pal.alignment
Class JumbledAlignment

java.lang.Object
  |
  +--pal.alignment.AbstractAlignment
        |
        +--pal.alignment.JumbledAlignment
All Implemented Interfaces:
Alignment, IdGroup, Report, java.io.Serializable

public class JumbledAlignment
extends AbstractAlignment

generates jumbled alignments (randomizing input order of sequences)

See Also:
Serialized Form

Fields inherited from class pal.alignment.AbstractAlignment
dataType, frequency, idGroup, numSeqs, numSites
 
Fields inherited from interface pal.alignment.Alignment
GAP
 
Constructor Summary
JumbledAlignment(Alignment raw)
           
 
Method Summary
 char getData(int seq, int site)
          sequence alignment at (sequence, site)
 void jumble()
          jumble sequences (rearrange input order)
 
Methods inherited from class pal.alignment.AbstractAlignment
getAlignedSequenceString, getDataType, getFrequency, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getStates, guessDataType, isGap, report, setDataType, setFrequency, setIdentifier, toString, whichIdNumber
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

JumbledAlignment

public JumbledAlignment(Alignment raw)
Method Detail

getData

public char getData(int seq,
                    int site)
sequence alignment at (sequence, site)
Overrides:
getData in class AbstractAlignment

jumble

public void jumble()
jumble sequences (rearrange input order)