/dports/biology/ncbi-toolkit/ncbi/tools/ |
H A D | salign.c | 175 if (slp1==NULL || slp2==NULL) in BandAlignTwoSeqLocsFunc() 239 ValNodeAddPointer (&vnp, 0, slp2); in BandAlignTwoSeqLocs() 537 if (slp1 == NULL || slp2 == NULL) in BlastTwoSeqLocs() 571 strand2=SeqLocStrand(slp2); in BlastTwoSeqLocs() 574 sit=(SeqIntPtr)slp2->data.ptrvalue; in BlastTwoSeqLocs() 814 sip2 = SeqLocId(slp2); in align_extrem() 819 slpstart2= SeqLocStart(slp2); in align_extrem() 820 slpstop2 = SeqLocStop(slp2); in align_extrem() 948 SeqLocPtr slp1, slp2; in align_btwhits() local 1531 ValNodeAddPointer (&vnp, 0, slp2); in AlignAnyway() [all …]
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H A D | urkbias.c | 246 SeqLocPtr slp1, slp2; in SeqLocCompProc() local 251 slp2 = *((SeqLocPtr PNTR) ptr2); in SeqLocCompProc() 252 if (slp1 != NULL && slp2 != NULL) in SeqLocCompProc() 306 SeqLocPtr slp1, slp2, slp = NULL; in RemoveInternalOrfs() local 317 slp2 = *slpFound; in RemoveInternalOrfs() 318 while (slp2 != NULL) in RemoveInternalOrfs() 320 start2 = SeqLocStart (slp2); in RemoveInternalOrfs() 321 stop2 = SeqLocStop (slp2); in RemoveInternalOrfs() 328 slp2 = slp2->next; in RemoveInternalOrfs() 337 slp2 = slp1->next; in RemoveInternalOrfs() [all …]
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H A D | urksigu.c | 112 SeqLocPtr slp1, slp2; in FilterSigSeq() local 171 slp2 = ssp2->loc; in FilterSigSeq() 172 cstart = SeqLocStart (slp2); in FilterSigSeq() 173 cstop = SeqLocStop (slp2); in FilterSigSeq()
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H A D | dotseq.c | 1926 if (mip == NULL || slp1 == NULL || slp2 == NULL) return MemFree (mip); in DOT_InitMainInfobyLoc() 1928 slen=SeqLocLen(slp2); in DOT_InitMainInfobyLoc() 1931 sslp=slp2; in DOT_InitMainInfobyLoc() 2018 mip = DOT_CreateAndStorebyLoc (slp1, slp2, wordsize, num_hits); in DOT_SPI_FindBestAlnByDotPlot() 2025 start2 = SeqLocStart(slp2); in DOT_SPI_FindBestAlnByDotPlot() 2026 strand = SeqLocStrand(slp2); in DOT_SPI_FindBestAlnByDotPlot() 2039 dsp->ids->next = SeqIdDup(SeqLocId(slp2)); in DOT_SPI_FindBestAlnByDotPlot() 2042 dsp->strands[1] = SeqLocStrand(slp2); in DOT_SPI_FindBestAlnByDotPlot() 2050 if (ddp->length > SeqLocLen(slp2)) in DOT_SPI_FindBestAlnByDotPlot() 2051 dsp->lens[0] = SeqLocLen(slp2); in DOT_SPI_FindBestAlnByDotPlot() [all …]
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H A D | actutils.c | 2013 start2 = SeqLocStart(slp2); in ACT_FindBestAlnByDotPlot() 2014 strand = SeqLocStrand(slp2); in ACT_FindBestAlnByDotPlot() 2104 SeqLocPtr slp2; in ACT_FindPiece() local 2115 sap = aln_piece_func (slp1, slp2); in ACT_FindPiece() 2118 SeqLocFree(slp2); in ACT_FindPiece() 2169 SeqLocFree(slp2); in ACT_FindPiece() 2180 SeqLocFree(slp2); in ACT_FindPiece() 2216 SeqLocFree(slp2); in ACT_FindPiece() 2237 SeqLocFree(slp2); in ACT_FindPiece() 3092 if (slp1 == NULL || slp2 == NULL) in GetOldBlastAlignmentPiece() [all …]
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H A D | dotseq.h | 186 DOTMainDataPtr DOT_CreateAndStorebyLoc (SeqLocPtr slp1, SeqLocPtr slp2, Int4 word_size, Int4 tree_l… 194 SeqAlignPtr DOT_SPI_FindBestAlnByDotPlot(SeqLocPtr slp1, SeqLocPtr slp2, Int4 wordsize, Int4 num_hi…
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H A D | bandalgn.c | 868 NLM_EXTERN GlobalBandStructPtr CreatBandStruct(SeqLocPtr slp1, SeqLocPtr slp2, Int4Ptr PNTR W, Bool… in CreatBandStruct() argument 884 len2 = SeqLocLen(slp2); in CreatBandStruct() 887 seq2 = load_data(slp2, is_prot); in CreatBandStruct() 894 gbsp->seqloc2 = slp2; in CreatBandStruct() 934 …Blast(PSUGapOptionsPtr opt, Boolean is_prot, Int2 type, Int2 width, SeqLocPtr slp1, SeqLocPtr slp2) in SetLowUpFromBlast() argument 955 …while ((seqalign = BlastTwoSequencesByLoc(slp1, slp2,NULL, options))==NULL && (is_prot==FALSE && o… in SetLowUpFromBlast() 961 len2 = SeqLocLen(slp2); in SetLowUpFromBlast() 1084 NLM_EXTERN SeqAlignPtr GlobalBandByLoc(GlobalBandStructPtr gbsp, SeqLocPtr slp1, SeqLocPtr slp2, B… in GlobalBandByLoc() argument 1090 SetLowUpFromBlast(opt, is_prot, band_method, 0, slp1, slp2); in GlobalBandByLoc() 1095 AdjustOffSetsInSeqAlign(seqalign, slp1, slp2); in GlobalBandByLoc()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/ |
H A D | blast_seqalign.cpp | 785 CRef<CSeq_loc> slp1, slp2; in s_OOFBlastHSP2SeqAlign() local 825 slp2.Reset(new CSeq_loc()); in s_OOFBlastHSP2SeqAlign() 838 slp2->SetEmpty(*id2); in s_OOFBlastHSP2SeqAlign() 862 slp2->SetInt().SetTo(to2); in s_OOFBlastHSP2SeqAlign() 906 slp2->SetInt().SetFrom(from2); in s_OOFBlastHSP2SeqAlign() 907 slp2->SetInt().SetTo(to2); in s_OOFBlastHSP2SeqAlign() 914 slp2->SetInt().SetId(*id2); in s_OOFBlastHSP2SeqAlign() 952 slp2->SetInt().SetFrom(from2); in s_OOFBlastHSP2SeqAlign() 953 slp2->SetInt().SetTo(to2); in s_OOFBlastHSP2SeqAlign() 954 slp2->SetInt().SetId(*id2); in s_OOFBlastHSP2SeqAlign() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/ |
H A D | blast_seqalign.cpp | 785 CRef<CSeq_loc> slp1, slp2; in s_OOFBlastHSP2SeqAlign() local 825 slp2.Reset(new CSeq_loc()); in s_OOFBlastHSP2SeqAlign() 838 slp2->SetEmpty(*id2); in s_OOFBlastHSP2SeqAlign() 862 slp2->SetInt().SetTo(to2); in s_OOFBlastHSP2SeqAlign() 906 slp2->SetInt().SetFrom(from2); in s_OOFBlastHSP2SeqAlign() 907 slp2->SetInt().SetTo(to2); in s_OOFBlastHSP2SeqAlign() 914 slp2->SetInt().SetId(*id2); in s_OOFBlastHSP2SeqAlign() 952 slp2->SetInt().SetFrom(from2); in s_OOFBlastHSP2SeqAlign() 953 slp2->SetInt().SetTo(to2); in s_OOFBlastHSP2SeqAlign() 954 slp2->SetInt().SetId(*id2); in s_OOFBlastHSP2SeqAlign() [all …]
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/dports/devel/valgrind-lts/valgrind-dragonfly-dragonfly/helgrind/tests/ |
H A D | bar_bad.c | 38 pthread_t thr1, thr2, slp1, slp2, ext1; in main() local 76 pthread_create(&slp2, NULL, sleep1, (void*)bar4); in main() 84 pthread_cancel(slp2); in main()
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/dports/devel/valgrind/valgrind-dragonfly-dragonfly/helgrind/tests/ |
H A D | bar_bad.c | 38 pthread_t thr1, thr2, slp1, slp2, ext1; in main() local 76 pthread_create(&slp2, NULL, sleep1, (void*)bar4); in main() 84 pthread_cancel(slp2); in main()
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/dports/biology/ncbi-toolkit/ncbi/algo/blast/api/ |
H A D | blast_seqalign.c | 623 SeqLocPtr slp, slp1, slp2; in s_GapMakeSeqAlign() local 676 slp2 = NULL; in s_GapMakeSeqAlign() 694 slp1->next = slp2; in s_GapMakeSeqAlign() 840 SeqLocPtr slp, slp1, slp2; in OOFBlastHSPToSeqAlign() local 898 slp2 = NULL; in OOFBlastHSPToSeqAlign() 975 slp = slp2; in OOFBlastHSPToSeqAlign() 976 slp2->next = slp1; in OOFBlastHSPToSeqAlign() 1001 slp2 = NULL; in OOFBlastHSPToSeqAlign() 1206 slp = slp2; in OOFBlastHSPToSeqAlign() 1207 slp2->next = slp1; in OOFBlastHSPToSeqAlign() [all …]
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/dports/biology/ncbi-toolkit/ncbi/demo/ |
H A D | dotmain.c | 248 if (slp1 == NULL || slp2 == NULL) in DOT_RunBlast2Seqs() 269 SeqLocPtr slp1=NULL, slp2=NULL; in DOT_RunRequest() local 309 slp2 = NULL; in DOT_RunRequest() 314 slp2 = SeqLocIntNew(s_start, s_stop, 1, sbsp->id); in DOT_RunRequest() 316 slp2 = SeqLocIntNew(s_start, s_stop,2, sbsp->id); in DOT_RunRequest() 321 slp2 = SeqLocIntNew(s_start, s_stop,1, sbsp->id); in DOT_RunRequest() 326 slp2 = SeqLocIntNew(s_start, s_stop,1, sbsp->id); in DOT_RunRequest() 328 slp2 = SeqLocIntNew(s_start, s_stop, 2, sbsp->id); in DOT_RunRequest() 332 sap = DOT_RunBlast2Seqs(qbsp, sbsp, slp1, slp2, sdata); in DOT_RunRequest() 376 SeqLocPtr slp1=NULL, slp2=NULL; in DOT_OpenAcceptProc() local [all …]
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H A D | bl2seq.c | 647 BL2SEQ_MakeSeqLoc(const BioseqPtr bsp1, const BioseqPtr bsp2, SeqLocPtr *slp1, SeqLocPtr *slp2, Uin… in BL2SEQ_MakeSeqLoc() argument 654 *slp2 = NULL; in BL2SEQ_MakeSeqLoc() 692 *slp2 = SeqLocIntNew(from, to, Seq_strand_plus, SeqIdFindBestAccession(bsp2->id)); in BL2SEQ_MakeSeqLoc() 694 ValNodeAddPointer(slp2, SEQLOC_WHOLE, SeqIdDup(SeqIdFindBestAccession(bsp2->id))); in BL2SEQ_MakeSeqLoc() 805 SeqLocPtr slp1, slp2; /* Used for actual search. */ in Main_new() local 870 if (BL2SEQ_MakeSeqLoc(bsp1, bsp2, &slp1, &slp2, strand_option) == FALSE) in Main_new() 892 status = BLAST_TwoSeqLocSets(options, slp1, slp2, lcase_mask, &seqalign_arr, in Main_new() 959 slp2 = SeqLocSetFree(slp2); in Main_new() 1113 SeqLocPtr slp1=NULL, slp2=NULL; in Main_old() local 1114 if (BL2SEQ_MakeSeqLoc(bsp1, bsp2, &slp1, &slp2, options->strand_option) == FALSE) in Main_old() [all …]
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/dports/math/gap/gap-4.11.0/pkg/recog-1.3.2/contrib/pete/ |
H A D | basics.g | 125 ProdProg := function(slp1, slp2) 126 return ProductOfStraightLinePrograms(slp1, slp2); 142 ConjProg := function(slp1, slp2) 143 return ProdProg( InvProg(slp2) , ProdProg(slp1,slp2) );
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/dports/devel/gettext-tools/gettext-0.21/gettext-tools/src/ |
H A D | msgl-equal.c | 118 string_list_equal (const string_list_ty *slp1, const string_list_ty *slp2) in string_list_equal() argument 123 i2 = (slp2 != NULL ? slp2->nitems : 0); in string_list_equal() 127 if (strcmp (slp1->item[i], slp2->item[i]) != 0) in string_list_equal()
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H A D | msgl-equal.h | 33 const string_list_ty *slp2);
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/dports/devel/gettext-runtime/gettext-0.21/gettext-tools/src/ |
H A D | msgl-equal.c | 118 string_list_equal (const string_list_ty *slp1, const string_list_ty *slp2) in string_list_equal() argument 123 i2 = (slp2 != NULL ? slp2->nitems : 0); in string_list_equal() 127 if (strcmp (slp1->item[i], slp2->item[i]) != 0) in string_list_equal()
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H A D | msgl-equal.h | 33 const string_list_ty *slp2);
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/dports/devel/gettext-po-mode/gettext-0.21/gettext-tools/src/ |
H A D | msgl-equal.c | 118 string_list_equal (const string_list_ty *slp1, const string_list_ty *slp2) in string_list_equal() argument 123 i2 = (slp2 != NULL ? slp2->nitems : 0); in string_list_equal() 127 if (strcmp (slp1->item[i], slp2->item[i]) != 0) in string_list_equal()
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H A D | msgl-equal.h | 33 const string_list_ty *slp2);
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/dports/devel/libtextstyle/gettext-0.21/gettext-tools/src/ |
H A D | msgl-equal.c | 118 string_list_equal (const string_list_ty *slp1, const string_list_ty *slp2) in string_list_equal() argument 123 i2 = (slp2 != NULL ? slp2->nitems : 0); in string_list_equal() 127 if (strcmp (slp1->item[i], slp2->item[i]) != 0) in string_list_equal()
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/dports/biology/ncbi-toolkit/ncbi/api/ |
H A D | needleman.c | 277 NLM_EXTERN SeqAlignPtr LIBCALL NeedlemanWunschQuadraticByLoc(SeqLocPtr slp1,SeqLocPtr slp2, Int4 **… in NeedlemanWunschQuadraticByLoc() argument 316 dbSequence = FetchSequenceByLoc(slp2,&dbLength,&BspLen2); in NeedlemanWunschQuadraticByLoc() 322 if(SeqLocStrand(slp2)!=Seq_strand_minus) { in NeedlemanWunschQuadraticByLoc() 323 slp_start2 = SeqLocStart(slp2); in NeedlemanWunschQuadraticByLoc() 325 slp_start2 = BspLen2-1-SeqLocStop(slp2); in NeedlemanWunschQuadraticByLoc() 574 if(SeqLocStrand(slp2)!=Seq_strand_minus) in NeedlemanWunschQuadraticByLoc() 618 dsp->ids->next = SeqIdDup(SeqLocId(slp2)); in NeedlemanWunschQuadraticByLoc()
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H A D | salutil.c | 1480 SeqLocPtr slp1, slp2; in SeqLocListMatch() local 1486 slp2 = (SeqLocPtr) tmp2->data.ptrvalue; in SeqLocListMatch() 1587 SeqLocPtr slp, slp2; in SelStructCpy() local 1603 if ( slp2 == NULL ) { in SelStructCpy() 1607 ssp2->region = (Pointer) slp2; in SelStructCpy() 1705 SeqLocPtr slp1, slp2; in is_samepos() local 1711 slp2 = (SeqLocPtr) ssp2->region; in is_samepos() 1785 && SeqLocStop(slp1) < SeqLocStop(slp2) ) in overlapp_startssp() 1992 SeqLocPtr slp, slp2; in SelEdStructCpy() local 2003 if ( slp2 == NULL ) { in SelEdStructCpy() [all …]
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H A D | salutil.h | 177 NLM_EXTERN Boolean include_ssp (SeqLocPtr slp1, SeqLocPtr slp2); 178 NLM_EXTERN Int4 overlapp_startssp (SeqLocPtr slp1, SeqLocPtr slp2); 179 NLM_EXTERN Boolean overlapp_ssp (SeqLocPtr slp1, SeqLocPtr slp2); 180 NLM_EXTERN Boolean precede_ssp (SeqLocPtr slp1, SeqLocPtr slp2); 181 NLM_EXTERN Boolean succeed_ssp (SeqLocPtr slp1, SeqLocPtr slp2);
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