Class MaxMismatchPattern

  • All Implemented Interfaces:
    BioPattern

    public class MaxMismatchPattern
    extends java.lang.Object
    implements BioPattern
    This class permits searching a SymbolList with another SymbolList while permitting a specified number of mismatches. The search pattern can include ambiguity Symbols.
    Author:
    Matthew Pocock (wrote original MaxMissmatchPattern class), David Huen (debugging and extension to permit ambiguity symbols)
    • Constructor Detail

      • MaxMismatchPattern

        public MaxMismatchPattern()
      • MaxMismatchPattern

        public MaxMismatchPattern​(SymbolList pattern,
                                  int mismatches)
    • Method Detail

      • getMismatches

        public int getMismatches()
      • setMismatches

        public void setMismatches​(int mismatches)
      • setPattern

        public void setPattern​(SymbolList pattern)
      • matcher

        public BioMatcher matcher​(SymbolList symList)
                           throws IllegalAlphabetException
        Description copied from interface: BioPattern
        Get a matcher that will use these parameters to search a SymbolList.

        The resulting BioMatcher is independant of this BioPattern. In particular, calling any mutator methods on this pattern will not affect the matcher.

        Specified by:
        matcher in interface BioPattern
        Parameters:
        symList - the SymbolList to match against
        Returns:
        a BioMatcher that will perform the search
        Throws:
        IllegalAlphabetException - if symList is not over the right alphabet