NCBI C++ ToolKit
Functions | Variables
cuCD.hpp File Reference
#include <corelib/ncbistd.hpp>
#include <objects/ncbimime/Ncbi_mime_asn1.hpp>
#include <algo/structure/cd_utils/cuCdCore.hpp>
+ Include dependency graph for cuCD.hpp:
+ This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Go to the SVN repository for this file.

Functions

int GetReMasterFailureCode (const CCdCore *cd)
 
bool Reorder (CCdCore *pCD, const vector< int > positions)
 
bool ReorderStructureAlignments (CCdCore *pCD, const vector< int > &positions)
 
bool remasterAlignannot (CCdCore &cd, unsigned int oldMasterRow=1)
 
void ResetFields (CCdCore *pCD)
 
CCdCoreExtractCDFromMime (CNcbi_mime_asn1 *ncbiMime)
 
CCdCoreCopyCD (const CCdCore *cd)
 
bool SetCreationDate (CCdCore *cd)
 
bool SetUpdateDate (CCdCore *cd)
 
int NumberOfOverlappedRows (CCdCore *cd1, CCdCore *cd2=NULL)
 
int GetOverlappedRows (CCdCore *cd1, CCdCore *cd2, vector< int > &rowsOfCD1, vector< int > &rowsOfCD2)
 
int GetMappedRowIds (CCdCore *cd1, int row1, CCdCore *cd2, vector< int > &rows2, bool cd1AsChild, bool overlapMode=false)
 
void SetConvertedSequencesForCD (CCdCore *cd, vector< string > &convertedSequences, bool forceRecompute=false)
 
void SetAlignedResiduesForCD (CCdCore *cd, char **&ppAlignedResidues, bool forceRecompute=false)
 
void GetAlignmentColumnsForCD (CCdCore *cd, map< unsigned int, string > &columns, unsigned int referenceRow=kMax_UInt)
 
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=true)
 
bool obeysParentTypeConstraints (const CCdCore *pCD)
 
int PurgeConsensusSequences (CCdCore *pCD, bool resetFields=true)
 
bool RemasterWithStructure (CCdCore *cd, string *msg=NULL)
 
bool ReMasterCdWithoutUnifiedBlocks (CCdCore *cd, int Row, bool resetFields=true)
 
int IntersectByMaster (CCdCore *ccd, double rowFraction=1.0)
 

Variables

const int ALIGN_ANNOTS_VALID_FAILURE = 1
 

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 = kMax_UInt 
)

◆ 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 = true 
)

◆ GetMappedRowIds()

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

◆ 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 = 1.0 
)

◆ NumberOfOverlappedRows()

int NumberOfOverlappedRows ( CCdCore cd1,
CCdCore cd2 = NULL 
)

Definition at line 403 of file cuCD.cpp.

References GetOverlappedRows().

◆ obeysParentTypeConstraints()

bool obeysParentTypeConstraints ( const CCdCore pCD)

◆ PurgeConsensusSequences()

int PurgeConsensusSequences ( CCdCore pCD,
bool  resetFields = true 
)

◆ remasterAlignannot()

bool remasterAlignannot ( CCdCore cd,
unsigned int  oldMasterRow = 1 
)

◆ ReMasterCdWithoutUnifiedBlocks()

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

◆ RemasterWithStructure()

bool RemasterWithStructure ( CCdCore cd,
string msg = NULL 
)

◆ Reorder()

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

◆ ReorderStructureAlignments()

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

◆ ResetFields()

void ResetFields ( CCdCore pCD)

◆ SetAlignedResiduesForCD()

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

◆ SetConvertedSequencesForCD()

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

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)

Variable Documentation

◆ ALIGN_ANNOTS_VALID_FAILURE

const int ALIGN_ANNOTS_VALID_FAILURE = 1

Definition at line 51 of file cuCD.hpp.

Referenced by GetReMasterFailureCode().

Modified on Thu Feb 22 17:15:08 2024 by modify_doxy.py rev. 669887