CompactedSubSequence Class Reference

#include <seq_search.hxx>

Public Member Functions
	CompactedSubSequence (const char *seq, int length_, const char *name_, int start_offset=0)
	CompactedSubSequence (const CompactedSubSequence &other)
	CompactedSubSequence (const CompactedSubSequence &other, int rel_pos, int length_)
	DECLARE_ASSIGNMENT_OPERATOR (CompactedSubSequence)
int	length () const
const char *	text () const
const char *	text (int i) const
const char *	name () const
char	operator[] (int i) const
int	no_of_gaps_before (int cPos) const
int	no_of_gaps_after (int cPos) const
int	expdStartPosition () const
int	expdPosition (int cPos) const
int	compPosition (int xPos) const
int	expdLength () const
const int *	gapsBefore (int offset=0) const
int	firstDotPosition () const
int	nextDotPosition () const
bool	may_refer_to_same_part_as (const CompactedSubSequence &other) const

Detailed Description

Definition at line 141 of file seq_search.hxx.

Constructor & Destructor Documentation

CompactedSubSequence::CompactedSubSequence ( const char *  seq, int  length_, const char *  name_, int  start_offset = 0  )

inline

Definition at line 163 of file seq_search.hxx.

CompactedSubSequence::CompactedSubSequence ( const CompactedSubSequence &  other )

inline

Definition at line 171 of file seq_search.hxx.

CompactedSubSequence::CompactedSubSequence ( const CompactedSubSequence &  other, int  rel_pos, int  length_  )

inline

Definition at line 178 of file seq_search.hxx.

Member Function Documentation

CompactedSubSequence::DECLARE_ASSIGNMENT_OPERATOR

(

CompactedSubSequence

)

int CompactedSubSequence::length ( ) const

inline

Definition at line 187 of file seq_search.hxx.

Referenced by alignToNextRelative(), expdLength(), FastSearchSequence::fast_align(), insertsToNextBase(), may_refer_to_same_part_as(), operator[](), and SequencePosition::rightOf().

const char* CompactedSubSequence::text ( ) const

inline

Definition at line 189 of file seq_search.hxx.

Referenced by cannot_fast_align(), may_refer_to_same_part_as(), and operator[]().

const char* CompactedSubSequence::text ( int  i ) const

inline

Definition at line 190 of file seq_search.hxx.

References text().

Referenced by text().

const char* CompactedSubSequence::name ( ) const

inline

Definition at line 192 of file seq_search.hxx.

References CompactedSequence::get_name().

Referenced by alignCompactedTo(), alignToNextRelative(), and AlignBuffer::restoreDots().

char CompactedSubSequence::operator[] ( int  i ) const

inline

Definition at line 194 of file seq_search.hxx.

References length(), and text().

int CompactedSubSequence::no_of_gaps_before ( int  cPos ) const

inline

Definition at line 196 of file seq_search.hxx.

References CompactedSequence::no_of_gaps_before().

Referenced by AliChange::follow().

int CompactedSubSequence::no_of_gaps_after ( int  cPos ) const

inline

Definition at line 197 of file seq_search.hxx.

References CompactedSequence::no_of_gaps_after().

Referenced by AliChange::follow().

int CompactedSubSequence::expdStartPosition ( ) const

inline

Definition at line 199 of file seq_search.hxx.

References CompactedSequence::expdPosition().

int CompactedSubSequence::expdPosition ( int  cPos ) const

inline

Definition at line 200 of file seq_search.hxx.

References CompactedSequence::expdPosition(), and fa_assert.

Referenced by cannot_fast_align(), expdLength(), SequencePosition::expdPosition(), AliChange::follow(), and insertsToNextBase().

int CompactedSubSequence::compPosition ( int  xPos ) const

inline

Definition at line 205 of file seq_search.hxx.

References CompactedSequence::compPosition().

Referenced by AliChange::follow().

int CompactedSubSequence::expdLength ( ) const

inline

Definition at line 207 of file seq_search.hxx.

References expdPosition(), and length().

const int* CompactedSubSequence::gapsBefore ( int  offset = 0 ) const

inline

Definition at line 208 of file seq_search.hxx.

References CompactedSequence::gapsBefore(), and offset.

Referenced by cannot_fast_align().

int CompactedSubSequence::firstDotPosition ( ) const

inline

Definition at line 210 of file seq_search.hxx.

References Dots::beforeBase(), CompactedSequence::getDotlist(), and Dots::next().

Referenced by AlignBuffer::restoreDots().

int CompactedSubSequence::nextDotPosition ( ) const

inline

Definition at line 224 of file seq_search.hxx.

References Dots::next().

Referenced by AlignBuffer::restoreDots().

bool CompactedSubSequence::may_refer_to_same_part_as ( const CompactedSubSequence &  other ) const

inline

Definition at line 236 of file seq_search.hxx.

References length(), and text().

Referenced by AliChange::AliChange().

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

• SL/FAST_ALIGNER/seq_search.hxx