pal.tree
Class SimulatedAlignment
java.lang.Object
pal.alignment.AbstractAlignment
pal.tree.SimulatedAlignment
- All Implemented Interfaces:
- java.io.Serializable, Alignment, IdGroup, Report
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
Nested Class Summary |
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 |
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, getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, report, setDataType, 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)
- Specified by:
getData
in interface Alignment
- Specified by:
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)