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Searched refs:SeqLocIntNew (Results 1 – 25 of 96) sorted by relevance

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/dports/biology/ncbi-toolkit/ncbi/tools/
H A Dtfuns.c885 m_slp = SeqLocIntNew(len-1-(stop+ir), in find_orf()
897 slp = SeqLocIntNew(start+ir, stop+ir, strand, id); in find_orf()
899 slp = SeqLocIntNew(len-1-(stop+ir), len-1-(start+ir), in find_orf()
939 m_slp = SeqLocIntNew(met_start+ir, stop, strand, id); in find_orf()
956 slp = SeqLocIntNew(start+ir, stop, strand, id); in find_orf()
1023 slp = SeqLocIntNew (start, stop, strand, id); in find_orf_from_circle()
1042 slp = SeqLocIntNew (stop, len-1, strand, id); in find_orf_from_circle()
1096 slp = SeqLocIntNew (start, len-1, strand, id); in find_orf_from_circle()
1098 slp = SeqLocIntNew (0, len-start-1, strand, id); in find_orf_from_circle()
1221 slp = SeqLocIntNew(from, to, Seq_strand_plus, bsp->id); in find_all_orf()
[all …]
H A Dsalign.c658 slpp = SeqLocIntNew (0, length-1, Seq_strand_plus, bsp->id); in TranslateSeqLoc()
702 newslp1=SeqLocIntNew (0, start1, strand1, sip1); in AlignExtreme5()
727 newslp1=SeqLocIntNew (0, start1, strand1, sip1); in AlignExtreme5()
728 newslp2=SeqLocIntNew (0, start2, strand2, sip2); in AlignExtreme5()
761 newslp1=SeqLocIntNew(stop1,slpstop1, strand1, sip1); in AlignExtreme3()
762 newslp2=SeqLocIntNew(0,stop2, strand2, sip2); in AlignExtreme3()
786 newslp1=SeqLocIntNew(stop1,slpstop1, strand1, sip1); in AlignExtreme3()
787 newslp2=SeqLocIntNew(stop2,slpstop2, strand2, sip2); in AlignExtreme3()
1035 slp1 = SeqLocIntNew (x1+1, y1-1, st1, sip1); in align_btwhits()
1037 slp2 = SeqLocIntNew (x2+1, y2-1, st2, sip2); in align_btwhits()
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H A Durkpcc.c408 slp = SeqLocIntNew (start, stop, Seq_strand_unknown, sip); in FilterCC()
431 slp = SeqLocIntNew (start, stop, Seq_strand_unknown, sip); in FilterCC()
522 slp = SeqLocIntNew (start, stop, Seq_strand_unknown, sip); in FilterCCVS()
545 slp = SeqLocIntNew (start, stop, Seq_strand_unknown, sip); in FilterCCVS()
H A Dsalptool.c332 loc_1_1 = SeqLocIntNew(start, stop, strand, dsp_1->ids); in MergeTwoDspBySIM4()
334 loc_1_2 = SeqLocIntNew(start, stop, strand, dsp_1->ids->next); in MergeTwoDspBySIM4()
345 loc_2_1 = SeqLocIntNew(0, -1, 0, dsp_1->ids); in MergeTwoDspBySIM4()
346 loc_2_2 = SeqLocIntNew(0, -1, 0, dsp_1->ids->next); in MergeTwoDspBySIM4()
372 loc_1_1 = SeqLocIntNew(0, -1, 0, dsp_1->ids); in MergeTwoDspBySIM4()
373 loc_1_2 = SeqLocIntNew(0, -1, 0, dsp_1->ids->next); in MergeTwoDspBySIM4()
523 loc_1_2 = SeqLocIntNew(match_start, match_stop, in MergeTwoDspBySIM4()
528 loc_1_1 = SeqLocIntNew(match_start, match_stop, in MergeTwoDspBySIM4()
530 loc_1_2 = SeqLocIntNew(start, stop, in MergeTwoDspBySIM4()
786 end_loc = SeqLocIntNew(start, stop, in check_polyA_tail()
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H A Dpobutil.c68 slp = SeqLocIntNew(0, bsp->length-1, Seq_strand_both, bsp->id); in make_repeat_lib()
83 slp = SeqLocIntNew(0, bsp->length-1, Seq_strand_both, bsp->id); in make_repeat_lib()
141 new = SeqLocIntNew(rep->start, rep->stop, rep->strand, sip); in store_align_ends()
199 new_sfp->location = SeqLocIntNew(rep->start, rep->stop, rep->strand, sip); in build_repeat_feat()
882 return SeqLocIntNew(start, stop, strand, sip); in break_blast_job()
895 new = SeqLocIntNew(start, stop, strand, sip); in break_blast_job()
2052 pbp->m_loc = SeqLocIntNew(m_start, m_stop, Seq_strand_plus, ddp->id); in check_sim_list()
2053 pbp->s_loc = SeqLocIntNew(s_start, s_stop, strand, ddp->id->next); in check_sim_list()
2116 slp = SeqLocIntNew(start, stop, strand, sip); in filter_redundent_sim_alignment()
2494 slp = SeqLocIntNew(start, start+dsp->lens[i]-1, strand, dsp->ids); in convert_align_to_interval()
H A Durkfltr.c435 slp = SeqLocIntNew (start, stop, Seq_strand_unknown, sip); in FilterFilter()
467 slp = SeqLocIntNew (start, stop, Seq_strand_unknown, sip); in FilterFilter()
H A Durksigu.c185 slp = SeqLocIntNew (lstart, cstop, Seq_strand_unknown, sip); in FilterSigSeq()
H A Durkepi.c1136 slp = SeqLocIntNew (start, stop, Seq_strand_unknown, sip); in FilterEpi()
1168 slp = SeqLocIntNew (start, stop, Seq_strand_unknown, sip); in FilterEpi()
1228 slptmp = SeqLocIntNew (stop+1, start-1, Seq_strand_unknown, sip); in FilterEpi()
1239 slptmp = SeqLocIntNew (stop+1, length-1, Seq_strand_unknown, sip); in FilterEpi()
H A Dblastconcat.c202 private_slp = SeqLocIntNew( query_loc_start, SeqLocStop( query_slp ), in GetNumSpacers()
205 private_slp = SeqLocIntNew( query_loc_start, SeqLocStop( query_slp ), in GetNumSpacers()
593 newloc = SeqLocIntNew( start, end, SeqLocStrand( loc ), tmpid ); in DivideSeqAligns()
995 newloc = SeqLocIntNew( start, end, SeqLocStrand( loc ), id ); in ConcatSeqLoc()
H A Dactutils.c1188 slp = SeqLocIntNew(amp->from_row, amp->to_row, amp->strand, sip); in ACT_MakeProfileFromSA()
2113 slp1 = SeqLocIntNew(start1, stop1, Seq_strand_plus, bsp1->id); in ACT_FindPiece()
2114 slp2 = SeqLocIntNew(start2, stop2, strand, bsp2->id); in ACT_FindPiece()
2165 slp1 = SeqLocIntNew(start1, nstart1, Seq_strand_plus, bsp1->id); in ACT_FindPiece()
2166 slp2 = SeqLocIntNew(start2, nstart2, strand, bsp2->id); in ACT_FindPiece()
2176 slp1 = SeqLocIntNew(start1, nstart1, Seq_strand_plus, bsp1->id); in ACT_FindPiece()
2177 slp2 = SeqLocIntNew(nstop2, stop2, strand, bsp2->id); in ACT_FindPiece()
2212 slp1 = SeqLocIntNew(nstop1, stop1, Seq_strand_plus, bsp1->id); in ACT_FindPiece()
2213 slp2 = SeqLocIntNew(nstop2, stop2, strand, bsp2->id); in ACT_FindPiece()
2233 slp1 = SeqLocIntNew(nstop1, stop1, Seq_strand_plus, bsp1->id); in ACT_FindPiece()
[all …]
H A Dspidey.c561 slp2 = SeqLocIntNew(spot->from, spot->to, spot->strand, spig->bsp->id); in SPI_AlnSinglemRNAToGen()
4198 slp1 = SeqLocIntNew(prevstop1+1, start1-1, strand1, sip1); in SPI_ConnectAln()
4467 slp1 = SeqLocIntNew(start1, stop1, Seq_strand_plus, sip1); in SPI_FillInIntron()
4482 slp2 = SeqLocIntNew(start, stop, strand2, sip2); in SPI_FillInIntron()
4693 slp2 = SeqLocIntNew(stop_m, start_m, strand, sip2); in SPI_FindPiece()
4750 slp2 = SeqLocIntNew(start_m, stop_m, strand, sip2); in SPI_FindPiece()
4815 slp2 = SeqLocIntNew(stop_m, start_m, strand, sip2); in SPI_FindPiece()
4872 slp2 = SeqLocIntNew(start_m, stop_m, strand, sip2); in SPI_FindPiece()
6372 slp2 = SeqLocIntNew(end2, prevstop2+1, strand, sip_mrna); in SPI_FillInLastmRNAHoles()
6374 slp2 = SeqLocIntNew(prevstop2+1, end2, strand, sip_mrna); in SPI_FillInLastmRNAHoles()
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/dports/biology/ncbi-toolkit/ncbi/desktop/
H A Dmapgene.c797 slp = SeqLocIntNew(start, stop, Seq_strand_plus, missing_id); in map_one_fish_loc()
909 slp = SeqLocIntNew(start, stop, Seq_strand_plus, missing_id); in map_one_fish_loc()
1106 slp = SeqLocIntNew(start, stop, Seq_strand_plus, sip); in figure_loc_by_position()
1249 n_fsp->slp = SeqLocIntNew(SeqLocStart(g_msp->slp), in AddSeqIndexLoc()
1261 n_fsp->slp = SeqLocIntNew(SeqLocStart(g_fsp->slp), in AddSeqIndexLoc()
1392 slp = SeqLocIntNew(start, stop, strand, sip); in find_gene_location()
1607 t_loc = SeqLocIntNew(start, stop, Seq_strand_plus, sip); in map_one_location_to_slp_list()
2016 return SeqLocIntNew(SeqLocStart(fsp->slp), in find_other_seqloc()
2050 slp = SeqLocIntNew(m_left, m_right, Seq_strand_plus, in cvt_loc_for_two_gene()
2150 return SeqLocIntNew(left, right, Seq_strand_plus, bsp->id); in find_band_location()
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H A Dgphview.c124 slp = SeqLocIntNew (0, len-1, Seq_strand_plus, SeqIdFindBest (bsp->id, 0)); in MakeMultiSlpList()
460 m_loc = SeqLocIntNew (0, bsp->length - 1, 0, bsp->id); in PopulateCompressedNoAlignment()
507 m_loc = SeqLocIntNew (0, bsp->length - 1, 0, bsp->id); in PopulateCompressed()
652 slp = SeqLocIntNew (0, len-1, Seq_strand_plus, SeqIdFindBest (bsp->id, 0)); in PopulateSimpleGraphic()
787 loc = SeqLocIntNew(m_start, m_stop, m_strand, sip); in load_seq_loc()
790 loc->next = SeqLocIntNew(m_start, m_stop, m_strand, sip); in load_seq_loc()
816 slp = SeqLocIntNew(m_start, m_stop, m_strand, sip); in load_seq_loc()
1175 slp = SeqLocIntNew (0, len-1, Seq_strand_plus, SeqIdFindBest (bsp->id, 0)); in PopulateGraphic()
1420 m_loc = SeqLocIntNew(start, stop, Seq_strand_plus, m_sip); in DrawAlignOnAllSequences()
1423 m_loc = SeqLocIntNew(0, mbsp->length-1, Seq_strand_plus, m_sip); in DrawAlignOnAllSequences()
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/dports/biology/ncbi-toolkit/ncbi/api/
H A Dsatutil.c191 t_loc = SeqLocIntNew(0, t_bsp->length-1, s_strand, target_sip); in bk_map_one_location()
233 slp = SeqLocIntNew(start, stop, strand, target_sip); in bk_map_one_location()
256 slp = SeqLocIntNew(start, stop, strand, target_sip); in bk_map_one_location()
375 slp = SeqLocIntNew(arp->sr.start, arp->sr.stop, strand, target_sip); in map_one_location()
383 slp = SeqLocIntNew(adp->seqends.start, adp->seqends.stop, strand, target_sip); in map_one_location()
768 return SeqLocIntNew(m_start, m_stop, strand, sip); in make_seq_loc_by_ends()
1070 source_slp = SeqLocIntNew(0, source_bsp->length-1, Seq_strand_plus, sip); in CopyFeatureFromAlign()
1110 c_slp = SeqLocIntNew(gr.left, gr.right, gr.strand, source_id); in CopyFeatureFromAlign()
1266 new_slp = SeqLocIntNew(a_start, a_stop, 0, SeqLocId(new_sfp->product)); in CopyFeatureFromAlign()
1291 c_slp = SeqLocIntNew(gr.left, gr.right, gr.strand, source_id); in CopyFeatureFromAlign()
H A Dsalutil.c572 slp = SeqLocIntNew (from, to, Seq_strand_plus, sip); in load_seq_data()
574 slp = SeqLocIntNew (to, from, Seq_strand_minus, sip); in load_seq_data()
1574 slp = SeqLocIntNew (from, to, strand, sip); in SelStructNew()
1601 slp2 = SeqLocIntNew (SeqLocStart(slp), SeqLocStop(slp), in SelStructCpy()
1838 slp = SeqLocIntNew (from, to, strand, sip); in new_seledstruct()
1935 slp = SeqLocIntNew (start, stop, SeqLocStrand (slptmp), sip); in sesp_to_slp()
1957 slpnew = SeqLocIntNew (start, stop, strand, sip); in sesp_to_slp()
1968 slpnew = SeqLocIntNew (start, stop, strand, sip); in sesp_to_slp()
1980 slpnew = SeqLocIntNew (start, stop, strand, sip); in sesp_to_slp()
2560 slp = SeqLocIntNew (start, stop, strand, sip); in checkseqlocfeature_for_editor()
[all …]
H A Dsalprop.c343 source_slp = SeqLocIntNew(0, source_bsp->length-1, Seq_strand_plus, sip); in CopySeqLocFromSeqAlign()
379 c_slp = SeqLocIntNew(gr.left, gr.right, gr.strand, source_id); in CopySeqLocFromSeqAlign()
1109 source_slp = SeqLocIntNew (0, source_bsp->length-1, Seq_strand_plus, source_id); in CreatePropaStruc()
1114 target_slp = SeqLocIntNew (0, target_bsp->length-1, Seq_strand_plus, in CreatePropaStruc()
1299 target_slp=SeqLocIntNew (from_overlapp, to_overlapp, Seq_strand_plus, target_id); in MergeFunc()
H A Dudvseq.c1253 slp=SeqLocIntNew(from, to, Seq_strand_plus, parent->id); in UDV_PopParaGFeaturesEx()
1258 slp=SeqLocIntNew (from_bsp, to_bsp, Seq_strand_plus, bsp->id);; in UDV_PopParaGFeaturesEx()
1344 slp = SeqLocIntNew (from, to, strand, sip); in UDV_Read_SequenceEx()
H A Dcodon.c425 loc = SeqLocIntNew(d_stop, d_start, strand, SeqLocId(slp)); in aa_to_dnaloc()
431 loc = SeqLocIntNew(d_start, d_stop, strand, SeqLocId(slp)); in aa_to_dnaloc()
H A Dmconsist.c266 t_slp = SeqLocIntNew(start, stop, Seq_strand_plus, anchor_id); in MapLocToAnchor()
/dports/biology/ncbi-toolkit/ncbi/demo/
H A Ddotmain.c312 slp1= SeqLocIntNew(q_start, q_stop, 1, qbsp->id); 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()
320 slp1 = SeqLocIntNew(q_start, q_stop, 1, qbsp->id); in DOT_RunRequest()
321 slp2 = SeqLocIntNew(s_start, s_stop,1, sbsp->id); in DOT_RunRequest()
324 slp1= SeqLocIntNew(q_start, q_stop, 1, qbsp->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()
H A Dtwop.c351 slpT = SeqLocIntNew (0, bspT->length-1, Seq_strand_unknown, bspT->id); in Main()
352 slpP = SeqLocIntNew (0, bspP->length-1, Seq_strand_unknown, bspP->id); in Main()
H A Dsigmev.c657 sgplead->loc = SeqLocIntNew (0, xosp->bsp->length-1, xosp->bsp->strand, in SigMeProc()
664 sgpcut->loc = SeqLocIntNew (0, xosp->bsp->length-1, xosp->bsp->strand, in SigMeProc()
671 sgptm->loc = SeqLocIntNew (0, xosp->bsp->length-1, xosp->bsp->strand, in SigMeProc()
H A Dbl2seq.c670 *slp1 = SeqLocIntNew(from, to, strand_option, in BL2SEQ_MakeSeqLoc()
673 *slp1 = SeqLocIntNew(0, bsp1->length-1, strand_option, in BL2SEQ_MakeSeqLoc()
692 *slp2 = SeqLocIntNew(from, to, Seq_strand_plus, SeqIdFindBestAccession(bsp2->id)); in BL2SEQ_MakeSeqLoc()
/dports/biology/ncbi-toolkit/ncbi/cn3d/
H A Dcn3dmatn.c342 slp = SeqLocIntNew(from, to, 0, pmmdThis->pSeqId); in MediaObjSelect()
/dports/biology/ncbi-toolkit/ncbi/ddv/
H A Dddvclick.c451 slp = SeqLocIntNew (bsp_pos, bsp_stop, strand/*Seq_strand_minus*/, sip); in DDV_GetClosetSeqLocGivenBspPos()
455 slp = SeqLocIntNew (bsp_start, bsp_stop, strand, sip); in DDV_GetClosetSeqLocGivenBspPos()
466 slp = SeqLocIntNew (bsp_start, bsp_pos, strand/*Seq_strand_plus*/, sip); in DDV_GetClosetSeqLocGivenBspPos()
470 slp = SeqLocIntNew (bsp_start, bsp_stop, strand, sip); in DDV_GetClosetSeqLocGivenBspPos()
490 slp = SeqLocIntNew (bsp_start, bsp_stop, strand, sip); in DDV_GetClosetSeqLocGivenBspPos()
1034 slp = SeqLocIntNew (first_bsp_coord, bsp_coord, direction, cur_pgp->sip); in DDV_SendBSPSelectMsg_OLD()
1127 slp = SeqLocIntNew (bsp_coord_start, bsp_coord_stop, direction, pgp->sip); in DDV_SendBSPSelectMsg()
1702 slp = SeqLocIntNew (bsp_start, bsp_stop, Seq_strand_plus, cur_pgp->sip); in DDV_ClickProc()

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