/dports/biology/ncbi-toolkit/ncbi/api/ |
H A D | edutil.h | 474 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);
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H A D | edutil.c | 744 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() [all …]
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H A D | asn2gnb6.c | 5614 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()
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H A D | seqport.c | 2642 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() [all …]
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H A D | seqmgr.c | 2602 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() [all …]
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H A D | asn2gnb3.c | 193 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()
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H A D | gather.c | 3027 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()
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H A D | wprint.c | 1934 DeltaSeqPtr dsp; in PrintGenome() 1958 for (dsp = (DeltaSeqPtr) gbp->bsp->seq_ext; dsp; dsp=dsp->next) { in PrintGenome()
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H A D | asn2ff2.c | 764 DeltaSeqPtr d; in GetCommentByChoice() 857 for (d=(DeltaSeqPtr)(bsp->seq_ext); d != NULL; d=d->next) { in GetCommentByChoice()
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H A D | valid.c | 4404 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() [all …]
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H A D | sqnutil2.c | 4369 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() [all …]
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H A D | sqnutils.h | 1678 NLM_EXTERN Int4 GetDeltaSeqLen (DeltaSeqPtr dsp); 1679 NLM_EXTERN DeltaSeqPtr GetDeltaSeqForPosition(Int4 pos, BioseqPtr bsp, Int4Ptr pStart);
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/dports/biology/ncbi-toolkit/ncbi/object/ |
H A D | objseq.h | 328 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));
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H A D | objseq.c | 796 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() [all …]
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/dports/biology/ncbi-toolkit/ncbi/demo/ |
H A D | sqn2agp.c | 260 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()
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H A D | fa2htgs.c | 276 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()
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H A D | idcleanscan.c | 211 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()
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H A D | asn2fsa.c | 183 DeltaSeqPtr dsp; in QueueFarBioseqs() 200 for (dsp = (DeltaSeqPtr) (bsp->seq_ext); dsp != NULL; dsp = dsp->next) { in QueueFarBioseqs()
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H A D | asnval.c | 506 DeltaSeqPtr dsp; in LookForBigFarSeqs() 524 for (dsp = (DeltaSeqPtr) bsp->seq_ext; dsp != NULL; dsp = dsp->next) { in LookForBigFarSeqs()
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H A D | tbl2asn.c | 3476 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()
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/dports/biology/ncbi-toolkit/ncbi/tools/ |
H A D | salptool.c | 1704 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()
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/dports/biology/ncbi-toolkit/ncbi/sequin/ |
H A D | sequin9.c | 4096 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() [all …]
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H A D | sequin10.c | 9204 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()
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/dports/biology/ncbi-toolkit/ncbi/desktop/ |
H A D | bspview.c | 497 DeltaSeqPtr delsp; in LaunchPrim() 527 delsp = (DeltaSeqPtr) gcp->thisitem; in LaunchPrim() 3578 DeltaSeqPtr dsp; in SetClickmeTitle() 3602 dsp = (DeltaSeqPtr) gcp->thisitem; in SetClickmeTitle()
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/dports/biology/ncbi-toolkit/ncbi/access/ |
H A D | pmfapi.c | 3174 DeltaSeqPtr dsp; in LookupBioseqs() 3191 for (dsp = (DeltaSeqPtr) (bsp->seq_ext); dsp != NULL; dsp = dsp->next) { in LookupBioseqs()
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