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

Nested Class Summary

Nested classes inherited from class 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

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, 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

JumbledAlignment

public JumbledAlignment(Alignment raw)

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

jumble

public void jumble()

jumble sequences (rearrange input order)