pal.tree
public class SimulatedAlignment extends AbstractAlignment
Modifier and Type | Class and Description |
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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
|
IdGroup.Utils
idGroup, numSeqs, numSites
Constructor and Description |
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SimulatedAlignment(int sites,
Tree t,
SubstitutionModel m)
Inititalisation
|
Modifier and Type | Method and Description |
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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)
|
getAlignedSequenceString, getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, report, setDataType, setIdentifier, toString, whichIdNumber
public SimulatedAlignment(int sites, Tree t, SubstitutionModel m)
sites
- number of sitest
- tree relating the sequencesm
- model of evolutionpublic char getData(int seq, int site)
getData
in interface Alignment
getData
in class AbstractAlignment
public void simulate()
public void simulate(java.lang.String givenRootSequence)
public void simulate(byte[] rootSeq)