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-rw-r--r--api/asn2gnb6.c247
1 files changed, 214 insertions, 33 deletions
diff --git a/api/asn2gnb6.c b/api/asn2gnb6.c
index a70c1f5c..62bd744a 100644
--- a/api/asn2gnb6.c
+++ b/api/asn2gnb6.c
@@ -30,7 +30,7 @@
*
* Version Creation Date: 10/21/98
*
-* $Revision: 1.227 $
+* $Revision: 1.257 $
*
* File Description: New GenBank flatfile generator - work in progress
*
@@ -477,6 +477,7 @@ NLM_EXTERN CharPtr legalDbXrefs [] = {
"HMP",
"HOMD",
"HSSP",
+ "IKMC",
"IMGT/GENE-DB",
"IMGT/HLA",
"IMGT/LIGM",
@@ -517,6 +518,7 @@ NLM_EXTERN CharPtr legalDbXrefs [] = {
"SGN",
"SoyBase",
"SubtiList",
+ "TAIR",
"taxon",
"TIGRFAM",
"UniGene",
@@ -547,6 +549,7 @@ NLM_EXTERN CharPtr legalSrcDbXrefs [] = {
"GRIN",
"HMP",
"HOMD",
+ "IKMC",
"IMGT/HLA",
"IMGT/LIGM",
"JCM",
@@ -562,6 +565,7 @@ NLM_EXTERN CharPtr legalSrcDbXrefs [] = {
NLM_EXTERN CharPtr legalRefSeqDbXrefs [] = {
"BEEBASE",
+ "BioProject",
"CCDS",
"CGNC",
"CloneID",
@@ -573,7 +577,6 @@ NLM_EXTERN CharPtr legalRefSeqDbXrefs [] = {
"PBR",
"REBASE",
"SK-FST",
- "TAIR",
"VBRC",
NULL
};
@@ -996,7 +999,7 @@ NLM_EXTERN CharPtr FormatSourceBlock (
/* If the organelle prefix is already on the */
/* name, don't add it. */
- if (StringNCmp (organelle, taxname, StringLen (organelle)) == 0)
+ if (StringNICmp (organelle, taxname, StringLen (organelle)) == 0)
organelle = "";
if (StringHasNoText (common)) {
@@ -1228,13 +1231,13 @@ NLM_EXTERN CharPtr FormatOrganismBlock (
} else {
FFAddOneString(temp, taxname, FALSE, FALSE, TILDE_IGNORE);
}
- FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
+ FFLineWrap(ajp, ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
FFRecycleString(ajp, temp);
temp = FFGetString(ajp);
FFStartPrint(temp, afp->format, 12, 12, NULL, 0, 5, 5, "OC", FALSE);
FFAddTextToString(temp, NULL, lineage, NULL, TRUE, FALSE, TILDE_TO_SPACES);
- FFLineWrap(ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
+ FFLineWrap(ajp, ffstring, temp, 12, 12, ASN2FF_GB_MAX, NULL);
FFRecycleString(ajp, temp);
/* optionally populate gbseq for XML-ized GenBank format */
@@ -1258,14 +1261,14 @@ NLM_EXTERN CharPtr FormatOrganismBlock (
} else if (afp->format == EMBL_FMT || afp->format == EMBLPEPT_FMT) {
FFStartPrint(temp, afp->format, 12, 12, NULL, 0, 5, 5, "OC", FALSE);
FFAddTextToString(temp, NULL, lineage, NULL, TRUE, FALSE, TILDE_TO_SPACES);
- FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "OC");
+ FFLineWrap(ajp, ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "OC");
FFRecycleString(ajp, temp);
if ( !StringHasNoText(organelle) ) {
temp = FFGetString(ajp);
if ( temp != NULL ) {
FFStartPrint(temp, afp->format, 12, 12, NULL, 0, 5, 5, "OG", FALSE);
FFAddTextToString(temp, NULL, organelle, NULL, TRUE, FALSE, TILDE_TO_SPACES);
- FFLineWrap(ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "OG");
+ FFLineWrap(ajp, ffstring, temp, 5, 5, ASN2FF_EMBL_MAX, "OG");
FFRecycleString(ajp, temp);
}
}
@@ -1428,9 +1431,9 @@ static CharPtr StrucCommentFFEndPrint (
if ( (ffstring == NULL) || (ajp == NULL) ) return NULL;
if (format == GENBANK_FMT || format == GENPEPT_FMT) {
- FFLineWrap (temp, ffstring, gb_init_indent, gb_cont_indent, ASN2FF_GB_MAX - 12, NULL);
+ FFLineWrap (ajp, temp, ffstring, gb_init_indent, gb_cont_indent, ASN2FF_GB_MAX - 12, NULL);
} else {
- FFLineWrap (temp, ffstring, eb_init_indent, eb_cont_indent, ASN2FF_EMBL_MAX - 5, eb_line_prefix);
+ FFLineWrap (ajp, temp, ffstring, eb_init_indent, eb_cont_indent, ASN2FF_EMBL_MAX - 5, eb_line_prefix);
}
result = FFToCharPtr (temp);
FFRecycleString (ajp, temp);
@@ -1573,6 +1576,10 @@ static CharPtr GetStrForStructuredComment (
FFAddOneString (ffstring, "</a>", FALSE, FALSE, TILDE_IGNORE);
} else if (GetWWW (ajp) && StringCmp (field, "url") == 0) {
AddCommentWithURLlinks (ajp, ffstring, NULL, str, NULL);
+ } else if (GetWWW (ajp) && StringNICmp (str, "http://", 7) == 0) {
+ AddCommentWithURLlinks (ajp, ffstring, NULL, str, NULL);
+ } else if (GetWWW (ajp) && StringNICmp (str, "https://", 8) == 0) {
+ AddCommentWithURLlinks (ajp, ffstring, NULL, str, NULL);
} else {
FFAddOneString (ffstring, str, FALSE, FALSE, TILDE_EXPAND);
}
@@ -1830,7 +1837,7 @@ static void CatenateCommentInGbseq (
if (gbseq->comment == NULL) {
gbseq->comment = cpy;
} else {
- tmp = (CharPtr) MemNew (StringLen (gbseq->comment) + StringLen (str) + 10);
+ tmp = (CharPtr) MemNew (StringLen (gbseq->comment) + StringLen (cpy) + 10);
if (tmp == NULL) return;
StringCpy (tmp, gbseq->comment);
if (ajp->oldXmlPolicy) {
@@ -3696,15 +3703,20 @@ static CharPtr FullNameFromInstCode (CharPtr code)
#define s_atcc_base "http://www.atcc.org/SearchCatalogs/linkin?id="
#define s_bcrc_base "http://strain.bcrc.firdi.org.tw/BSAS/controller?event=SEARCH&bcrc_no="
-#define s_ccmp_base "http://ccmp.bigelow.org/SD/display.php?strain=CCMP"
+#define s_cbs_base "http://www.cbs.knaw.nl/collections/BioloMICS.aspx?Fields=All&ExactMatch=T&Table=CBS+strain+database&Name=CBS+"
+#define s_ccap_base "http://www.ccap.ac.uk/strain_info.php?Strain_No="
+#define s_ccmp_base "https://ccmp.bigelow.org/node/1/strain/CCMP"
#define s_ccug_base "http://www.ccug.se/default.cfm?page=search_record.cfm&db=mc&s_tests=1&ccugno="
+#define s_cori_base "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref="
#define s_dsmz_base "http://www.dsmz.de/microorganisms/search_no.php?q="
#define s_fsu_base "http://www.prz.uni-jena.de/data.php?fsu="
#define s_icmp_base "http://nzfungi.landcareresearch.co.nz/icmp/results_cultures.asp?ID=&icmpVAR="
+#define s_kctc_base "http://www.brc.re.kr/English/_SearchView.aspx?sn="
#define s_ku_base "http://collections.nhm.ku.edu/"
-#define s_pcc_base "http://www.pasteur.fr/recherche/banques/PCC/docs/pcc"
+#define s_pcc_base "http://www.crbip.pasteur.fr/fiches/fichecata.jsp?crbip=PCC+"
#define s_pcmb_base "http://www2.bishopmuseum.org/HBS/PCMB/results3.asp?searchterm3="
#define s_pdd_base "http://nzfungi.landcareresearch.co.nz/html/data_collections_details.asp?CID="
+#define s_sag_base "http://sagdb.uni-goettingen.de/detailedList.php?str_number="
#define s_tgrc_base "http://tgrc.ucdavis.edu/Data/Acc/AccDetail.aspx?AccessionNum="
#define s_uam_base "http://arctos.database.museum/guid/"
#define s_ypm_base "http://peabody.research.yale.edu/cgi-bin/Query.Ledger?"
@@ -3723,7 +3735,6 @@ static CharPtr FullNameFromInstCode (CharPtr code)
#define s_ypmorn_pfx "LE=orn&ID="
#define s_bcrc_sfx "&type_id=6&keyword=;;"
-#define s_pcc_sfx ".htm"
typedef struct vouch {
CharPtr sites;
@@ -3736,17 +3747,23 @@ typedef struct vouch {
static VouchData Nlm_spec_vouchers [] = {
{ "ATCC", s_atcc_base, FALSE, NULL, NULL },
{ "BCRC", s_bcrc_base, FALSE, NULL, s_bcrc_sfx },
+ { "CBS", s_cbs_base, FALSE, NULL, NULL },
+ { "CCAP", s_ccap_base, FALSE, NULL, NULL },
{ "CCMP", s_ccmp_base, FALSE, NULL, NULL },
{ "CCUG", s_ccug_base, FALSE, NULL, NULL },
+ { "Coriell", s_cori_base, FALSE, NULL, NULL },
{ "CRCM:Bird", s_uam_base, TRUE, s_colon_pfx, NULL },
{ "DGR:Bird", s_uam_base, TRUE, s_colon_pfx, NULL },
{ "DGR:Ento", s_uam_base, TRUE, s_colon_pfx, NULL },
{ "DGR:Fish", s_uam_base, TRUE, s_colon_pfx, NULL },
{ "DGR:Herp", s_uam_base, TRUE, s_colon_pfx, NULL },
{ "DGR:Mamm", s_uam_base, TRUE, s_colon_pfx, NULL },
+ { "DMNS:Bird", s_uam_base, TRUE, s_colon_pfx, NULL },
+ { "DMNS:Mamm", s_uam_base, TRUE, s_colon_pfx, NULL },
{ "DSM", s_dsmz_base, FALSE, NULL, NULL },
{ "FSU<DEU>", s_fsu_base, FALSE, NULL, NULL },
{ "ICMP", s_icmp_base, FALSE, NULL, NULL },
+ { "KCTC", s_kctc_base, FALSE, NULL, NULL },
{ "KU:I", s_ku_base, FALSE, s_kui_pfx, NULL },
{ "KU:IT", s_ku_base, FALSE, s_kuit_pfx, NULL },
{ "KWP:Ento", s_uam_base, TRUE, s_colon_pfx, NULL },
@@ -3762,10 +3779,11 @@ static VouchData Nlm_spec_vouchers [] = {
{ "MVZ:Page", s_uam_base, TRUE, s_colon_pfx, NULL },
{ "MVZObs:Herp", s_uam_base, TRUE, s_colon_pfx, NULL },
{ "NBSB:Bird", s_uam_base, TRUE, s_colon_pfx, NULL },
- { "PCC", s_pcc_base, FALSE, NULL, s_pcc_sfx },
+ { "PCC", s_pcc_base, FALSE, NULL, NULL },
{ "PCMB", s_pcmb_base, FALSE, NULL, NULL },
{ "PDD", s_pdd_base, FALSE, NULL, NULL },
{ "PSU<USA-OR>:Mamm", s_uam_base, FALSE, s_psu_pfx, NULL },
+ { "SAG", s_sag_base, FALSE, NULL, NULL },
{ "TGRC", s_tgrc_base, FALSE, NULL, NULL },
{ "UAM:Bird", s_uam_base, TRUE, s_colon_pfx, NULL },
{ "UAM:Bryo", s_uam_base, TRUE, s_colon_pfx, NULL },
@@ -4061,14 +4079,16 @@ NLM_EXTERN CharPtr FormatSourceFeatBlock (
BioSourcePtr biop = NULL;
BioseqPtr bsp;
BioseqSetPtr bssp;
- Char buf [80];
+ Char buf [128], pfx [512], sfx [128];
CharPtr common = NULL;
+ Int4 currGi = 0;
DbtagPtr dbt;
SeqMgrDescContext dcontext;
SeqMgrFeatContext fcontext;
GBFeaturePtr gbfeat = NULL;
GBSeqPtr gbseq;
Int2 i;
+ IntAsn2gbSectPtr iasp;
Uint1 idx;
IntSrcBlockPtr isp;
Boolean is_desc = TRUE;
@@ -4121,6 +4141,9 @@ NLM_EXTERN CharPtr FormatSourceFeatBlock (
qvp = afp->qvp;
if (qvp == NULL) return NULL;
+ pfx [0] = '\0';
+ sfx [0] = '\0';
+
if (ajp->gbseq) {
gbseq = &asp->gbseq;
} else {
@@ -4164,6 +4187,26 @@ NLM_EXTERN CharPtr FormatSourceFeatBlock (
if ( ffstring == NULL ) return NULL;
FFStartPrint (ffstring, afp->format, 5, 21, NULL, 0, 5, 21, "FT", FALSE);
+
+ for (sip = bsp->id; sip != NULL; sip = sip->next) {
+ if (sip->choice == SEQID_GI) {
+ currGi = (Int4) sip->data.intvalue;
+ }
+ }
+
+ iasp = (IntAsn2gbSectPtr) asp;
+
+ if (iasp != NULL && GetWWW (ajp) && ajp->mode == ENTREZ_MODE &&
+ (ajp->format == GENBANK_FMT || ajp->format == GENPEPT_FMT)) {
+ if (! iasp->feat_js_prefix_added) {
+ sprintf (pfx, "<span id=\"feature_%ld_source_%ld\" class=\"feature\"><script>if (typeof(oData) == \"undefined\") oData = []; oData.push ({gi:%s,acc:\"%s\",features: {}});</script>",
+ (long) currGi, (long) isp->source_count, iasp->gi, iasp->acc);
+ iasp->feat_js_prefix_added = TRUE;
+ } else {
+ sprintf (pfx, "<span id=\"feature_%ld_source_%ld\" class=\"feature\">", (long) currGi, (long) isp->source_count);
+ }
+ }
+
FFAddOneString (ffstring, "source", FALSE, FALSE, TILDE_IGNORE);
FFAddNChar(ffstring, ' ', 21 - 5 - StringLen("source"), FALSE);
@@ -4878,7 +4921,12 @@ NLM_EXTERN CharPtr FormatSourceFeatBlock (
/* and then deal with the various note types separately (not in order table) */
- str = FFEndPrint(ajp, ffstring, afp->format, 21, 21, 5, 21, "FT");
+ if (GetWWW (ajp) && ajp->mode == ENTREZ_MODE &&
+ (ajp->format == GENBANK_FMT || ajp->format == GENPEPT_FMT)) {
+ sprintf (sfx, "</span>");
+ }
+
+ str = FFEndPrintEx (ajp, ffstring, afp->format, 21, 21, 5, 21, "FT", pfx, sfx);
/* optionally populate gbseq for XML-ized GenBank format */
@@ -5034,12 +5082,12 @@ static void PrintSeqLine (
sprintf (pos, "%9ld", (long) (start + 1));
FFAddOneString(ffstring, pos, FALSE, FALSE, TILDE_TO_SPACES);
FFAddOneChar(ffstring, ' ', FALSE);
- if (ajp != NULL && ajp->seqspans) {
+ if (ajp != NULL && GetWWW (ajp)) {
sprintf (tmp, "<span class=\"ff_line\" id=\"gi_%ld_%ld\">", (long) gi, (long) (start + 1));
FFAddOneString(ffstring, tmp, FALSE, FALSE, TILDE_TO_SPACES);
}
FFAddOneString(ffstring, buf, FALSE, FALSE, TILDE_TO_SPACES);
- if (ajp != NULL && ajp->seqspans) {
+ if (ajp != NULL && GetWWW (ajp)) {
FFAddOneString(ffstring, "</span>", FALSE, FALSE, TILDE_TO_SPACES);
}
FFAddOneChar(ffstring, '\n', FALSE);
@@ -5117,7 +5165,7 @@ static void PrintGenome (
Boolean first = TRUE;
SeqIdPtr freeid = NULL, sid = NULL, newid = NULL;
SeqLocPtr slp = NULL;
- Int4 from = 0, to = 0, start = 0, stop = 0, gi = 0;
+ Int4 start = 0, stop = 0, gi = 0;
BioseqPtr bsp = NULL;
Int2 p1 = 0, p2 = 0;
@@ -5125,12 +5173,11 @@ static void PrintGenome (
gibuf [0] = '\0';
vbuf [0] = '\0';
for (slp = slp_head; slp; slp = slp->next) {
- from = to = 0;
sid = SeqLocId (slp);
- if (slp->choice == SEQLOC_INT || slp->choice == SEQLOC_WHOLE) {
- start = from = SeqLocStart (slp);
- stop = to = SeqLocStop (slp);
- } else if (slp->choice == SEQLOC_NULL){
+ if (slp->choice == SEQLOC_INT || slp->choice == SEQLOC_PNT || slp->choice == SEQLOC_WHOLE) {
+ start = SeqLocStart (slp);
+ stop = SeqLocStop (slp);
+ } else if (slp->choice == SEQLOC_NULL) {
sprintf (vbuf, ",%s", "gap()");
FFAddOneString (ffstring, vbuf, FALSE, FALSE, TILDE_IGNORE);
continue;
@@ -5230,6 +5277,82 @@ static void PrintGenome (
}
}
+static DeltaSeqPtr RevCompDelta (
+ DeltaSeqPtr seq_ext
+)
+
+{
+ DeltaSeqPtr dsp;
+ ValNodePtr head = NULL;
+ Int4 from, to, tmp;
+ SeqLocPtr nslp, slp;
+ Boolean partial5, partial3;
+ SeqIntPtr sintp;
+ SeqLitPtr slitp, slip;
+ ValNodePtr vnp;
+
+ for (dsp = seq_ext; dsp != NULL; dsp = dsp->next) {
+ vnp = NULL;
+
+ if (dsp->choice == 1) {
+
+ slp = (SeqLocPtr) dsp->data.ptrvalue;
+ if (slp != NULL) {
+
+ if (slp->choice == SEQLOC_NULL) {
+
+ nslp = ValNodeAddPointer (NULL, SEQLOC_NULL, NULL);
+
+ vnp = ValNodeAddPointer (NULL, 1, nslp);
+
+ } else if (slp->choice == SEQLOC_INT) {
+
+ sintp = (SeqIntPtr) slp->data.ptrvalue;
+ if (sintp != NULL) {
+ CheckSeqLocForPartial (slp, &partial5, &partial3);
+ from = sintp->from;
+ to = sintp->to;
+ if (sintp->strand != Seq_strand_minus) {
+ tmp = from;
+ from = to;
+ to = tmp;
+ }
+ nslp = AddIntervalToLocation (NULL, sintp->id, from, to, partial3, partial5);
+
+ vnp = ValNodeAddPointer (NULL, 1, nslp);
+
+ }
+ }
+ }
+
+ } else if (dsp->choice == 2) {
+
+ slitp = (SeqLitPtr) dsp->data.ptrvalue;
+ if (slitp != NULL && slitp->seq_data == NULL) {
+ slip = SeqLitNew ();
+ if (slip != NULL) {
+ slip->length = slitp->length;
+ /* not copying fuzz */
+ slip->seq_data_type = slitp->seq_data_type;
+ vnp = ValNodeAddPointer (NULL, 2, (Pointer) slip);
+ }
+ } else {
+ ValNodeFree (head);
+ return NULL;
+ }
+ }
+
+ /* save in new list in reverse order */
+
+ if (vnp != NULL) {
+ vnp->next = head;
+ head = vnp;
+ }
+ }
+
+ return head;
+}
+
NLM_EXTERN CharPtr FormatContigBlock (
Asn2gbFormatPtr afp,
BaseBlockPtr bbp
@@ -5239,13 +5362,19 @@ NLM_EXTERN CharPtr FormatContigBlock (
IntAsn2gbJobPtr ajp;
Asn2gbSectPtr asp;
BioseqPtr bsp;
+ DeltaSeqPtr delta_head = NULL;
DeltaSeqPtr dsp;
+ DeltaSeqPtr dspnext;
IntFuzzPtr fuzz;
GBSeqPtr gbseq;
Boolean is_na;
SeqLitPtr litp;
+ DeltaSeqPtr new_delta = NULL;
CharPtr prefix = NULL;
+ Boolean rev_comp = FALSE;
Boolean segWithParts = FALSE;
+ SeqIntPtr sintp;
+ SeqLocPtr slp;
SeqLocPtr slp_head = NULL;
CharPtr str;
Char tmp [16];
@@ -5267,6 +5396,18 @@ NLM_EXTERN CharPtr FormatContigBlock (
is_na = ISA_na (bsp->mol);
+ if (ajp->ajp.slp != NULL) {
+ slp = ajp->ajp.slp;
+ if (slp->choice == SEQLOC_INT) {
+ sintp = (SeqIntPtr) slp->data.ptrvalue;
+ if (sintp != NULL) {
+ if (sintp->from == 0 && sintp->to == bsp->length - 1 && sintp->strand == Seq_strand_minus) {
+ rev_comp = TRUE;
+ }
+ }
+ }
+ }
+
FFStartPrint (ffstring, afp->format, 0, 0, "CONTIG", 12, 5, 5, "CO", FALSE);
/*
if ( GetWWW(ajp) ) {
@@ -5292,7 +5433,14 @@ NLM_EXTERN CharPtr FormatContigBlock (
} else if (bsp->seq_ext_type == 4) {
- for (dsp = (DeltaSeqPtr) bsp->seq_ext; dsp != NULL; dsp=dsp->next) {
+ if (rev_comp) {
+ new_delta = RevCompDelta ((DeltaSeqPtr) bsp->seq_ext);
+ delta_head = new_delta;
+ } else {
+ delta_head = (DeltaSeqPtr) bsp->seq_ext;
+ }
+
+ for (dsp = delta_head; dsp != NULL; dsp = dsp->next) {
if (dsp->choice == 1) {
slp_head = (SeqLocPtr) dsp->data.ptrvalue;
@@ -5359,6 +5507,16 @@ NLM_EXTERN CharPtr FormatContigBlock (
StripAllSpaces (gbseq->contig);
}
+ if (new_delta != NULL) {
+ dsp = new_delta;
+ while (dsp != NULL) {
+ dspnext = dsp->next;
+ dsp->next = NULL;
+ DeltaSeqFree (dsp);
+ dsp = dsp->next;
+ }
+ }
+
return str;
}
@@ -5536,8 +5694,11 @@ static Int2 ProcessGapSpecialFormat (
Char gi_buf [16];
Boolean is_na;
Char pad;
+ Char rgn_buf [64];
SeqIdPtr sip;
+ SeqLocPtr slp;
Int2 startgapgap = 0, endgap = 0;
+ Int4 from, to;
is_na = ISA_na (bsp->mol);
if (is_na) {
@@ -5574,6 +5735,13 @@ static Int2 ProcessGapSpecialFormat (
sprintf(fmt_buf, "?fmt_mask=%ld", (long) EXPANDED_GAP_DISPLAY);
if (bsp->repr == Seq_repr_delta && (! DeltaLitOnly (bsp))) {
StringCat (fmt_buf, "&report=gbwithparts");
+ if (ajp->ajp.slp != NULL) {
+ slp = ajp->ajp.slp;
+ from = SeqLocStart (slp) + 1;
+ to = SeqLocStop (slp) + 1;
+ sprintf (rgn_buf, "&from=%ld&to=%ld", (long) from, (long) to);
+ StringCat (fmt_buf, rgn_buf);
+ }
}
FFAddOneString (ffstring, " <a href=\"", FALSE, FALSE, TILDE_IGNORE);
if (is_na) {
@@ -5592,6 +5760,7 @@ static Int2 ProcessGapSpecialFormat (
FixGapAtStart (buf, ' ');
} else if (startgapgap > 0) {
FixGapAtStart (buf, pad);
+ startgapgap = 0;
}
endgap = GapAtEnd (buf);
@@ -5870,13 +6039,15 @@ NLM_EXTERN CharPtr FormatSlashBlock (
)
{
- IntAsn2gbJobPtr ajp;
- Asn2gbSectPtr asp;
- GBFeaturePtr currf, headf, nextf;
- GBReferencePtr currr, headr, nextr;
- GBSeqPtr gbseq, gbtmp;
- IndxPtr index;
- INSDSeq is;
+ IntAsn2gbJobPtr ajp;
+ Asn2gbSectPtr asp;
+ GBFeaturePtr currf, headf, nextf;
+ GBReferencePtr currr, headr, nextr;
+ Uint1 featdeftype;
+ GBSeqPtr gbseq, gbtmp;
+ IntAsn2gbSectPtr iasp;
+ IndxPtr index;
+ INSDSeq is;
/*
Int2 moltype, strandedness, topology;
*/
@@ -5887,6 +6058,8 @@ NLM_EXTERN CharPtr FormatSlashBlock (
asp = afp->asp;
if (asp == NULL) return NULL;
+ iasp = (IntAsn2gbSectPtr) asp;
+
/* sort and unique indexes */
index = ajp->index;
@@ -6017,7 +6190,15 @@ NLM_EXTERN CharPtr FormatSlashBlock (
GBSeqFree (gbtmp);
}
- /* slash always has string pre-allocated by add slash block function */
+ /* then clean up javascript components */
+
+ iasp->gi = MemFree (iasp->gi);
+ iasp->acc = MemFree (iasp->acc);
+ for (featdeftype = 0; featdeftype < FEATDEF_MAX; featdeftype++) {
+ iasp->feat_key [featdeftype] = MemFree (iasp->feat_key [featdeftype]);
+ }
+
+ /* slash has string pre-allocated by add slash block function */
return StringSaveNoNull (bbp->string);
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-02 20:19:21 +0000