NCBI C++ ToolKit
Functions
cuCD.cpp File Reference
#include <ncbi_pch.hpp>
#include <objects/cdd/Align_annot.hpp>
#include <objects/cdd/Align_annot_set.hpp>
#include <objects/cdd/Cdd.hpp>
#include <objects/cdd/Cdd_id.hpp>
#include <objects/cdd/Cdd_descr_set.hpp>
#include <objects/ncbimime/Ncbi_mime_asn1.hpp>
#include <objects/ncbimime/Biostruc_seqs_aligns_cdd.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/seqalign/Dense_diag.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqloc/PDB_seq_id.hpp>
#include <objects/seqloc/PDB_mol_id.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/taxon1/taxon1.hpp>
#include <objects/taxon1/Taxon2_data.hpp>
#include "corelib/ncbitime.hpp"
#include <objects/general/Date.hpp>
#include <algo/structure/cd_utils/cuCdCore.hpp>
#include <algo/structure/cd_utils/cuCdReadWriteASN.hpp>
#include <algo/structure/cd_utils/cuAlign.hpp>
#include <algo/structure/cd_utils/cuSequence.hpp>
#include <algo/structure/cd_utils/cuCD.hpp>
#include <algo/structure/cd_utils/cuBlockIntersector.hpp>
#include <algo/structure/cd_utils/cuAlignmentCollection.hpp>
#include <math.h>
+ Include dependency graph for cuCD.cpp:

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Functions

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)
 
CCdCoreExtractCDFromMime (CNcbi_mime_asn1 *ncbiMime)
 
CCdCoreCopyCD (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< CBioseqGetMasterBioseqWithFootprintOld (CCdCore *cd)
 
CRef< CBioseqGetMasterBioseqWithFootprint (CCdCore *cd)
 
CRef< CBioseqGetBioseqWithFootprintForNthRow (CCdCore *cd, int N, string &errstr)
 
bool GetBioseqWithFootprintForNRows (CCdCore *cd, int N, vector< CRef< CBioseq > > &bioseqs, string &errstr)
 
CRef< COrg_refGetCommonTax (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)
 

Function Documentation

◆ CopyCD()

CCdCore* CopyCD ( const CCdCore cd)

Definition at line 281 of file cuCD.cpp.

References CopyASNObject(), and NULL.

Referenced by ExtractCDFromMime().

◆ ExtractCDFromMime()

CCdCore* ExtractCDFromMime ( CNcbi_mime_asn1 ncbiMime)

◆ GetAlignmentColumnsForCD()

void GetAlignmentColumnsForCD ( CCdCore cd,
map< unsigned int, string > &  columns,
unsigned int  referenceRow 
)

◆ GetBioseqWithFootprintForNRows()

bool GetBioseqWithFootprintForNRows ( CCdCore cd,
int  N,
vector< CRef< CBioseq > > &  bioseqs,
string errstr 
)

Definition at line 624 of file cuCD.cpp.

References GetBioseqWithFootprintForNthRow(), CCdCore::GetNumRows(), i, and N.

◆ GetBioseqWithFootprintForNthRow()

CRef< CBioseq > GetBioseqWithFootprintForNthRow ( CCdCore cd,
int  N,
string errstr 
)

◆ GetCommonTax()

CRef< COrg_ref > GetCommonTax ( CCdCore cd,
bool  useRootWhenNoTaxInfo 
)

◆ GetMappedRowIds()

int GetMappedRowIds ( CCdCore cd1,
int  row1,
CCdCore cd2,
vector< int > &  rows2,
bool  cd1AsChild,
bool  overlapMode 
)

◆ GetMasterBioseqWithFootprint()

CRef< CBioseq > GetMasterBioseqWithFootprint ( CCdCore cd)

Definition at line 580 of file cuCD.cpp.

References GetBioseqWithFootprintForNthRow().

◆ GetMasterBioseqWithFootprintOld()

CRef< CBioseq > GetMasterBioseqWithFootprintOld ( CCdCore cd)

◆ GetOverlappedRows()

int GetOverlappedRows ( CCdCore cd1,
CCdCore cd2,
vector< int > &  rowsOfCD1,
vector< int > &  rowsOfCD2 
)

Definition at line 352 of file cuCD.cpp.

References GetMappedRowIds(), CCdCore::GetNumRows(), and NULL.

Referenced by NumberOfOverlappedRows().

◆ GetReMasterFailureCode()

int GetReMasterFailureCode ( const CCdCore cd)

Definition at line 73 of file cuCD.cpp.

References ALIGN_ANNOTS_VALID_FAILURE.

◆ GetVerboseNameStr()

string GetVerboseNameStr ( const CCdCore cd)

Definition at line 551 of file cuCD.cpp.

References CCdCore::GetAccession(), and CCdd_Base::GetName().

◆ IntersectByMaster()

int IntersectByMaster ( CCdCore ccd,
double  rowFraction 
)

◆ NumberOfOverlappedRows()

int NumberOfOverlappedRows ( CCdCore cd1,
CCdCore cd2 
)

Definition at line 403 of file cuCD.cpp.

References GetOverlappedRows().

◆ obeysParentTypeConstraints()

bool obeysParentTypeConstraints ( const CCdCore pCD)

◆ PurgeConsensusSequences()

int PurgeConsensusSequences ( CCdCore pCD,
bool  resetFields 
)

◆ remasterAlignannot()

bool remasterAlignannot ( CCdCore cd,
unsigned int  oldMasterRow 
)

◆ ReMasterCdWithoutUnifiedBlocks()

bool ReMasterCdWithoutUnifiedBlocks ( CCdCore cd,
int  Row,
bool  resetFields 
)

◆ RemasterWithStructure()

bool RemasterWithStructure ( CCdCore cd,
string msg 
)

◆ Reorder()

bool Reorder ( CCdCore pCD,
const vector< int positions 
)

◆ ReorderStructureAlignments()

bool ReorderStructureAlignments ( CCdCore pCD,
const vector< int > &  positions 
)

◆ ResetFields()

void ResetFields ( CCdCore cd)

◆ SetAlignedResiduesForCD()

void SetAlignedResiduesForCD ( CCdCore cd,
char **&  ppAlignedResidues,
bool  forceRecompute 
)

◆ SetConvertedSequencesForCD()

void SetConvertedSequencesForCD ( CCdCore cd,
vector< string > &  convertedSequences,
bool  forceRecompute 
)

Definition at line 408 of file cuCD.cpp.

References CCdCore::GetNumSequences(), CCdCore::GetSequenceStringByIndex(), and i.

◆ SetCreationDate()

bool SetCreationDate ( CCdCore cd)

Definition at line 207 of file cuCD.cpp.

References CTime::eCurrent, CDate::ePrecision_day, result, and CCdd_Base::SetDescription().

Referenced by CCdCore::AddCreateDate().

◆ SetUpdateDate()

bool SetUpdateDate ( CCdCore cd)
Modified on Sat Jul 13 13:36:11 2024 by modify_doxy.py rev. 669887