Package pal.alignment
Class JumbledAlignment
java.lang.Object
pal.alignment.AbstractAlignment
pal.alignment.JumbledAlignment
- All Implemented Interfaces:
Serializable
,Alignment
,IdGroup
,Report
generates jumbled alignments (randomizing input order of sequences)
- Version:
- $Id: JumbledAlignment.java,v 1.4 2001/07/13 14:39:12 korbinian Exp $
- Author:
- Korbinian Strimmer, Alexei Drummond
- 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
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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JumbledAlignment
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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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jumble
public void jumble()jumble sequences (rearrange input order)
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