org.biojava3.phylo

Class TreeConstructor<C extends AbstractSequence<D>,D extends Compound>

java.lang.Object

java.lang.Thread

org.biojava3.phylo.TreeConstructor<C,D>

All Implemented Interfaces:

java.lang.Runnable

public class TreeConstructor<C extends AbstractSequence<D>,D extends Compound>
extends java.lang.Thread

Tree constructor uses the forrester tree library to build phylogenetic trees using neighbor joining algorithm. The distance matrix is calculated using code from JalView.

Author:

Scooter Willis

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors

Constructor and Description
TreeConstructor(BasicSymmetricalDistanceMatrix _matrix, TreeType _treeType, TreeConstructionAlgorithm _treeConstructionAlgorithm, NJTreeProgressListener _treeProgessListener)
TreeConstructor(MultipleSequenceAlignment<C,D> multipleSequenceAlignment, TreeType _treeType, TreeConstructionAlgorithm _treeConstructionAlgorithm, NJTreeProgressListener _treeProgessListener)

Method Summary

Methods

Modifier and Type	Method and Description
void	addProgessListener(NJTreeProgressListener treeProgessListener)
void	broadcastComplete()
void	cancel()
DistanceMatrix	getDistanceMatrix()
java.lang.String	getNewickString(boolean simpleNewick, boolean writeDistanceToParent)
static void	main(java.lang.String[] args)
void	outputPhylipDistances(java.lang.String fileName)
void	process()
void	removeProgessListener(NJTreeProgressListener treeProgessListener)
void	run()
void	updateProgress(java.lang.String state, int percentage)
void	updateProgress(java.lang.String state, int currentCount, int totalCount)

Methods inherited from class java.lang.Thread

activeCount, checkAccess, clone, countStackFrames, currentThread, destroy, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, stop, suspend, toString, yield

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

TreeConstructor

public TreeConstructor(MultipleSequenceAlignment<C,D> multipleSequenceAlignment,
               TreeType _treeType,
               TreeConstructionAlgorithm _treeConstructionAlgorithm,
               NJTreeProgressListener _treeProgessListener)

TreeConstructor

public TreeConstructor(BasicSymmetricalDistanceMatrix _matrix,
               TreeType _treeType,
               TreeConstructionAlgorithm _treeConstructionAlgorithm,
               NJTreeProgressListener _treeProgessListener)

Method Detail

outputPhylipDistances

public void outputPhylipDistances(java.lang.String fileName)
                           throws java.lang.Exception

Throws:

java.lang.Exception

getDistanceMatrix

public DistanceMatrix getDistanceMatrix()

cancel

public void cancel()

process

public void process()
             throws java.lang.Exception

Throws:

java.lang.Exception

run

public void run()

Specified by:

run in interface java.lang.Runnable

Overrides:

run in class java.lang.Thread

getNewickString

public java.lang.String getNewickString(boolean simpleNewick,
                               boolean writeDistanceToParent)
                                 throws java.lang.Exception

Throws:

java.lang.Exception

addProgessListener

public void addProgessListener(NJTreeProgressListener treeProgessListener)

removeProgessListener

public void removeProgessListener(NJTreeProgressListener treeProgessListener)

broadcastComplete

public void broadcastComplete()

updateProgress

public void updateProgress(java.lang.String state,
                  int percentage)

updateProgress

public void updateProgress(java.lang.String state,
                  int currentCount,
                  int totalCount)

main

public static void main(java.lang.String[] args)