pal.alignment
Class GapBalancedAlignment

java.lang.Object
  extended by pal.alignment.AbstractAlignment
      extended by pal.alignment.GapBalancedAlignment
All Implemented Interfaces:
java.io.Serializable, Alignment, IdGroup, Report

public class GapBalancedAlignment
extends AbstractAlignment
implements java.io.Serializable

Creates a "Gap-Balanced" alignment.

Version:
$Id: GapBalancedAlignment.java,v 1.14 2003/04/10 05:53:47 matt Exp $
Author:
Matthew Goode
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
 
Field Summary
 
Fields inherited from class pal.alignment.AbstractAlignment
idGroup, numSeqs, numSites
 
Fields inherited from interface pal.alignment.Alignment
GAP, GAP_TLA, GAPS, UNKNOWN, UNKNOWN_TLA
 
Constructor Summary
GapBalancedAlignment(Alignment base, int startingCodonPosition, boolean alignGap)
          The standard GapBalanced constructor
GapBalancedAlignment(Alignment base, int startingCodonPosition, boolean alignGap, int codonLength)
          GapBalanced power user constructor
GapBalancedAlignment(Alignment base, int startingCodonPosition, int codonLength)
          GapBalanced power user constructor
 
Method Summary
 char getData(int seq, int site)
          sequence alignment at (sequence, site)
 
Methods inherited from class pal.alignment.AbstractAlignment
getAlignedSequenceString, getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, report, setDataType, setIdentifier, toString, whichIdNumber
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

GapBalancedAlignment

public GapBalancedAlignment(Alignment base,
                            int startingCodonPosition,
                            boolean alignGap)
The standard GapBalanced constructor

Parameters:
Alignment - on which to based this gap balanced alignment
the - estimated startingCodonPosition of the alignment

GapBalancedAlignment

public GapBalancedAlignment(Alignment base,
                            int startingCodonPosition,
                            int codonLength)
GapBalanced power user constructor

Parameters:
Alignment - on which to based this gap balanced alignment
startingCodonPosition - the starting codon position of the alignment
codonLength - the length of a codon (to make things general, - the author is a Computer Scientist)

GapBalancedAlignment

public GapBalancedAlignment(Alignment base,
                            int startingCodonPosition,
                            boolean alignGap,
                            int codonLength)
GapBalanced power user constructor

Parameters:
Alignment - on which to based this gap balanced alignment
startingCodonPosition - the starting codon position of the alignment
alignGap - sometimes a large cap may occur in the middle of a sequence's codon. If this is true than no columns can match up in this area (it's hard to explain - for safety choose true!)
codonLength - the length of a codon (to make things general, - the author is a Computer Scientist)
Method Detail

getData

public char getData(int seq,
                    int site)
sequence alignment at (sequence, site)

Specified by:
getData in interface Alignment
Specified by:
getData in class AbstractAlignment