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Searched refs:slp2 (Results 1 – 25 of 74) sorted by relevance

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/dports/biology/ncbi-toolkit/ncbi/tools/
H A Dsalign.c175 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()
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H A Durkbias.c246 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()
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H A Durksigu.c112 SeqLocPtr slp1, slp2; in FilterSigSeq() local
171 slp2 = ssp2->loc; in FilterSigSeq()
172 cstart = SeqLocStart (slp2); in FilterSigSeq()
173 cstop = SeqLocStop (slp2); in FilterSigSeq()
H A Ddotseq.c1926 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()
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H A Dactutils.c2013 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()
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H A Ddotseq.h186 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…
H A Dbandalgn.c868 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/
H A Dblast_seqalign.cpp785 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/
H A Dblast_seqalign.cpp785 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()
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/dports/devel/valgrind-lts/valgrind-dragonfly-dragonfly/helgrind/tests/
H A Dbar_bad.c38 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()
/dports/devel/valgrind/valgrind-dragonfly-dragonfly/helgrind/tests/
H A Dbar_bad.c38 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()
/dports/biology/ncbi-toolkit/ncbi/algo/blast/api/
H A Dblast_seqalign.c623 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()
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/dports/biology/ncbi-toolkit/ncbi/demo/
H A Ddotmain.c248 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
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H A Dbl2seq.c647 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()
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/dports/math/gap/gap-4.11.0/pkg/recog-1.3.2/contrib/pete/
H A Dbasics.g125 ProdProg := function(slp1, slp2)
126 return ProductOfStraightLinePrograms(slp1, slp2);
142 ConjProg := function(slp1, slp2)
143 return ProdProg( InvProg(slp2) , ProdProg(slp1,slp2) );
/dports/devel/gettext-tools/gettext-0.21/gettext-tools/src/
H A Dmsgl-equal.c118 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()
H A Dmsgl-equal.h33 const string_list_ty *slp2);
/dports/devel/gettext-runtime/gettext-0.21/gettext-tools/src/
H A Dmsgl-equal.c118 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()
H A Dmsgl-equal.h33 const string_list_ty *slp2);
/dports/devel/gettext-po-mode/gettext-0.21/gettext-tools/src/
H A Dmsgl-equal.c118 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()
H A Dmsgl-equal.h33 const string_list_ty *slp2);
/dports/devel/libtextstyle/gettext-0.21/gettext-tools/src/
H A Dmsgl-equal.c118 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()
/dports/biology/ncbi-toolkit/ncbi/api/
H A Dneedleman.c277 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()
H A Dsalutil.c1480 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()
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H A Dsalutil.h177 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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