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:
- Runnable
public class TreeConstructor<C extends AbstractSequence<D>,D extends Compound>
- extends 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
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 |
TreeConstructor
public TreeConstructor(MultipleSequenceAlignment<C,D> multipleSequenceAlignment,
TreeType _treeType,
TreeConstructionAlgorithm _treeConstructionAlgorithm,
NJTreeProgressListener _treeProgessListener)
TreeConstructor
public TreeConstructor(DistanceMatrix _matrix,
TreeType _treeType,
TreeConstructionAlgorithm _treeConstructionAlgorithm,
NJTreeProgressListener _treeProgessListener)
outputPhylipDistances
public void outputPhylipDistances(String fileName)
throws Exception
- Throws:
Exception
getDistanceMatrix
public DistanceMatrix getDistanceMatrix()
cancel
public void cancel()
process
public void process()
throws Exception
- Throws:
Exception
run
public void run()
- Specified by:
run
in interface Runnable
- Overrides:
run
in class Thread
getNewickString
public String getNewickString(boolean simpleNewick,
boolean writeDistanceToParent)
throws Exception
- Throws:
Exception
addProgessListener
public void addProgessListener(NJTreeProgressListener treeProgessListener)
removeProgessListener
public void removeProgessListener(NJTreeProgressListener treeProgessListener)
broadcastComplete
public void broadcastComplete()
updateProgress
public void updateProgress(String state,
int percentage)
updateProgress
public void updateProgress(String state,
int currentCount,
int totalCount)
main
public static void main(String[] args)