bpp-seq-omics  2.4.1
Public Member Functions | Static Public Attributes | Private Member Functions | Private Attributes | List of all members
bpp::GtfFeatureReader Class Reference

A simple reader implementing the Gene Transfer Format. More...

#include <Bpp/Seq/Feature/Gtf/GtfFeatureReader.h>

+ Inheritance diagram for bpp::GtfFeatureReader:
+ Collaboration diagram for bpp::GtfFeatureReader:

Public Member Functions

 GtfFeatureReader (std::istream &input)
 
bool hasMoreFeature () const
 
const BasicSequenceFeature nextFeature ()
 
void getAllFeatures (SequenceFeatureSet &features)
 
void getFeaturesOfType (const std::string &type, SequenceFeatureSet &features)
 
void getFeaturesOfSequence (const std::string &seqId, SequenceFeatureSet &features)
 

Static Public Attributes

static const std::string GTF_PHASE = "GTF_PHASE"
 
static const std::string GTF_GENE_ID = "gene_id"
 
static const std::string GTF_TRANSCRIPT_ID = "transcript_id"
 

Private Member Functions

void getNextLine_ ()
 

Private Attributes

std::istream & input_
 
std::string nextLine_
 

Detailed Description

A simple reader implementing the Gene Transfer Format.

The reference norm in use is the one of GTF2.2 http://mblab.wustl.edu/GTF22.html . This class is a "beta" class, and may undeavour interface changes in the future.

Note that in GTF, coordinates are [a, b] 1-based. They will therefore be converted to [a, b[ 0-based, as specified for the SequenceFeature object.

Author
Sylvain Gaillard

Definition at line 66 of file GtfFeatureReader.h.

Constructor & Destructor Documentation

◆ GtfFeatureReader()

bpp::GtfFeatureReader::GtfFeatureReader ( std::istream &  input)
inline

Definition at line 79 of file GtfFeatureReader.h.

References getNextLine_().

Member Function Documentation

◆ getAllFeatures()

void bpp::GtfFeatureReader::getAllFeatures ( SequenceFeatureSet &  features)
inlinevirtual

Implements bpp::FeatureReader.

Definition at line 89 of file GtfFeatureReader.h.

References bpp::SequenceFeatureSet::addFeature(), hasMoreFeature(), and nextFeature().

◆ getFeaturesOfSequence()

void bpp::GtfFeatureReader::getFeaturesOfSequence ( const std::string &  seqId,
SequenceFeatureSet &  features 
)
inlinevirtual

Implements bpp::FeatureReader.

Definition at line 101 of file GtfFeatureReader.h.

References bpp::SequenceFeatureSet::addFeature(), bpp::BasicSequenceFeature::getSequenceId(), hasMoreFeature(), and nextFeature().

◆ getFeaturesOfType()

void bpp::GtfFeatureReader::getFeaturesOfType ( const std::string &  type,
SequenceFeatureSet &  features 
)
inlinevirtual

Implements bpp::FeatureReader.

Definition at line 94 of file GtfFeatureReader.h.

References bpp::SequenceFeatureSet::addFeature(), bpp::BasicSequenceFeature::getType(), hasMoreFeature(), and nextFeature().

◆ getNextLine_()

void GtfFeatureReader::getNextLine_ ( )
private

Definition at line 58 of file GtfFeatureReader.cpp.

References bpp::TextTools::isEmpty().

Referenced by GtfFeatureReader().

◆ hasMoreFeature()

bool bpp::GtfFeatureReader::hasMoreFeature ( ) const
inlinevirtual

Implements bpp::FeatureReader.

Definition at line 86 of file GtfFeatureReader.h.

References nextLine_.

Referenced by getAllFeatures(), getFeaturesOfSequence(), and getFeaturesOfType().

◆ nextFeature()

const BasicSequenceFeature GtfFeatureReader::nextFeature ( )
virtual

Implements bpp::FeatureReader.

Definition at line 73 of file GtfFeatureReader.cpp.

References bpp::StringTokenizer::hasMoreToken(), bpp::TextTools::isEmpty(), bpp::TextTools::isWhiteSpaceCharacter(), bpp::StringTokenizer::nextToken(), bpp::StringTokenizer::numberOfRemainingTokens(), bpp::TextTools::removeSurroundingWhiteSpaces(), and bpp::BasicSequenceFeature::setAttribute().

Referenced by getAllFeatures(), getFeaturesOfSequence(), and getFeaturesOfType().

Member Data Documentation

◆ GTF_GENE_ID

const string GtfFeatureReader::GTF_GENE_ID = "gene_id"
static

Definition at line 71 of file GtfFeatureReader.h.

◆ GTF_PHASE

const string GtfFeatureReader::GTF_PHASE = "GTF_PHASE"
static

Definition at line 70 of file GtfFeatureReader.h.

◆ GTF_TRANSCRIPT_ID

const string GtfFeatureReader::GTF_TRANSCRIPT_ID = "transcript_id"
static

Definition at line 72 of file GtfFeatureReader.h.

◆ input_

std::istream& bpp::GtfFeatureReader::input_
private

Definition at line 75 of file GtfFeatureReader.h.

◆ nextLine_

std::string bpp::GtfFeatureReader::nextLine_
private

Definition at line 76 of file GtfFeatureReader.h.

Referenced by hasMoreFeature().

The documentation for this class was generated from the following files: