#include <ncbi_pch.hpp>#include <corelib/ncbistd.hpp>#include <objects/seqalign/Dense_diag.hpp>#include <objects/seqalign/Dense_seg.hpp>#include <objects/seqset/Bioseq_set.hpp>#include <objects/scoremat/scoremat__.hpp>#include <objects/cdd/Cdd_id.hpp>#include <objects/cdd/Cdd_id_set.hpp>#include "remove_header_conflicts.hpp"#include "alignment_manager.hpp"#include "sequence_set.hpp"#include "alignment_set.hpp"#include "block_multiple_alignment.hpp"#include "messenger.hpp"#include "structure_set.hpp"#include "sequence_viewer.hpp"#include "molecule.hpp"#include "show_hide_manager.hpp"#include "cn3d_threader.hpp"#include "update_viewer.hpp"#include "sequence_display.hpp"#include "cn3d_tools.hpp"#include "molecule_identifier.hpp"#include "cn3d_blast.hpp"#include "style_manager.hpp"#include "cn3d_ba_interface.hpp"#include "cn3d_pssm.hpp"#include "progress_meter.hpp"
Include dependency graph for alignment_manager.cpp:
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Classes | |
| struct | ExtendInfo |
Functions | |
| USING_SCOPE (objects) | |
| static bool | AlignedToAllDependents (int masterResidue, const AlignmentManager::PairwiseAlignmentList &alignments) |
| static bool | NoDependentInsertionsBetween (int masterFrom, int masterTo, const AlignmentManager::PairwiseAlignmentList &alignments) |
| static bool | NoBlockBoundariesBetween (int masterFrom, int masterTo, const AlignmentManager::PairwiseAlignmentList &alignments) |
| static int | GetAlignedResidueIndexes (BlockMultipleAlignment::UngappedAlignedBlockList::const_iterator &b, BlockMultipleAlignment::UngappedAlignedBlockList::const_iterator &be, int row, int *seqIndexes, bool countHighlights=false, const BlockMultipleAlignment *multiple=NULL) |
| static bool | CreateNewPairwiseAlignmentsByBlockExtension (const BlockMultipleAlignment &multiple, const UpdateViewer::AlignmentList &toExtend, UpdateViewer::AlignmentList *newAlignments) |
Variables | |
| USING_NCBI_SCOPE | |
Function Documentation
◆ AlignedToAllDependents()
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static |
Definition at line 277 of file alignment_manager.cpp.
References a.
Referenced by AlignmentManager::CreateMultipleFromPairwiseWithIBM().
◆ CreateNewPairwiseAlignmentsByBlockExtension()
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static |
Definition at line 976 of file alignment_manager.cpp.
References available, BlockMultipleAlignment::Clone(), BlockMultipleAlignment::eLeft, ERRORMSG, Block::Range::from, BlockMultipleAlignment::GetAlignedBlockNumber(), BlockMultipleAlignment::GetAlignmentIndex(), BlockMultipleAlignment::GetUnalignedBlockAfter(), BlockMultipleAlignment::GetUnalignedBlockBefore(), BlockMultipleAlignment::GetUngappedAlignedBlocks(), BlockMultipleAlignment::HasNoAlignedBlocks(), i, if(), BlockMultipleAlignment::IsAligned(), BlockMultipleAlignment::MergeBlocks(), BlockMultipleAlignment::MoveBlockBoundary(), NULL, pb, t, Block::Range::to, TRACEMSG, and U.
Referenced by AlignmentManager::ExtendAllUpdates(), and AlignmentManager::ExtendUpdate().
◆ GetAlignedResidueIndexes()
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static |
Definition at line 384 of file alignment_manager.cpp.
References b, GlobalMessenger(), i, compile_time_bits::range(), and row.
Referenced by AlignmentManager::RealignAllDependentStructures().
◆ NoBlockBoundariesBetween()
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static |
Definition at line 298 of file alignment_manager.cpp.
References a.
Referenced by AlignmentManager::CreateMultipleFromPairwiseWithIBM().
◆ NoDependentInsertionsBetween()
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static |
Definition at line 287 of file alignment_manager.cpp.
References a.
Referenced by AlignmentManager::CreateMultipleFromPairwiseWithIBM().
◆ USING_SCOPE()
| USING_SCOPE | ( | objects | ) |
Variable Documentation
◆ USING_NCBI_SCOPE
| USING_NCBI_SCOPE |
Definition at line 66 of file alignment_manager.cpp.
