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int GetReMasterFailureCode (const CCdCore *cd) void ResetFields (CCdCore *cd) bool Reorder (CCdCore *pCD, const vector< int > positions) bool ReorderStructureAlignments (CCdCore *pCD, const vector< int > &positions) bool SetCreationDate (CCdCore *cd) bool SetUpdateDate (CCdCore *cd) CCdCore * ExtractCDFromMime (CNcbi_mime_asn1 *ncbiMime) CCdCore * CopyCD (const CCdCore *cd) int GetMappedRowIds (CCdCore *cd1, int row1, CCdCore *cd2, vector< int > &rows2, bool cd1AsChild, bool overlapMode) int GetOverlappedRows (CCdCore *cd1, CCdCore *cd2, vector< int > &rowsOfCD1, vector< int > &rowsOfCD2) int NumberOfOverlappedRows (CCdCore *cd1, CCdCore *cd2) void SetConvertedSequencesForCD (CCdCore *cd, vector< string > &convertedSequences, bool forceRecompute) void SetAlignedResiduesForCD (CCdCore *cd, char **&ppAlignedResidues, bool forceRecompute) void GetAlignmentColumnsForCD (CCdCore *cd, map< unsigned int, string > &columns, unsigned int referenceRow) string GetVerboseNameStr (const CCdCore *cd) CRef< CBioseq > GetMasterBioseqWithFootprintOld (CCdCore *cd) CRef< CBioseq > GetMasterBioseqWithFootprint (CCdCore *cd) CRef< CBioseq > GetBioseqWithFootprintForNthRow (CCdCore *cd, int N, string &errstr) bool GetBioseqWithFootprintForNRows (CCdCore *cd, int N, vector< CRef< CBioseq > > &bioseqs, string &errstr) CRef< COrg_ref > GetCommonTax (CCdCore *cd, bool useRootWhenNoTaxInfo) bool obeysParentTypeConstraints (const CCdCore *pCD) bool RemasterWithStructure (CCdCore *cd, string *msg) bool ReMasterCdWithoutUnifiedBlocks (CCdCore *cd, int Row, bool resetFields) bool remasterAlignannot (CCdCore &cd, unsigned int oldMasterRow) int PurgeConsensusSequences (CCdCore *pCD, bool resetFields) int IntersectByMaster (CCdCore *ccd, double rowFraction) ◆ CopyCD() ◆ ExtractCDFromMime() ◆ GetAlignmentColumnsForCD() void GetAlignmentColumnsForCD ( CCdCore * cd, map< unsigned int, string > & columns, unsigned int referenceRow )Definition at line 455 of file cuCD.cpp.
References columns, ERR_POST, CCdCore::GetAccession(), CCdCore::GetAlignmentLength(), GetBlockLengths(), GetBlockStarts(), CCdCore::GetNumRows(), CCdCore::GetSeqAlign(), i, MultipleAlignment::isBlockAligned(), nRows, NULL, row, and SetAlignedResiduesForCD().
◆ GetBioseqWithFootprintForNRows() ◆ GetBioseqWithFootprintForNthRow()Definition at line 587 of file cuCD.cpp.
References CSerialObject::Assign(), CSeq_id_Base::e_Local, CCdCore::GetAccession(), CCdCore::GetBioseqForRow(), CCdCore::GetLowerBound(), CCdCore::GetNumRows(), CCdCore::GetUpperBound(), NStr::IntToString(), N, CBioseq_Base::SetAnnot(), CSeq_annot_Base::SetData(), and CBioseq_Base::SetId().
Referenced by GetBioseqWithFootprintForNRows(), and GetMasterBioseqWithFootprint().
◆ GetCommonTax()Definition at line 636 of file cuCD.cpp.
References CSerialObject::Assign(), CCdCore::GetBioseqForRow(), CCdCore::GetGI(), CCdCore::GetNumRows(), CTaxon1::GetOrgRef(), CTaxon1::GetTaxId4GI(), GetTaxIdInBioseq(), i, CTaxon1::Init(), INVALID_GI, CTaxon1::Join(), LOG_POST, CRef< C, Locker >::Reset(), TAX_ID_CONST, ZERO_GI, and ZERO_TAX_ID.
◆ GetMappedRowIds() ◆ GetMasterBioseqWithFootprint() ◆ GetMasterBioseqWithFootprintOld() ◆ GetOverlappedRows() ◆ GetReMasterFailureCode() ◆ GetVerboseNameStr() ◆ IntersectByMaster() int IntersectByMaster ( CCdCore * ccd, double rowFraction )Definition at line 903 of file cuCD.cpp.
References BlockModel::addBlock(), BlockIntersector::addOneAlignment(), assert, b, bmp, BlockModel::getBlock(), BlockModel::getBlocks(), BlockModel::getGapToCTerminal(), Block::getId(), BlockIntersector::getIntersectedAlignment(), Block::getLen(), CCdCore::GetNumRows(), CCdCore::GetSeqAligns(), CCdCore::GetSequenceStringByRow(), Block::getStart(), BlockModel::getTotalBlockLength(), i, set< Key, Compare >::insert(), MultipleAlignment::isBlockAligned(), nRows, result, and BlockModel::toSeqAlign().
◆ NumberOfOverlappedRows() ◆ obeysParentTypeConstraints() ◆ PurgeConsensusSequences() ◆ remasterAlignannot()Definition at line 800 of file cuCD.cpp.
References BlockModelPair::getMaster(), CCdCore::GetNumRows(), CCdCore::GetSeqAlign(), BlockModel::getSeqId(), BlockModelPair::getSlave(), int, CCdd_Base::IsSetAlignannot(), BlockModelPair::mapToMaster(), CSeq_id::Match(), ok, and CCdd_Base::SetAlignannot().
Referenced by ReMasterCdWithoutUnifiedBlocks().
◆ ReMasterCdWithoutUnifiedBlocks()Definition at line 754 of file cuCD.cpp.
References bmp, CCdCore::GetSeqAlign(), CCdCore::GetSeqAligns(), CCdCore::GetSeqIDForRow(), i, CSeq_id_Base::IsPdb(), CCdd_Base::IsSetMaster3d(), remasterAlignannot(), ResetFields(), BlockModelPair::reverse(), CCdd_Base::SetMaster3d(), and BlockModelPair::toSeqAlign().
Referenced by CDUpdater::mergePending(), PurgeConsensusSequences(), RemasterWithStructure(), and SeqSwapper::swapSequences().
◆ RemasterWithStructure() ◆ Reorder() ◆ ReorderStructureAlignments()Definition at line 145 of file cuCD.cpp.
References CCdd_Base::GetFeatures(), CBiostruc_annot_set_Base::GetFeatures(), CCdCore::GetNumRows(), CCdCore::GetPDB(), CCdCore::Has3DMaster(), i, int, CCdCore::IsSeqAligns(), CCdd_Base::IsSetFeatures(), nRows, NULL, CCdCore::Num3DAlignments(), result, CCdd_Base::SetFeatures(), and si.
Referenced by Reorder().
◆ ResetFields() ◆ SetAlignedResiduesForCD() void SetAlignedResiduesForCD ( CCdCore * cd, char **& ppAlignedResidues, bool forceRecompute ) ◆ SetConvertedSequencesForCD() void SetConvertedSequencesForCD ( CCdCore * cd, vector< string > & convertedSequences, bool forceRecompute ) ◆ SetCreationDate() ◆ SetUpdateDate()RetroSearch is an open source project built by @garambo | Open a GitHub Issue
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