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NCBI C++ ToolKit: MultipleAlignment Class Reference
Search Toolkit Book for MultipleAlignment
#include <algo/structure/cd_utils/cuAlignmentCollection.hpp>
MultipleAlignment (CCdCore *cd, bool scoped=true) MultipleAlignment (const CDFamily &family) MultipleAlignment () bool setAlignment (const CDFamily &family) bool setAlignment (const CDFamily &family, CDFamilyIterator &start) void setAlignment (CCdCore *cd, bool scoped=true) void setAlignment (CRef< CSeq_align > &seqAlign) bool setAlignment (const AlignmentCollection &ac, int row) bool isBlockAligned () const int appendAlignment (MultipleAlignment &malign, bool includeUnScoped=true) bool findParentalEquivalent (const cd_utils::BlockModel &bar, int &pRow, bool inputAsChild=true) const bool findParentalCastible (const cd_utils::BlockModel &bar, int &pRow) const bool locateChildRow (const cd_utils::BlockModel &childRow, int &pRow) const const cd_utils::BlockModel & getBlockModel (int row) const void copyRowSource (int currentRow, const AlignmentCollection &malign, int rowInAc) bool transferToCD (CCdCore *cd=0) bool extractAlignedSubset (const AlignmentCollection &ac, const set< int > &normalRows, int master) AlignmentCollection (CCdCore *cd, CCdCore::AlignmentUsage alignUse=CCdCore::USE_PENDING_ALIGNMENT, bool uniqueSeqId=false, bool scoped=true) AlignmentCollection () void AddAlignment (CCdCore *cd, CCdCore::AlignmentUsage alignUse=CCdCore::USE_PENDING_ALIGNMENT, bool uniqueSeqId=false, bool scoped=true) void AddAlignment (const AlignmentCollection &ac) void AddSequence (CCdCore *cd) void AddSequence (const AlignmentCollection &ac) int getNumFamilies () const void setNumFamilies (int num) void clear () CCdCore * getFirstCD () const int GetNumRows () const int GetNumPendingRows () const int GetAlignmentLength (int row=0) const bool Get_GI_or_PDB_String_FromAlignment (int row, std::string &result) const bool GetSeqIDForRow (int row, CRef< CSeq_id > &SeqID) const bool GetSeqEntryForRow (int row, CRef< CSeq_entry > &seqEntry) const string GetDefline (int row) const bool GetGI (int row, TGi &gi, bool ignorePDBs=true) const int GetLowerBound (int row) const int GetUpperBound (int row) const int FindSeqInterval (const CSeq_interval &seqLoc) const bool IsPending (int row) const bool wasMaster (int row) const void removeRowSourcesForCD (CCdCore *cd) void addRowSources (const vector< int > &rows, CCdCore *cd, bool scoped=true) const RowSource & GetRowSource (int row) const RowSource & GetRowSource (int row) CRef< CSeq_align > getSeqAlign (int row) const const RowSourceTable & GetRowSourceTable () const int getCDs (vector< CCdCore * > &cds) int getCDsInScope (vector< CCdCore * > &cds) int getCDsOutofScope (vector< CCdCore * > &cds) bool isCDInScope (CCdCore *cd) const bool isRowInScope (int row) const CCdCore * GetLeafDescendentCD (int row, bool includeSelf=false) const CCdCore * GetScopedLeafCD (int row) const CCdCore * GetSeniorMemberCD (int row, bool scopedOnly=true) const void convertFromCDRows (CCdCore *cd, const vector< int > &cdRows, set< int > &colRows) const void convertToCDRows (const vector< int > &colRows, CDRowsMap &cdRows) const void mapRows (const AlignmentCollection &ac, const set< int > &rows, set< int > &convertedRows) const int mapRow (const AlignmentCollection &ac, int row) const void getAllRowsForCD (CCdCore *cd, vector< int > &colRows) const bool GetSpeciesForRow (int row, string &species) const bool GetBioseqForRow (int rowId, CRef< CBioseq > &bioseq) int GetRowsWithSameSeqID (int rowToMatch, vector< int > &rows, bool inclusive=true) const int GetRowsWithSeqID (const CRef< CSeq_id > &SeqID, vector< int > &rows) const bool IsStruct (int row) bool IsPdb (int row) const void GetAllSequences (vector< string > &sequences) string GetSequenceForRow (int row) void GetAlignedResiduesForRow (int row, char *&) void GetAlignedResiduesForAll (char **&ppAlignedResidues, bool forceRecompute) bool isInstanceOf (MultipleAlignment *ma) void getNormalRowsNotInChild (vector< int > &childless, bool excludeMaster=false) const virtual ~AlignmentCollection () bool AreNonOverlapping () const bool IsNonOverlapping (const CRef< CSeq_align > &align, int &blockIndex) const string & getLastError ()
Definition at line 111 of file cuAlignmentCollection.hpp.
◆ MultipleAlignment() [1/3] ◆ MultipleAlignment() [2/3] ◆ MultipleAlignment() [3/3] ◆ AddAlignment() ◆ appendAlignment()
Definition at line 847 of file cuAlignmentCollection.cpp.
References assert, copyRowSource(), CRef< C, Locker >::Empty(), findParentalEquivalent(), GetAccession(), CCdCore::GetAccession(), AlignmentCollection::getFirstCD(), AlignmentCollection::GetSequenceForRow(), i, AlignmentCollection::isRowInScope(), locateChildRow(), LOG_POST, m_blockTable, AlignmentCollection::m_err, and AlignmentCollection::m_seqAligns.
Referenced by setAlignment().
◆ copyRowSource() ◆ extractAlignedSubset()
Definition at line 1057 of file cuAlignmentCollection.cpp.
References set< Key, Compare >::begin(), BlockModel::blockMatch(), copyRowSource(), set< Key, Compare >::end(), AlignmentCollection::GetRowSource(), AlignmentCollection::getSeqAlign(), m_blockTable, AlignmentCollection::m_seqAligns, RowSource::master, BlockModel::toSeqAlign(), and AlignmentCollection::wasMaster().
◆ findParentalCastible() bool MultipleAlignment::findParentalCastible ( const cd_utils::BlockModel & bar, int & pRow ) const ◆ findParentalEquivalent() bool MultipleAlignment::findParentalEquivalent ( const cd_utils::BlockModel & bar, int & pRow, bool inputAsChild = true ) const ◆ getBlockModel() ◆ isBlockAligned() bool MultipleAlignment::isBlockAligned ( ) const ◆ locateChildRow() bool MultipleAlignment::locateChildRow ( const cd_utils::BlockModel & childRow, int & pRow ) const ◆ makeBlockTable() void MultipleAlignment::makeBlockTable ( ) private ◆ setAlignment() [1/5] ◆ setAlignment() [2/5] ◆ setAlignment() [3/5] ◆ setAlignment() [4/5] ◆ setAlignment() [5/5] void MultipleAlignment::setAlignment ( CRef< CSeq_align > & seqAlign ) ◆ transferOneRow() ◆ transferToCD() bool MultipleAlignment::transferToCD ( CCdCore * cd = 0 ) ◆ m_blockTable vector<cd_utils::BlockModel> MultipleAlignment::m_blockTable private
The documentation for this class was generated from the following files:
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