diff options
Diffstat (limited to 'api/sqnutil1.c')
| -rw-r--r-- | api/sqnutil1.c | 70 |
1 files changed, 61 insertions, 9 deletions
diff --git a/api/sqnutil1.c b/api/sqnutil1.c index e44797e5..432b130c 100644 --- a/api/sqnutil1.c +++ b/api/sqnutil1.c @@ -29,7 +29,7 @@ * * Version Creation Date: 9/2/97 * -* $Revision: 6.369 $ +* $Revision: 6.376 $ * * File Description: * @@ -2685,9 +2685,7 @@ static Boolean HandledGBQualOnGene (SeqFeatPtr sfp, GBQualPtr gbq) Int2 choice = 0; GeneRefPtr grp; - if (StringICmp (gbq->qual, "pseudo") == 0) { - choice = 1; - } else if (StringICmp (gbq->qual, "map") == 0) { + if (StringICmp (gbq->qual, "map") == 0) { choice = 2; } else if (StringICmp (gbq->qual, "allele") == 0) { choice = 3; @@ -2698,9 +2696,6 @@ static Boolean HandledGBQualOnGene (SeqFeatPtr sfp, GBQualPtr gbq) grp = (GeneRefPtr) sfp->data.value.ptrvalue; if (grp == NULL) return FALSE; switch (choice) { - case 1 : - grp->pseudo = TRUE; - break; case 2 : if (grp->maploc != NULL) return FALSE; if (StringHasNoText (gbq->val)) return FALSE; @@ -2785,6 +2780,7 @@ extern Boolean ParseAnticodon (SeqFeatPtr sfp, CharPtr val, Int4 offset) { Int4 diff; + Int2 j; Boolean locmap; int num_errs; CharPtr pos; @@ -2809,6 +2805,12 @@ extern Boolean ParseAnticodon (SeqFeatPtr sfp, CharPtr val, Int4 offset) rrp->ext.choice = 2; trp = (tRNAPtr) MemNew (sizeof (tRNA)); rrp->ext.value.ptrvalue = (Pointer) trp; + if (trp != NULL) { + trp->aatype = 2; + for (j = 0; j < 6; j++) { + trp->codon [j] = 255; + } + } } if (rrp->ext.choice != 2) return FALSE; @@ -5201,7 +5203,8 @@ static void FixOldDbxrefs (ValNodePtr vnp) dbt->db = MemFree (dbt->db); dbt->db = StringSave ("SubtiList"); } - if (StringICmp (dbt->db, "Swiss-Prot") == 0) { + if (StringICmp (dbt->db, "Swiss-Prot") == 0 || + StringICmp (dbt->db, "SWISSPROT") == 0) { dbt->db = MemFree (dbt->db); dbt->db = StringSave ("UniProt/Swiss-Prot"); } else if (StringICmp (dbt->db, "TrEMBL") == 0) { @@ -7658,6 +7661,7 @@ NLM_EXTERN void CleanUpSeqFeat ( BioseqPtr bsp; CodeBreakPtr cbp; CdRegionPtr crp; + GeneRefPtr grp; Boolean hasNulls; SeqIdPtr id; ImpFeatPtr ifp; @@ -7774,7 +7778,15 @@ NLM_EXTERN void CleanUpSeqFeat ( CleanupSeqLoc (sfp->location); strand = SeqLocStrand (sfp->location); id = SeqLocId (sfp->location); - if (sfp->data.choice == SEQFEAT_CDREGION) { + if (sfp->data.choice == SEQFEAT_GENE) { + grp = (GeneRefPtr) sfp->data.value.ptrvalue; + if (grp != NULL) { + if (grp->pseudo) { + sfp->pseudo = TRUE; + grp->pseudo = FALSE; + } + } + } else if (sfp->data.choice == SEQFEAT_CDREGION) { crp = (CdRegionPtr) sfp->data.value.ptrvalue; if (crp != NULL) { crp->code_break = SortCodeBreaks (sfp, crp->code_break); @@ -7797,6 +7809,12 @@ NLM_EXTERN void CleanUpSeqFeat ( } } else if (sfp->data.choice == SEQFEAT_RNA) { rrp = (RnaRefPtr) sfp->data.value.ptrvalue; + if (rrp != NULL) { + if (rrp->pseudo) { + sfp->pseudo = TRUE; + rrp->pseudo = FALSE; + } + } if (rrp != NULL && rrp->ext.choice == 2) { trp = (tRNAPtr) rrp->ext.value.ptrvalue; if (trp != NULL && trp->anticodon != NULL) { @@ -9827,6 +9845,40 @@ NLM_EXTERN Int4 VisitUserObjectsInUop (UserObjectPtr uop, Pointer userdata, Visi return index; } +typedef struct uopdata { + UserObjectPtr rsult; + CharPtr tag; +} UopData, PNTR UopDataPtr; + +static void FindUopProc ( + UserObjectPtr uop, + Pointer userdata +) + +{ + ObjectIdPtr oip; + UopDataPtr udp; + + if (uop == NULL || userdata == NULL) return; + oip = uop->type; + if (oip == NULL) return; + udp = (UopDataPtr) userdata; + if (StringICmp (oip->str, udp->tag) != 0) return; + udp->rsult = uop; +} + +NLM_EXTERN UserObjectPtr FindUopByTag (UserObjectPtr top, CharPtr tag) + +{ + UopData ud; + + if (top == NULL || StringHasNoText (tag)) return NULL; + ud.rsult = NULL; + ud.tag = tag; + VisitUserObjectsInUop (top, (Pointer) &ud, FindUopProc); + return ud.rsult; +} + NLM_EXTERN UserObjectPtr CombineUserObjects (UserObjectPtr origuop, UserObjectPtr newuop) { |