public class SimulatedAlignment extends AbstractAlignment
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
|
IdGroup.Utils
idGroup, numSeqs, numSites
Constructor | Description |
---|---|
SimulatedAlignment(int sites,
Tree t,
SubstitutionModel m) |
Inititalisation
|
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)
|
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)