Package pal.alignment
Class IndelAlignment
- java.lang.Object
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- pal.alignment.AbstractAlignment
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- pal.alignment.IndelAlignment
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- 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
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Field Summary
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Fields inherited from class pal.alignment.AbstractAlignment
idGroup, numSeqs, numSites
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Constructor Summary
Constructors Constructor Description IndelAlignment(Alignment a, boolean anchored)
Basic constructor.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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
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Constructor Detail
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IndelAlignment
public IndelAlignment(Alignment a, boolean anchored)
Basic constructor.- Parameters:
anchored
- sets to score anchored indels as same position
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Method Detail
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getData
public char getData(int seq, int site)
sequence alignment at (sequence, site)- Specified by:
getData
in interfaceAlignment
- Specified by:
getData
in classAbstractAlignment
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