CompactedSequence Class Reference

#include <seq_search.hxx>

Inheritance diagram for CompactedSequence:

Collaboration diagram for CompactedSequence:

Public Member Functions
	CompactedSequence (const char *text, int length, const char *name, int start_offset=0)
	~CompactedSequence ()
const char *	get_name () const
int	length () const
const char *	text (int i=0) const
char	operator[] (int i) const
int	expdPosition (int cPos) const
int	compPosition (int xPos) const
const int *	gapsBefore (int offset=0) const
int	no_of_gaps_before (int cPos) const
int	no_of_gaps_after (int cPos) const
void	storeDots (int beforePos)
const Dots *	getDotlist () const

Detailed Description

Definition at line 70 of file seq_search.hxx.

Constructor & Destructor Documentation

CompactedSequence::CompactedSequence	(	const char *	text,
		int	length,
		const char *	name,
		int	start_offset = 0
	)

Definition at line 52 of file seq_search.cxx.

References BasePosition::abs_2_rel(), fa_assert(), BasePosition::first_base_abspos(), BasePosition::last_base_abspos(), length(), no_of_gaps_before(), BasePosition::rel_2_abs(), and storeDots().

CompactedSequence::~CompactedSequence

(

)

Definition at line 92 of file seq_search.cxx.

Member Function Documentation

const char* CompactedSequence::get_name ( ) const

inline

Definition at line 86 of file seq_search.hxx.

Referenced by CompactedSubSequence::name().

int CompactedSequence::length ( ) const

inline

Definition at line 88 of file seq_search.hxx.

References BasePosition::base_count().

Referenced by CompactedSequence(), expdPosition(), no_of_gaps_after(), and operator[]().

const char* CompactedSequence::text ( int  i = 0 ) const

inline

Definition at line 89 of file seq_search.hxx.

Referenced by operator[]().

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

inline

Definition at line 90 of file seq_search.hxx.

References length(), and text().

int CompactedSequence::expdPosition ( int  cPos ) const

inline

Definition at line 92 of file seq_search.hxx.

References BasePosition::abs_count(), fa_assert, length(), and BasePosition::rel_2_abs().

Referenced by CompactedSubSequence::expdPosition(), CompactedSubSequence::expdStartPosition(), no_of_gaps_after(), and no_of_gaps_before().

int CompactedSequence::compPosition ( int  xPos ) const

inline

Definition at line 103 of file seq_search.hxx.

References BasePosition::abs_2_rel().

Referenced by CompactedSubSequence::compPosition().

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

inline

Definition at line 108 of file seq_search.hxx.

References offset.

Referenced by CompactedSubSequence::gapsBefore().

int CompactedSequence::no_of_gaps_before ( int  cPos ) const

inline

Definition at line 110 of file seq_search.hxx.

References expdPosition().

Referenced by CompactedSequence(), and CompactedSubSequence::no_of_gaps_before().

int CompactedSequence::no_of_gaps_after ( int  cPos ) const

inline

Definition at line 121 of file seq_search.hxx.

References BasePosition::abs_count(), expdPosition(), and length().

Referenced by CompactedSubSequence::no_of_gaps_after().

void CompactedSequence::storeDots ( int  beforePos )

inline

Definition at line 133 of file seq_search.hxx.

References Dots::append().

Referenced by CompactedSequence().

const Dots* CompactedSequence::getDotlist ( ) const

inline

Definition at line 138 of file seq_search.hxx.

Referenced by CompactedSubSequence::firstDotPosition().

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

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