/dports/biology/ncbi-toolkit/ncbi/tools/ |
H A D | actutils.h | 218 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 D | actutils.c | 2082 (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() [all …]
|
H A D | salign.h | 53 NLM_EXTERN SeqLocPtr AlignmRNA2genomic (BioseqPtr bsp1, BioseqPtr bsp2);
|
H A D | blast.h | 551 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 D | bl2seq.c | 663 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() [all …]
|
H A D | asnmacro.c | 66 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 D | dotmain.c | 165 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 D | ShapeFix_Wire_1.cxx | 383 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() [all …]
|
/dports/lang/fpc-source/fpc-3.2.2/tests/test/ |
H A D | trtti20.pp | 121 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 D | spline.dem | 37 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 D | spline.dem | 37 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 D | spline.dem | 39 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 D | twoseq_api.c | 240 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 D | twoseq_api.h | 179 Bioseq *bsp1,
|
/dports/biology/ncbi-toolkit/ncbi/desktop/ |
H A D | ingenext.h | 107 BioseqPtr bsp1; member 127 BioseqPtr bsp1; member
|
H A D | dotvibrant.c | 5423 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() [all …]
|
H A D | ingenext.c | 1364 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() [all …]
|
H A D | seqpanel.h | 57 NLM_EXTERN SeqAlignPtr Sequin_GlobalAlign2Seq (BioseqPtr bsp1, BioseqPtr bsp2, BoolPtr revcomp);
|
H A D | ingenwin.h | 213 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 D | dotviewer.h | 67 BioseqPtr bsp1; member 384 NLM_EXTERN SCP_ResultPtr SCP_CompareOrderOrganizeBioseqs(BioseqPtr bsp1, BioseqPtr bsp2, SeqLocPtr …
|
/dports/biology/ncbi-toolkit/ncbi/ddv/ |
H A D | ddvopen.c | 2646 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() [all …]
|
/dports/biology/ncbi-toolkit/ncbi/biostruc/cblast/ |
H A D | cblastutil.h | 38 extern SeqEntryPtr GetSeqEntry(BioseqPtr bsp1, BioseqPtr bsp2);
|
/dports/biology/ncbi-toolkit/ncbi/biostruc/cdd/ |
H A D | cddutil.c | 3085 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() [all …]
|
/dports/biology/ncbi-toolkit/ncbi/api/ |
H A D | salpstat.h | 249 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 D | salpstat.c | 1906 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() [all …]
|