pal.alignment
Class ConcatenatedAlignment

java.lang.Object
  pal.alignment.AbstractAlignment
      pal.alignment.ConcatenatedAlignment

All Implemented Interfaces:

java.io.Serializable, Alignment, IdGroup, Report

public class ConcatenatedAlignment
extends AbstractAlignment

concatenates a list of alignments to one single alignment, increasing the number of sites

Version:

$Id: ConcatenatedAlignment.java,v 1.3 2001/07/13 14:39:12 korbinian 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

ConcatenatedAlignment(Alignment[] list)
concatenate alignments

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

ConcatenatedAlignment

public ConcatenatedAlignment(Alignment[] list)
                      throws java.lang.IllegalArgumentException

concatenate alignments

Parameters:

Alignment - array with alignment to concatenate

Throws:

java.lang.IllegalArgumentException

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