pal.alignment
Class BootstrappedAlignment

java.lang.Object
  pal.alignment.AbstractAlignment
      pal.alignment.BootstrappedAlignment

All Implemented Interfaces:

java.io.Serializable, Alignment, IdGroup, Report

public class BootstrappedAlignment
extends AbstractAlignment

generates bootstrapped alignments from a raw alignment

Version:

$Id: BootstrappedAlignment.java,v 1.6 2003/03/23 00:12:57 matt Exp $

Author:

Korbinian Strimmer

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

BootstrappedAlignment(Alignment raw)
Constructor

Method Summary

void	bootstrap() bootstrap alignment
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

BootstrappedAlignment

public BootstrappedAlignment(Alignment raw)

Constructor

Parameters:

raw - original alignment

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

bootstrap

public void bootstrap()

bootstrap alignment