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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/SearchIO/
H A Dcross_match.pm259 my $subject_start;
265 $subject_start = $r[11];
270 $subject_start = $r[9];
281 -hit_start => $subject_start,
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/io/
H A DMSPcrunchStreamFeature.java211 final String subject_start; in MSPcrunchStreamFeature() local
219 subject_start = line_bits[4]; in MSPcrunchStreamFeature()
237 subject_start = line_bits[5]; in MSPcrunchStreamFeature()
249 new Qualifier ("subject_start", subject_start); in MSPcrunchStreamFeature()
H A DBlastStreamFeature.java157 int subject_start = Integer.valueOf (subject_start_string).intValue (); in BlastStreamFeature() local
166 note_values.add ("hit to " + subject_id + " " + subject_start + in BlastStreamFeature()
178 if (subject_end < subject_start) { in BlastStreamFeature()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/core/
H A Dblast_hits.h247 Int4 subject_start, Int4 subject_end,
286 const Uint1* subject_start, const Int4 subject_length,
304 const Uint1* query_start, const Uint1* subject_start,
H A Dblast_gapalign.h86 Int4 subject_start; /**< subject start offset current alignment */ member
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/core/
H A Dblast_hits.h247 Int4 subject_start, Int4 subject_end,
286 const Uint1* subject_start, const Int4 subject_length,
304 const Uint1* query_start, const Uint1* subject_start,
/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/
H A Dblast_hits.h247 Int4 subject_start, Int4 subject_end,
286 const Uint1* subject_start, const Int4 subject_length,
304 const Uint1* query_start, const Uint1* subject_start,
H A Dphi_gapalign.c704 gap_align->subject_start = s_length - private_s_start + 1; in s_PHIGappedAlignment()
726 gap_align->subject_start = subject_offset; in s_PHIGappedAlignment()
811 gap_align->subject_start, gap_align->subject_stop, in PHIGetGappedScore()
865 gap_align->subject_start = s_start - private_s_length; in PHIGappedAlignmentWithTraceback()
H A Dblast_hits.c126 Blast_HSPInit(Int4 query_start, Int4 query_end, Int4 subject_start, in Blast_HSPInit() argument
146 new_hsp->subject.offset = subject_start; in Blast_HSPInit()
432 hsp->subject.offset = best_s_start - subject_start; in s_UpdateReevaluatedHSP()
646 subject_start, best_q_start, best_q_end, in s_UpdateReevaluatedHSPUngapped()
652 const Uint1* subject_start, const BlastInitialWordParameters* word_params, in Blast_HSPReevaluateWithAmbiguitiesUngapped() argument
668 subject = subject_start + hsp->subject.offset; in Blast_HSPReevaluateWithAmbiguitiesUngapped()
2502 const Uint1* subject_start = NULL; in Blast_HSPListReevaluateUngapped() local
2565 subject_start = subject_blk->sequence_start + 1; in Blast_HSPListReevaluateUngapped()
2567 subject_start = subject_blk->sequence; in Blast_HSPListReevaluateUngapped()
2589 subject_start, word_params, sbp, kTranslateSubject); in Blast_HSPListReevaluateUngapped()
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/util/unit_test/data/
H A Dfilters71 subject_start < 50
/dports/devel/cgit/cgit-1.2.3/git/builtin/
H A Dtag.c308 const char *subject_start; in create_reflog_msg() local
326 subject_len = find_commit_subject(buf, &subject_start); in create_reflog_msg()
327 strbuf_insert(sb, sb->len, subject_start, subject_len); in create_reflog_msg()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/
H A Dblastextend_unit_test.cpp444 const int subject_start = 291; in BOOST_AUTO_TEST_CASE() local
527 BOOST_REQUIRE_EQUAL(hsp_list->hsp_array[0]->subject.offset, subject_start); in BOOST_AUTO_TEST_CASE()
534 BOOST_REQUIRE(m_ipGapAlign->greedy_subject_seed_start >= subject_start); in BOOST_AUTO_TEST_CASE()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/
H A Dblastextend_unit_test.cpp444 const int subject_start = 291; in BOOST_AUTO_TEST_CASE() local
527 BOOST_REQUIRE_EQUAL(hsp_list->hsp_array[0]->subject.offset, subject_start); in BOOST_AUTO_TEST_CASE()
534 BOOST_REQUIRE(m_ipGapAlign->greedy_subject_seed_start >= subject_start); in BOOST_AUTO_TEST_CASE()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/
H A Dphi_gapalign.c704 gap_align->subject_start = s_length - private_s_start + 1; in s_PHIGappedAlignment()
726 gap_align->subject_start = subject_offset; in s_PHIGappedAlignment()
811 gap_align->subject_start, gap_align->subject_stop, in PHIGetGappedScore()
865 gap_align->subject_start = s_start - private_s_length; in PHIGappedAlignmentWithTraceback()
H A Dblast_hits.c151 Blast_HSPInit(Int4 query_start, Int4 query_end, Int4 subject_start, in Blast_HSPInit() argument
171 new_hsp->subject.offset = subject_start; in Blast_HSPInit()
457 hsp->subject.offset = best_s_start - subject_start; in s_UpdateReevaluatedHSP()
671 subject_start, best_q_start, best_q_end, in s_UpdateReevaluatedHSPUngapped()
677 const Uint1* subject_start, const BlastInitialWordParameters* word_params, in Blast_HSPReevaluateWithAmbiguitiesUngapped() argument
693 subject = subject_start + hsp->subject.offset; in Blast_HSPReevaluateWithAmbiguitiesUngapped()
2610 const Uint1* subject_start = NULL; in Blast_HSPListReevaluateUngapped() local
2673 subject_start = subject_blk->sequence_start + 1; in Blast_HSPListReevaluateUngapped()
2675 subject_start = subject_blk->sequence; in Blast_HSPListReevaluateUngapped()
2697 subject_start, word_params, sbp, kTranslateSubject); in Blast_HSPListReevaluateUngapped()
[all …]
H A Djumper.c490 gap_align->subject_start, query_length, in s_ShiftGaps()
2561 s_length = subject_start + offset_adjustment; in JumperGappedAlignmentCompressedWithTraceback()
2564 if (query_start > 0 && subject_start > 0) { in JumperGappedAlignmentCompressedWithTraceback()
2583 gap_align->subject_start = s_length - s_ext_len + 1; in JumperGappedAlignmentCompressedWithTraceback()
2586 ASSERT(gap_align->subject_start >= 0); in JumperGappedAlignmentCompressedWithTraceback()
2590 gap_align->subject_start = subject_start; in JumperGappedAlignmentCompressedWithTraceback()
2619 gap_align->subject_stop = subject_start; in JumperGappedAlignmentCompressedWithTraceback()
2760 Int4 s_pos = gap_align->subject_start; in JumperFindEdits()
3214 gap_align->subject_start, in s_CreateHSP()
3217 gap_align->subject_start, in s_CreateHSP()
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/
H A Dphi_gapalign.c704 gap_align->subject_start = s_length - private_s_start + 1; in s_PHIGappedAlignment()
726 gap_align->subject_start = subject_offset; in s_PHIGappedAlignment()
811 gap_align->subject_start, gap_align->subject_stop, in PHIGetGappedScore()
865 gap_align->subject_start = s_start - private_s_length; in PHIGappedAlignmentWithTraceback()
H A Dblast_hits.c151 Blast_HSPInit(Int4 query_start, Int4 query_end, Int4 subject_start, in Blast_HSPInit() argument
171 new_hsp->subject.offset = subject_start; in Blast_HSPInit()
457 hsp->subject.offset = best_s_start - subject_start; in s_UpdateReevaluatedHSP()
671 subject_start, best_q_start, best_q_end, in s_UpdateReevaluatedHSPUngapped()
677 const Uint1* subject_start, const BlastInitialWordParameters* word_params, in Blast_HSPReevaluateWithAmbiguitiesUngapped() argument
693 subject = subject_start + hsp->subject.offset; in Blast_HSPReevaluateWithAmbiguitiesUngapped()
2610 const Uint1* subject_start = NULL; in Blast_HSPListReevaluateUngapped() local
2673 subject_start = subject_blk->sequence_start + 1; in Blast_HSPListReevaluateUngapped()
2675 subject_start = subject_blk->sequence; in Blast_HSPListReevaluateUngapped()
2697 subject_start, word_params, sbp, kTranslateSubject); in Blast_HSPListReevaluateUngapped()
[all …]
H A Djumper.c490 gap_align->subject_start, query_length, in s_ShiftGaps()
2561 s_length = subject_start + offset_adjustment; in JumperGappedAlignmentCompressedWithTraceback()
2564 if (query_start > 0 && subject_start > 0) { in JumperGappedAlignmentCompressedWithTraceback()
2583 gap_align->subject_start = s_length - s_ext_len + 1; in JumperGappedAlignmentCompressedWithTraceback()
2586 ASSERT(gap_align->subject_start >= 0); in JumperGappedAlignmentCompressedWithTraceback()
2590 gap_align->subject_start = subject_start; in JumperGappedAlignmentCompressedWithTraceback()
2619 gap_align->subject_stop = subject_start; in JumperGappedAlignmentCompressedWithTraceback()
2760 Int4 s_pos = gap_align->subject_start; in JumperFindEdits()
3214 gap_align->subject_start, in s_CreateHSP()
3217 gap_align->subject_start, in s_CreateHSP()
[all …]
/dports/devel/git-svn/git-2.34.1/builtin/
H A Dtag.c350 const char *subject_start; in create_reflog_msg() local
368 subject_len = find_commit_subject(buf, &subject_start); in create_reflog_msg()
369 strbuf_insert(sb, sb->len, subject_start, subject_len); in create_reflog_msg()
/dports/devel/git-p4/git-2.34.1/builtin/
H A Dtag.c350 const char *subject_start; in create_reflog_msg() local
368 subject_len = find_commit_subject(buf, &subject_start); in create_reflog_msg()
369 strbuf_insert(sb, sb->len, subject_start, subject_len); in create_reflog_msg()
/dports/devel/git/git-2.34.1/builtin/
H A Dtag.c350 const char *subject_start; in create_reflog_msg() local
368 subject_len = find_commit_subject(buf, &subject_start); in create_reflog_msg()
369 strbuf_insert(sb, sb->len, subject_start, subject_len); in create_reflog_msg()
/dports/devel/git-gui/git-2.34.1/builtin/
H A Dtag.c350 const char *subject_start; in create_reflog_msg() local
368 subject_len = find_commit_subject(buf, &subject_start); in create_reflog_msg()
369 strbuf_insert(sb, sb->len, subject_start, subject_len); in create_reflog_msg()
/dports/devel/git-cvs/git-2.34.1/builtin/
H A Dtag.c350 const char *subject_start; in create_reflog_msg() local
368 subject_len = find_commit_subject(buf, &subject_start); in create_reflog_msg()
369 strbuf_insert(sb, sb->len, subject_start, subject_len); in create_reflog_msg()
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/
H A DAlignmentViewer.java939 final int subject_start = last_subject_event.getStart(); in getAlignMatchFromPosition() local
953 subject_flipped, query_flipped, base_width, query_base_width, subject_start, in getAlignMatchFromPosition()
1383 final int subject_start = last_subject_event.getStart(); in drawAlignments() local
1399 subject_flipped, query_flipped, base_width, query_base_width, subject_start, in drawAlignments()
2055 final int subject_start, final int query_start, in getMatchCoords() argument
2086 subject_start); in getMatchCoords()
2088 subject_start); in getMatchCoords()

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