ARB
Public Member Functions | List of all members
AlignBuffer Class Reference

#include <seq_search.hxx>

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Collaboration diagram for AlignBuffer:
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Public Member Functions

 AlignBuffer (long size)
 
 ~AlignBuffer ()
 
const chartext () const
 
const charquality () 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
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)
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: