FastSearchSequence Class Reference

#include <seq_search.hxx>

Inheritance diagram for FastSearchSequence:

Collaboration diagram for FastSearchSequence:

Public Member Functions
	FastSearchSequence (const CompactedSubSequence &seq)
	~FastSearchSequence ()
ARB_ERROR	fast_align (const CompactedSubSequence &align_to, AlignBuffer *alignBuffer, int max_seq_length, int matchScore, int mismatchScore, FastAlignReport *report) const
const CompactedSubSequence &	sequence () const
const TripleOffset *	find (const char *triple) const

Detailed Description

Definition at line 481 of file seq_search.hxx.

Constructor & Destructor Documentation

FastSearchSequence::FastSearchSequence

(

const CompactedSubSequence &

seq

)

Definition at line 103 of file seq_search.cxx.

References SequencePosition::leftOf(), MAX_TRIPLES, SequencePosition::rightOf(), seq, and SequencePosition::text().

FastSearchSequence::~FastSearchSequence

(

)

Definition at line 118 of file seq_search.cxx.

References MAX_TRIPLES.

Member Function Documentation

ARB_ERROR FastSearchSequence::fast_align	(	const CompactedSubSequence &	align_to,
		AlignBuffer *	alignBuffer,
		int	max_seq_length,
		int	matchScore,
		int	mismatchScore,
		FastAlignReport *	report
	)		const

Definition at line 807 of file fast_aligner.cxx.

References CAN_SCORE_LEFT, CAN_SCORE_RIGHT, cannot_fast_align(), error(), fast_align(), insertAligned(), SequencePosition::leftOf(), length, CompactedSubSequence::length(), log3(), MIN_ALIGNMENT_RANGE, NULp, offset, AlignBuffer::offset(), partSignificance(), SequencePosition::rightOf(), SCORE_LEFT, SCORE_RIGHT, sequence(), SequencePosition::text(), and AlignBuffer::text().

Referenced by alignCompactedTo(), and fast_align().

const CompactedSubSequence& FastSearchSequence::sequence ( ) const

inline

Definition at line 504 of file seq_search.hxx.

Referenced by alignCompactedTo(), fast_align(), and FastSearchOccurrence::sequence().

const TripleOffset* FastSearchSequence::find ( const char *  triple ) const

inline

Definition at line 505 of file seq_search.hxx.

Referenced by FastSearchOccurrence::FastSearchOccurrence().

---

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

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