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

Fields inherited from class pal.alignment.AbstractAlignment
dataType, frequency, idGroup, numSeqs, numSites
 
Fields inherited from interface pal.alignment.Alignment
GAP
 
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, 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
 

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)
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)