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

Nested Classes
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

Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils

Field Summary
- Fields inherited from class pal.alignment.AbstractAlignment
  idGroup, numSeqs, numSites
- Fields inherited from interface pal.alignment.Alignment
  GAP, GAP_TLA, GAPS, UNKNOWN, UNKNOWN_TLA

Constructor Summary

Constructors
Constructor Description

SimulatedAlignment(int sites, Tree t, SubstitutionModel m)
Inititalisation

Method Summary

All Methods Instance Methods Concrete Methods
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)

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

- Constructor Detail
  - SimulatedAlignment
```
public SimulatedAlignment(int sites,
                          Tree t,
                          SubstitutionModel m)
```
    Inititalisation
    
    Parameters:
    
    sites - number of sites
    
    t - tree relating the sequences
    
    m - model of evolution
- Method Detail
  - 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)