pal.alignment
Class BootstrappedAlignment

java.lang.Object
  extended by pal.alignment.AbstractAlignment
      extended by 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