Package pal.alignment
Class JumbledAlignment
- java.lang.Object
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- pal.alignment.AbstractAlignment
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- pal.alignment.JumbledAlignment
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public class JumbledAlignment extends AbstractAlignment
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:
- 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 JumbledAlignment(Alignment raw)
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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)void
jumble()
jumble sequences (rearrange input order)-
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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JumbledAlignment
public JumbledAlignment(Alignment raw)
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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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jumble
public void jumble()
jumble sequences (rearrange input order)
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