hultig.align
Class SimpleChaining

java.lang.Object
  extended by hultig.align.SimpleChaining

public class SimpleChaining
extends Object

NOT YET WELL COMMENTED.


Nested Class Summary
static class SimpleChaining.Match
          Match class defintion
 
Field Summary
static Comparator FROMA_COMPARATOR
           
 
Constructor Summary
SimpleChaining()
           
 
Method Summary
static List chaining(List matches, boolean debug)
          Identify the best chain from given list of match
static void main(String[] args)
           
static void printLowerMatrix(double[] m, int size)
          System out the input array as an strict lower diagonal matrix
static void test()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

FROMA_COMPARATOR

public static Comparator FROMA_COMPARATOR
Constructor Detail

SimpleChaining

public SimpleChaining()
Method Detail

chaining

public static List chaining(List matches,
                            boolean debug)
Identify the best chain from given list of match

Parameters:
matches - a list of match
debug - if true, print list of input match, adjacency, score matrix, best chain found.
Returns:
the optimal chain as a list of match

printLowerMatrix

public static void printLowerMatrix(double[] m,
                                    int size)
System out the input array as an strict lower diagonal matrix


test

public static void test()

main

public static void main(String[] args)