Public Member Functions | List of all members
FastSearchSequence Class Reference

#include <seq_search.hxx>

Inheritance diagram for FastSearchSequence:
Inheritance graph
Collaboration diagram for FastSearchSequence:
Collaboration graph

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 CompactedSubSequencesequence () const
const TripleOffsetfind (const char *triple) const

Detailed Description

Definition at line 481 of file seq_search.hxx.

Constructor & Destructor Documentation

FastSearchSequence::FastSearchSequence ( const CompactedSubSequence seq)
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
const CompactedSubSequence& FastSearchSequence::sequence ( ) const

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

Definition at line 505 of file seq_search.hxx.

Referenced by FastSearchOccurrence::FastSearchOccurrence().

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