Package pal.alignment
Class IndelAlignment
java.lang.Object
pal.alignment.AbstractAlignment
pal.alignment.IndelAlignment
- All Implemented Interfaces:
Serializable
,Alignment
,IdGroup
,Report
- Direct Known Subclasses:
IndelAnnotatedAlignment
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:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Field Summary
Fields inherited from class pal.alignment.AbstractAlignment
idGroup, numSeqs, numSites
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionchar
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 Details
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IndelAlignment
Basic constructor.- Parameters:
anchored
- sets to score anchored indels as same position
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Method Details
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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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