NCBI C++ ToolKit
Classes | Functions | Variables
alignment_manager.cpp File Reference
#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()

static bool AlignedToAllDependents ( int  masterResidue,
const AlignmentManager::PairwiseAlignmentList alignments 
)
static

Definition at line 277 of file alignment_manager.cpp.

References a.

Referenced by AlignmentManager::CreateMultipleFromPairwiseWithIBM().

◆ CreateNewPairwiseAlignmentsByBlockExtension()

static bool CreateNewPairwiseAlignmentsByBlockExtension ( const BlockMultipleAlignment multiple,
const UpdateViewer::AlignmentList toExtend,
UpdateViewer::AlignmentList newAlignments 
)
static

◆ GetAlignedResidueIndexes()

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

◆ NoBlockBoundariesBetween()

static bool NoBlockBoundariesBetween ( int  masterFrom,
int  masterTo,
const AlignmentManager::PairwiseAlignmentList alignments 
)
static

Definition at line 298 of file alignment_manager.cpp.

References a.

Referenced by AlignmentManager::CreateMultipleFromPairwiseWithIBM().

◆ NoDependentInsertionsBetween()

static bool NoDependentInsertionsBetween ( int  masterFrom,
int  masterTo,
const AlignmentManager::PairwiseAlignmentList alignments 
)
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.

Modified on Tue Feb 27 05:56:07 2024 by modify_doxy.py rev. 669887