/* tofasta.h * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * 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 have not placed any restriction on its use or reproduction. * * 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. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * File Name: tofasta.h * * Author: James Ostell * * Version Creation Date: 7/12/91 * * $Revision: 6.16 $ * * File Description: various sequence objects to fasta output * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * $Log: tofasta.h,v $ * Revision 6.16 2001/08/31 15:29:54 kans * added CreateDefLineEx to ignore existing title descriptor, force generation of protein title computationally * * Revision 6.15 2001/08/17 13:27:26 kans * ClearProteinTitlesInNucProts, do not do it for outside protein databases * * Revision 6.14 2001/06/25 23:47:48 kans * added InstantiateProteinTitles and ClearProteinTitles * * Revision 6.13 2001/02/27 21:52:37 madden * Added BioseqToFastaDump and FastaDumpFileFunc for dumping BLAST db in FASTA * * Revision 6.12 2000/10/12 16:03:58 kans * added SeqEntryToFastaEx, printid_general field to MyFsa structure, to support processing software that requires gnl ID in FASTA defline even in the presence of higher-priority ref ID * * Revision 6.11 2000/07/20 17:48:28 dondosha * Added function FastaToSeqBuffForDb analogous to FastaToSeqEntryForDbtofasta.c * * Revision 6.10 2000/05/30 19:44:45 ostell * added FastaSeqLineEx() with another parameter, do_virtual * * Revision 6.9 2000/04/03 22:09:26 kans * added ClearGenBankKeywords for RefSeq processing * * Revision 6.8 2000/03/29 22:00:23 kans * added NC_Cleanup function used internally for genome RefSeq processing * * Revision 6.7 2000/02/17 17:20:58 sicotte * Add Reading of Lowercase Characters as SeqLoc for inputting masking informatioin. Use FastaToSeqEntryForDb or FastaToSeqEntryInternalEx * * Revision 6.6 2000/02/04 16:38:29 kans * added FastaToSeqEntryForDb and FastaToSeqEntryInternalEx, giving control over generation of unique SeqID * * Revision 6.5 1999/09/20 18:37:55 shavirin * Added definition of the function Int4 GetOrderBySeqId(). * * Revision 6.4 1998/02/23 16:51:27 egorov * Changes to make the tofasta.c independent on readdb.h * * Revision 6.2 1998/01/27 20:28:10 madden * Added BioseqRawToFastaExtra with line_length arg * * Revision 6.1 1997/10/22 16:44:07 shavirin * Added definitions for functions: FastaReadSequence() and FastaReadSequenceMem() * * Revision 6.0 1997/08/25 18:07:48 madden * Revision changed to 6.0 * * Revision 5.6 1997/06/19 18:39:21 vakatov * [WIN32,MSVC++] Adopted for the "NCBIOBJ.LIB" DLL'ization * * Revision 5.5 1996/10/22 16:00:50 shavirin * Added new Boolean no_sequence in MyFsa structure to disable * sequence printing * * Revision 5.4 1996/10/21 21:37:24 shavirin * Added definition for function SeqEntrysToDefline() * * Revision 5.3 1996/10/08 22:27:05 shavirin * Moved definition of functions FastaToSeqEntryEx and FastaToSeqBuffEx * into include file * * Revision 5.2 1996/08/15 18:15:23 tatiana * CreateDefLine() added * * Revision 5.1 1996/06/15 17:29:44 ostell * changed MyFsa structure by adding do_virtual and tech fields * added value of 3 for group_segs * addes support of tech to FastaDefLine() * * Revision 5.0 1996/05/28 13:23:23 ostell * Set to revision 5.0 * * Revision 4.1 1996/03/13 19:50:23 shavirin * Added definition for new external function FastaToSeqBuff() * * Revision 4.0 1995/07/26 13:49:01 ostell * force revision to 4.0 * * Revision 2.7 1995/05/09 18:43:09 ostell * added support for (accession) on GenPept deflines and [organism] on * GenPept and PRF deflines * * * ========================================================================== */ #ifndef _NCBI_Tofasta_ #define _NCBI_Tofasta_ #include #undef NLM_EXTERN #ifdef NLM_IMPORT #define NLM_EXTERN NLM_IMPORT #else #define NLM_EXTERN extern #endif #ifdef __cplusplus extern "C" { #endif /* keys returned by FastaWriteFunc */ #define FASTA_ID ((Int2)1) /* the SeqId string */ #define FASTA_DEFLINE ((Int2)2) /* the definition line */ #define FASTA_SEQLINE ((Int2)3) /* a line of sequence */ #define FASTA_EOS ((Int2)4) /* all the sequence has been printed */ #define FASTA_FORMATDB_AMB ((Int2)5) /* make conversion to standard form for nucleotides */ typedef Boolean (* FastaWriteFunc) PROTO ((BioseqPtr bsp, Int2 key, CharPtr buf, Uint4 buflen, Pointer data)); typedef struct iteminfo { /* struct used for defline */ Uint2 entityID, itemID, itemtype; } ItemInfo, PNTR ItemInfoPtr; typedef struct descrinfo { /* struct used for defline */ BioseqPtr bsp; ValNodePtr vnp; ItemInfoPtr iip; Uint1 choice; } DescrInfo, PNTR DescrInfoPtr; typedef struct myfsa { /* struct used for fasta searches */ CharPtr buf; /* buffer for strings (suggest 255 minimum) */ Int2 buflen, /* length of buf */ seqlen; /* length of sequence lines (must be buflen-1 or less) */ Pointer mydata; /* pointer to your own data */ FastaWriteFunc myfunc; /* callback to process parts of fasta file */ BioseqPtr bsp; /* Bioseq being processed */ Boolean bad_asn1; /* set if error in input object like mol not set */ CharPtr accession; /* used internally for GenPept def lines */ CharPtr organism; /* used internally for GenPept/PRF def lines */ Uint1 order; /* used to order def lines for BLAST */ Boolean do_virtual; /* if TRUE, instantiate virtual sequences */ Uint1 tech; /* for MolInfo.tech */ Boolean no_sequence; /* used to disable sequence printing */ Uint1 code; /* coding of sequence */ Boolean formatdb; /* TRUE, if is used in formatdb */ Boolean printid_general; /* show gi and gnl for SeqId */ } MyFsa, PNTR MyFsaPtr; typedef struct tofasta { Boolean is_na; Boolean got_one; MyFsaPtr mfp; Uint1 group_segs; Int2 last_indent, parts, seg; } FastaDat, PNTR FastaPtr; NLM_EXTERN Boolean BioseqRawToFastaExtra PROTO((BioseqPtr bsp, FILE *fp, Int2 line_length)); NLM_EXTERN Boolean BioseqRawToFasta PROTO((BioseqPtr bsp, FILE * fp, Boolean is_na)); NLM_EXTERN Boolean SeqEntryToFasta PROTO((SeqEntryPtr sep, FILE * fp, Boolean is_na)); NLM_EXTERN Boolean SeqEntryToFastaEx PROTO((SeqEntryPtr sep, FILE * fp, Boolean is_na, Boolean printid_general)); NLM_EXTERN Boolean BioseqToFasta PROTO((BioseqPtr bsp, FILE *fp, Boolean is_na)); NLM_EXTERN Boolean BioseqToFastaDump PROTO((BioseqPtr bsp, FILE *fp, Boolean is_na)); NLM_EXTERN void SeqEntryFasta PROTO ((SeqEntryPtr sep, Pointer data, Int4 index, Int2 indent)); /***************************************************************************** * * SeqEntrysToFasta(sep, fp, is_na, group_segs) * * group_segs = 0 ... take only raw Bioseqs * group_segs = 1 ... group segmented seqs into single entry.. no parts * group_segs = 2 ... show only parts of segmented seqs * group_segs = 3 ... like 1, but also instantiate virtual sequences * *****************************************************************************/ NLM_EXTERN Boolean SeqEntrysToFasta PROTO((SeqEntryPtr sep, FILE *fp, Boolean is_na, Uint1 group_segs)); NLM_EXTERN Boolean SeqEntrysToFastaX PROTO((SeqEntryPtr sep, MyFsaPtr mfp, Boolean is_na, Uint1 group_segs)); NLM_EXTERN Boolean SeqEntrysToDefline PROTO((SeqEntryPtr sep, FILE *fp, Boolean is_na, Uint1 group_segs)); NLM_EXTERN Boolean BioseqRawToFastaX PROTO((BioseqPtr bsp, MyFsaPtr mfp, Boolean is_na)); NLM_EXTERN Boolean BioseqToFastaX PROTO((BioseqPtr bsp, MyFsaPtr mfp, Boolean is_na)); /***************************************************************************** * * FastaFileFunc(key, buf, data) * standard "write to file" callback * *****************************************************************************/ NLM_EXTERN Boolean FastaFileFunc PROTO((BioseqPtr bsp, Int2 key, CharPtr buf, Uint4 buflen, Pointer data)); /***************************************************************************** * * FastaDumpFileFunc(key, buf, data) * standard "write to file" callback * * Used for BLAST (FASTA) databases. If the defline is * longer than buflen, then check that an ID is not * truncated in the middle. * *****************************************************************************/ NLM_EXTERN Boolean FastaDumpFileFunc PROTO((BioseqPtr bsp, Int2 key, CharPtr buf, Uint4 buflen, Pointer data)); /***************************************************************************** * * Reads a Fasta File into a SeqEntry structure * Conventions: * >name def * agaggagagagagag * agagagagagagagag * * "name" = string is considered SEQID_LOCAL until first white space * "def" = after first white space, and before first newline will be "title" * "agaga.." = sequence follows until EOF. can be upper or lower case IUPAC * *****************************************************************************/ NLM_EXTERN SeqEntryPtr FastaToSeqEntry PROTO((FILE *fp, Boolean is_na)); /***************************************************************************** * * Reads a Fasta Buffer into a SeqEntry structure * Conventions: * >name def * agaggagagagagag * agagagagagagagag * * "name" = string is considered SEQID_LOCAL until first white space * "def" = after first white space, and before first newline will be "title" * "agaga.." = sequence follows until EOF. can be upper or lower case IUPAC * *****************************************************************************/ NLM_EXTERN SeqEntryPtr FastaToSeqBuff PROTO((CharPtr buffer, CharPtr PNTR last_char,Boolean is_na)); NLM_EXTERN SeqEntryPtr FastaToSeqBuffEx(CharPtr buffer, CharPtr PNTR last_char, Boolean is_na, CharPtr PNTR errormsg, Boolean parseSeqId); NLM_EXTERN SeqEntryPtr FastaToSeqBuffForDb(CharPtr buffer, CharPtr PNTR last_char, Boolean is_na, CharPtr PNTR errormsg, Boolean parseSeqId, CharPtr prefix, Int2Ptr ctrptr, SeqLocPtr PNTR mask_ptr); NLM_EXTERN SeqEntryPtr FastaToSeqEntryEx (FILE *fp, Boolean is_na, CharPtr PNTR errormsg, Boolean parseSeqId); NLM_EXTERN SeqEntryPtr FastaToSeqEntryForDb ( FILE *fp, Boolean is_na, CharPtr PNTR errormsg, Boolean parseSeqId, CharPtr prefix, Int2Ptr ctrptr, SeqLocPtr PNTR mask_ptr); /********* DEFINES for input type *********/ #define FASTA_MEM_IO 1 /* type of reading from buffer in memory */ #define FASTA_FILE_IO 2 /* type of reading from file */ NLM_EXTERN SeqEntryPtr FastaToSeqEntryInternalEx ( VoidPtr input, Int4 type, CharPtr PNTR next_char, Boolean is_na, CharPtr PNTR errormsg, Boolean parseSeqId, CharPtr special_symbol, CharPtr prefix, Int2Ptr ctrptr, SeqLocPtr PNTR mask_ptr); /***************************************************************************** * * Boolean FastaReadSequence() - read sequence from file * *****************************************************************************/ Boolean FastaReadSequence ( FILE *fd, /* input file pointer) */ Boolean is_na, /* type of sequence */ Int4Ptr seq_length, /* Returned length of sequence in residues */ ByteStorePtr PNTR bs_out, /* Returned pointer to sequence ByteStore */ CharPtr PNTR errormsg /* error message for debugging */ ); /***************************************************************************** * * Boolean FastaReadSequenceMem() - read sequence from buffer * *****************************************************************************/ Boolean FastaReadSequenceMem ( CharPtr buffer, /* input buffer with sequence */ CharPtr PNTR next_char, /* returned pointer to next FASTA sequence */ Boolean is_na, /* type of sequence */ Int4Ptr seq_length, /* Returned length of sequence in residues */ ByteStorePtr PNTR bs_out, /* Returned pointer to sequence ByteStore */ CharPtr PNTR errormsg /* error message for debugging */ ); /***************************************************************************** * * This routines get parts needed to make FASTA format from ASN.1 * *****************************************************************************/ /***************************************************************************** * * FastaId(bsp, buf, buflen) * Makes the string for the id part of fasta format. * buf should be at least 40 bytes * *****************************************************************************/ NLM_EXTERN Boolean FastaId PROTO((BioseqPtr bsp, CharPtr buf, Int2 buflen)); /***************************************************************************** * * FastaDefLine(bsp, buf, buflen, accession, organism) * Finds or makes a FASTA format defline (just locates the string) * buf should be very long if possible * function truncates if buf not long enough * a few deflines are longer than 255 * if (accession != NULL) prefixes defline with (accession) * used for translated GenBank records * if (organism != NULL) adds [organism] to end * if (tech == MI_TECH_phase1 or phase2, adds order comment to defline) * *****************************************************************************/ NLM_EXTERN Boolean FastaDefLine PROTO((BioseqPtr bsp, CharPtr buf, Int2 buflen, CharPtr accession, CharPtr organism, Uint1 tech)); NLM_EXTERN Boolean CreateDefLine PROTO((ItemInfoPtr dip, BioseqPtr bsp, CharPtr buf, Int2 buflen, Uint1 tech, CharPtr accession, CharPtr organism)); NLM_EXTERN Boolean CreateDefLineEx (ItemInfoPtr iip, BioseqPtr bsp, CharPtr buf, Int2 buflen, Uint1 tech, CharPtr accession, CharPtr organism, Boolean ignoreTitle); /***************************************************************************** * * FastaSeqPort(bsp, is_na, do_virtual) * opens a SeqPort for a fasta output of bsp * *****************************************************************************/ NLM_EXTERN SeqPortPtr FastaSeqPort PROTO((BioseqPtr bsp, Boolean is_na, Boolean do_virtual, Uint1 code)); /***************************************************************************** * * FastaSeqLine(spp, buf, linelen) * an open seqport is passed in. * fills buf with linelen bases * assumes buf[linelen] = '\0' * returns FALSE when no more residues to print * here for backward compatibility. Is the same as calling * FastaSeqLineEx() with do_virtual = FALSE; * *****************************************************************************/ NLM_EXTERN Boolean FastaSeqLine PROTO((SeqPortPtr spp, CharPtr buf, Int2 linelen, Boolean is_na)); /**************************************************************************** * * FastaSeqLineEx(spp, buf, linelen, is_na, do_virtual) * * adds a parameter to indicate if virtual sequences should be shown * this is necessary in order to avoid showing SEQPORT_VIRT return * (gap of 0 length) as '-', when do_virtual is TRUE. * *****************************************************************************/ NLM_EXTERN Boolean FastaSeqLineEx(SeqPortPtr spp, CharPtr buf, Int2 linelen, Boolean is_na, Boolean do_virtual); Int4 GetOrderBySeqId(Int4 choice, Boolean is_prot); /***************************************************************************** * * NC_Cleanup (entityID, ptr) and ClearGenBankKeywords (entityID, ptr) * internal functions for genome RefSeq processing * *****************************************************************************/ NLM_EXTERN void NC_Cleanup (Uint2 entityID, Pointer ptr); NLM_EXTERN void ClearGenBankKeywords (Uint2 entityID, Pointer ptr); /***************************************************************************** * * InstantiateProteinTitles (entityID, ptr) and ClearProteinTitles (entityID, ptr) * allows proteins titles to be kept as Seq_descr_title rather than always * being generated on the fly * *****************************************************************************/ NLM_EXTERN void InstantiateProteinTitles (Uint2 entityID, Pointer ptr); NLM_EXTERN void ClearProteinTitlesInNucProts (Uint2 entityID, Pointer ptr); #ifdef __cplusplus } #endif #undef NLM_EXTERN #ifdef NLM_EXPORT #define NLM_EXTERN NLM_EXPORT #else #define NLM_EXTERN #endif #endif