gkarrays::readIterator Class Reference

#include <readsReader.h>

Inheritance diagram for gkarrays::readIterator:

List of all members.

Public Member Functions
virtual	~readIterator ()
virtual readIterator &	operator++ ()=0
virtual kseq_t &	operator* ()=0
virtual size_t	getLength ()=0
virtual char *	getName ()=0
virtual char *	getQuality ()=0
virtual uint	getReadNumber ()=0
virtual char *	getSequence ()=0
virtual bool	isFinished ()=0
bool	printWarnings ()
void	setPrintWarnings (bool isVisible)

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Detailed Description

readIterator allows to retrieve information on each read by traversing them in order, one after one. If the k-mer length or the read length are given, only reads that are long enough to fulfill those values are considered.

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Constructor & Destructor Documentation

virtual gkarrays::readIterator::~readIterator

(

)

[inline, virtual]

Virtual destructor, necessary in c++

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Member Function Documentation

virtual size_t gkarrays::readIterator::getLength

(

)

[pure virtual]

Returns:

the length of the read

Implemented in gkarrays::pairedEndReadIterator, and gkarrays::singleReadIterator.

virtual char* gkarrays::readIterator::getName

(

)

[pure virtual]

Returns:

the name of the read

Implemented in gkarrays::pairedEndReadIterator, and gkarrays::singleReadIterator.

virtual char* gkarrays::readIterator::getQuality

(

)

[pure virtual]

Returns:

the quality of the read

Implemented in gkarrays::pairedEndReadIterator, and gkarrays::singleReadIterator.

virtual uint gkarrays::readIterator::getReadNumber

(

)

[pure virtual]

Returns:

the number of the read in the file

Implemented in gkarrays::pairedEndReadIterator, and gkarrays::singleReadIterator.

virtual char* gkarrays::readIterator::getSequence

(

)

[pure virtual]

Returns:

the sequence of the read

Implemented in gkarrays::pairedEndReadIterator, and gkarrays::singleReadIterator.

virtual bool gkarrays::readIterator::isFinished

(

)

[pure virtual]

Returns:

true iff we have read the whole file

Implemented in gkarrays::pairedEndReadIterator, and gkarrays::singleReadIterator.

virtual kseq_t& gkarrays::readIterator::operator*

(

)

[pure virtual]

Returns:

the kseq_t related to the current read

Implemented in gkarrays::pairedEndReadIterator, and gkarrays::singleReadIterator.

virtual readIterator& gkarrays::readIterator::operator++

(

)

[pure virtual]

Go to next sequence

Implemented in gkarrays::pairedEndReadIterator, and gkarrays::singleReadIterator.

bool gkarrays::readIterator::printWarnings

(

)

Returns:

true if warnings are visible false either.

void gkarrays::readIterator::setPrintWarnings

(

bool

isVisible

)

Parameters:

isVisible

Printwarnins visible value.

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

• readsReader.h
• readsReader.cpp