pal.alignment
Class ConcatenatedAlignment

java.lang.Object
  |
  +--pal.alignment.AbstractAlignment
        |
        +--pal.alignment.ConcatenatedAlignment
All Implemented Interfaces:
Alignment, IdGroup, Report, java.io.Serializable

public class ConcatenatedAlignment
extends AbstractAlignment

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

See Also:
Serialized Form

Fields inherited from class pal.alignment.AbstractAlignment
dataType, frequency, idGroup, numSeqs, numSites
 
Fields inherited from interface pal.alignment.Alignment
GAP
 
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, getDataType, getFrequency, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getStates, guessDataType, isGap, report, setDataType, setFrequency, 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
Method Detail

getData

public char getData(int seq,
                    int site)
sequence alignment at (sequence, site)
Overrides:
getData in class AbstractAlignment