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.UtilsidGroup, 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, whichIdNumberpublic 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 AlignmentgetData in class AbstractAlignmentpublic void simulate()
public void simulate(java.lang.String givenRootSequence)
public void simulate(byte[] rootSeq)