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-rw-r--r--api/sqnutil3.c444
1 files changed, 339 insertions, 105 deletions
diff --git a/api/sqnutil3.c b/api/sqnutil3.c
index ef2a21bf..007ce12f 100644
--- a/api/sqnutil3.c
+++ b/api/sqnutil3.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 2/7/00
*
-* $Revision: 6.69 $
+* $Revision: 6.74 $
*
* File Description:
*
@@ -115,7 +115,7 @@ static void SfpClearFeatIDs (
ClearFeatIDXrefs (sfp);
}
-NLM_EXTERN void ClearCDSmRNAfeatureIDs (
+NLM_EXTERN void ClearFeatureIDs (
SeqEntryPtr sep
)
@@ -123,11 +123,20 @@ NLM_EXTERN void ClearCDSmRNAfeatureIDs (
VisitFeaturesInSep (sep, NULL, SfpClearFeatIDs);
}
+typedef struct idpair {
+ Int4 before;
+ Int4 after;
+} IdPairData, PNTR IdPairPtr;
+
typedef struct fiddata {
- Int4 highestID;
+ Int4 highestID;
+ Int4 highestRef;
+ Int4 offset;
+ Int4 count;
+ IdPairPtr pairs;
} FidData, PNTR FidDataPtr;
-static void FindHighestFeatureID (
+static void FindHighestFeatID (
SeqFeatPtr sfp,
Pointer userdata
)
@@ -138,7 +147,6 @@ static void FindHighestFeatureID (
SeqFeatXrefPtr xref;
if (sfp == NULL) return;
- if (sfp->idx.subtype != FEATDEF_CDS && sfp->idx.subtype != FEATDEF_mRNA) return;
fip = (FidDataPtr) userdata;
if (fip == NULL) return;
@@ -147,7 +155,7 @@ static void FindHighestFeatureID (
if (oip != NULL) {
if (oip->str == NULL) {
if (oip->id >= fip->highestID) {
- fip->highestID = oip->id + 1;
+ fip->highestID = oip->id;
}
}
}
@@ -158,15 +166,29 @@ static void FindHighestFeatureID (
oip = (ObjectIdPtr) xref->id.value.ptrvalue;
if (oip != NULL) {
if (oip->str == NULL) {
- if (oip->id >= fip->highestID) {
- fip->highestID = oip->id + 1;
+ if (oip->id >= fip->highestRef) {
+ fip->highestRef = oip->id;
}
}
}
}
}
-static void SfpAssignCDSmRNAfeatureIDs (
+NLM_EXTERN Int4 FindHighestFeatureID (
+ SeqEntryPtr sep
+)
+
+{
+ FidData fd;
+
+ MemSet ((Pointer) &fd, 0, sizeof (FidData));
+ fd.highestID = 0;
+ fd.highestRef = 0;
+ VisitFeaturesInSep (sep, (Pointer) &fd, FindHighestFeatID);
+ return fd.highestID;
+}
+
+static void SfpAssignFeatIDs (
SeqFeatPtr sfp,
Pointer userdata
)
@@ -176,32 +198,241 @@ static void SfpAssignCDSmRNAfeatureIDs (
ObjectIdPtr oip;
if (sfp == NULL) return;
- if (sfp->idx.subtype != FEATDEF_CDS && sfp->idx.subtype != FEATDEF_mRNA) return;
fip = (FidDataPtr) userdata;
if (fip == NULL) return;
if (sfp->id.choice == 3) return;
oip = ObjectIdNew ();
if (oip == NULL) return;
+
+ (fip->highestID)++;
oip->id = fip->highestID;
sfp->id.value.ptrvalue = (Pointer) oip;
sfp->id.choice = 3;
+}
+
+NLM_EXTERN void AssignFeatureIDs (
+ SeqEntryPtr sep
+)
+
+{
+ FidData fd;
+
+ MemSet ((Pointer) &fd, 0, sizeof (FidData));
+ fd.highestID = 0;
+ fd.highestRef = 0;
+ VisitFeaturesInSep (sep, (Pointer) &fd, FindHighestFeatID);
+ VisitFeaturesInSep (sep, (Pointer) &fd, SfpAssignFeatIDs);
+}
+
+static void SfpOffsetFeatIDs (
+ SeqFeatPtr sfp,
+ Pointer userdata
+)
+
+{
+ FidDataPtr fip;
+ ObjectIdPtr oip;
+
+ if (sfp == NULL) return;
+ fip = (FidDataPtr) userdata;
+ if (fip == NULL) return;
+
+ if (sfp->id.choice == 3) {
+ oip = (ObjectIdPtr) sfp->id.value.ptrvalue;
+ if (oip != NULL) {
+ if (oip->str == NULL) {
+ oip->id += fip->offset;
+ }
+ }
+ }
+}
+
+NLM_EXTERN void OffsetFeatureIDs (
+ SeqEntryPtr sep,
+ Int4 offset
+)
+
+{
+ FidData fd;
+
+ MemSet ((Pointer) &fd, 0, sizeof (FidData));
+ fd.offset = offset;
+ VisitFeaturesInSep (sep, (Pointer) &fd, SfpOffsetFeatIDs);
+}
+
+static void SfpOffsetFeatIDXrefs (
+ SeqFeatPtr sfp,
+ Pointer userdata
+)
+
+{
+ FidDataPtr fip;
+ ObjectIdPtr oip;
+ SeqFeatXrefPtr xref;
+
+ if (sfp == NULL) return;
+ fip = (FidDataPtr) userdata;
+ if (fip == NULL) return;
+
+ for (xref = sfp->xref; xref != NULL; xref = xref->next) {
+ if (xref->id.choice != 3) continue;
+ oip = (ObjectIdPtr) xref->id.value.ptrvalue;
+ if (oip != NULL) {
+ if (oip->str == NULL) {
+ oip->id += fip->offset;
+ }
+ }
+ }
+}
+
+NLM_EXTERN void OffsetFeatureIDXrefs (
+ SeqEntryPtr sep,
+ Int4 offset
+)
+
+{
+ FidData fd;
+
+ MemSet ((Pointer) &fd, 0, sizeof (FidData));
+ fd.offset = offset;
+ VisitFeaturesInSep (sep, (Pointer) &fd, SfpOffsetFeatIDXrefs);
+}
+
+static void SfpMakePairList (
+ SeqFeatPtr sfp,
+ Pointer userdata
+)
+
+{
+ FidDataPtr fip;
+ Int4 idx;
+ IdPairPtr ipp;
+ ObjectIdPtr oip;
+
+ if (sfp == NULL) return;
+ fip = (FidDataPtr) userdata;
+ if (fip == NULL) return;
+ if (fip->pairs == NULL) return;
+
+ if (sfp->id.choice != 3) return;
+ oip = (ObjectIdPtr) sfp->id.value.ptrvalue;
+ if (oip == NULL) return;
+
+ idx = fip->highestID;
+ ipp = &(fip->pairs [idx]);
(fip->highestID)++;
+ ipp->before = oip->id;
+ ipp->after = fip->highestID;
+}
+
+static int LIBCALLBACK SortPairList (VoidPtr ptr1, VoidPtr ptr2)
+
+{
+ IdPairPtr ipp1 = (IdPairPtr) ptr1;
+ IdPairPtr ipp2 = (IdPairPtr) ptr2;
+
+ if (ipp1 == NULL || ipp2 == NULL) return 0;
+ if (ipp1->before > ipp2->before) return 1;
+ if (ipp1->before < ipp2->before) return -1;
+ return 0;
+}
+
+static Int4 LookupNewFeatID (
+ FidDataPtr fip,
+ Int4 before
+)
+
+{
+ IdPairPtr ipp;
+ Int4 L;
+ Int4 mid;
+ Int4 R;
+
+ if (fip == NULL || fip->pairs == NULL || fip->count < 1) return 0;
+
+ L = 0;
+ R = fip->count - 1;
+ while (L < R) {
+ mid = (L + R) / 2;
+ ipp = &(fip->pairs [mid]);
+ if (ipp->before < before) {
+ L = mid + 1;
+ } else {
+ R = mid;
+ }
+ }
+
+ if (R < fip->count) {
+ ipp = &(fip->pairs [R]);
+ if (ipp->before == before) return ipp->after;
+ }
+
+ return 0;
+}
+
+static void SfpReassignPairList (
+ SeqFeatPtr sfp,
+ Pointer userdata
+)
+
+{
+ FidDataPtr fip;
+ ObjectIdPtr oip;
+ SeqFeatXrefPtr xref;
+
+ if (sfp == NULL) return;
+ fip = (FidDataPtr) userdata;
+ if (fip == NULL) return;
+ if (fip->pairs == NULL) return;
+
+ if (sfp->id.choice == 3) {
+ oip = (ObjectIdPtr) sfp->id.value.ptrvalue;
+ if (oip != NULL) {
+ if (oip->str == NULL) {
+ oip->id = LookupNewFeatID (fip, oip->id);
+ }
+ }
+ }
+
+ for (xref = sfp->xref; xref != NULL; xref = xref->next) {
+ if (xref->id.choice != 3) continue;
+ oip = (ObjectIdPtr) xref->id.value.ptrvalue;
+ if (oip != NULL) {
+ if (oip->str == NULL) {
+ oip->id = LookupNewFeatID (fip, oip->id);
+ }
+ }
+ }
}
-NLM_EXTERN void AssignCDSmRNAfeatureIDs (
+NLM_EXTERN void ReassignFeatureIDs (
SeqEntryPtr sep
)
{
+ Int4 count;
FidData fd;
+ count = VisitFeaturesInSep (sep, NULL, NULL);
+ if (count < 1) return;
+
MemSet ((Pointer) &fd, 0, sizeof (FidData));
- fd.highestID = 1;
- VisitFeaturesInSep (sep, (Pointer) &fd, FindHighestFeatureID);
- VisitFeaturesInSep (sep, (Pointer) &fd, SfpAssignCDSmRNAfeatureIDs);
+ fd.highestID = 0;
+ fd.highestRef = 0;
+ fd.count = count;
+ fd.pairs = (IdPairPtr) MemNew (sizeof (IdPairData) * (count + 1));
+ if (fd.pairs == NULL) return;
+
+ VisitFeaturesInSep (sep, (Pointer) &fd, SfpMakePairList);
+
+ HeapSort (fd.pairs, (size_t) count, sizeof (IdPairData), SortPairList);
+
+ VisitFeaturesInSep (sep, (Pointer) &fd, SfpReassignPairList);
+
+ MemFree (fd.pairs);
}
typedef struct vcmdata {
@@ -368,7 +599,7 @@ NLM_EXTERN void LinkCDSmRNAbyOverlap (
)
{
- AssignCDSmRNAfeatureIDs (sep);
+ AssignFeatureIDs (sep);
VisitBioseqsInSep (sep, NULL, BspLinkCDSmRNAbyOverlap);
}
@@ -515,97 +746,100 @@ static void BspLinkCDSmRNAbyProduct (
if (cdna->idx.parenttype == OBJ_BIOSEQSET) {
bssp = (BioseqSetPtr) cdna->idx.parentptr;
if (bssp == NULL) continue;
- if (bssp->_class != BioseqseqSet_class_nuc_prot) continue;
- prot = NULL;
- if (VisitBioseqsInSet (bssp, (Pointer) &prot, FindProtBsp) != 2) continue;
- for (sip = prot->id; sip != NULL; sip = sip->next) {
- MakeReversedSeqIdString (sip, buf, sizeof (buf) - 1);
-
- /* binary search */
-
- L = 0;
- R = numcds - 1;
- while (L < R) {
- mid = (L + R) / 2;
- odp = cdsarray [mid];
- compare = StringCmp (odp->revstr, buf);
- if (compare < 0) {
- L = mid + 1;
- } else {
- R = mid;
- }
- }
- odp = cdsarray [R];
- if (odp != NULL && StringCmp (odp->revstr, buf) == 0) {
- cds = odp->sfp;
- if (cds == NULL) continue;
-
- /* make reciprocal feature ID xrefs */
-
- if (cds->id.choice == 3) {
- oip = (ObjectIdPtr) cds->id.value.ptrvalue;
- if (oip != NULL && oip->str == NULL) {
- id = oip->id;
- if (id > 0) {
- for (xref = mrna->xref; xref != NULL && xref->id.choice != 3; xref = xref->next) continue;
- if (xref != NULL) {
- oip = (ObjectIdPtr) xref->id.value.ptrvalue;
- if (oip != NULL) {
- if (oip->str != NULL) {
- oip->str = MemFree (oip->str);
- }
- oip->id = id;
- }
- } else {
- xref = SeqFeatXrefNew ();
- if (xref != NULL) {
- oip = ObjectIdNew ();
- if (oip != NULL) {
- oip->id = id;
- xref->id.choice = 3;
- xref->id.value.ptrvalue = (Pointer) oip;
- xref->next = mrna->xref;
- mrna->xref = xref;
- }
- }
- }
- }
- }
- }
-
- if (mrna->id.choice == 3) {
- oip = (ObjectIdPtr) mrna->id.value.ptrvalue;
- if (oip != NULL && oip->str == NULL) {
- id = oip->id;
- if (id > 0) {
- for (xref = cds->xref; xref != NULL && xref->id.choice != 3; xref = xref->next) continue;
- if (xref != NULL) {
- oip = (ObjectIdPtr) xref->id.value.ptrvalue;
- if (oip != NULL) {
- if (oip->str != NULL) {
- oip->str = MemFree (oip->str);
- }
- oip->id = id;
- }
- } else {
- xref = SeqFeatXrefNew ();
- if (xref != NULL) {
- oip = ObjectIdNew ();
- if (oip != NULL) {
- oip->id = id;
- xref->id.choice = 3;
- xref->id.value.ptrvalue = (Pointer) oip;
- xref->next = cds->xref;
- cds->xref = xref;
- }
- }
- }
- }
- }
- }
- }
+ if (bssp->_class == BioseqseqSet_class_nuc_prot) {
+ prot = NULL;
+ if (VisitBioseqsInSet (bssp, (Pointer) &prot, FindProtBsp) == 2) {
+ for (sip = prot->id; sip != NULL; sip = sip->next) {
+ MakeReversedSeqIdString (sip, buf, sizeof (buf) - 1);
+
+ /* binary search */
+
+ L = 0;
+ R = numcds - 1;
+ while (L < R) {
+ mid = (L + R) / 2;
+ odp = cdsarray [mid];
+ compare = StringCmp (odp->revstr, buf);
+ if (compare < 0) {
+ L = mid + 1;
+ } else {
+ R = mid;
+ }
+ }
+ odp = cdsarray [R];
+ if (odp != NULL && StringCmp (odp->revstr, buf) == 0) {
+ cds = odp->sfp;
+ if (cds == NULL) continue;
+
+ /* make reciprocal feature ID xrefs */
+
+ if (cds->id.choice == 3) {
+ oip = (ObjectIdPtr) cds->id.value.ptrvalue;
+ if (oip != NULL && oip->str == NULL) {
+ id = oip->id;
+ if (id > 0) {
+ for (xref = mrna->xref; xref != NULL && xref->id.choice != 3; xref = xref->next) continue;
+ if (xref != NULL) {
+ oip = (ObjectIdPtr) xref->id.value.ptrvalue;
+ if (oip != NULL) {
+ if (oip->str != NULL) {
+ oip->str = MemFree (oip->str);
+ }
+ oip->id = id;
+ }
+ } else {
+ xref = SeqFeatXrefNew ();
+ if (xref != NULL) {
+ oip = ObjectIdNew ();
+ if (oip != NULL) {
+ oip->id = id;
+ xref->id.choice = 3;
+ xref->id.value.ptrvalue = (Pointer) oip;
+ xref->next = mrna->xref;
+ mrna->xref = xref;
+ }
+ }
+ }
+ }
+ }
+ }
+
+ if (mrna->id.choice == 3) {
+ oip = (ObjectIdPtr) mrna->id.value.ptrvalue;
+ if (oip != NULL && oip->str == NULL) {
+ id = oip->id;
+ if (id > 0) {
+ for (xref = cds->xref; xref != NULL && xref->id.choice != 3; xref = xref->next) continue;
+ if (xref != NULL) {
+ oip = (ObjectIdPtr) xref->id.value.ptrvalue;
+ if (oip != NULL) {
+ if (oip->str != NULL) {
+ oip->str = MemFree (oip->str);
+ }
+ oip->id = id;
+ }
+ } else {
+ xref = SeqFeatXrefNew ();
+ if (xref != NULL) {
+ oip = ObjectIdNew ();
+ if (oip != NULL) {
+ oip->id = id;
+ xref->id.choice = 3;
+ xref->id.value.ptrvalue = (Pointer) oip;
+ xref->next = cds->xref;
+ cds->xref = xref;
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
}
}
+ BioseqUnlock (cdna);
}
}
@@ -626,7 +860,7 @@ NLM_EXTERN void LinkCDSmRNAbyProduct (
)
{
- AssignCDSmRNAfeatureIDs (sep);
+ AssignFeatureIDs (sep);
VisitBioseqsInSep (sep, NULL, BspLinkCDSmRNAbyProduct);
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-02 20:43:09 +0000