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-rw-r--r--api/sqnutil2.c174
1 files changed, 166 insertions, 8 deletions
diff --git a/api/sqnutil2.c b/api/sqnutil2.c
index f2e27242..a5817f57 100644
--- a/api/sqnutil2.c
+++ b/api/sqnutil2.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 9/2/97
*
-* $Revision: 6.144 $
+* $Revision: 6.152 $
*
* File Description:
*
@@ -3054,14 +3054,17 @@ static SimpleSeqPtr ByteStoreToSimpleSeq (ByteStorePtr bs, CharPtr seqid, CharPt
#define strandStr field [STRAND_TAG]
static Boolean ParseFeatTableLine (CharPtr line, Int4Ptr startP, Int4Ptr stopP,
- BoolPtr partial5P, BoolPtr partial3P,
- CharPtr PNTR featP, CharPtr PNTR qualP,
+ BoolPtr partial5P, BoolPtr partial3P, BoolPtr ispointP,
+ BoolPtr isminusP, CharPtr PNTR featP, CharPtr PNTR qualP,
CharPtr PNTR valP, Int4 offset)
{
Boolean badNumber;
CharPtr field [NUM_FTABLE_COLUMNS];
Int2 i;
+ Boolean isminus = FALSE;
+ Boolean ispoint = FALSE;
+ size_t len;
ValNodePtr parsed;
Boolean partial5 = FALSE;
Boolean partial3 = FALSE;
@@ -3098,6 +3101,11 @@ static Boolean ParseFeatTableLine (CharPtr line, Int4Ptr startP, Int4Ptr stopP,
partial5 = TRUE;
str++;
}
+ len = StringLen (str);
+ if (len > 1 && str [len - 1] == '^') {
+ ispoint = TRUE;
+ str [len - 1] = '\0';
+ }
if (str != NULL && sscanf (str, "%ld", &val) == 1) {
start = val;
} else {
@@ -3131,6 +3139,7 @@ static Boolean ParseFeatTableLine (CharPtr line, Int4Ptr startP, Int4Ptr stopP,
start = stop;
stop = tmp;
}
+ isminus = TRUE;
}
}
}
@@ -3139,6 +3148,8 @@ static Boolean ParseFeatTableLine (CharPtr line, Int4Ptr startP, Int4Ptr stopP,
*stopP = stop + offset;
*partial5P = partial5;
*partial3P = partial3;
+ *ispointP = ispoint;
+ *isminusP = isminus;
*featP = featType;
*qualP = qualType;
*valP = qualVal;
@@ -3297,7 +3308,8 @@ NLM_EXTERN Uint1 ParseTRnaString (CharPtr strx, BoolPtr justTrnaText, Uint1Ptr c
}
} else if (StringICmp ("tRNA", str) != 0 &&
StringICmp ("transfer", str) != 0 &&
- StringICmp ("RNA", str) != 0) {
+ StringICmp ("RNA", str) != 0 &&
+ StringICmp ("product", str) != 0) {
if (cdP != NULL && StringLen (str) == 3) {
StringCpy (codon, str);
for (i = 0; i < 3; i++) {
@@ -3323,7 +3335,8 @@ NLM_EXTERN Uint1 ParseTRnaString (CharPtr strx, BoolPtr justTrnaText, Uint1Ptr c
if (curraa != 0) {
} else if (StringICmp ("tRNA", str) != 0 &&
StringICmp ("transfer", str) != 0 &&
- StringICmp ("RNA", str) != 0) {
+ StringICmp ("RNA", str) != 0 &&
+ StringICmp ("product", str) != 0) {
if (cdP != NULL && StringLen (str) == 3) {
StringCpy (codon, str);
for (i = 0; i < 3; i++) {
@@ -4127,6 +4140,12 @@ NLM_EXTERN void AddQualifierToFeature (SeqFeatPtr sfp, CharPtr qual, CharPtr val
prp->desc = StringSaveNoNull (val);
} else if (sfp->data.choice == SEQFEAT_CDREGION && StringCmp (qual, "prot_note") == 0) {
bail = FALSE;
+ } else if (sfp->data.choice == SEQFEAT_PROT && StringCmp (qual, "prot_desc") == 0) {
+ prp = (ProtRefPtr) sfp->data.value.ptrvalue;
+ if (prp != NULL) {
+ prp->desc = MemFree (prp->desc);
+ prp->desc = StringSaveNoNull (val);
+ }
} else if (ifp != NULL && StringICmp (ifp->key, "variation") == 0 && ParseQualIntoSnpUserObject (sfp, qual, val)) {
} else if (ifp != NULL && StringICmp (ifp->key, "STS") == 0 && ParseQualIntoStsUserObject (sfp, qual, val)) {
} else if (ifp != NULL && StringICmp (ifp->key, "misc_feature") == 0 && ParseQualIntoCloneUserObject (sfp, qual, val)) {
@@ -4313,6 +4332,20 @@ NLM_EXTERN void AddQualifierToFeature (SeqFeatPtr sfp, CharPtr qual, CharPtr val
}
}
}
+ } else if (sfp->data.choice == SEQFEAT_PROT) {
+ if (qnum == GBQUAL_function || qnum == GBQUAL_EC_number || qnum == GBQUAL_product) {
+ prp = (ProtRefPtr) sfp->data.value.ptrvalue;
+ if (prp != NULL) {
+ if (qnum == GBQUAL_function) {
+ ValNodeCopyStr (&(prp->activity), 0, val);
+ } else if (qnum == GBQUAL_EC_number) {
+ ValNodeCopyStr (&(prp->ec), 0, val);
+ } else if (qnum == GBQUAL_product) {
+ ValNodeCopyStr (&(prp->name), 0, val);
+ }
+ return;
+ }
+ }
} else if (sfp->data.choice == SEQFEAT_RNA) {
if (qnum == GBQUAL_product) {
rrp = (RnaRefPtr) sfp->data.value.ptrvalue;
@@ -4485,16 +4518,94 @@ NLM_EXTERN SeqLocPtr AddIntervalToLocation (SeqLocPtr loc, SeqIdPtr sip,
return rsult;
}
+static CharPtr TokenizeAtWhiteSpace (CharPtr str)
+
+{
+ Char ch;
+ CharPtr ptr;
+
+ if (str == NULL) return NULL;
+ ptr = str;
+ ch = *ptr;
+
+ while (ch != '\0' && (IS_WHITESP (ch))) {
+ ptr++;
+ ch = *ptr;
+ }
+ while (ch != '\0' && (! IS_WHITESP (ch))) {
+ ptr++;
+ ch = *ptr;
+ }
+ if (ch != '\0') {
+ *ptr = '\0';
+ ptr++;
+ }
+
+ return ptr;
+}
+
+static void ParseWhitespaceIntoTabs (CharPtr line)
+
+{
+ Char ch;
+ size_t len;
+ CharPtr ptr;
+ CharPtr str;
+ CharPtr tmp;
+
+ if (StringHasNoText (line)) return;
+ len = StringLen (line) + 10;
+
+ str = MemNew (len);
+ if (str == NULL) return;
+
+ ptr = line;
+ ch = *ptr;
+ if (IS_WHITESP (ch)) {
+ /* qualifier value line */
+ StringCat (str, "\t\t\t");
+ TrimSpacesAroundString (ptr);
+ tmp = TokenizeAtWhiteSpace (ptr);
+ StringCat (str, ptr);
+ StringCat (str, "\t");
+ StringCat (str, tmp);
+ } else {
+ /* location and possible feature key line */
+ TrimSpacesAroundString (ptr);
+ tmp = TokenizeAtWhiteSpace (ptr);
+ StringCat (str, ptr);
+ StringCat (str, "\t");
+ ptr = tmp;
+ tmp = TokenizeAtWhiteSpace (ptr);
+ StringCat (str, ptr);
+ ptr = tmp;
+ if (! StringHasNoText (ptr)) {
+ tmp = TokenizeAtWhiteSpace (ptr);
+ StringCat (str, "\t");
+ StringCat (str, ptr);
+ }
+ }
+
+ /* replace original with tab-delimited table */
+ StringCpy (line, str);
+
+ MemFree (str);
+}
+
static SeqAnnotPtr ReadFeatureTable (FILE *fp, CharPtr seqid, CharPtr annotname)
{
+ Boolean allowWhitesp = TRUE;
BioSourcePtr biop;
CdRegionPtr crp;
AnnotDescrPtr desc;
CharPtr feat;
+ IntFuzzPtr fuzz;
GeneRefPtr grp;
Int2 idx;
ImpFeatPtr ifp;
+ Boolean isminus;
+ Boolean ispoint;
Int2 j;
CharPtr label;
Char line [2047];
@@ -4508,12 +4619,15 @@ static SeqAnnotPtr ReadFeatureTable (FILE *fp, CharPtr seqid, CharPtr annotname)
PubdescPtr pdp;
Int4 pos;
SeqFeatPtr prev = NULL;
+ ProtRefPtr prp;
CharPtr qual;
Uint1 rnatype;
RnaRefPtr rrp;
SeqAnnotPtr sap = NULL;
SeqFeatPtr sfp = NULL;
SeqIdPtr sip;
+ SeqLocPtr slp;
+ SeqPntPtr spp;
Int4 start;
Int4 stop;
SqnTagPtr stp;
@@ -4543,7 +4657,11 @@ static SeqAnnotPtr ReadFeatureTable (FILE *fp, CharPtr seqid, CharPtr annotname)
return sap;
}
- if (ParseFeatTableLine (line, &start, &stop, &partial5, &partial3, &feat, &qual, &val, offset)) {
+ if (allowWhitesp) {
+ ParseWhitespaceIntoTabs (line);
+ }
+
+ if (ParseFeatTableLine (line, &start, &stop, &partial5, &partial3, &ispoint, &isminus, &feat, &qual, &val, offset)) {
if (feat != NULL && start >= 0 && stop >= 0) {
if (sap == NULL) {
@@ -4620,6 +4738,23 @@ static SeqAnnotPtr ReadFeatureTable (FILE *fp, CharPtr seqid, CharPtr annotname)
rrp->type = rnatype;
}
+ } else if (StringCmp (feat, "Protein") == 0) {
+
+ sfp->data.choice = SEQFEAT_PROT;
+ prp = ProtRefNew ();
+ if (prp != NULL) {
+ sfp->data.value.ptrvalue = (Pointer) prp;
+ }
+
+ } else if (StringCmp (feat, "proprotein") == 0) {
+
+ sfp->data.choice = SEQFEAT_PROT;
+ prp = ProtRefNew ();
+ if (prp != NULL) {
+ sfp->data.value.ptrvalue = (Pointer) prp;
+ prp->processed = 1;
+ }
+
} else if (StringCmp (feat, "source") == 0) {
sfp->data.choice = SEQFEAT_BIOSRC;
@@ -4672,7 +4807,30 @@ static SeqAnnotPtr ReadFeatureTable (FILE *fp, CharPtr seqid, CharPtr annotname)
}
}
- sfp->location = AddIntervalToLocation (NULL, sip, start, stop, partial5, partial3);
+ if (ispoint) {
+ spp = SeqPntNew ();
+ if (spp != NULL) {
+ spp->point = start;
+ if (isminus) {
+ spp->strand = Seq_strand_minus;
+ }
+ spp->id = SeqIdDup (sip);
+ fuzz = IntFuzzNew ();
+ if (fuzz != NULL) {
+ fuzz->choice = 4;
+ fuzz->a = 3;
+ spp->fuzz = fuzz;
+ }
+ slp = ValNodeNew (NULL);
+ if (slp != NULL) {
+ slp->choice = SEQLOC_PNT;
+ slp->data.ptrvalue = (Pointer) spp;
+ sfp->location = slp;
+ }
+ }
+ } else {
+ sfp->location = AddIntervalToLocation (NULL, sip, start, stop, partial5, partial3);
+ }
if (partial5 || partial3) {
sfp->partial = TRUE;
@@ -5250,7 +5408,7 @@ NLM_EXTERN Pointer ReadAsnFastaOrFlatFile (FILE *fp, Uint2Ptr datatypeptr, Uint2
Boolean inLetters;
Boolean isProt = FALSE;
Int4 j;
- Char line [1023];
+ Char line [4096];
Boolean mayBeAccessionList = TRUE;
Boolean mayBePlainFasta = TRUE;
SeqFeatPtr nextsfp;
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-02 21:12:39 +0000