Package pal.tree
Class SimulatedAlignment
java.lang.Object
pal.alignment.AbstractAlignment
pal.tree.SimulatedAlignment
- All Implemented Interfaces:
Serializable
,Alignment
,IdGroup
,Report
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:
-
Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic final class
A utility class that can be used to generate Simulated alignments based on a tree with predefined sequence length and substitution modelNested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
-
Field Summary
Fields inherited from class pal.alignment.AbstractAlignment
idGroup, numSeqs, numSites
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionchar
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
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
-
Constructor Details
-
SimulatedAlignment
Inititalisation- Parameters:
sites
- number of sitest
- tree relating the sequencesm
- model of evolution
-
-
Method Details
-
getData
public char getData(int seq, int site) sequence alignment at (sequence, site)- Specified by:
getData
in interfaceAlignment
- Specified by:
getData
in classAbstractAlignment
-
simulate
public void simulate()generate new artificial data set (random root sequence) -
simulate
generate new artificial data set (random root sequence) -
simulate
public void simulate(byte[] rootSeq) generate new artificial data set (specified root sequence)
-