Package org.biojava.utils.regex

Class Search

java.lang.Object
org.biojava.utils.regex.Search
public class Search extends Object
A utility class to make searching a Sequence with many regex patterns easier.
Since:
1.4
Author:
David Huen

  • Constructor Details

  • Method Details

    • setListener

      public void setListener(Search.Listener listener)

    • addPattern

      public void addPattern(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(String label, 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.