Package pal.tree
Class SimulatedAlignment
- java.lang.Object
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- pal.alignment.AbstractAlignment
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- pal.tree.SimulatedAlignment
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public class SimulatedAlignment extends AbstractAlignment
generates an artificial data set- Version:
- $Id: SimulatedAlignment.java,v 1.19 2003/03/23 00:21:33 matt Exp $
- Author:
- Korbinian Strimmer, Alexei Drummond
- See Also:
- Serialized Form
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
SimulatedAlignment.Factory
A utility class that can be used to generate Simulated alignments based on a tree with predefined sequence length and substitution model-
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 SimulatedAlignment(int sites, Tree t, SubstitutionModel m)
Inititalisation
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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
simulate()
generate new artificial data set (random root sequence)void
simulate(byte[] rootSeq)
generate new artificial data set (specified root sequence)void
simulate(java.lang.String givenRootSequence)
generate new artificial data set (random root sequence)-
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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SimulatedAlignment
public SimulatedAlignment(int sites, Tree t, SubstitutionModel m)
Inititalisation- Parameters:
sites
- number of sitest
- tree relating the sequencesm
- model of evolution
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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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simulate
public void simulate()
generate new artificial data set (random root sequence)
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simulate
public void simulate(java.lang.String givenRootSequence)
generate new artificial data set (random root sequence)
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simulate
public void simulate(byte[] rootSeq)
generate new artificial data set (specified root sequence)
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