diff options
Diffstat (limited to 'api/asn2gnb4.c')
| -rw-r--r-- | api/asn2gnb4.c | 196 |
1 files changed, 143 insertions, 53 deletions
diff --git a/api/asn2gnb4.c b/api/asn2gnb4.c index 7788e925..6b60cc6a 100644 --- a/api/asn2gnb4.c +++ b/api/asn2gnb4.c @@ -30,7 +30,7 @@ * * Version Creation Date: 10/21/98 * -* $Revision: 1.11 $ +* $Revision: 1.18 $ * * File Description: New GenBank flatfile generator - work in progress * @@ -135,6 +135,7 @@ static FtQualType feat_qual_order [] = { FTQUAL_organism, FTQUAL_label, FTQUAL_cds_product, + FTQUAL_extra_products, FTQUAL_protein_id, FTQUAL_transcript_id, FTQUAL_db_xref, @@ -218,6 +219,7 @@ static FeaturQual asn2gnbk_featur_quals [ASN2GNBK_TOTAL_FEATUR] = { { "evidence", Qual_class_evidence }, { "exception", Qual_class_string }, { "exception_note", Qual_class_string }, + { "product", Qual_class_valnode }, { "figure", Qual_class_string }, { "frequency", Qual_class_quote }, { "function", Qual_class_quote }, @@ -1347,13 +1349,9 @@ static CharPtr validRefSeqExceptionString [] = { "RNA editing", "reasons given in citation", "ribosomal slippage", - "ribosome slippage", - "trans splicing", "trans-splicing", "alternative processing", - "alternate processing", "artificial frameshift", - "non-consensus splice site", "nonconsensus splice site", "rearrangement required for product", "modified codon recognition", @@ -1431,7 +1429,7 @@ NLM_EXTERN Int2 ValidateAccn ( if (numAlpha == 3 && numDigits == 5) return 0; if (numAlpha == 4 && numDigits == 8) return 0; } else if (numUndersc == 1) { - if (numAlpha != 2 || (numDigits != 6 && numDigits != 8)) return -2; + if (numAlpha != 2 || (numDigits != 6 && numDigits != 8 && numDigits != 9)) return -2; if (accession [0] == 'N' || accession [0] == 'X' || accession [0] == 'Z') { if (accession [1] == 'M' || accession [1] == 'C' || @@ -1575,20 +1573,27 @@ NLM_EXTERN CharPtr goFieldType [] = { }; static CharPtr GetGOtext ( - UserFieldPtr topufp + UserFieldPtr topufp, + IntAsn2gbJobPtr ajp ) { - CharPtr evidence = NULL; - Char gid [32]; - CharPtr goid = NULL; - Int2 j; - ObjectIdPtr oip; - Int4 pmid = 0; - CharPtr str; - CharPtr textstr = NULL; - Char tmp [32]; - UserFieldPtr ufp; + CharPtr evidence = NULL; + StringItemPtr ffstring; + Char gid [32]; + CharPtr goid = NULL; + Boolean is_www; + Int2 j; + ObjectIdPtr oip; + Int4 pmid = 0; + CharPtr ptr; + CharPtr str; + CharPtr textstr = NULL; + Char tmp [32]; + UserFieldPtr ufp; + + if (topufp == NULL || ajp == NULL) return NULL; + is_www = GetWWW (ajp); for (ufp = topufp; ufp != NULL; ufp = ufp->next) { oip = ufp->label; @@ -1627,13 +1632,31 @@ static CharPtr GetGOtext ( } /* if (StringHasNoText (textstr)) return NULL; */ - str = (CharPtr) MemNew (StringLen (textstr) + StringLen (goid) + StringLen (evidence) + 50); + str = (CharPtr) MemNew (StringLen (textstr) + StringLen (goid) + StringLen (evidence) + StringLen (link_go) + 80); if (str == NULL) return NULL; StringCpy (str, textstr); if (! StringHasNoText (goid)) { StringCat (str, " [goid "); - StringCat (str, goid); + if (is_www) { + ffstring = FFGetString (ajp); + if (ffstring != NULL) { + FFAddOneString(ffstring, "<a href=", FALSE, FALSE, TILDE_IGNORE); + FFAddOneString(ffstring, link_go, FALSE, FALSE, TILDE_IGNORE); + FFAddOneString(ffstring, goid, FALSE, FALSE, TILDE_IGNORE); + FFAddOneChar(ffstring, '>', FALSE); + FFAddOneString(ffstring, goid, FALSE, FALSE, TILDE_IGNORE); + FFAddOneString(ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE); + ptr = FFToCharPtr (ffstring); + FFRecycleString (ajp, ffstring); + StringCat (str, ptr); + MemFree (ptr); + } else { + StringCat (str, goid); + } + } else { + StringCat (str, goid); + } StringCat (str, "]"); } if (! StringHasNoText (evidence)) { @@ -1751,6 +1774,26 @@ static void LIBCALLBACK SaveGBSeqSequence ( *tmpp = tmp; } +static int LIBCALLBACK SortVnpByInt (VoidPtr ptr1, VoidPtr ptr2) + +{ + 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; + + if (vnp1->data.intvalue > vnp2->data.intvalue) { + return 1; + } else if (vnp1->data.intvalue < vnp2->data.intvalue) { + return -1; + } + + return 0; +} + static void FormatFeatureBlockQuals ( StringItemPtr ffstring, IntAsn2gbJobPtr ajp, @@ -1784,9 +1827,7 @@ static void FormatFeatureBlockQuals ( CodeBreakPtr cbp; Char ch; Uint1 choice; - /* - Uint1 code = Seq_code_ncbieaa; - */ + ValNodePtr citlist; Int4 gi; Boolean hadProtDesc = FALSE; DbtagPtr dbt; @@ -1823,9 +1864,6 @@ static void FormatFeatureBlockQuals ( SeqIdPtr sip; SeqLocPtr slp; Boolean split; - /* - SeqPortPtr spp; - */ CharPtr start; CharPtr str; Boolean suppress_period; @@ -2525,15 +2563,24 @@ static void FormatFeatureBlockQuals ( case Qual_class_pubset : vnp = qvp [idx].vnp; if (vnp != NULL && asp != NULL && asp->referenceArray != NULL) { + citlist = NULL; for (ppr = vnp->data.ptrvalue; ppr != NULL; ppr = ppr->next) { j = MatchRef (ppr, asp->referenceArray, asp->numReferences); if (j > 0) { + ValNodeAddInt (&citlist, 0, (Int4) j); + } + } + citlist = ValNodeSort (citlist, SortVnpByInt); + for (vnp = citlist; vnp != NULL; vnp = vnp->next) { + j = (Int2) vnp->data.intvalue; + if (j > 0) { sprintf (numbuf, "%d", (int) j); FFAddTextToString(ffstring, "/citation=[", numbuf, "]", FALSE, TRUE, TILDE_TO_SPACES); FFAddOneChar(ffstring, '\n', FALSE); } } + citlist = ValNodeFree (citlist); } break; @@ -2677,7 +2724,7 @@ static void FormatFeatureBlockQuals ( ajp->relModeError = TRUE; } } else { - sip = GetSeqIdForGI(gi); + sip = GetSeqIdForGI (gi); if (sip != NULL && SeqIdWrite (sip, seqid, PRINTID_TEXTID_ACC_VER, sizeof (seqid)) != NULL) { if ((! ajp->flags.dropIllegalQuals) || ValidateAccn (seqid) == 0) { FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals [idx].name, "=\"", @@ -2777,29 +2824,6 @@ static void FormatFeatureBlockQuals ( FFAddOneChar(ffstring, '\n', FALSE); } MemFree (str); - /* - 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 (! StringHasNoText (str)) { - FFAddTextToString(ffstring, "/translation=\"", str, "\"", - FALSE, TRUE, TILDE_TO_SPACES); - FFAddOneChar(ffstring, '\n', FALSE); - } - MemFree (str); - } else { - ajp->relModeError = TRUE; - } - SeqPortFree (spp); - */ } else { ajp->relModeError = TRUE; } @@ -2876,7 +2900,7 @@ static void FormatFeatureBlockQuals ( for (entry = qvp [jdx].ufp; entry != NULL; entry = entry->next) { if (entry == NULL || entry->choice != 11) break; ufp = (UserFieldPtr) entry->data.ptrvalue; - str = GetGOtext (ufp); + str = GetGOtext (ufp, ajp); if (! StringHasNoText (str)) { FFAddTextToString(ffstring, "/", asn2gnbk_featur_quals[jdx].name, "=", FALSE, TRUE, TILDE_IGNORE); @@ -2997,7 +3021,7 @@ static void FormatFeatureBlockQuals ( for (entry = qvp [jdx].ufp; entry != NULL; entry = entry->next) { if (entry == NULL || entry->choice != 11) break; ufp = (UserFieldPtr) entry->data.ptrvalue; - str = GetGOtext (ufp); + str = GetGOtext (ufp, ajp); if (! StringHasNoText (str)) { if (StringCmp (prefix, "; ") == 0) { prefix = ";\n"; @@ -3241,7 +3265,7 @@ static void FormatFeatureBlockQuals ( FALSE, FALSE, TILDE_IGNORE); } } else { - sip = GetSeqIdForGI(gi); + sip = GetSeqIdForGI (gi); if (sip != NULL && SeqIdWrite (sip, seqid, PRINTID_TEXTID_ACC_VER, sizeof (seqid)) != NULL) { if ((! ajp->flags.dropIllegalQuals) || ValidateAccn (seqid) == 0) { FFAddTextToString(unique, prefix, "transcript found in: ", seqid, @@ -4264,7 +4288,11 @@ static CharPtr FormatFeatureBlockEx ( 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; + if (ajp->flags.extraProductsToNote) { + qvp [FTQUAL_prot_names].vnp = vnp; + } else { + qvp [FTQUAL_extra_products].vnp = vnp; + } } qvp [FTQUAL_prot_desc].str = prp->desc; qvp [FTQUAL_prot_activity].vnp = prp->activity; @@ -4998,8 +5026,10 @@ NLM_EXTERN CharPtr FormatFeatureBlock ( BioseqPtr bsp; SeqMgrFeatContext fcontext; FmtType format; + ValNodePtr head; QualValPtr qvp; SeqFeatPtr sfp; + CharPtr str; BioseqPtr target; if (afp == NULL || bbp == NULL) return NULL; @@ -5019,10 +5049,70 @@ NLM_EXTERN CharPtr FormatFeatureBlock ( sfp = SeqMgrGetDesiredFeature (bbp->entityID, NULL, bbp->itemID, 0, NULL, &fcontext); if (sfp == NULL) return NULL; + /* five-column feature table uses special code for formatting */ + + if (ajp->format == FTABLE_FMT) { + head = NULL; + PrintFtableLocAndQuals (ajp, &head, target, sfp, &fcontext); + str = MergeFFValNodeStrs (head); + ValNodeFreeData (head); + return str; + } + + /* otherwise do regular flatfile formatting */ + return FormatFeatureBlockEx (ajp, asp, bsp, target, sfp, &fcontext, qvp, format, (IntFeatBlockPtr) bbp, ISA_aa (bsp->mol), TRUE); } +NLM_EXTERN CharPtr FormatFeatHeaderBlock ( + Asn2gbFormatPtr afp, + BaseBlockPtr bbp +) + +{ + IntAsn2gbJobPtr ajp; + Asn2gbSectPtr asp; + BioseqPtr bsp; + Char id [64]; + SeqIdPtr sip; + SeqIdPtr sip2; + CharPtr str = NULL; + BioseqPtr target; + Char tmp [53]; + + if (afp == NULL || bbp == NULL) return NULL; + ajp = afp->ajp; + if (ajp == NULL) return NULL; + asp = afp->asp; + if (asp == NULL) return NULL; + target = asp->target; + bsp = asp->bsp; + if (target == NULL || bsp == NULL) return NULL; + + /* five-column feature table uses special code for formatting */ + + if (ajp->format == FTABLE_FMT) { + sip = SeqIdFindBest (target->id, 0); + if (sip != NULL && sip->choice == SEQID_GI) { + sip2 = GetSeqIdForGI (sip->data.intvalue); + if (sip2 != NULL) { + sip = sip2; + } + } + SeqIdWrite (sip, id, PRINTID_FASTA_LONG, sizeof (id) - 1); + if (! StringHasNoText (id)) { + sprintf (tmp, ">Feature %s\n", id); + str = StringSave (tmp); + } + return str; + } + + /* otherwise do regular flatfile formatting */ + + return StringSaveNoNull (bbp->string); +} + /* stand alone function to produce qualifiers in genbank style */ |