Public Member Functions | List of all members
CompactedSequence Class Reference

#include <seq_search.hxx>

Inheritance diagram for CompactedSequence:
Inheritance graph
Collaboration diagram for CompactedSequence:
Collaboration graph

Public Member Functions

 CompactedSequence (const char *text, int length, const char *name, int start_offset=0)
 ~CompactedSequence ()
const charget_name () const
int length () const
const chartext (int i=0) const
char operator[] (int i) const
int expdPosition (int cPos) const
int compPosition (int xPos) const
const intgapsBefore (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 DotsgetDotlist () 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 
CompactedSequence::~CompactedSequence ( )

Definition at line 92 of file seq_search.cxx.

Member Function Documentation

const char* CompactedSequence::get_name ( ) const

Definition at line 86 of file seq_search.hxx.

Referenced by CompactedSubSequence::name().

int CompactedSequence::length ( ) const

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

Definition at line 89 of file seq_search.hxx.

Referenced by operator[]().

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

Definition at line 90 of file seq_search.hxx.

References length(), and text().

int CompactedSequence::expdPosition ( int  cPos) const
int CompactedSequence::compPosition ( int  xPos) const

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

Definition at line 108 of file seq_search.hxx.

References offset.

Referenced by CompactedSubSequence::gapsBefore().

int CompactedSequence::no_of_gaps_before ( int  cPos) const

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
void CompactedSequence::storeDots ( int  beforePos)

Definition at line 133 of file seq_search.hxx.

References Dots::append().

Referenced by CompactedSequence().

const Dots* CompactedSequence::getDotlist ( ) const

Definition at line 138 of file seq_search.hxx.

Referenced by CompactedSubSequence::firstDotPosition().

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