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java.lang.Object | +--pal.alignment.AbstractAlignment | +--pal.alignment.JumbledAlignment
generates jumbled alignments (randomizing input order of sequences)
Fields inherited from class pal.alignment.AbstractAlignment |
dataType, frequency, idGroup, numSeqs, numSites |
Fields inherited from interface pal.alignment.Alignment |
GAP |
Constructor Summary | |
JumbledAlignment(Alignment raw)
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Method Summary | |
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, getDataType, getFrequency, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getStates, guessDataType, isGap, report, setDataType, setFrequency, setIdentifier, toString, whichIdNumber |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
public JumbledAlignment(Alignment raw)
Method Detail |
public char getData(int seq, int site)
getData
in class AbstractAlignment
public void jumble()
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