/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/format/ |
H A D | blast_format.cpp | 596 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 …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/format/ |
H A D | blast_format.cpp | 596 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 …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/format/ |
H A D | blast_format.hpp | 442 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);
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/format/ |
H A D | blast_format.hpp | 442 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);
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/format/ |
H A D | sam_formatter.cpp | 337 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/format/ |
H A D | sam_formatter.cpp | 337 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/data_loaders/lds2/ |
H A D | lds2_dataloader.cpp | 646 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/ |
H A D | bl2seq_unit_test.cpp | 383 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 …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/ |
H A D | bl2seq_unit_test.cpp | 383 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 …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/align_format/ |
H A D | align_format_util.hpp | 1069 objects::CSeq_align_set& aln_set, 1078 SortSeqalignForSortableFormat(objects::CSeq_align_set& aln_set,
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/align_format/ |
H A D | align_format_util.hpp | 1069 objects::CSeq_align_set& aln_set, 1078 SortSeqalignForSortableFormat(objects::CSeq_align_set& aln_set,
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/align_format/ |
H A D | align_format_util.cpp | 2884 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/align_format/ |
H A D | align_format_util.cpp | 2883 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/seq/ |
H A D | seq_loc_mapper_base.cpp | 1472 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/seq/ |
H A D | seq_loc_mapper_base.cpp | 1472 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/ |
H A D | blast_seqalign.cpp | 1887 CRef<CSeq_align_set> aln_set = alnvec[iLinearIndex]; in s_TransposeSeqAlignVector() local 1888 result_alnvec.push_back(aln_set); in s_TransposeSeqAlignVector()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/ |
H A D | blast_seqalign.cpp | 1887 CRef<CSeq_align_set> aln_set = alnvec[iLinearIndex]; in s_TransposeSeqAlignVector() local 1888 result_alnvec.push_back(aln_set); in s_TransposeSeqAlignVector()
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