pal.alignment
Class IndelAlignment

java.lang.Object
  extended by pal.alignment.AbstractAlignment
      extended by pal.alignment.IndelAlignment
All Implemented Interfaces:
java.io.Serializable, Alignment, IdGroup, Report
Direct Known Subclasses:
IndelAnnotatedAlignment

public class IndelAlignment
extends AbstractAlignment

This class extracts indels (insertion/deletion) out of an alignment, and creates an alignment of indel polymorphisms. It uses the NumericDataType, so that the length of each indel is recorded in the alignment. If anchored is true, then SSR-like (microsatellites) indels will be identified as the same indel locus. If anchored is false, then the same indel start and end at the exact same position.

Version:
$Id: IndelAlignment.java,v 1.4 2002/10/14 06:54:24 matt Exp $
Author:
Ed Buckler
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
IndelAlignment(Alignment a, boolean anchored)
          Basic constructor.
 
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

IndelAlignment

public IndelAlignment(Alignment a,
                      boolean anchored)
Basic constructor.

Parameters:
anchored - sets to score anchored indels as same position
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