NCBI C++ ToolKit
Public Member Functions | Protected Attributes | List of all members
CBedFeatureRecord Class Reference

Search Toolkit Book for CBedFeatureRecord

Encapsulation of the BED feature record. More...

#include <objtools/writers/bed_feature_record.hpp>

+ Collaboration diagram for CBedFeatureRecord:

Public Member Functions

 CBedFeatureRecord ()
 
 ~CBedFeatureRecord ()
 
bool AssignLocation (CScope &, const CSeq_interval &)
 
bool AssignDisplayData (const CMappedFeat &, bool)
 
bool AssignName (const CMappedFeat &)
 
bool Write (CNcbiOstream &, unsigned int)
 
bool SetLocation (const CSeq_loc &)
 
bool SetName (const CSeqFeatData &)
 
bool SetScore (int)
 
bool SetThick (const CSeq_loc &)
 
bool SetNoThick (const CSeq_loc &)
 
bool SetRgb (const string &)
 
bool SetBlocks (const CSeq_loc &, const CSeq_loc &)
 
const stringChrom () const
 
const stringChromStart () const
 
const stringChromEnd () const
 
const stringName () const
 
const stringScore () const
 
const stringStrand () const
 
const stringThickStart () const
 
const stringThickEnd () const
 
const stringItemRgb () const
 
const stringBlockCount () const
 
const stringBlockSizes () const
 
const stringBlockStarts () const
 
size_t ColumnCount () const
 

Protected Attributes

size_t m_uColumnCount
 
string m_strChrom
 
string m_strChromStart
 
string m_strChromEnd
 
string m_strName
 
string m_strScore
 
string m_strStrand
 
string m_strThickStart
 
string m_strThickEnd
 
string m_strItemRgb
 
string m_strBlockCount
 
string m_strBlockSizes
 
string m_strBlockStarts
 

Detailed Description

Encapsulation of the BED feature record.

That's columnar data with at least three and at most twelve columns. Each column has a fixed, well defined meaning, and all records of the same track must have the same number of columns.

Definition at line 44 of file bed_feature_record.hpp.

Constructor & Destructor Documentation

◆ CBedFeatureRecord()

CBedFeatureRecord::CBedFeatureRecord ( )

Definition at line 55 of file bed_feature_record.cpp.

◆ ~CBedFeatureRecord()

CBedFeatureRecord::~CBedFeatureRecord ( )

Definition at line 74 of file bed_feature_record.cpp.

Member Function Documentation

◆ AssignDisplayData()

bool CBedFeatureRecord::AssignDisplayData ( const CMappedFeat mf,
bool  bUseScore 
)

◆ AssignLocation()

bool CBedFeatureRecord::AssignLocation ( CScope scope,
const CSeq_interval interval 
)

◆ AssignName()

bool CBedFeatureRecord::AssignName ( const CMappedFeat mf)

◆ BlockCount()

const string& CBedFeatureRecord::BlockCount ( ) const
inline

Definition at line 75 of file bed_feature_record.hpp.

References m_strBlockCount.

Referenced by Write().

◆ BlockSizes()

const string& CBedFeatureRecord::BlockSizes ( ) const
inline

Definition at line 76 of file bed_feature_record.hpp.

References m_strBlockSizes.

Referenced by Write().

◆ BlockStarts()

const string& CBedFeatureRecord::BlockStarts ( ) const
inline

Definition at line 77 of file bed_feature_record.hpp.

References m_strBlockStarts.

Referenced by Write().

◆ Chrom()

const string& CBedFeatureRecord::Chrom ( ) const
inline

Definition at line 66 of file bed_feature_record.hpp.

References m_strChrom.

Referenced by Write().

◆ ChromEnd()

const string& CBedFeatureRecord::ChromEnd ( ) const
inline

Definition at line 68 of file bed_feature_record.hpp.

References m_strChromEnd.

Referenced by Write().

◆ ChromStart()

const string& CBedFeatureRecord::ChromStart ( ) const
inline

Definition at line 67 of file bed_feature_record.hpp.

References m_strChromStart.

Referenced by Write().

◆ ColumnCount()

size_t CBedFeatureRecord::ColumnCount ( ) const
inline

Definition at line 79 of file bed_feature_record.hpp.

References m_uColumnCount.

◆ ItemRgb()

const string& CBedFeatureRecord::ItemRgb ( ) const
inline

Definition at line 74 of file bed_feature_record.hpp.

References m_strItemRgb.

Referenced by Write().

◆ Name()

const string& CBedFeatureRecord::Name ( ) const
inline

Definition at line 69 of file bed_feature_record.hpp.

References m_strName.

Referenced by Write().

◆ Score()

const string& CBedFeatureRecord::Score ( ) const
inline

Definition at line 70 of file bed_feature_record.hpp.

References m_strScore.

Referenced by Write().

◆ SetBlocks()

bool CBedFeatureRecord::SetBlocks ( const CSeq_loc chrom,
const CSeq_loc blocks 
)

◆ SetLocation()

bool CBedFeatureRecord::SetLocation ( const CSeq_loc loc)

◆ SetName()

bool CBedFeatureRecord::SetName ( const CSeqFeatData data)

Definition at line 355 of file bed_feature_record.cpp.

References data, and m_strName.

◆ SetNoThick()

bool CBedFeatureRecord::SetNoThick ( const CSeq_loc loc)

◆ SetRgb()

bool CBedFeatureRecord::SetRgb ( const string color)

Definition at line 454 of file bed_feature_record.cpp.

References color, NStr::Join(), m_strItemRgb, and NStr::Split().

◆ SetScore()

bool CBedFeatureRecord::SetScore ( int  score)

Definition at line 369 of file bed_feature_record.cpp.

References NStr::IntToString(), and m_strScore.

◆ SetThick()

bool CBedFeatureRecord::SetThick ( const CSeq_loc loc)

◆ Strand()

const string& CBedFeatureRecord::Strand ( ) const
inline

Definition at line 71 of file bed_feature_record.hpp.

References m_strStrand.

Referenced by Write().

◆ ThickEnd()

const string& CBedFeatureRecord::ThickEnd ( ) const
inline

Definition at line 73 of file bed_feature_record.hpp.

References m_strThickEnd.

Referenced by Write().

◆ ThickStart()

const string& CBedFeatureRecord::ThickStart ( ) const
inline

Definition at line 72 of file bed_feature_record.hpp.

References m_strThickStart.

Referenced by Write().

◆ Write()

bool CBedFeatureRecord::Write ( CNcbiOstream ostr,
unsigned int  columnCount 
)

Member Data Documentation

◆ m_strBlockCount

string CBedFeatureRecord::m_strBlockCount
protected

Definition at line 92 of file bed_feature_record.hpp.

Referenced by AssignDisplayData(), BlockCount(), and SetBlocks().

◆ m_strBlockSizes

string CBedFeatureRecord::m_strBlockSizes
protected

Definition at line 93 of file bed_feature_record.hpp.

Referenced by AssignDisplayData(), BlockSizes(), and SetBlocks().

◆ m_strBlockStarts

string CBedFeatureRecord::m_strBlockStarts
protected

Definition at line 94 of file bed_feature_record.hpp.

Referenced by AssignDisplayData(), BlockStarts(), and SetBlocks().

◆ m_strChrom

string CBedFeatureRecord::m_strChrom
protected

Definition at line 83 of file bed_feature_record.hpp.

Referenced by AssignLocation(), Chrom(), and SetLocation().

◆ m_strChromEnd

string CBedFeatureRecord::m_strChromEnd
protected

Definition at line 85 of file bed_feature_record.hpp.

Referenced by AssignLocation(), ChromEnd(), and SetLocation().

◆ m_strChromStart

string CBedFeatureRecord::m_strChromStart
protected

Definition at line 84 of file bed_feature_record.hpp.

Referenced by AssignLocation(), ChromStart(), and SetLocation().

◆ m_strItemRgb

string CBedFeatureRecord::m_strItemRgb
protected

Definition at line 91 of file bed_feature_record.hpp.

Referenced by AssignDisplayData(), ItemRgb(), and SetRgb().

◆ m_strName

string CBedFeatureRecord::m_strName
protected

Definition at line 86 of file bed_feature_record.hpp.

Referenced by AssignDisplayData(), AssignName(), Name(), and SetName().

◆ m_strScore

string CBedFeatureRecord::m_strScore
protected

Definition at line 87 of file bed_feature_record.hpp.

Referenced by AssignDisplayData(), Score(), and SetScore().

◆ m_strStrand

string CBedFeatureRecord::m_strStrand
protected

Definition at line 88 of file bed_feature_record.hpp.

Referenced by AssignLocation(), SetLocation(), and Strand().

◆ m_strThickEnd

string CBedFeatureRecord::m_strThickEnd
protected

Definition at line 90 of file bed_feature_record.hpp.

Referenced by AssignDisplayData(), SetNoThick(), SetThick(), and ThickEnd().

◆ m_strThickStart

string CBedFeatureRecord::m_strThickStart
protected

Definition at line 89 of file bed_feature_record.hpp.

Referenced by AssignDisplayData(), SetNoThick(), SetThick(), and ThickStart().

◆ m_uColumnCount

size_t CBedFeatureRecord::m_uColumnCount
protected

Definition at line 82 of file bed_feature_record.hpp.

Referenced by AssignDisplayData(), AssignLocation(), and ColumnCount().


The documentation for this class was generated from the following files:
Modified on Wed May 29 18:43:04 2024 by modify_doxy.py rev. 669887