IndelAlignment

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java.lang.Object
- pal.alignment.AbstractAlignment
- - 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
  
  Constructors
  Constructor and Description
  
  IndelAlignment(Alignment a, boolean anchored)
  Basic constructor.
- Method Summary
  
  All Methods Instance Methods Concrete Methods
  Modifier and Type Method and Description
  
  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

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