/dports/biology/ncbi-toolkit/ncbi/tools/ |
H A D | tfuns.c | 885 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 D | salign.c | 658 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() [all …]
|
H A D | urkpcc.c | 408 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 D | salptool.c | 332 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() [all …]
|
H A D | pobutil.c | 68 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 D | urkfltr.c | 435 slp = SeqLocIntNew (start, stop, Seq_strand_unknown, sip); in FilterFilter() 467 slp = SeqLocIntNew (start, stop, Seq_strand_unknown, sip); in FilterFilter()
|
H A D | urksigu.c | 185 slp = SeqLocIntNew (lstart, cstop, Seq_strand_unknown, sip); in FilterSigSeq()
|
H A D | urkepi.c | 1136 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 D | blastconcat.c | 202 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 D | actutils.c | 1188 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 D | spidey.c | 561 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() [all …]
|
/dports/biology/ncbi-toolkit/ncbi/desktop/ |
H A D | mapgene.c | 797 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() [all …]
|
H A D | gphview.c | 124 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() [all …]
|
/dports/biology/ncbi-toolkit/ncbi/api/ |
H A D | satutil.c | 191 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 D | salutil.c | 572 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 D | salprop.c | 343 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 D | udvseq.c | 1253 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 D | codon.c | 425 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 D | mconsist.c | 266 t_slp = SeqLocIntNew(start, stop, Seq_strand_plus, anchor_id); in MapLocToAnchor()
|
/dports/biology/ncbi-toolkit/ncbi/demo/ |
H A D | dotmain.c | 312 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 D | twop.c | 351 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 D | sigmev.c | 657 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 D | bl2seq.c | 670 *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 D | cn3dmatn.c | 342 slp = SeqLocIntNew(from, to, 0, pmmdThis->pSeqId); in MediaObjSelect()
|
/dports/biology/ncbi-toolkit/ncbi/ddv/ |
H A D | ddvclick.c | 451 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()
|