org.biojava.utils.regex
Class Search

java.lang.Object
  extended by org.biojava.utils.regex.Search

public class Search
extends java.lang.Object

A utility class to make searching a Sequence with many regex patterns easier.

Since:
1.4
Author:
David Huen

Nested Class Summary
static interface Search.Listener
          Interface for a class that will recieve match information from this class.
 
Constructor Summary
Search(FiniteAlphabet alfa)
           
 
Method Summary
 void addPattern(java.lang.String patternString, boolean overlap)
          add a search pattern to the searches to be conducted by this object.
 void addPattern(java.lang.String label, java.lang.String patternString, boolean overlap)
          add a search pattern to the searches to be conducted by this object.
 char charValue(Symbol sym)
           
 void clearPatterns()
          remove all patterns from the pattern cache.
 void search(SymbolList seq)
          search the Sequence with the patterns already registered with this object.
 void search(SymbolList seq, int loLimit, int hiLimit)
          search part of the SymbolList with the patterns already registered with this object.
 void setListener(Search.Listener listener)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Search

public Search(FiniteAlphabet alfa)
Method Detail

setListener

public void setListener(Search.Listener listener)

addPattern

public void addPattern(java.lang.String patternString,
                       boolean overlap)
                throws RegexException,
                       IllegalAlphabetException
add a search pattern to the searches to be conducted by this object.

Parameters:
patternString - String representation of the pattern.
overlap - if true, the search continues at the base following the start to the previous hit. If false, it continues at the base after the existing hit.
Throws:
RegexException - if the requested pattern is not valid
IllegalAlphabetException - if the requested pattern is not valid

addPattern

public void addPattern(java.lang.String label,
                       java.lang.String patternString,
                       boolean overlap)
                throws RegexException,
                       IllegalAlphabetException
add a search pattern to the searches to be conducted by this object.

Parameters:
patternString - String representation of the pattern.
overlap - if true, the search continues at the base following the start to the previous hit. If false, it continues at the base after the existing hit.
Throws:
RegexException - if the requested pattern is not valid
IllegalAlphabetException - if the requested pattern is not valid

clearPatterns

public void clearPatterns()
remove all patterns from the pattern cache.


charValue

public char charValue(Symbol sym)
               throws IllegalSymbolException
Throws:
IllegalSymbolException

search

public void search(SymbolList seq)
search the Sequence with the patterns already registered with this object.


search

public void search(SymbolList seq,
                   int loLimit,
                   int hiLimit)
search part of the SymbolList with the patterns already registered with this object.

Parameters:
loLimit - low limit of search range.
hiLimit - high limit of search range.