pal.tree
Class SimulatedAlignment

java.lang.Object
  extended by pal.alignment.AbstractAlignment
      extended by 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
 
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
SimulatedAlignment(int sites, Tree t, SubstitutionModel m)
          Inititalisation
 
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
 

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)