charite.christo.strap
Class AcceptAlignment2

java.lang.Object
  charite.christo.strap.AcceptAlignment2

public class AcceptAlignment2
extends java.lang.Object

Constructor Summary

AcceptAlignment2(Protein[] pp, int startCol, byte[][] alignment)

Method Summary

static void	delGaps(Protein[] pp, int startCol, int endCol, byte[][] alignment)
static int	eliminateCommonGaps(Protein[] pp, int startCol, int endCol, byte[][] alignment, int[] wide2narrow)
int[]	getCountInserts()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AcceptAlignment2

public AcceptAlignment2(Protein[] pp,
                        int startCol,
                        byte[][] alignment)

Method Detail

eliminateCommonGaps

public static int eliminateCommonGaps(Protein[] pp,
                                      int startCol,
                                      int endCol,
                                      byte[][] alignment,
                                      int[] wide2narrow)

delGaps

public static void delGaps(Protein[] pp,
                           int startCol,
                           int endCol,
                           byte[][] alignment)

getCountInserts

public int[] getCountInserts()