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java.lang.Objectpal.alignment.AbstractAlignment
pal.alignment.BootstrappedAlignment
public class BootstrappedAlignment
generates bootstrapped alignments from a raw alignment
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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BootstrappedAlignment(Alignment raw)
Constructor |
Method Summary | |
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void |
bootstrap()
bootstrap alignment |
char |
getData(int seq,
int site)
sequence alignment at (sequence, site) |
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 BootstrappedAlignment(Alignment raw)
raw
- original alignmentMethod Detail |
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public char getData(int seq, int site)
getData
in interface Alignment
getData
in class AbstractAlignment
public void bootstrap()
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