Search Toolkit Book for AlignmentCollection
#include <algo/structure/cd_utils/cuAlignmentCollection.hpp>
Definition at line 19 of file cuAlignmentCollection.hpp.
◆ AlignmentCollection() [1/2] ◆ AlignmentCollection() [2/2] AlignmentCollection::AlignmentCollection ( ) ◆ ~AlignmentCollection() ◆ AddAlignment() [1/2] ◆ AddAlignment() [2/2] ◆ addNormalAlignment() ◆ addPendingAlignment() ◆ addRowSources() ◆ AddSequence() [1/2] void AlignmentCollection::AddSequence ( CCdCore * cd ) ◆ AddSequence() [2/2] ◆ AreNonOverlapping() bool AlignmentCollection::AreNonOverlapping ( ) const ◆ clear() void AlignmentCollection::clear ( void ) inline ◆ convertFromCDRows() void AlignmentCollection::convertFromCDRows ( CCdCore * cd, const vector< int > & cdRows, set< int > & colRows ) const ◆ convertToCDRows() void AlignmentCollection::convertToCDRows ( const vector< int > & colRows, CDRowsMap & cdRows ) const ◆ FindSeqInterval() ◆ Get_GI_or_PDB_String_FromAlignment() bool AlignmentCollection::Get_GI_or_PDB_String_FromAlignment ( int row, std::string & result ) const ◆ GetAlignedResiduesForAll() void AlignmentCollection::GetAlignedResiduesForAll ( char **& ppAlignedResidues, bool forceRecompute ) ◆ GetAlignedResiduesForRow() void AlignmentCollection::GetAlignedResiduesForRow ( int row, char *& aseq ) ◆ GetAlignmentLength() int AlignmentCollection::GetAlignmentLength ( int row =0 ) const ◆ getAllRowsForCD() void AlignmentCollection::getAllRowsForCD ( CCdCore * cd, vector< int > & colRows ) const ◆ GetAllSequences() void AlignmentCollection::GetAllSequences ( vector< string > & sequences ) ◆ GetBioseqForRow()
Definition at line 442 of file cuAlignmentCollection.cpp.
References RowSource::cd, Empty(), RowSourceTable::findEntry(), SequenceTable::findSequence(), CCdCore::GetBioseqForIndex(), GetNumRows(), GetSeqIDForRow(), CCdCore::GetSeqIndex(), m_bioseqs, m_rowSources, m_seqTable, and row.
Referenced by CdBlaster::blast(), GetSequenceForRow(), IsStruct(), and CdBlaster::truncateBioseq().
◆ getCDs() int AlignmentCollection::getCDs ( vector< CCdCore * > & cds ) ◆ getCDsInScope() int AlignmentCollection::getCDsInScope ( vector< CCdCore * > & cds ) ◆ getCDsOutofScope() int AlignmentCollection::getCDsOutofScope ( vector< CCdCore * > & cds ) ◆ GetDefline() string AlignmentCollection::GetDefline ( int row ) const ◆ getFirstCD() CCdCore* AlignmentCollection::getFirstCD ( ) const inline ◆ GetGI() ◆ getLastError() string& AlignmentCollection::getLastError ( ) inline ◆ GetLeafDescendentCD() ◆ GetLowerBound() int AlignmentCollection::GetLowerBound ( int row ) const ◆ getNormalRowsNotInChild() void AlignmentCollection::getNormalRowsNotInChild ( vector< int > & childless, bool excludeMaster =false ) const ◆ getNumFamilies() int AlignmentCollection::getNumFamilies ( ) const inline ◆ GetNumPendingRows() int AlignmentCollection::GetNumPendingRows ( ) const ◆ GetNumRows() int AlignmentCollection::GetNumRows ( ) const
Definition at line 194 of file cuAlignmentCollection.cpp.
References m_seqAligns.
Referenced by TaxTreeData::addRows(), SeqTreeAPI::annotateLeafNode(), AreNonOverlapping(), CdBlaster::blast(), DM_AlignedScore::CalcPairwiseScores(), DM_BlastScore::CalcPairwiseScoresOnTheFly(), CdBlaster::CdBlaster(), DMAlignedOptimalScore::ComputeMatrix(), DM_AlignedScore::ConvertScoresToDistances(), SeqSwapper::findStructuralPendings(), SeqTree::fixRowName(), GetAlignedResiduesForAll(), getAllRowsForCD(), GetAllSequences(), GetBioseqForRow(), CdBlaster::getCompositeIndex(), AlignedDM::GetMaxScoreForAligned(), getNormalRowsNotInChild(), GetNumPendingRows(), DM_Identities::GetPercentIdentities(), FlexiDm::GetPercentIdentities(), AlignedDM::GetResidueListsWithShifts(), GetRowsWithSeqID(), SeqTree::getSequenceComposition(), MultipleAlignment::makeBlockTable(), SeqSwapper::makeClusters(), CDUpdater::processPendingToNormal(), CdBlaster::psiBlast(), RemasterWithStructure(), BlockExtender::setAlignments(), DistanceMatrix::SetData(), and MultipleAlignment::transferToCD().
◆ GetRowSource() [1/2] ◆ GetRowSource() [2/2] ◆ GetRowSourceTable() ◆ GetRowsWithSameSeqID() int AlignmentCollection::GetRowsWithSameSeqID ( int rowToMatch, vector< int > & rows, bool inclusive =true ) const ◆ GetRowsWithSeqID() ◆ GetScopedLeafCD() CCdCore * AlignmentCollection::GetScopedLeafCD ( int row ) const ◆ GetSeniorMemberCD() CCdCore * AlignmentCollection::GetSeniorMemberCD ( int row, bool scopedOnly = true ) const ◆ getSeqAlign() ◆ GetSeqEntryForRow() ◆ GetSeqIDForRow()
Definition at line 240 of file cuAlignmentCollection.cpp.
References GetSeqID(), m_seqAligns, row, and wasMaster().
Referenced by SeqTreeAsnizer::fillAsnSeqTreeNode(), SeqSwapper::findReplacements(), Get_GI_or_PDB_String_FromAlignment(), GetBioseqForRow(), GetGI(), GetRowsWithSameSeqID(), GetRowsWithSeqID(), GetSeqEntryForRow(), GetSpeciesForRow(), IsPdb(), RemasterWithStructure(), MultipleAlignment::setAlignment(), SeqSwapper::swapSequences(), and MultipleAlignment::transferOneRow().
◆ GetSequenceForRow() string AlignmentCollection::GetSequenceForRow ( int row ) ◆ GetSpeciesForRow() bool AlignmentCollection::GetSpeciesForRow ( int row, string & species ) const ◆ GetUpperBound() int AlignmentCollection::GetUpperBound ( int row ) const ◆ isCDInScope() bool AlignmentCollection::isCDInScope ( CCdCore * cd ) const ◆ isInstanceOf() ◆ IsNonOverlapping() ◆ IsPdb() bool AlignmentCollection::IsPdb ( int row ) const ◆ IsPending() bool AlignmentCollection::IsPending ( int row ) const ◆ isRowInScope() bool AlignmentCollection::isRowInScope ( int row ) const ◆ IsStruct() bool AlignmentCollection::IsStruct ( int row ) ◆ mapRow() ◆ mapRows() ◆ removeRowSourcesForCD() void AlignmentCollection::removeRowSourcesForCD ( CCdCore * cd ) ◆ setNumFamilies() void AlignmentCollection::setNumFamilies ( int num ) inline ◆ wasMaster() bool AlignmentCollection::wasMaster ( int row ) const ◆ m_bioseqs vector<CRef< CBioseq > > AlignmentCollection::m_bioseqs protected ◆ m_err string AlignmentCollection::m_err protected ◆ m_firstCd CCdCore* AlignmentCollection::m_firstCd protected ◆ m_numFamilies int AlignmentCollection::m_numFamilies protected ◆ m_rowSourcesDefinition at line 96 of file cuAlignmentCollection.hpp.
Referenced by AddAlignment(), addNormalAlignment(), addPendingAlignment(), addRowSources(), clear(), convertFromCDRows(), convertToCDRows(), MultipleAlignment::copyRowSource(), getAllRowsForCD(), GetBioseqForRow(), getCDs(), getCDsInScope(), getCDsOutofScope(), GetLeafDescendentCD(), GetRowSource(), GetRowSourceTable(), GetScopedLeafCD(), GetSeniorMemberCD(), GetSpeciesForRow(), isCDInScope(), mapRow(), and removeRowSourcesForCD().
◆ m_seqAlignsDefinition at line 93 of file cuAlignmentCollection.hpp.
Referenced by AddAlignment(), addNormalAlignment(), addPendingAlignment(), MultipleAlignment::appendAlignment(), AreNonOverlapping(), clear(), MultipleAlignment::extractAlignedSubset(), GetAlignedResiduesForRow(), GetAlignmentLength(), GetLowerBound(), GetNumRows(), getSeqAlign(), GetSeqIDForRow(), GetUpperBound(), MultipleAlignment::makeBlockTable(), MultipleAlignment::setAlignment(), and MultipleAlignment::transferOneRow().
◆ m_seqTableThe documentation for this class was generated from the following files:
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