/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/SearchIO/ |
H A D | cross_match.pm | 259 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 D | MSPcrunchStreamFeature.java | 211 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 D | BlastStreamFeature.java | 157 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 D | blast_hits.h | 247 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 D | blast_gapalign.h | 86 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 D | blast_hits.h | 247 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 D | blast_hits.h | 247 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 D | phi_gapalign.c | 704 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 D | blast_hits.c | 126 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 D | filters | 71 subject_start < 50
|
/dports/devel/cgit/cgit-1.2.3/git/builtin/ |
H A D | tag.c | 308 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 D | blastextend_unit_test.cpp | 444 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 D | blastextend_unit_test.cpp | 444 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 D | phi_gapalign.c | 704 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 D | blast_hits.c | 151 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 D | jumper.c | 490 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 D | phi_gapalign.c | 704 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 D | blast_hits.c | 151 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 D | jumper.c | 490 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 D | tag.c | 350 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 D | tag.c | 350 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 D | tag.c | 350 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 D | tag.c | 350 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 D | tag.c | 350 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 D | AlignmentViewer.java | 939 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()
|