Cassiopee  1.0
Suffix indexer and search tool
Public Member Functions | Public Attributes | List of all members
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

map< std::string, string > morphisms
 
Matchmatch_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::CassieSearch ( CassieIndexer index_ref)

Main constructor

Parameters
index_refIndexer for sequence

Member Function Documentation

◆ isequal()

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

Compare two chars, with ambiguity is option is set

◆ removeDuplicates()

void CassieSearch::removeDuplicates ( )

Remove matches with same position and same length.

◆ search() [1/3]

void CassieSearch::search ( string  suffix)

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

Parameters
suffixpattern to search

◆ search() [2/3]

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

Search for a string in the indexed sequence

Parameters
suffixpattern to search
clearClear existing matches?

◆ search() [3/3]

void CassieSearch::search ( string  suffixes[])

Search for multiple strings

Parameters
arrayof patterns to search

◆ sort()

void CassieSearch::sort ( )

Sort matches according to positions i nascending order

Member Data Documentation

◆ ambiguity

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_limits

Match* CassieSearch::match_limits

Used to store max errors allowed

◆ matches

list<Match*> CassieSearch::matches

List of positions in original sequence matching the search

◆ max_indel

int CassieSearch::max_indel

Maximum number of insertion or deletion

◆ max_subst

int CassieSearch::max_subst

Maximum number of substitution

◆ mode

int CassieSearch::mode

Search mode:

  • 0: DNA
  • 1: RNA
  • 2: Protein

◆ nmax

int CassieSearch::nmax

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


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