AlignBuffer Class Reference

#include <seq_search.hxx>

Inheritance diagram for AlignBuffer:

Collaboration diagram for AlignBuffer:

Public Member Functions
	AlignBuffer (long size)
	~AlignBuffer ()
const char *	text () const
const char *	quality () const
long	length () const
long	offset () const
long	free () const
void	copy (const char *s, char q, long len)
void	set (char c, char q)
void	set (char c, char q, long len)
void	reset (long newOffset=0)
void	correctUnalignedPositions ()
void	restoreDots (CompactedSubSequence &slaveSequence)
void	setDotsAtEOSequence ()

Detailed Description

Definition at line 300 of file seq_search.hxx.

Constructor & Destructor Documentation

AlignBuffer::AlignBuffer ( long  size )

inline

Definition at line 337 of file seq_search.hxx.

AlignBuffer::~AlignBuffer ( )

inline

Definition at line 345 of file seq_search.hxx.

Member Function Documentation

const char* AlignBuffer::text ( ) const

inline

Definition at line 350 of file seq_search.hxx.

References fa_assert, and free().

Referenced by alignCompactedTo(), and FastSearchSequence::fast_align().

const char* AlignBuffer::quality ( ) const

inline

Definition at line 351 of file seq_search.hxx.

References fa_assert, and free().

Referenced by alignCompactedTo(), and correctUnalignedPositions().

long AlignBuffer::length ( ) const

inline

Definition at line 352 of file seq_search.hxx.

Referenced by alignCompactedTo().

long AlignBuffer::offset ( ) const

inline

Definition at line 354 of file seq_search.hxx.

Referenced by FastSearchSequence::fast_align(), and insertsToNextBase().

long AlignBuffer::free ( ) const

inline

Definition at line 355 of file seq_search.hxx.

Referenced by alignCompactedTo(), copy(), insertAligned(), insertClustalValigned(), quality(), set(), and text().

void AlignBuffer::copy ( const char *  s, char  q, long  len  )

inline

Definition at line 357 of file seq_search.hxx.

References fa_assert, and free().

Referenced by cannot_fast_align(), and insertSlaveBases().

void AlignBuffer::set ( char  c, char  q  )

inline

Definition at line 363 of file seq_search.hxx.

References fa_assert, and free().

Referenced by alignCompactedTo(), insertAligned(), insertBase(), insertClustalValigned(), and insertGap().

void AlignBuffer::set ( char  c, char  q, long  len  )

inline

Definition at line 369 of file seq_search.hxx.

References fa_assert, and free().

void AlignBuffer::reset ( long  newOffset = 0 )

inline

Definition at line 375 of file seq_search.hxx.

References fa_assert.

void AlignBuffer::correctUnalignedPositions

(

)

Definition at line 124 of file seq_search.cxx.

References after(), before(), and quality().

Referenced by alignCompactedTo().

void AlignBuffer::restoreDots

(

CompactedSubSequence &

slaveSequence

)

Definition at line 168 of file seq_search.cxx.

References CompactedSubSequence::firstDotPosition(), is_gap(), CompactedSubSequence::name(), and CompactedSubSequence::nextDotPosition().

Referenced by alignCompactedTo().

void AlignBuffer::setDotsAtEOSequence

(

)

Definition at line 197 of file seq_search.cxx.

References is_gap().

Referenced by alignCompactedTo().

---

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

• SL/FAST_ALIGNER/seq_search.hxx
• SL/FAST_ALIGNER/seq_search.cxx