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-rw-r--r--api/sequtil.c135
1 files changed, 103 insertions, 32 deletions
diff --git a/api/sequtil.c b/api/sequtil.c
index 07cb6305..3b41b818 100644
--- a/api/sequtil.c
+++ b/api/sequtil.c
@@ -29,13 +29,50 @@
*
* Version Creation Date: 4/1/91
*
-* $Revision: 6.196 $
+* $Revision: 6.207 $
*
* File Description: Sequence Utilities for objseq and objsset
*
* Modifications:
* --------------------------------------------------------------------------
* $Log: sequtil.c,v $
+* Revision 6.207 2006/09/28 20:19:26 bollin
+* fixed buffer overrun problem in SeqPointWriteEx, increased size of buffer used
+* by SeqLocPrintProc
+*
+* Revision 6.206 2006/09/20 14:53:18 kans
+* ExtendSingleGeneOnMRNA and CorrectGeneFeatLocation look for origin artificial and taxname synthetic construct, do not extend gene
+*
+* Revision 6.205 2006/09/18 17:58:41 kans
+* added EG to WHICH_db_accession
+*
+* Revision 6.204 2006/08/21 20:02:31 kans
+* assign EF to NCBI dirsub in WHICH_db_accession
+*
+* Revision 6.203 2006/07/13 17:06:39 bollin
+* use Uint4 instead of Uint2 for itemID values
+* removed unused variables
+* resolved compiler warnings
+*
+* Revision 6.202 2006/07/06 15:05:02 kans
+* added EE to WHICH_db_accession as NCBI EST
+*
+* Revision 6.201 2006/06/29 20:31:19 kans
+* only AH may be segmented protein, CH, CM, DS are nucleotide
+*
+* Revision 6.200 2006/06/29 14:24:05 kans
+* added ED to WHICH_db_accession as NCBI GSS
+*
+* Revision 6.199 2006/06/20 20:49:21 kans
+* added CU to WHICH_db_accession as EMBL genome project data
+*
+* Revision 6.198 2006/05/30 14:54:06 kans
+* added EC as NCBI EST prefix
+*
+* Revision 6.197 2006/05/11 17:08:13 bollin
+* corrected problem in GetThePointForOffset for SeqLocStart and SeqLocStop for
+* all-minus strand interval locations
+*
* Revision 6.196 2006/04/06 15:41:19 kans
* added DG to WHICH_db_accession
*
@@ -1506,7 +1543,7 @@ NLM_EXTERN ByteStorePtr BSPack (ByteStorePtr from, Uint1 oldcode,
j = 0;
}
/* byte = (Uint1) BSGetByte(from); */
- byte = (Int2) (Uint1) tmp [j];
+ byte = (Uint1) tmp [j];
j++;
if(Code4na[byte]) {
newcode = Seq_code_ncbi4na;
@@ -1540,7 +1577,7 @@ NLM_EXTERN ByteStorePtr BSPack (ByteStorePtr from, Uint1 oldcode,
j = 0;
}
/* byte = (Uint1) BSGetByte(from); */
- byte = (Int2) (Uint1) tmp [j];
+ byte = (Uint1) tmp [j];
j++;
if(CodeIna[byte]) {
newcode = Seq_code_ncbi4na;
@@ -1827,7 +1864,7 @@ NLM_EXTERN Boolean RebuildDNA_4na (Uint1Ptr buffer, Int4 length, Uint4Ptr lbytes
{
Boolean new = FALSE;
- Int4 i;
+ Uint4 i;
Uint4 amb_num;
Uint4Ptr amb_buff;
Uint1 char_l, char_r;
@@ -2413,13 +2450,16 @@ NLM_EXTERN ByteStorePtr BSCompressDNAOld(ByteStorePtr from, Int4 len,
NLM_EXTERN void CorrectGeneFeatLocation(SeqEntryPtr sep, Pointer data,
Int4 n, Int2 m)
{
- BioseqPtr bsp;
- ValNodePtr vnp;
- MolInfoPtr mip;
- SeqAnnotPtr sap;
- SeqFeatPtr sfp;
- SeqIntPtr sip;
-
+ BioseqPtr bsp;
+ ValNodePtr vnp;
+ MolInfoPtr mip;
+ SeqAnnotPtr sap;
+ SeqFeatPtr sfp;
+ SeqIntPtr sip;
+ SeqDescrPtr sdp;
+ BioSourcePtr biop;
+ OrgRefPtr orp;
+
if(sep == NULL)
return;
@@ -2453,6 +2493,19 @@ NLM_EXTERN void CorrectGeneFeatLocation(SeqEntryPtr sep, Pointer data,
if(vnp == NULL)
return;
+ sdp = GetNextDescriptorUnindexed (bsp, Seq_descr_source, NULL);
+ if (sdp != NULL) {
+ biop = (BioSourcePtr) sdp->data.ptrvalue;
+ if (biop != NULL) {
+ if (biop->origin == ORG_ARTIFICIAL) {
+ orp = biop->org;
+ if (orp != NULL) {
+ if (StringICmp (orp->taxname, "synthetic construct") == 0) return;
+ }
+ }
+ }
+ }
+
/* Otherwise go ahead
*/
for(sap = bsp->annot; sap != NULL; sap = sap->next) {
@@ -6814,8 +6867,8 @@ Boolean GetThePointForOffset(SeqLocPtr of, SeqPntPtr target, Uint1 which_end)
case SEQLOC_START:
if (all_minus)
{
- target->point = SeqLocStop (last);
- target->id = last_sip;
+ target->point = SeqLocStop (first);
+ target->id = first_sip;
}
else
{
@@ -6833,8 +6886,8 @@ Boolean GetThePointForOffset(SeqLocPtr of, SeqPntPtr target, Uint1 which_end)
case SEQLOC_STOP:
if (all_minus)
{
- target->point = SeqLocStart (first);
- target->id = first_sip;
+ target->point = SeqLocStart (last);
+ target->id = last_sip;
}
else
{
@@ -7092,7 +7145,7 @@ SeqLocPrintProc
SeqIdPtr lastid,
Boolean use_best_id)
{
- Char buf[41];
+ Char buf[128];
SeqBondPtr sbp;
PackSeqPntPtr pspp;
SeqIntPtr sip;
@@ -7118,7 +7171,7 @@ SeqLocPrintProc
sbp = (SeqBondPtr)(slp->data.ptrvalue);
if (sbp->a != NULL)
{
- lastid = SeqPointWriteEx(sbp->a, buf, lastid, 40, use_best_id);
+ lastid = SeqPointWriteEx(sbp->a, buf, lastid, sizeof(buf) - 1, use_best_id);
BSstring(bsp, buf);
}
else
@@ -7128,7 +7181,7 @@ SeqLocPrintProc
if (sbp->b != NULL)
{
- lastid = SeqPointWriteEx(sbp->b, buf, lastid, 40, use_best_id);
+ lastid = SeqPointWriteEx(sbp->b, buf, lastid, sizeof(buf) - 1, use_best_id);
BSstring(bsp, buf);
}
else
@@ -7143,13 +7196,13 @@ SeqLocPrintProc
case SEQLOC_EMPTY: /* empty */
BSPutByte(bsp, '{');
SeqIdWrite((SeqIdPtr)(slp->data.ptrvalue),
- buf, PRINTID_FASTA_SHORT, 40);
+ buf, PRINTID_FASTA_SHORT, sizeof(buf) - 1);
BSstring(bsp, buf);
BSPutByte(bsp, '}');
break;
case SEQLOC_WHOLE: /* whole */
SeqIdWrite((SeqIdPtr)(slp->data.ptrvalue),
- buf, PRINTID_FASTA_SHORT, 40);
+ buf, PRINTID_FASTA_SHORT, sizeof(buf) - 1);
BSstring(bsp, buf);
break;
case SEQLOC_MIX: /* mix -- more than one seq */
@@ -7179,7 +7232,7 @@ SeqLocPrintProc
}
if (! SeqIdMatch(sip->id, lastid))
{
- SeqIdWrite(thisid, buf, PRINTID_FASTA_SHORT, 40);
+ SeqIdWrite(thisid, buf, PRINTID_FASTA_SHORT, sizeof(buf) - 1);
BSstring(bsp, buf);
BSPutByte(bsp, ':');
}
@@ -7211,7 +7264,7 @@ SeqLocPrintProc
break;
case SEQLOC_PNT: /* pnt */
lastid = SeqPointWriteEx((SeqPntPtr)(slp->data.ptrvalue),
- buf, lastid, 40, use_best_id);
+ buf, lastid, sizeof(buf) - 1, use_best_id);
BSstring(bsp, buf);
break;
case SEQLOC_PACKED_PNT: /* packed pnt */
@@ -7281,11 +7334,15 @@ SeqPointWriteEx
CharPtr tmp;
SeqIdPtr best_id, tmp_next;
BioseqPtr bsp;
+ Int4 fuzzlen, id_len;
+ Char fuzzbuf[100];
if ((spp == NULL) || (buf == NULL)) return NULL;
tmp = buf;
*tmp = '\0';
+ if (buflen < 2) return NULL;
+
best_id = spp->id;
if (use_best_id)
{
@@ -7298,9 +7355,12 @@ SeqPointWriteEx
tmp_next = best_id->next;
best_id->next = NULL;
+ IntFuzzPrint(spp->fuzz, spp->point, fuzzbuf, TRUE);
+ fuzzlen = StringLen (fuzzbuf);
+
if (! SeqIdMatch(best_id, lastid))
{
- SeqIdWrite(best_id, tmp, PRINTID_FASTA_SHORT, buflen);
+ SeqIdWrite(best_id, tmp, PRINTID_FASTA_SHORT, buflen - 2);
while (*tmp != '\0') tmp++;
*tmp = ':';
tmp++; *tmp = '\0';
@@ -7310,7 +7370,12 @@ SeqPointWriteEx
*tmp = strandsymbol[spp->strand];
tmp++; *tmp = '\0';
}
- IntFuzzPrint(spp->fuzz, spp->point, tmp, TRUE);
+
+ id_len = StringLen (buf);
+ if (id_len < buflen - 1) {
+ StringNCat (buf, fuzzbuf, buflen - id_len - 1);
+ buf[buflen - 1] = 0;
+ }
best_id->next = tmp_next;
@@ -9379,7 +9444,10 @@ NLM_EXTERN Uint4 LIBCALL WHICH_db_accession (CharPtr s)
(StringICmp(temp,"DV") == 0) ||
(StringICmp(temp,"DW") == 0) ||
(StringICmp(temp,"DY") == 0) ||
- (StringICmp(temp,"EB") == 0) ) { /* NCBI EST */
+ (StringICmp(temp,"EB") == 0) ||
+ (StringICmp(temp,"EC") == 0) ||
+ (StringICmp(temp,"EE") == 0) ||
+ (StringICmp(temp,"EG") == 0) ) { /* NCBI EST */
retcode = ACCN_NCBI_EST;
} else if ((StringICmp(temp,"BV") == 0)) { /* NCBI STS */
retcode = ACCN_NCBI_STS;
@@ -9388,18 +9456,19 @@ NLM_EXTERN Uint4 LIBCALL WHICH_db_accession (CharPtr s)
retcode = ACCN_NCBI_HTGS;
} else if ((StringICmp(temp,"AF") == 0) ||
(StringICmp(temp,"AY") == 0) ||
- (StringICmp(temp,"DQ") == 0)) { /* NCBI direct submission */
+ (StringICmp(temp,"DQ") == 0) ||
+ (StringICmp(temp,"EF") == 0)) { /* NCBI direct submission */
retcode = ACCN_NCBI_DIRSUB;
} else if ((StringICmp(temp,"AE") == 0) ||
(StringICmp(temp,"CP") == 0) ||
(StringICmp(temp,"CY") == 0)) { /* NCBI genome project data */
retcode = ACCN_NCBI_GENOME;
- } else if ((StringICmp(temp,"AH") == 0) ||
- (StringICmp(temp,"CH") == 0) ||
+ } else if ((StringICmp(temp,"AH") == 0)) { /* NCBI segmented set header Bioseq */
+ retcode = ACCN_NCBI_SEGSET | ACCN_AMBIGOUS_MOL; /* A few segmented proteins are AH */
+ } else if ((StringICmp(temp,"CH") == 0) ||
(StringICmp(temp,"CM") == 0) ||
(StringICmp(temp,"DS") == 0)) { /* NCBI segmented set header Bioseq */
- retcode = ACCN_NCBI_SEGSET | ACCN_AMBIGOUS_MOL; /* A few segmented
- proteins are AH */
+ retcode = ACCN_NCBI_SEGSET;
} else if ((StringICmp(temp,"AS") == 0)) { /* NCBI "other" */
retcode = ACCN_NCBI_OTHER;
} else if ((StringICmp(temp,"AD") == 0)) { /* NCBI accessions assigned to GSDB entries */
@@ -9415,7 +9484,8 @@ NLM_EXTERN Uint4 LIBCALL WHICH_db_accession (CharPtr s)
(StringICmp(temp,"CW") == 0) ||
(StringICmp(temp,"CZ") == 0) ||
(StringICmp(temp,"DU") == 0) ||
- (StringICmp(temp,"DX") == 0) ) { /* NCBI GSS */
+ (StringICmp(temp,"DX") == 0) ||
+ (StringICmp(temp,"ED") == 0) ) { /* NCBI GSS */
retcode = ACCN_NCBI_GSS;
} else if ((StringICmp(temp,"AR") == 0) ||
(StringICmp(temp,"DZ") == 0) ||
@@ -9438,7 +9508,8 @@ NLM_EXTERN Uint4 LIBCALL WHICH_db_accession (CharPtr s)
} else if ((StringICmp(temp,"AL") == 0) ||
(StringICmp(temp,"BX") == 0)||
(StringICmp(temp,"CR") == 0)||
- (StringICmp(temp,"CT") == 0)) { /* EMBL genome project data */
+ (StringICmp(temp,"CT") == 0)||
+ (StringICmp(temp,"CU") == 0)) { /* EMBL genome project data */
retcode = ACCN_EMBL_GENOME;
} else if ((StringICmp(temp,"AN") == 0)) { /* EMBL CON division */
retcode = ACCN_EMBL_CON;
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-08 17:42:03 +0000