Package org.biojava.bio.search

Interface BioMatcher

  • All Known Implementing Classes:
    MaxMismatchMatcher
    public interface BioMatcher
    Interface for things that perform matches.

    These will almost always be produced by a factory method on a BioPattern object.

    Author:
    Matthew Pocock

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      int end()
      Get the last symbol index that matches the pattern.
      boolean find()
      Attempt to find the next match.
      SymbolList group()
      Get the matching region as a SymbolList.
      int start()
      Get the first symbol index that matches the pattern.

    • Method Detail

      • find

        boolean find()
        Attempt to find the next match.

        If the pattern can be found, then this will return true. If it could not, then it will return false. This is convenient within for or while loops.

        Each time this is called, the next match will be found. The start() and end() values will increase each time, regardless of wether you called any other methods.

        Returns:
        true if there is another match

      • start

        int start()
        Get the first symbol index that matches the pattern.
        Returns:
        the start of the current match
        Throws:
        IllegalStateException - if there is no current match

      • end

        int end()
        Get the last symbol index that matches the pattern.
        Returns:
        the end of the current match
        Throws:
        IllegalStateException - if there is no current match