org.biojava.bio.search
Class MaxMismatchMatcher

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

public class MaxMismatchMatcher
extends java.lang.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 Summary
 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 mismatchCount()
          Returns number of mismatches
 int start()
          Get the first symbol index that matches the pattern.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Method Detail

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