pal.alignment
Class ConcatenatedAlignment

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