Class MaxMismatchMatcher

java.lang.Object
org.biojava.bio.search.MaxMismatchMatcher
All Implemented Interfaces:
BioMatcher

public class MaxMismatchMatcher extends Object implements BioMatcher
A BioMatcher class returned by MaxMismatchPattern.matcher() that implements searching of a SymbolList.

This class is public only to allow access to the mismatchCount() method.

Author:
Matthew Pocock (wrote original MaxMissmatchMatcher class), David Huen (debugging and extension of functionality)
  • Method Details

    • find

      public boolean find()
      Description copied from interface: BioMatcher
      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.

      Specified by:
      find in interface BioMatcher
      Returns:
      true if there is another match
    • start

      public int start()
      Description copied from interface: BioMatcher
      Get the first symbol index that matches the pattern.
      Specified by:
      start in interface BioMatcher
      Returns:
      the start of the current match
    • end

      public int end()
      Description copied from interface: BioMatcher
      Get the last symbol index that matches the pattern.
      Specified by:
      end in interface BioMatcher
      Returns:
      the end of the current match
    • group

      public SymbolList group()
      Description copied from interface: BioMatcher
      Get the matching region as a SymbolList.
      Specified by:
      group in interface BioMatcher
      Returns:
      the matching symbols
    • mismatchCount

      public int mismatchCount()
      Returns number of mismatches