summaryrefslogtreecommitdiff
path: root/api/tofasta.c
diff options
context:
space:
mode:
Diffstat (limited to 'api/tofasta.c')
-rw-r--r--api/tofasta.c390
1 files changed, 368 insertions, 22 deletions
diff --git a/api/tofasta.c b/api/tofasta.c
index 58797c41..38c1280e 100644
--- a/api/tofasta.c
+++ b/api/tofasta.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 7/12/91
*
-* $Revision: 6.219 $
+* $Revision: 6.230 $
*
* File Description: various sequence objects to fasta output
*
@@ -876,6 +876,7 @@ static SeqIdPtr ChooseFastaID (BioseqPtr bsp, Boolean allow_mult)
static Int4 BioseqFastaStreamInternal (
BioseqPtr bsp,
SeqLocPtr slp,
+ SeqLitPtr lit,
CharPtr str,
FILE *fp,
ByteStorePtr bs,
@@ -890,16 +891,22 @@ static Int4 BioseqFastaStreamInternal (
)
{
+ Char acc [41];
+ SeqIdPtr accn = NULL;
Char buf [4096];
- Char ch;
+ Char ch, ch1, ch2, ch3;
Int4 count = 0;
+ Int4 gi = -1;
+ SeqIdPtr gpp = NULL;
Char id [128];
+ Uint1 id_format = PRINTID_FASTA_LONG;
+ CharPtr ptr;
StreamFsa sf;
SeqIdPtr sip = NULL;
Char spn [64];
CharPtr tmp;
- if (bsp == NULL && slp == NULL && str == NULL) return 0;
+ if (bsp == NULL && slp == NULL && lit == NULL && str == NULL) return 0;
if (fp == NULL && bs == NULL) return 0;
if (bsp != NULL && bsp->repr == Seq_repr_virtual) return 0;
if (linelen > 128) {
@@ -920,6 +927,7 @@ static Int4 BioseqFastaStreamInternal (
if (grouplen < 1) {
grouplen = 0;
}
+ acc [0] = '\0';
MemSet ((Pointer) &sf, 0, sizeof (StreamFsa));
sf.fp = fp;
sf.bs = bs;
@@ -932,15 +940,108 @@ static Int4 BioseqFastaStreamInternal (
sf.grouplen = grouplen;
sf.skip = skip;
sf.gi = 0;
- if (bsp != NULL) {
- for (sip = bsp->id; sip != NULL; sip = sip->next) {
- if (sip->choice != SEQID_GI) continue;
- sf.gi = sip->data.intvalue;
- }
- }
sf.start = 0;
sf.seqpos = 0;
sf.seqspans = (Boolean) ((flags & STREAM_HTML_SPANS) != 0);
+ if (sf.seqspans) {
+ if (bsp != NULL) {
+ 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;
+ case SEQID_GPIPE :
+ /* should not override better accession */
+ gpp = sip;
+ break;
+ default :
+ break;
+ }
+ }
+ } else if (slp != NULL) {
+ /* PUBSEQ_OS will send a SeqInt with a chain of Seq-ids */
+ for (sip = SeqLocId (slp); 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;
+ case SEQID_GPIPE :
+ /* should not override better accession */
+ gpp = sip;
+ break;
+ default :
+ break;
+ }
+ }
+ if (sip != NULL && sip->choice == SEQID_GI) {
+ sf.gi = sip->data.intvalue;
+ }
+ }
+ if (gi > 0) {
+ sf.gi = gi;
+ }
+ if (accn == NULL) {
+ accn = gpp;
+ }
+ if (accn != NULL) {
+ SeqIdWrite (accn, acc, PRINTID_TEXTID_ACC_ONLY, sizeof (acc) - 1);
+
+ if (accn->choice == SEQID_PDB) {
+ ptr = StringChr (acc, '_');
+ if (ptr != NULL) {
+ ch1 = ptr [1];
+ if (ch1 != '\0') {
+ ch2 = ptr [2];
+ if (ch2 != '\0') {
+ ch3 = ptr [3];
+ if (ch3 == '\0') {
+ if (ch1 == ch2) {
+ if (IS_UPPER (ch1)) {
+ ptr [1] = TO_LOWER (ch1);
+ ptr [2] = '\0';
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
if (do_defline) {
id [0] = '\0';
if (substitute_ids) {
@@ -948,7 +1049,10 @@ static Int4 BioseqFastaStreamInternal (
} else if (bsp != NULL) {
sip = bsp->id;
}
- SeqIdWrite (sip, id, PRINTID_FASTA_LONG, sizeof (id) - 1);
+ if ((flags & STREAM_ALL_FASTA_IDS) != 0) {
+ id_format = PRINTID_FASTA_ALL;
+ }
+ SeqIdWrite (sip, id, id_format, sizeof (id) - 1);
/* no longer need to do feature indexing if title not present to speed up creation */
/*
sdp = GetNextDescriptorUnindexed (bsp, Seq_descr_title, NULL);
@@ -984,6 +1088,8 @@ static Int4 BioseqFastaStreamInternal (
count = SeqPortStream (bsp, flags, (Pointer) &sf, FsaStreamProc);
} else if (slp != NULL) {
count = SeqPortStreamLoc (slp, flags, (Pointer) &sf, FsaStreamProc);
+ } else if (lit != NULL) {
+ count = SeqPortStreamLit (lit, flags, (Pointer) &sf, FsaStreamProc);
} else if (str != NULL) {
count = StringLen (str);
FsaStreamProc (str, (Pointer) &sf);
@@ -1007,6 +1113,12 @@ static Int4 BioseqFastaStreamInternal (
fprintf (sf.fp, "</span>");
}
fprintf (sf.fp, "\n");
+ if (sf.seqspans) {
+ fprintf (sf.fp, "<script type=\"text/javascript\">");
+ fprintf (sf.fp, "if (typeof(oData) == \"undefined\") oData = []; ");
+ fprintf (sf.fp, "oData.push({gi:%ld,acc:\"%s\"})", (long) sf.gi, acc);
+ fprintf (sf.fp, "</script>\n");
+ }
} else if (sf.bs != NULL) {
if (sf.seqspans) {
sprintf (spn, "<span class=\"ff_line\" id=\"gi_%ld_%ld\">", (long) sf.gi, (long) (sf.start + 1));
@@ -1017,6 +1129,16 @@ static Int4 BioseqFastaStreamInternal (
BSWrite (sf.bs, "</span>", sizeof ("</span>"));
}
BSWrite (sf.bs, "\n", sizeof ("\n"));
+ if (sf.seqspans) {
+ sprintf (spn, "<script type=\"text/javascript\">");
+ BSWrite (sf.bs, spn, StringLen (spn));
+ sprintf (spn, "if (typeof(oData) == \"undefined\") oData = []; ");
+ BSWrite (sf.bs, spn, StringLen (spn));
+ sprintf (spn, "oData.push({gi:%ld,acc:\"%s\"})", (long) sf.gi, acc);
+ BSWrite (sf.bs, spn, StringLen (spn));
+ sprintf (spn, "</script>\n");
+ BSWrite (sf.bs, spn, StringLen (spn));
+ }
}
}
return count;
@@ -1033,7 +1155,7 @@ NLM_EXTERN Int4 BioseqFastaStream (
)
{
- return BioseqFastaStreamInternal (bsp, NULL, NULL, fp, NULL, flags,
+ return BioseqFastaStreamInternal (bsp, NULL, NULL, NULL, fp, NULL, flags,
linelen, blocklen, grouplen,
do_defline, FALSE, FALSE, 0);
}
@@ -1051,7 +1173,7 @@ NLM_EXTERN Int4 BioseqFastaStreamEx (
)
{
- return BioseqFastaStreamInternal (bsp, NULL, NULL, fp, NULL, flags,
+ return BioseqFastaStreamInternal (bsp, NULL, NULL, NULL, fp, NULL, flags,
linelen, blocklen, grouplen,
do_defline, substitute_ids, sorted_protein, 0);
}
@@ -1067,7 +1189,7 @@ NLM_EXTERN Int4 BioseqFastaMemStream (
)
{
- return BioseqFastaStreamInternal (bsp, NULL, NULL, NULL, bs, flags,
+ return BioseqFastaStreamInternal (bsp, NULL, NULL, NULL, NULL, bs, flags,
linelen, blocklen, grouplen,
do_defline, FALSE, FALSE, 0);
}
@@ -1084,7 +1206,24 @@ NLM_EXTERN Int4 SeqLocFastaStream (
{
if (slp == NULL || fp == NULL) return 0;
- return BioseqFastaStreamInternal (NULL, slp, NULL, fp, NULL, flags,
+ return BioseqFastaStreamInternal (NULL, slp, NULL, NULL, fp, NULL, flags,
+ linelen, blocklen, grouplen,
+ FALSE, FALSE, FALSE, 0);
+}
+
+NLM_EXTERN Int4 SeqLitFastaStream (
+ SeqLitPtr lit,
+ FILE *fp,
+ StreamFlgType flags,
+ Int2 linelen,
+ Int2 blocklen,
+ Int2 grouplen
+)
+
+{
+ if (lit == NULL || fp == NULL) return 0;
+
+ return BioseqFastaStreamInternal (NULL, NULL, lit, NULL, fp, NULL, flags,
linelen, blocklen, grouplen,
FALSE, FALSE, FALSE, 0);
}
@@ -1275,7 +1414,7 @@ NLM_EXTERN Int4 CdRegionFastaStream (
skip = 2;
}
- return BioseqFastaStreamInternal (NULL, sfp->location, NULL, fp, NULL, flags,
+ return BioseqFastaStreamInternal (NULL, sfp->location, NULL, NULL, fp, NULL, flags,
linelen, blocklen, grouplen,
FALSE, FALSE, FALSE, skip);
}
@@ -1330,7 +1469,7 @@ NLM_EXTERN Int4 TranslationFastaStream (
}
}
- count = BioseqFastaStreamInternal (NULL, NULL, str, fp, NULL, flags,
+ count = BioseqFastaStreamInternal (NULL, NULL, NULL, str, fp, NULL, flags,
linelen, blocklen, grouplen,
FALSE, FALSE, FALSE, 0);
@@ -1339,6 +1478,153 @@ NLM_EXTERN Int4 TranslationFastaStream (
return count;
}
+static void DoGeneDefline (
+ SeqFeatPtr sfp,
+ FILE *fp,
+ GeneRefPtr grp,
+ CharPtr idSuffix
+)
+
+{
+ BioseqPtr bsp = NULL;
+ Char buf [512];
+ Boolean do_defline = TRUE;
+ Uint2 entityID;
+ SeqMgrFeatContext genecontext;
+ IntAsn2gbJob iaj;
+ Boolean partial5;
+ Boolean partial3;
+ SeqIdPtr sip;
+ CharPtr str;
+ Char tmp [64];
+
+ if (sfp == NULL || fp == NULL || grp == NULL) return;
+ if (sfp == NULL || fp == NULL || sfp->data.choice != SEQFEAT_GENE) return;
+ grp = (GeneRefPtr) sfp->data.value.ptrvalue;
+ if (grp == NULL) return;
+
+ if (do_defline) {
+ bsp = BioseqFindFromSeqLoc (sfp->location);
+ if (bsp == NULL) {
+ do_defline = FALSE;
+ StringCpy (buf, "lcl|");
+ sip = SeqLocId (sfp->location);
+ if (sip != NULL) {
+ SeqIdWrite (sip, tmp, PRINTID_TEXTID_ACC_VER, sizeof (tmp) - 1);
+ StringCat (buf, tmp);
+ }
+ if (StringDoesHaveText (idSuffix) && StringLen (idSuffix) < 200) {
+ StringCat (buf, idSuffix);
+ }
+ FastaFileFunc (bsp, FASTA_ID, buf, sizeof (buf), (Pointer) fp);
+ StringCpy (buf, "?");
+ FastaFileFunc (bsp, FASTA_DEFLINE, buf, sizeof (buf), (Pointer) fp);
+ fflush (fp);
+ }
+ }
+
+ if (do_defline && bsp != NULL) {
+ if (sfp != SeqMgrGetDesiredFeature (0, bsp, 0, 0, sfp, &genecontext)) {
+ do_defline = FALSE;
+ StringCpy (buf, "lcl|");
+ sip = SeqIdFindWorst (bsp->id);
+ if (sip != NULL) {
+ SeqIdWrite (sip, tmp, PRINTID_TEXTID_ACC_VER, sizeof (tmp) - 1);
+ StringCat (buf, tmp);
+ }
+ if (StringDoesHaveText (idSuffix) && StringLen (idSuffix) < 200) {
+ StringCat (buf, idSuffix);
+ }
+ FastaFileFunc (bsp, FASTA_ID, buf, sizeof (buf), (Pointer) fp);
+ StringCpy (buf, "?");
+ FastaFileFunc (bsp, FASTA_DEFLINE, buf, sizeof (buf), (Pointer) fp);
+ fflush (fp);
+ }
+ }
+
+ if (do_defline) {
+ entityID = ObjMgrGetEntityIDForPointer (bsp);
+ if (SeqMgrFeaturesAreIndexed (entityID) == 0) {
+ SeqMgrIndexFeatures (entityID, NULL);
+ }
+
+ CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
+
+ MemSet ((Pointer) &iaj, 0, sizeof (IntAsn2gbJob));
+ iaj.flags.iupacaaOnly = FALSE;
+ iaj.relModeError = FALSE;
+
+ StringCpy (buf, "lcl|");
+ sip = SeqIdFindWorst (bsp->id);
+ if (sip != NULL) {
+ SeqIdWrite (sip, tmp, PRINTID_TEXTID_ACC_VER, sizeof (tmp) - 1);
+ StringCat (buf, tmp);
+ }
+ if (StringDoesHaveText (idSuffix) && StringLen (idSuffix) < 200) {
+ StringCat (buf, idSuffix);
+ }
+
+ FastaFileFunc (bsp, FASTA_ID, buf, sizeof (buf), (Pointer) fp);
+
+ buf [0] = '\0';
+ if (StringDoesHaveText (grp->locus)) {
+ StringCat (buf, "[gene=");
+ StringCat (buf, grp->locus);
+ StringCat (buf, "] ");
+ }
+ if (StringDoesHaveText (grp->locus_tag)) {
+ StringCat (buf, "[locus_tag=");
+ StringCat (buf, grp->locus_tag);
+ StringCat (buf, "] ");
+ }
+ if (StringLen (buf) == 0 && StringDoesHaveText (genecontext.label)) {
+ StringCat (buf, "[gene=");
+ StringCat (buf, genecontext.label);
+ StringCat (buf, "] ");
+ }
+ str = FFFlatLoc (&iaj, bsp, sfp->location, FALSE, FALSE);
+ if (str != NULL && StringLen (str) + StringLen (buf) < sizeof (buf) - 10) {
+ StringCat (buf, "[location=");
+ StringCat (buf, str);
+ StringCat (buf, "] ");
+ MemFree (str);
+ }
+ TrimSpacesAroundString (buf);
+
+ FastaFileFunc (bsp, FASTA_DEFLINE, buf, sizeof (buf), (Pointer) fp);
+
+ fflush (fp);
+ }
+}
+
+NLM_EXTERN Int4 GeneFastaStream (
+ SeqFeatPtr sfp,
+ FILE *fp,
+ StreamFlgType flags,
+ Int2 linelen,
+ Int2 blocklen,
+ Int2 grouplen,
+ Boolean do_defline,
+ CharPtr idSuffix
+)
+
+{
+ GeneRefPtr grp;
+
+ if (sfp == NULL || sfp->data.choice != SEQFEAT_GENE) return 0;
+ if (fp == NULL) return 0;
+ grp = (GeneRefPtr) sfp->data.value.ptrvalue;
+ if (grp == NULL) return 0;
+
+ if (do_defline) {
+ DoGeneDefline (sfp, fp, grp, idSuffix);
+ }
+
+ return BioseqFastaStreamInternal (NULL, sfp->location, NULL, NULL, fp, NULL, flags,
+ linelen, blocklen, grouplen,
+ FALSE, FALSE, FALSE, 0);
+}
+
/*****************************************************************************
*
* SeqEntryFastaStream (bsp, fp, flags, linelen, blocklen, grouplen,
@@ -5109,6 +5395,7 @@ typedef struct deflinestruct {
/* subsource fields */
CharPtr m_chromosome;
CharPtr m_clone;
+ Boolean m_has_clone;
CharPtr m_map;
CharPtr m_plasmid;
CharPtr m_segment;
@@ -5117,6 +5404,9 @@ typedef struct deflinestruct {
CharPtr m_isolate;
CharPtr m_strain;
+ /* user object fields */
+ Boolean m_is_unverified;
+
/* exception fields */
TextFsaPtr m_low_quality_fsa;
} DefLineData, PNTR DefLinePtr;
@@ -5176,6 +5466,7 @@ static void x_SetFlags (
SeqIdPtr sip;
CharPtr str;
TextSeqIdPtr tsip;
+ UserObjectPtr uop;
ValNodePtr vnp;
if (dlp == NULL) return;
@@ -5307,6 +5598,19 @@ static void x_SetFlags (
}
}
+ /* process Unverified user object */
+ for (sdp = GetNextDescriptorUnindexed (bsp, Seq_descr_user, NULL);
+ sdp != NULL;
+ sdp = GetNextDescriptorUnindexed (bsp, Seq_descr_user, sdp)) {
+ if (sdp->choice != Seq_descr_user) continue;
+ uop = (UserObjectPtr) sdp->data.ptrvalue;
+ if (uop == NULL) continue;
+ oip = uop->type;
+ if (oip == NULL) continue;
+ if (StringICmp (oip->str, "Unverified") != 0) continue;
+ dlp->m_is_unverified = TRUE;
+ }
+
if (dlp->m_htg_tech || dlp->m_third_party) {
/* process keywords */
keywords = NULL;
@@ -5365,6 +5669,31 @@ static void x_SetFlags (
}
/* set instance variables from BioSource */
+static void x_SetSrcClone (
+ SeqFeatPtr sfp,
+ Pointer userdata
+)
+
+{
+ BioSourcePtr biop;
+ DefLinePtr dlp;
+ SubSourcePtr ssp;
+
+ if (sfp == NULL || sfp->data.choice != SEQFEAT_BIOSRC) return;
+ dlp = (DefLinePtr) userdata;
+ if (dlp == NULL) return;
+
+ biop = (BioSourcePtr) sfp->data.value.ptrvalue;
+ if (biop == NULL) return;
+
+ /* look for clones on source features */
+ for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next) {
+ if (StringHasNoText (ssp->name)) continue;
+ if (ssp->subtype != SUBSRC_clone) continue;
+ dlp->m_has_clone = TRUE;
+ }
+}
+
static void x_SetBioSrc (
DefLinePtr dlp
)
@@ -5404,6 +5733,7 @@ static void x_SetBioSrc (
break;
case SUBSRC_clone :
dlp->m_clone = ssp->name;
+ dlp->m_has_clone = TRUE;
break;
case SUBSRC_map :
dlp->m_map = ssp->name;
@@ -5444,6 +5774,10 @@ static void x_SetBioSrc (
}
}
}
+
+ if (dlp->m_has_clone) return;
+
+ VisitFeaturesOnBsp (bsp, (Pointer) dlp, x_SetSrcClone);
}
static CharPtr x_TrimFirstNCharacters (
@@ -5593,6 +5927,11 @@ static CharPtr x_DescribeClones (
if (dlp == NULL) return NULL;
+ if (dlp->m_htgs_unfinished && dlp->m_htgs_pooled && dlp->m_has_clone) {
+ result = StringSave (", pooled multiple clones");
+ return result;
+ }
+
str = dlp->m_clone;
if (StringHasNoText (str)) return NULL;
@@ -5606,9 +5945,7 @@ static CharPtr x_DescribeClones (
ch = *str;
}
- if (dlp->m_htgs_unfinished && dlp->m_htgs_pooled) {
- result = StringSave (", pooled multiple clones");
- } else if (count > 3) {
+ if (count > 3) {
sprintf (buf, ", %d clones", (int) count);
result = StringSave (buf);
} else {
@@ -6817,7 +7154,8 @@ static CharPtr x_TitleFromWGS (
}
static CharPtr x_SetPrefix (
- DefLinePtr dlp
+ DefLinePtr dlp,
+ CharPtr title
)
{
@@ -6825,7 +7163,11 @@ static CharPtr x_SetPrefix (
if (dlp == NULL) return NULL;
- if (dlp->m_is_tsa) {
+ if (dlp->m_is_unverified) {
+ if (StringStr (title, "UNVERIFIED") == NULL) {
+ prefix = "UNVERIFIED: ";
+ }
+ } else if (dlp->m_is_tsa) {
prefix = "TSA: ";
} else if (dlp->m_third_party) {
if (dlp->m_tpa_exp) {
@@ -7062,6 +7404,8 @@ NLM_EXTERN CharPtr NewCreateDefLine (
x_TrimFirstNCharacters (title, 10);
} else if (StringNICmp (title, "TSA:", 4) == 0) {
x_TrimFirstNCharacters (title, 4);
+ } else if (StringNICmp (title, "UNVERIFIED:", 11) == 0) {
+ x_TrimFirstNCharacters (title, 11);
}
/* strip leading spaces remaining after removal of old TPA or TSA prefixes */
@@ -7071,7 +7415,7 @@ NLM_EXTERN CharPtr NewCreateDefLine (
x_TrimMostPunctFromEnd (title);
/* calcualte prefix */
- prefix = x_SetPrefix (dlp);
+ prefix = x_SetPrefix (dlp, title);
/* calculate suffix */
suffix = x_SetSuffix (dlp, title);
@@ -7093,6 +7437,8 @@ NLM_EXTERN CharPtr NewCreateDefLine (
dlp = MemFree (dlp);
+ Asn2gnbkCompressSpaces (result);
+
return result;
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-02 19:59:20 +0000