; DescrStructPtr descr; /* keeps entityID, itemID, itemtype for descr */ DescrStructPtr source_info; /* keeps org info if no source feature found */ Int4 feat_num; /* number of printed features */ Int2 comm_num; /* number of printed cooment blocks */ ComStructPtr comm; /* CharPtr in com.data.ptrvalue are comments */ Boolean map; CharPtr defline; struct gbentry PNTR next; Char version[60]; /* accession.version */ } GBEntry, PNTR GBEntryPtr; /***************************************************************************** * * Asn2ffWE * asn2ff working environment. Keeps top level information about current * unit under construction. Serves as head of chain of structs, one for * GenBank record finally produced. * *****************************************************************************/ typedef struct asn2ffwe { /* Working environment for data object */ SeqEntryPtr current_sep; /* current SeqEntry ???? Tatiana*/ BioseqPtr current_bsp; /* current Bioseq ???? Tatiana*/ BioseqSetPtr current_bssp;/* current BioseqSet ???? Tatiana*/ /* SeqSubmit Only */ ValNodePtr cit_sub; /* if a SeqSubmit, the Cit-sub for it */ /* Segmented Set Only */ Char base_name[25]; /* base LOCUS name if segmented set */ Int2 total_seg; /* number of segments in segmented set */ BioseqPtr seg; /* segmented Bioseq in segmented set */ BioseqSetPtr parts; /* parts set for segmented set */ Boolean only_one; /* only one segment of set being shown (current bsp) */ GBEntryPtr gbp; /* chain of data for each GB record */ } Asn2ffWE, PNTR Asn2ffWEPtr; /***************************************************************************** * * Asn2ffJob * top level job control structure to be filled in by caller * sets global options and I/O information * sets overall scope and target for formatting * points to function working environment (added by function) * *****************************************************************************/ typedef struct asn2ff_job { /* Set formatting options */ Boolean show_gene, /* show the gene feature */ show_seq, /* do not show the sequence */ show_gi, /* do not show the GI id */ error_msgs, /* do not show feature validator messages */ non_strict, /* only strict gene/protein binding allowed */ null_str, /* error msg if printing NULL string */ no_hold, /* if TRUE, do not use ObjMgrSetHold around asn2ff_print */ free_cache; /* if TRUE, ObjMgrFreeCache() after asn2ff_print */ Uint1 format, /* from _FMT above */ mode; /* from _MODE above */ FILE * fp; /* if not NULL, output goes to file */ StdPrintOptionsPtr Spop; /* for templates */ /* Specify the data to be formatted */ Uint2 entityID, /* could be a data object */ itemID, /* specified by ID or by pointer */ itemtype; Boolean only_one, /* show only one top-level bioseq */ ignore_top; /* do not show features from top-level bioseq */ SeqSubmitPtr ssp; /* alternative data object pointers */ SeqEntryPtr sep; SeqLocPtr slp; /* or could be a location on a sequence */ Boolean gb_style; /* only complete features are shown e.g. join cds on the last segmented bioseq */ Boolean genome_view; /* not printing the sequence and features*/ Boolean map_view; /* not printing the sequence */ Boolean hup; /* for submissions */ /* taken directly from Biotable, used for printing and formatting */ Int4 pap_index; Uint1 pap_last; Boolean pseudo; SeqFeatPtr sfp_out; Int2 number_of_cds; Boolean help; /** this section filled in by function **************/ Asn2ffWEPtr asn2ffwep; Boolean orgname; /* new algorithm for /organism in source feature*/ SeqIdPtr id_print; Boolean useSeqMgrIndexes; /* new style indexing to eliminate nested gathers */ Boolean show_version; ByteStorePtr byte_st; Boolean contig_view; /* CONTIG line and features*/ Boolean bankit; /* show Bankit comments*/ Boolean forgbrel; Pointer user_data; Int4 (*ajp_print_data)(struct asn2ff_job *ajp, CharPtr str, Pointer user_data); Int4 (*ajp_print_index)(struct asn2ff_job *ajp, Pointer user_data); Int4 (*ajp_count_index)(struct asn2ff_job *ajp, Int4 num, Pointer user_data); Boolean new_locus_fmt; /* TRUE if utilizing the new format for the LOCUS line */ } Asn2ffJob, PNTR Asn2ffJobPtr; /*----------- Estimates for the number of lines returned for each of the following------------------------------------------*/ #define NUM_SEQ_LINES 10 typedef void (* FFPapFct) PROTO ((Asn2ffJobPtr ajp, GBEntryPtr gbp)); typedef struct ffprintarray { FFPapFct fct; Asn2ffJobPtr ajp; GBEntryPtr gbp; Int4 index; Uint1 last; Uint1 printxx; Int2 estimate; DescrStructPtr descr; /* keeps entityID, itemID, itemtype for descr */ } FFPrintArray, PNTR FFPrintArrayPtr; /***************************************************************************** * * Main asn2ff entry points * *****************************************************************************/ Boolean Asn2ff PROTO((Asn2ffJobPtr ajp)); #endif