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Searched refs:bsp1 (Results 1 – 25 of 54) sorted by relevance

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/dports/biology/ncbi-toolkit/ncbi/tools/
H A Dactutils.h218 NLM_EXTERN SeqAlignPtr Sqn_GlobalAlign2Seq (BioseqPtr bsp1, BioseqPtr bsp2, BoolPtr revcomp);
225 typedef SeqAlignPtr (LIBCALLBACK *GetAlignmentFunc) (BioseqPtr bsp1, BioseqPtr bsp2);
226 typedef SeqAlignPtr (LIBCALLBACK *GetAlignmentPieceFunc) (SeqLocPtr bsp1, SeqLocPtr bsp2);
228 NLM_EXTERN SeqAlignPtr ACT_FindPiece(BioseqPtr bsp1, BioseqPtr bsp2, Int4 start1, Int4 stop1, Int4 …
231 (BioseqPtr bsp1,
H A Dactutils.c2082 (BioseqPtr bsp1, in ACT_FindPiece() argument
2602 BioseqPtr bsp1; in SQN_ExtendAlnAlg() local
2637 BioseqUnlock(bsp1); in SQN_ExtendAlnAlg()
2668 BioseqUnlock(bsp1); in SQN_ExtendAlnAlg()
2711 BioseqUnlock(bsp1); in SQN_ExtendAlnAlg()
2782 …spp = SeqPortNew(bsp1, MIN(stop1, bsp1->length-1), MIN(stop1+SQN_MAXGAP, bsp1->length-1), Seq_stra… in SQN_ExtendAlnAlg()
2848 BioseqUnlock(bsp1); in SQN_ExtendAlnAlg()
3105 if (ISA_aa(bsp1->mol)) in GetOldBlastAlignmentPiece()
3147 (BioseqPtr bsp1, in Sqn_GlobalAlign2SeqEx() argument
3261 if (bsp1->length-stop1 > 6 && bsp1->length-stop1 < extnd) in Sqn_GlobalAlign2SeqEx()
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H A Dsalign.h53 NLM_EXTERN SeqLocPtr AlignmRNA2genomic (BioseqPtr bsp1, BioseqPtr bsp2);
H A Dblast.h551 SeqAlignPtr LIBCALL BlastTwoSequences PROTO((BioseqPtr bsp1, BioseqPtr bsp2, CharPtr progname, BLAS…
592 SeqAlignPtr LIBCALL BlastTwoSequencesEx PROTO((BioseqPtr bsp1, BioseqPtr bsp2, CharPtr progname, BL…
594 SeqAlignPtr LIBCALL BlastTwoSequencesWithCallback PROTO((BioseqPtr bsp1, BioseqPtr bsp2, CharPtr pr…
/dports/biology/ncbi-toolkit/ncbi/demo/
H A Dbl2seq.c663 to = bsp1->length - 1; in BL2SEQ_MakeSeqLoc()
664 to = MIN(to, bsp1->length - 1); in BL2SEQ_MakeSeqLoc()
665 if (from >= bsp1->length) { in BL2SEQ_MakeSeqLoc()
671 SeqIdFindBestAccession(bsp1->id)); in BL2SEQ_MakeSeqLoc()
673 *slp1 = SeqLocIntNew(0, bsp1->length-1, strand_option, in BL2SEQ_MakeSeqLoc()
789 BioseqPtr bsp1=NULL, bsp2=NULL; in Main_new() local
863 bsp1 = (believe_query ? query_bsp : fake_bsp); in Main_new()
866 bsp1 = query_bsp; in Main_new()
975 BioseqPtr bsp1, bsp2; in Main_old() local
1056 bsp1 = (believe_query ? query_bsp : fake_bsp); in Main_old()
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H A Dasnmacro.c66 static SeqAlignPtr LIBCALLBACK GetSeqAlign (BioseqPtr bsp1, BioseqPtr bsp2) in GetSeqAlign() argument
71 if (bsp1 == NULL || bsp2 == NULL) return NULL; in GetSeqAlign()
74 if (bsp1->length > 10000 || bsp2->length > 10000) in GetSeqAlign()
85 if (ISA_na (bsp1->mol)) in GetSeqAlign()
94 BLAST_TwoSequencesSearch(options, bsp1, bsp2, &salp); in GetSeqAlign()
147 static SeqAlignPtr GlobalAlign2Seq (BioseqPtr bsp1, BioseqPtr bsp2, BoolPtr revcomp) in GlobalAlign2Seq() argument
149 return Sqn_GlobalAlign2SeqEx (bsp1, bsp2, revcomp, GetSeqAlign, GetSeqAlignPiece, TRUE); in GlobalAlign2Seq()
293 static SeqAlignPtr Sequin_GlobalAlign2Seq (BioseqPtr bsp1, BioseqPtr bsp2, BoolPtr revcomp) in Sequin_GlobalAlign2Seq() argument
295 return Sqn_GlobalAlign2SeqEx (bsp1, bsp2, revcomp, GetSeqAlign, GetSeqAlignPiece, TRUE); in Sequin_GlobalAlign2Seq()
H A Ddotmain.c165 static void DOT_AlignTwoSeqsAndDisplay(BioseqPtr bsp1, BioseqPtr bsp2, SeqLocPtr slp1, SeqLocPtr sl… in DOT_AlignTwoSeqsAndDisplay() argument
169 scp=SCP_CompareOrderOrganizeBioseqs(bsp1, bsp2, slp1, slp2, program, word_size, tree_limit); in DOT_AlignTwoSeqsAndDisplay()
203 static SeqAlignPtr DOT_RunBlast2Seqs(BioseqPtr bsp1, BioseqPtr bsp2, SeqLocPtr slp1, SeqLocPtr slp2… in DOT_RunBlast2Seqs() argument
249 sap = BlastTwoSequences(bsp1, bsp2, progname, options); in DOT_RunBlast2Seqs()
/dports/cad/opencascade/opencascade-7.6.0/src/ShapeFix/
H A DShapeFix_Wire_1.cxx383 if (!bsp1.IsNull()) in FixGap3d()
385 if(bsp1->Degree() == 1) bsp1->IncreaseDegree(2); //gka in FixGap3d()
388 bsp1->SetPole(1,vpnt); bsp1->SetPole(bsp1->NbPoles(),vpnt); in FixGap3d()
393 else bsp1->SetPole(bsp1->NbPoles(),vpnt); in FixGap3d()
395 first1 = bsp1->FirstParameter(); last1 = bsp1->LastParameter(); in FixGap3d()
396 c1 = bsp1; in FixGap3d()
969 if(bsp1->Degree() == 1) bsp1->IncreaseDegree(2); in FixGap2d()
972 bsp1->SetPole(1,mpnt); bsp1->SetPole(bsp1->NbPoles(),mpnt); in FixGap2d()
977 else bsp1->SetPole(bsp1->NbPoles(),mpnt); in FixGap2d()
979 first1 = bsp1->FirstParameter(); last1 = bsp1->LastParameter(); in FixGap2d()
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/dports/lang/fpc-source/fpc-3.2.2/tests/test/
H A Dtrtti20.pp121 bsp1, bsp2: TByteSetP;
130 bsp1 := [be1, be6];
144 if SetToString(PTypeInfo(TypeInfo(TByteSetP)), @bsp1, True) <> StrBS then
170 if bsp2<>bsp1 then
/dports/math/gnuplot/gnuplot-5.4.1/demo/
H A Dspline.dem37 bsp1(x) = ( 4 - 6 * x**2 + 3 * x**3 ) / 6;
41 plot bsp0(x), bsp1(x), bsp2(x), bsp3(x)
65 cub_bsplin_x(t) = bsp0(t) * x0 + bsp1(t) * x1 + bsp2(t) * x2 + bsp3(t) * x3
66 cub_bsplin_y(t) = bsp0(t) * y0 + bsp1(t) * y1 + bsp2(t) * y2 + bsp3(t) * y3
/dports/math/gnuplot-lite/gnuplot-5.4.1/demo/
H A Dspline.dem37 bsp1(x) = ( 4 - 6 * x**2 + 3 * x**3 ) / 6;
41 plot bsp0(x), bsp1(x), bsp2(x), bsp3(x)
65 cub_bsplin_x(t) = bsp0(t) * x0 + bsp1(t) * x1 + bsp2(t) * x2 + bsp3(t) * x3
66 cub_bsplin_y(t) = bsp0(t) * y0 + bsp1(t) * y1 + bsp2(t) * y2 + bsp3(t) * y3
/dports/math/gnuplot-tex-extras/gnuplot-5.2.8/demo/
H A Dspline.dem39 bsp1(x) = ( 4 - 6 * x**2 + 3 * x**3 ) / 6;
43 plot bsp0(x), bsp1(x), bsp2(x), bsp3(x)
67 cub_bsplin_x(t) = bsp0(t) * x0 + bsp1(t) * x1 + bsp2(t) * x2 + bsp3(t) * x3
68 cub_bsplin_y(t) = bsp0(t) * y0 + bsp1(t) * y1 + bsp2(t) * y2 + bsp3(t) * y3
/dports/biology/ncbi-toolkit/ncbi/algo/blast/api/
H A Dtwoseq_api.c240 BioseqPtr bsp1, BioseqPtr bsp2, in BLAST_TwoSequencesSearch() argument
253 if (bsp1 == NULL || bsp2 == NULL) in BLAST_TwoSequencesSearch()
256 seq1_is_aa = ISA_aa(bsp1->mol); in BLAST_TwoSequencesSearch()
283 SeqIdDup(SeqIdFindBest(bsp1->id, SEQID_GI))); in BLAST_TwoSequencesSearch()
H A Dtwoseq_api.h179 Bioseq *bsp1,
/dports/biology/ncbi-toolkit/ncbi/desktop/
H A Dingenext.h107 BioseqPtr bsp1; member
127 BioseqPtr bsp1; member
H A Ddotvibrant.c5423 BioseqUnlock(bsp1); in DOT_GetAlign()
5657 BioseqUnlock(bsp1); in DOT_FillAlignInfoPointer()
5661 BioseqUnlock(bsp1); in DOT_FillAlignInfoPointer()
5726 if (bsp1 != NULL) in DOT_Prob_FillAlignInfoPointer()
5727 BioseqUnlock(bsp1); in DOT_Prob_FillAlignInfoPointer()
5776 BioseqUnlock(bsp1); in DOT_Prob_FillAlignInfoPointer()
5780 BioseqUnlock(bsp1); in DOT_Prob_FillAlignInfoPointer()
5836 if (bsp1 != NULL) in DOT_FillFromScp()
5880 BioseqUnlock(bsp1); in DOT_FillFromScp()
5884 BioseqUnlock(bsp1); in DOT_FillFromScp()
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H A Dingenext.c1364 stop = bip->bsp1->length-1; in Ing_DoBlast2Seqs()
1513 bip->bsp1 = bsp1; in Ing_CreateBlast2SeqsForm()
1547 stop = bsp1->length; in Ing_CreateBlast2SeqsForm()
1784 bsp1=BioseqLockById(sip1); in Ing_CreateDotMatrixForm()
1789 bsp1 = igvp->bsp; in Ing_CreateDotMatrixForm()
1790 sip1 = bsp1->id; in Ing_CreateDotMatrixForm()
1793 stop = bsp1->length - 1; in Ing_CreateDotMatrixForm()
1797 if (bsp1){ in Ing_CreateDotMatrixForm()
1821 BioseqUnlock(bsp1); in Ing_CreateDotMatrixForm()
4691 sfp->bsp1 = bsp1; in Ing_CreateSpideyForm()
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H A Dseqpanel.h57 NLM_EXTERN SeqAlignPtr Sequin_GlobalAlign2Seq (BioseqPtr bsp1, BioseqPtr bsp2, BoolPtr revcomp);
H A Dingenwin.h213 extern void Ing_CreateSpideyForm(IngGenomeViewerPtr igvp, BioseqPtr bsp1, CharPtr path, CharPtr GI_…
228 extern void Ing_CreateBlast2SeqsForm(IngGenomeViewerPtr igvp, BioseqPtr bsp1, CharPtr path, CharPtr…
H A Ddotviewer.h67 BioseqPtr bsp1; member
384 NLM_EXTERN SCP_ResultPtr SCP_CompareOrderOrganizeBioseqs(BioseqPtr bsp1, BioseqPtr bsp2, SeqLocPtr …
/dports/biology/ncbi-toolkit/ncbi/ddv/
H A Dddvopen.c2646 Bioseq *bsp1 = NULL, *bsp2 = NULL; in DDV_DoAlign() local
2659 } else bsp1 = BioseqLockById(idp->sip); in DDV_DoAlign()
2660 if (bsp1 == NULL) { in DDV_DoAlign()
2679 BioseqUnlock(bsp1); in DDV_DoAlign()
2684 if(ISA_aa(bsp1->mol) != ISA_aa(bsp2->mol) || in DDV_DoAlign()
2685 ISA_na(bsp1->mol) != ISA_na(bsp1->mol)) { in DDV_DoAlign()
2687 BioseqUnlock(bsp1); in DDV_DoAlign()
2695 if(ISA_aa(bsp1->mol)) in DDV_DoAlign()
2696 sap = DDV_Blast2Seqs(bsp1, bsp2, idp->Gap, "blastp"); in DDV_DoAlign()
2701 BioseqUnlock(bsp1); in DDV_DoAlign()
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/dports/biology/ncbi-toolkit/ncbi/biostruc/cblast/
H A Dcblastutil.h38 extern SeqEntryPtr GetSeqEntry(BioseqPtr bsp1, BioseqPtr bsp2);
/dports/biology/ncbi-toolkit/ncbi/biostruc/cdd/
H A Dcddutil.c3085 BioseqPtr bsp1; in SeqAlignToCddExpAlign() local
3094 bsp1 = CddRetrieveBioseqById(sip,sep); in SeqAlignToCddExpAlign()
3096 CddExpAlignAlloc(pCDea,bsp1->length); in SeqAlignToCddExpAlign()
3434 if (!bsp1) { in CddCalculateTriangle()
3437 spp1 = SeqPortNew(bsp1, 0, bsp1->length-1, Seq_strand_unknown, Seq_code_ncbistdaa); in CddCalculateTriangle()
3456 for (i=0;i<bsp1->length;i++) { in CddCalculateTriangle()
3534 if (sip1) SeqIdFree(sip1); if (bsp1) bsp1 = NULL; in CddCalculateTriangle()
3547 BioseqPtr bsp1, bsp2, bsp3; in CddCalculateQuerySim() local
3572 spp1 = SeqPortNew(bsp1, 0, bsp1->length-1, Seq_strand_unknown, Seq_code_ncbistdaa); in CddCalculateQuerySim()
3588 for (i=0;i<bsp1->length;i++) { in CddCalculateQuerySim()
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/dports/biology/ncbi-toolkit/ncbi/api/
H A Dsalpstat.h249 NLM_EXTERN FloatHi PNTR LIBCALL SeqAlignWindowScoreFN(SeqAlignPtr align, BioseqPtr bsp1, BioseqPtr …
259 NLM_EXTERN FloatHi PNTR LIBCALL SeqAlignWindowScore(SeqAlignPtr align, BioseqPtr bsp1, BioseqPtr bs…
H A Dsalpstat.c1906 NLM_EXTERN FloatHi PNTR LIBCALL SeqAlignWindowScoreFN(SeqAlignPtr align, BioseqPtr bsp1, BioseqPtr … in SeqAlignWindowScoreFN() argument
1937 if(!bsp1 || !bsp2) { in SeqAlignWindowScoreFN()
1938 if(!bsp1) in SeqAlignWindowScoreFN()
1945 if((bsp1->mol == Seq_mol_aa)) in SeqAlignWindowScoreFN()
1957 a_len = bsp1->length; in SeqAlignWindowScoreFN()
1982 SeqAlignBioseqsOrder(align,bsp1,bsp2 ,&a_order, &b_order); in SeqAlignWindowScoreFN()
1986 spp_1 = SeqPortNew(bsp1, 0, -1, strand==NULL ? ((Uint1) 0) : strand[a_order], code1); in SeqAlignWindowScoreFN()
2138 NLM_EXTERN FloatHi PNTR LIBCALL SeqAlignWindowScore(SeqAlignPtr align, BioseqPtr bsp1, BioseqPtr bs… in SeqAlignWindowScore() argument
2146 if(bsp1) { in SeqAlignWindowScore()
2147 bsp_1 = bsp1; in SeqAlignWindowScore()
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