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Searched refs:DeltaSeqPtr (Results 1 – 25 of 42) sorted by relevance

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/dports/biology/ncbi-toolkit/ncbi/api/
H A Dedutil.h474 NLM_EXTERN SeqLocPtr LIBCALL DeltaSeqsToSeqLocs (DeltaSeqPtr dsp);
484 NLM_EXTERN DeltaSeqPtr LIBCALL SeqLocsToDeltaSeqs (DeltaSeqPtr dsp, SeqLocPtr slp);
623 NLM_EXTERN DeltaSeqPtr LIBCALL GappedSeqLocsToDeltaSeqs(SeqLocPtr slp);
782 extern Boolean IsDeltaSeqGap (DeltaSeqPtr dsp);
783 extern Boolean IsDeltaSeqUnknownGap (DeltaSeqPtr dsp);
784 extern Boolean IsDeltaSeqKnownGap (DeltaSeqPtr dsp);
786 extern Boolean DoesDeltaSeqHaveGapTypeOrLinkage (DeltaSeqPtr dsp);
H A Dedutil.c744 DeltaSeqPtr curr; in DeltaSeqsToSeqLocs()
790 NLM_EXTERN DeltaSeqPtr LIBCALL SeqLocsToDeltaSeqs (DeltaSeqPtr dsp, SeqLocPtr slp) in SeqLocsToDeltaSeqs()
931 DeltaSeqPtr tdsp = NULL; in BioseqDeleteEx()
2007 static DeltaSeqPtr CopyDeltaSeqPtrChain (DeltaSeqPtr dsp) in CopyDeltaSeqPtrChain()
2009 DeltaSeqPtr new_chain = NULL; in CopyDeltaSeqPtrChain()
2058 DeltaSeqPtr dsp; in BioseqCopyEx()
4116 DeltaSeqPtr res; in GappedSeqLocsToDeltaSeqs()
4117 DeltaSeqPtr dsp; in GappedSeqLocsToDeltaSeqs()
5413 DeltaSeqPtr dsp; in GetDeltaSeqForOffset()
5526 (DeltaSeqPtr dsp, in SeqEdInsertIntoDeltaGap()
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H A Dasn2gnb6.c5614 static DeltaSeqPtr RevCompDelta ( in RevCompDelta()
5615 DeltaSeqPtr seq_ext in RevCompDelta()
5619 DeltaSeqPtr dsp; in RevCompDelta()
5699 DeltaSeqPtr delta_head = NULL; in FormatContigBlock()
5700 DeltaSeqPtr dsp; in FormatContigBlock()
5701 DeltaSeqPtr dspnext; in FormatContigBlock()
5706 DeltaSeqPtr new_delta = NULL; in FormatContigBlock()
5771 new_delta = RevCompDelta ((DeltaSeqPtr) bsp->seq_ext); in FormatContigBlock()
5774 delta_head = (DeltaSeqPtr) bsp->seq_ext; in FormatContigBlock()
H A Dseqport.c2642 DeltaSeqPtr dsp; in SeqPortStreamDelta()
2660 for (dsp = (DeltaSeqPtr) bsp->seq_ext, cumulative = 0; in SeqPortStreamDelta()
4979 DeltaSeqPtr dsp; in DeltaBioseqComplement()
4988 dsp = (DeltaSeqPtr) bsp->seq_ext; in DeltaBioseqComplement()
4999 dsp = (DeltaSeqPtr) bsp->seq_ext; in DeltaBioseqComplement()
5239 DeltaSeqPtr dsp, next_dsp, newchain = NULL; in DeltaBioseqReverse()
5248 dsp = (DeltaSeqPtr) bsp->seq_ext; in DeltaBioseqReverse()
5259 dsp = (DeltaSeqPtr) bsp->seq_ext; in DeltaBioseqReverse()
5388 DeltaSeqPtr dsp, dspnext; in DeltaRevComp()
5397 for (dsp = (DeltaSeqPtr) bsp->seq_ext; dsp != NULL; dsp = dsp->next) { in DeltaRevComp()
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H A Dseqmgr.c2602 DeltaSeqPtr dsp; in SpreadGapsInDeltaSeq()
2613 for (dsp = (DeltaSeqPtr)(bsp->seq_ext); dsp != NULL; dsp = dsp->next) in SpreadGapsInDeltaSeq()
2734 static Boolean NextLitLength (DeltaSeqPtr next, Int4Ptr lenp) in NextLitLength()
2760 DeltaSeqPtr dsp, next; in CountGapsInDeltaSeq()
2775 for (dsp = (DeltaSeqPtr)(bsp->seq_ext); dsp != NULL; dsp = next) in CountGapsInDeltaSeq()
4071 DeltaSeqPtr dsp; in IsNonGappedLiteral()
4077 for (dsp = (DeltaSeqPtr) bsp->seq_ext; dsp != NULL; dsp = dsp->next) { in IsNonGappedLiteral()
6249 DeltaSeqPtr dsp; in RecordSegmentsInBioseqs()
6280 dsp = (DeltaSeqPtr) gop->dataptr; in RecordSegmentsInBioseqs()
11202 DeltaSeqPtr dsp; in CollectAllBioseqs()
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H A Dasn2gnb3.c193 DeltaSeqPtr dsp; in AddUnorderedCommentString()
203 for (dsp = (DeltaSeqPtr) bsp->seq_ext; dsp != NULL; dsp = dsp->next) { in AddUnorderedCommentString()
253 DeltaSeqPtr dsp; in AddHTGSCommentString()
262 for (dsp = (DeltaSeqPtr) bsp->seq_ext, buflen = 0; dsp != NULL; dsp = dsp->next) { in AddHTGSCommentString()
1681 DeltaSeqPtr deltasp; in GetPrimaryStrForDelta()
1693 for (deltasp = (DeltaSeqPtr) bsp->seq_ext; deltasp != NULL; deltasp = deltasp->next) { in GetPrimaryStrForDelta()
2620 DeltaSeqPtr dsp; in AddCommentBlock()
2950 for (dsp = (DeltaSeqPtr) (bsp->seq_ext); dsp != NULL; dsp = dsp->next) { in AddCommentBlock()
H A Dgather.c3027 DeltaSeqPtr dsp = NULL; in GatherBioseqFunc()
3166 dsp = (DeltaSeqPtr)(bsp->seq_ext); /* real data is here */ in GatherBioseqFunc()
3927 DeltaSeqPtr dsp; in IGCCBuild()
4016 dsp = (DeltaSeqPtr) bsp->seq_ext; in IGCCBuild()
6294 static Boolean VisitDelta (InternalACCPtr iap, DeltaSeqPtr dsp, Pointer parent, Uint2 parenttype, P… in VisitDelta()
6379 …if (! VisitDelta (iap, (DeltaSeqPtr) bsp->seq_ext, (Pointer) bsp, itemtype, (Pointer PNTR) &(bsp->… in VisitBioseq()
H A Dwprint.c1934 DeltaSeqPtr dsp; in PrintGenome()
1958 for (dsp = (DeltaSeqPtr) gbp->bsp->seq_ext; dsp; dsp=dsp->next) { in PrintGenome()
H A Dasn2ff2.c764 DeltaSeqPtr d; in GetCommentByChoice()
857 for (d=(DeltaSeqPtr)(bsp->seq_ext); d != NULL; d=d->next) { in GetCommentByChoice()
H A Dvalid.c4404 DeltaSeqPtr dsp; in ValLookForBigFarSeqs()
6990 DeltaSeqPtr dsp; in IsConWithGaps()
6997 for (dsp = (DeltaSeqPtr) bsp->seq_ext; dsp; dsp=dsp->next) { in IsConWithGaps()
9035 vnp = (DeltaSeqPtr) bsp->seq_ext; in ValidateBioseqInst()
18862 DeltaSeqPtr dsp; in GetFeatsInGaps()
21008 DeltaSeqPtr dsp; in LocationIsFar()
21027 for (dsp = (DeltaSeqPtr) bsp->seq_ext; in LocationIsFar()
21078 DeltaSeqPtr dsp; in HasAssemblyOrNullGap()
21097 DeltaSeqPtr dsp; in ReportBadAssemblyGap()
21145 DeltaSeqPtr dsp; in ReportBadWGSGap()
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H A Dsqnutil2.c4369 DeltaSeqPtr dsp; in ReadContigListExEx()
13570 DeltaSeqPtr dsp; in PrintQualityScoresForContig()
13602 for (dsp = (DeltaSeqPtr) bsp->seq_ext; dsp != NULL; dsp = dsp->next) { in PrintQualityScoresForContig()
13674 DeltaSeqPtr dsp; in PhrapGraphForContig()
13705 for (dsp = (DeltaSeqPtr) bsp->seq_ext; dsp != NULL; dsp = dsp->next) { in PhrapGraphForContig()
14701 NLM_EXTERN Int4 GetDeltaSeqLen (DeltaSeqPtr dsp) in GetDeltaSeqLen()
14720 DeltaSeqPtr dsp; in GetDeltaSeqForPosition()
15272 DeltaSeqPtr dsp; in LocationContainsGaps()
15300 for (dsp = (DeltaSeqPtr) bsp->seq_ext; in LocationContainsGaps()
15471 DeltaSeqPtr dsp; in RemoveGapsFromDeltaLocation()
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H A Dsqnutils.h1678 NLM_EXTERN Int4 GetDeltaSeqLen (DeltaSeqPtr dsp);
1679 NLM_EXTERN DeltaSeqPtr GetDeltaSeqForPosition(Int4 pos, BioseqPtr bsp, Int4Ptr pStart);
/dports/biology/ncbi-toolkit/ncbi/object/
H A Dobjseq.h328 typedef ValNode DeltaSeq, PNTR DeltaSeqPtr; typedef
330 NLM_EXTERN Boolean LIBCALL DeltaSeqAsnWrite PROTO((DeltaSeqPtr dsp, AsnIoPtr aip, AsnTypePtr atp…
331 NLM_EXTERN DeltaSeqPtr LIBCALL DeltaSeqAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
332 NLM_EXTERN DeltaSeqPtr LIBCALL DeltaSeqFree PROTO((DeltaSeqPtr dsp));
336 NLM_EXTERN Boolean LIBCALL DeltaSeqSetAsnWrite PROTO((DeltaSeqPtr dsp, AsnIoPtr aip, AsnTypePtr …
337 NLM_EXTERN DeltaSeqPtr LIBCALL DeltaSeqSetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr set, AsnTypePtr e…
338 NLM_EXTERN DeltaSeqPtr LIBCALL DeltaSeqSetFree PROTO((DeltaSeqPtr dsp));
H A Dobjseq.c796 DeltaSeqPtr dsp, dspnext; in BioseqFreeComponents()
822 dsp = (DeltaSeqPtr)(bsp->seq_ext); in BioseqFreeComponents()
4354 NLM_EXTERN DeltaSeqPtr LIBCALL DeltaSeqFree (DeltaSeqPtr dsp) in DeltaSeqFree()
4368 return (DeltaSeqPtr)MemFree(dsp); in DeltaSeqFree()
4378 NLM_EXTERN Boolean LIBCALL DeltaSeqAsnWrite (DeltaSeqPtr dsp, AsnIoPtr aip, AsnTypePtr orig) in DeltaSeqAsnWrite()
4428 NLM_EXTERN DeltaSeqPtr LIBCALL DeltaSeqAsnRead (AsnIoPtr aip, AsnTypePtr orig) in DeltaSeqAsnRead()
4432 DeltaSeqPtr dsp=NULL; in DeltaSeqAsnRead()
4490 DeltaSeqPtr olddsp; in DeltaSeqSetAsnWrite()
4538 DeltaSeqPtr dsp, first=NULL, prev; in DeltaSeqSetAsnRead()
4587 NLM_EXTERN DeltaSeqPtr LIBCALL DeltaSeqSetFree (DeltaSeqPtr dsp) in DeltaSeqSetFree()
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/dports/biology/ncbi-toolkit/ncbi/demo/
H A Dsqn2agp.c260 DeltaSeqPtr dsp; in DoOneBioseq()
328 for (dsp = (DeltaSeqPtr) bsp->seq_ext; dsp != NULL; dsp = dsp->next, cumulative += len) { in DoOneBioseq()
331 if (dsp == (DeltaSeqPtr) bsp->seq_ext || dsp->next == NULL) { in DoOneBioseq()
H A Dfa2htgs.c276 DeltaSeqPtr dsp; in OffsetAndLinkSeqGraph()
287 for (dsp = (DeltaSeqPtr) (bsp->seq_ext); in OffsetAndLinkSeqGraph()
448 DeltaSeqPtr dsp; in MakeAssemblyFragments()
462 for (dsp = (DeltaSeqPtr) (bsp->seq_ext); in MakeAssemblyFragments()
H A Didcleanscan.c211 DeltaSeqPtr dsp; in DoGraphs()
270 for (dsp = (DeltaSeqPtr) (bsp->seq_ext); dsp != NULL; dsp = dsp->next) { in DoGraphs()
297 for (dsp = (DeltaSeqPtr) (bsp->seq_ext), vnp = head; in DoGraphs()
H A Dasn2fsa.c183 DeltaSeqPtr dsp; in QueueFarBioseqs()
200 for (dsp = (DeltaSeqPtr) (bsp->seq_ext); dsp != NULL; dsp = dsp->next) { in QueueFarBioseqs()
H A Dasnval.c506 DeltaSeqPtr dsp; in LookForBigFarSeqs()
524 for (dsp = (DeltaSeqPtr) bsp->seq_ext; dsp != NULL; dsp = dsp->next) { in LookForBigFarSeqs()
H A Dtbl2asn.c3476 DeltaSeqPtr dsp; in AddAssemblyGapFeatures()
3484 for (dsp = (DeltaSeqPtr) (bsp->seq_ext); in AddAssemblyGapFeatures()
3768 DeltaSeqPtr dsp; in OffsetAndLinkSeqGraph()
3779 for (dsp = (DeltaSeqPtr) (bsp->seq_ext); in OffsetAndLinkSeqGraph()
4021 DeltaSeqPtr dsp = NULL; in MakeAssemblyFragments()
4035 for (dsp = (DeltaSeqPtr) (bsp->seq_ext); in MakeAssemblyFragments()
/dports/biology/ncbi-toolkit/ncbi/tools/
H A Dsalptool.c1704 DeltaSeqPtr dsp; in CutAlignmentAtGaps()
1735 dsp = (DeltaSeqPtr) bsp->seq_ext; in CutAlignmentAtGaps()
1809 DeltaSeqPtr dsp; in RemoveSequencesInGapFromAlignments()
1843 dsp = (DeltaSeqPtr) bsp->seq_ext; in RemoveSequencesInGapFromAlignments()
/dports/biology/ncbi-toolkit/ncbi/sequin/
H A Dsequin9.c4096 DeltaSeqPtr dsp_new; in SplitDeltaSeq()
4190 DeltaSeqPtr dspold, dspnew; in PatchDeltaSequence()
4192 DeltaSeqPtr new_list = NULL; in PatchDeltaSequence()
10822 static DeltaSeqPtr DeltaSeqListFree (DeltaSeqPtr list) in DeltaSeqListFree()
10824 DeltaSeqPtr dsp; in DeltaSeqListFree()
10846 DeltaSeqPtr dspold, dspnew, dspold_prev; in UpdateSequenceExtendDelta5Prime()
10848 DeltaSeqPtr new_list = NULL; in UpdateSequenceExtendDelta5Prime()
11088 DeltaSeqPtr dspold, dspnew, dspold_prev; in UpdateSequenceExtendDelta3Prime()
11090 DeltaSeqPtr new_list = NULL; in UpdateSequenceExtendDelta3Prime()
11449 DeltaSeqPtr dspold, dspnew; in UpdateSequencePatchDelta()
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H A Dsequin10.c9204 DeltaSeqPtr dsp; in GetRevSectionInterval()
9216 for (dsp = (DeltaSeqPtr)(bsp->seq_ext); dsp != NULL; dsp = dsp->next) { in GetRevSectionInterval()
9279 DeltaSeqPtr dsp; in ListDeltaSeqIntervalsCallback()
9293 for (dsp = (DeltaSeqPtr)(bsp->seq_ext); dsp != NULL; dsp = dsp->next) { in ListDeltaSeqIntervalsCallback()
11745 DeltaSeqPtr dsp; in GetContigsInScaffoldsCallback()
11754 for (dsp = (DeltaSeqPtr)(bsp->seq_ext); dsp != NULL; dsp = dsp->next) { in GetContigsInScaffoldsCallback()
11796 DeltaSeqPtr dsp, dsp_prev = NULL, dsp_next; in RemoveContigFromScaffold()
11806 for (dsp = (DeltaSeqPtr)(bsp->seq_ext); dsp != NULL; dsp = dsp_next) { in RemoveContigFromScaffold()
11863 if ((dsp = (DeltaSeqPtr) bsp->seq_ext) != NULL && dsp->choice == 2 in RemoveContigFromScaffold()
/dports/biology/ncbi-toolkit/ncbi/desktop/
H A Dbspview.c497 DeltaSeqPtr delsp; in LaunchPrim()
527 delsp = (DeltaSeqPtr) gcp->thisitem; in LaunchPrim()
3578 DeltaSeqPtr dsp; in SetClickmeTitle()
3602 dsp = (DeltaSeqPtr) gcp->thisitem; in SetClickmeTitle()
/dports/biology/ncbi-toolkit/ncbi/access/
H A Dpmfapi.c3174 DeltaSeqPtr dsp; in LookupBioseqs()
3191 for (dsp = (DeltaSeqPtr) (bsp->seq_ext); dsp != NULL; dsp = dsp->next) { in LookupBioseqs()

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