Home
last modified time | relevance | path

Searched refs:aln_set (Results 1 – 17 of 17) sorted by relevance

/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/format/
H A Dblast_format.cpp596 CShowBlastDefline showdef(*aln_set, *m_Scope, in x_DisplayDeflines()
754 aln_set.Reset(CDisplaySeqalign::PrepareBlastUngappedSeqalign(*aln_set)); in x_PrintTabularReport()
881 aln_set.Reset(CDisplaySeqalign::PrepareBlastUngappedSeqalign(*aln_set)); in x_PrintTaxReport()
939 aln_set, subject_bioseq); in x_PrintIgTabularReport()
942 for (; itr != aln_set->Get().end(); ++itr) { in x_PrintIgTabularReport()
1370 aln_set.Reset(CDisplaySeqalign::PrepareBlastUngappedSeqalign(*aln_set)); in PrintReport()
1374 x_DisplayDeflinesWithTemplates(aln_set); in PrintReport()
1377 x_CreateDeflinesJson(aln_set); in PrintReport()
1494 aln_set.Reset(CDisplaySeqalign::PrepareBlastUngappedSeqalign(*aln_set)); in PrintOneResultSet()
1506 const bool kIsGlobal = s_IsGlobalSeqAlign(aln_set); in PrintOneResultSet()
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/format/
H A Dblast_format.cpp596 CShowBlastDefline showdef(*aln_set, *m_Scope, in x_DisplayDeflines()
754 aln_set.Reset(CDisplaySeqalign::PrepareBlastUngappedSeqalign(*aln_set)); in x_PrintTabularReport()
881 aln_set.Reset(CDisplaySeqalign::PrepareBlastUngappedSeqalign(*aln_set)); in x_PrintTaxReport()
939 aln_set, subject_bioseq); in x_PrintIgTabularReport()
942 for (; itr != aln_set->Get().end(); ++itr) { in x_PrintIgTabularReport()
1370 aln_set.Reset(CDisplaySeqalign::PrepareBlastUngappedSeqalign(*aln_set)); in PrintReport()
1374 x_DisplayDeflinesWithTemplates(aln_set); in PrintReport()
1377 x_CreateDeflinesJson(aln_set); in PrintReport()
1494 aln_set.Reset(CDisplaySeqalign::PrepareBlastUngappedSeqalign(*aln_set)); in PrintOneResultSet()
1506 const bool kIsGlobal = s_IsGlobalSeqAlign(aln_set); in PrintOneResultSet()
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/format/
H A Dblast_format.hpp442 void x_DisplayDeflines(CConstRef<CSeq_align_set> aln_set,
534 void x_DisplayDeflinesWithTemplates(CConstRef<CSeq_align_set> aln_set);
536 …void x_DisplayAlignsWithTemplates(CConstRef<CSeq_align_set> aln_set,const blast::CSearchResults& r…
538 void x_CreateDeflinesJson(CConstRef<CSeq_align_set> aln_set);
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/format/
H A Dblast_format.hpp442 void x_DisplayDeflines(CConstRef<CSeq_align_set> aln_set,
534 void x_DisplayDeflinesWithTemplates(CConstRef<CSeq_align_set> aln_set);
536 …void x_DisplayAlignsWithTemplates(CConstRef<CSeq_align_set> aln_set,const blast::CSearchResults& r…
538 void x_CreateDeflinesJson(CConstRef<CSeq_align_set> aln_set);
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/format/
H A Dsam_formatter.cpp337 CSAM_Formatter& CSAM_Formatter::Print(const CSeq_align_set& aln_set, in Print() argument
342 disc.SetSegs().SetDisc().Assign(aln_set); in Print()
348 CSAM_Formatter& CSAM_Formatter::Print(const CSeq_align_set& aln_set, in Print() argument
353 disc.SetSegs().SetDisc().Assign(aln_set); in Print()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/format/
H A Dsam_formatter.cpp337 CSAM_Formatter& CSAM_Formatter::Print(const CSeq_align_set& aln_set, in Print() argument
342 disc.SetSegs().SetDisc().Assign(aln_set); in Print()
348 CSAM_Formatter& CSAM_Formatter::Print(const CSeq_align_set& aln_set, in Print() argument
353 disc.SetSegs().SetDisc().Assign(aln_set); in Print()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/data_loaders/lds2/
H A Dlds2_dataloader.cpp646 CSeq_align_set aln_set; in GetChunk() local
647 *obj_in >> aln_set; in GetChunk()
648 ITERATE(CSeq_align_set::Tdata, it, aln_set.Set()) { in GetChunk()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/
H A Dbl2seq_unit_test.cpp383 BOOST_REQUIRE(aln_set.NotNull()); in testResultAlignments()
387 if (aln_set->Get().size() > 0) in testResultAlignments()
3052 CRef<CSeq_align_set> aln_set; in BOOST_AUTO_TEST_CASE() local
3053 aln_set.Reset(const_cast<CSeq_align_set*> in BOOST_AUTO_TEST_CASE()
3055 sas_v.push_back(aln_set); in BOOST_AUTO_TEST_CASE()
3137 CRef<CSeq_align_set> aln_set; in BOOST_AUTO_TEST_CASE() local
3138 aln_set.Reset(const_cast<CSeq_align_set*> in BOOST_AUTO_TEST_CASE()
3140 sas_v.push_back(aln_set); in BOOST_AUTO_TEST_CASE()
3220 CRef<CSeq_align_set> aln_set; in BOOST_AUTO_TEST_CASE() local
3222 aln_set.Reset(const_cast<CSeq_align_set*> in BOOST_AUTO_TEST_CASE()
[all …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/
H A Dbl2seq_unit_test.cpp383 BOOST_REQUIRE(aln_set.NotNull()); in testResultAlignments()
387 if (aln_set->Get().size() > 0) in testResultAlignments()
3052 CRef<CSeq_align_set> aln_set; in BOOST_AUTO_TEST_CASE() local
3053 aln_set.Reset(const_cast<CSeq_align_set*> in BOOST_AUTO_TEST_CASE()
3055 sas_v.push_back(aln_set); in BOOST_AUTO_TEST_CASE()
3137 CRef<CSeq_align_set> aln_set; in BOOST_AUTO_TEST_CASE() local
3138 aln_set.Reset(const_cast<CSeq_align_set*> in BOOST_AUTO_TEST_CASE()
3140 sas_v.push_back(aln_set); in BOOST_AUTO_TEST_CASE()
3220 CRef<CSeq_align_set> aln_set; in BOOST_AUTO_TEST_CASE() local
3222 aln_set.Reset(const_cast<CSeq_align_set*> in BOOST_AUTO_TEST_CASE()
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/align_format/
H A Dalign_format_util.hpp1069 objects::CSeq_align_set& aln_set,
1078 SortSeqalignForSortableFormat(objects::CSeq_align_set& aln_set,
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/align_format/
H A Dalign_format_util.hpp1069 objects::CSeq_align_set& aln_set,
1078 SortSeqalignForSortableFormat(objects::CSeq_align_set& aln_set,
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/align_format/
H A Dalign_format_util.cpp2884 CSeq_align_set& aln_set, in SortSeqalignForSortableFormat() argument
2894 return (CRef<CSeq_align_set>) &aln_set; in SortSeqalignForSortableFormat()
2902 SplitSeqalignByMolecularType(seqalign_vec, db_sort, aln_set, scope, in SortSeqalignForSortableFormat()
2905 seqalign_vec[0] = const_cast<CSeq_align_set*>(&aln_set); in SortSeqalignForSortableFormat()
2960 CAlignFormatUtil::SortSeqalignForSortableFormat(CSeq_align_set& aln_set, in SortSeqalignForSortableFormat() argument
2966 return (CRef<CSeq_align_set>) &aln_set; in SortSeqalignForSortableFormat()
2970 …list< CRef<CSeq_align_set> > seqalign_hit_total_list = SortOneSeqalignForSortableFormat(aln_set, … in SortSeqalignForSortableFormat()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/align_format/
H A Dalign_format_util.cpp2883 CSeq_align_set& aln_set, in SortSeqalignForSortableFormat() argument
2893 return (CRef<CSeq_align_set>) &aln_set; in SortSeqalignForSortableFormat()
2901 SplitSeqalignByMolecularType(seqalign_vec, db_sort, aln_set, scope, in SortSeqalignForSortableFormat()
2904 seqalign_vec[0] = const_cast<CSeq_align_set*>(&aln_set); in SortSeqalignForSortableFormat()
2959 CAlignFormatUtil::SortSeqalignForSortableFormat(CSeq_align_set& aln_set, in SortSeqalignForSortableFormat() argument
2965 return (CRef<CSeq_align_set>) &aln_set; in SortSeqalignForSortableFormat()
2969 …list< CRef<CSeq_align_set> > seqalign_hit_total_list = SortOneSeqalignForSortableFormat(aln_set, … in SortSeqalignForSortableFormat()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/seq/
H A Dseq_loc_mapper_base.cpp1472 const CSeq_align_set& aln_set = map_align.GetSegs().GetDisc(); in x_InitializeAlign() local
1473 ITERATE(CSeq_align_set::Tdata, aln, aln_set.Get()) { in x_InitializeAlign()
1550 const CSeq_align_set& aln_set = map_align.GetSegs().GetDisc(); in x_InitializeAlign() local
1551 ITERATE(CSeq_align_set::Tdata, aln, aln_set.Get()) { in x_InitializeAlign()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/seq/
H A Dseq_loc_mapper_base.cpp1472 const CSeq_align_set& aln_set = map_align.GetSegs().GetDisc(); in x_InitializeAlign() local
1473 ITERATE(CSeq_align_set::Tdata, aln, aln_set.Get()) { in x_InitializeAlign()
1550 const CSeq_align_set& aln_set = map_align.GetSegs().GetDisc(); in x_InitializeAlign() local
1551 ITERATE(CSeq_align_set::Tdata, aln, aln_set.Get()) { in x_InitializeAlign()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/
H A Dblast_seqalign.cpp1887 CRef<CSeq_align_set> aln_set = alnvec[iLinearIndex]; in s_TransposeSeqAlignVector() local
1888 result_alnvec.push_back(aln_set); in s_TransposeSeqAlignVector()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/
H A Dblast_seqalign.cpp1887 CRef<CSeq_align_set> aln_set = alnvec[iLinearIndex]; in s_TransposeSeqAlignVector() local
1888 result_alnvec.push_back(aln_set); in s_TransposeSeqAlignVector()