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java.lang.Objectpal.alignment.AbstractAlignment
pal.alignment.JumbledAlignment
public class JumbledAlignment
generates jumbled alignments (randomizing input order of sequences)
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.misc.IdGroup |
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IdGroup.Utils |
Field Summary |
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Fields inherited from class pal.alignment.AbstractAlignment |
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idGroup, numSeqs, numSites |
Fields inherited from interface pal.alignment.Alignment |
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GAP, GAP_TLA, GAPS, UNKNOWN, UNKNOWN_TLA |
Constructor Summary | |
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JumbledAlignment(Alignment raw)
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Method Summary | |
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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 |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public JumbledAlignment(Alignment raw)
Method Detail |
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public char getData(int seq, int site)
getData
in interface Alignment
getData
in class AbstractAlignment
public void jumble()
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