org.biojava3.phylo
public class TreeConstructor<C extends AbstractSequence<D>,D extends Compound> extends java.lang.Thread
Constructor and Description |
---|
TreeConstructor(DistanceMatrix _matrix,
TreeType _treeType,
TreeConstructionAlgorithm _treeConstructionAlgorithm,
NJTreeProgressListener _treeProgessListener) |
TreeConstructor(MultipleSequenceAlignment<C,D> multipleSequenceAlignment,
TreeType _treeType,
TreeConstructionAlgorithm _treeConstructionAlgorithm,
NJTreeProgressListener _treeProgessListener) |
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) |
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
public TreeConstructor(MultipleSequenceAlignment<C,D> multipleSequenceAlignment, TreeType _treeType, TreeConstructionAlgorithm _treeConstructionAlgorithm, NJTreeProgressListener _treeProgessListener)
public TreeConstructor(DistanceMatrix _matrix, TreeType _treeType, TreeConstructionAlgorithm _treeConstructionAlgorithm, NJTreeProgressListener _treeProgessListener)
public void outputPhylipDistances(java.lang.String fileName) throws java.lang.Exception
java.lang.Exception
public DistanceMatrix getDistanceMatrix()
public void cancel()
public void process() throws java.lang.Exception
java.lang.Exception
public void run()
run
in interface java.lang.Runnable
run
in class java.lang.Thread
public java.lang.String getNewickString(boolean simpleNewick, boolean writeDistanceToParent) throws java.lang.Exception
java.lang.Exception
public void addProgessListener(NJTreeProgressListener treeProgessListener)
public void removeProgessListener(NJTreeProgressListener treeProgessListener)
public void broadcastComplete()
public void updateProgress(java.lang.String state, int percentage)
public void updateProgress(java.lang.String state, int currentCount, int totalCount)
public static void main(java.lang.String[] args)