CassieSearch Class Reference

#include <Cassiopee.h>

Public Member Functions
	CassieSearch (CassieIndexer *index_ref)
void	removeDuplicates ()
void	search (string suffix, bool clear)
void	search (string suffix)
void	search (string suffixes[])
bool	isequal (char a, char b)
void	sort ()

Public Attributes
Match *	match_limits
list< Match * >	matches
bool	ambiguity
int	nmax
int	mode
int	max_indel
int	max_subst
long	pattern_length

Detailed Description

Search object

Constructor & Destructor Documentation

CassieSearch::CassieSearch

(

CassieIndexer *

index_ref

)

Main constructor

Parameters

index_ref

Indexer for sequence

Member Function Documentation

bool CassieSearch::isequal	(	char	a,
		char	b
	)

Compare two chars, with ambiguity is option is set

void CassieSearch::removeDuplicates

(

)

Remove matches with same position and same length.

void CassieSearch::search	(	string	suffix,
		bool	clear
	)

Search for a string in the indexed sequence

Parameters

suffix	pattern to search
clear	Clear existing matches?

void CassieSearch::search

(

string

suffix

)

Search for a string in the indexed sequence. Clear all previous matches.

Parameters

suffix

pattern to search

void CassieSearch::search

(

string

suffixes[]

)

Search for multiple strings

Parameters

array

of patterns to search

void CassieSearch::sort

(

)

Sort matches according to positions i nascending order

Member Data Documentation

bool CassieSearch::ambiguity

Allow alphabet ambiguity search. False by default. N are by default ignored. To allow N matching, the nmax attribute must be set

Match* CassieSearch::match_limits

Used to store max errors allowed

list<Match*> CassieSearch::matches

List of positions in original sequence matching the search

int CassieSearch::max_indel

Maximum number of insertion or deletion

int CassieSearch::max_subst

Maximum number of substitution

int CassieSearch::mode

Search mode:

• 0: DNA
• 1: RNA
• 2: Protein

int CassieSearch::nmax

Allow N matching with alphabet ambiguity. nmax defines the maximum number of consecutive N allowed in match.

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

• src/Cassiopee.h
• src/cassiopee.cxx