pal.tree
Class SimulatedAlignment
java.lang.Object
|
+--pal.alignment.AbstractAlignment
|
+--pal.tree.SimulatedAlignment
- All Implemented Interfaces:
- Alignment, IdGroup, Report, java.io.Serializable
- public class SimulatedAlignment
- extends AbstractAlignment
generates an artificial data set
- See Also:
- Serialized Form
Method Summary |
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, getDataType, getFrequency, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getStates, guessDataType, isGap, report, setDataType, setFrequency, setIdentifier, toString, whichIdNumber |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
SimulatedAlignment
public SimulatedAlignment(int sites,
Tree t,
SubstitutionModel m)
- Inititalisation
- Parameters:
sites
- number of sitest
- tree relating the sequencesm
- model of evolution
getData
public char getData(int seq,
int site)
- sequence alignment at (sequence, site)
- Overrides:
getData
in class AbstractAlignment
simulate
public void simulate()
- generate new artificial data set (random root sequence)
simulate
public void simulate(java.lang.String givenRootSequence)
- generate new artificial data set (random root sequence)
simulate
public void simulate(byte[] rootSeq)
- generate new artificial data set (specified root sequence)