IMPACT_S

Class PhyMLTask

java.lang.Object

javax.swing.SwingWorker<java.lang.String,java.lang.Void>

IMPACT_S.PhyMLTask

All Implemented Interfaces:

java.lang.Runnable, java.util.concurrent.Future<java.lang.String>, java.util.concurrent.RunnableFuture<java.lang.String>

public class PhyMLTask
extends javax.swing.SwingWorker<java.lang.String,java.lang.Void>

Implementation of a background task for PhyML execution.

Author:

Emanuel Maldonado

See Also:

GUIAlignmentEditor, GUIPhyMLOptions, AlignmentEditor, GUI, CodemlTP

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.SwingWorker

javax.swing.SwingWorker.StateValue

Constructor Summary

Constructors

Constructor and Description
PhyMLTask(java.lang.String location, java.lang.String seqfile, java.lang.String[] options, int pmlen) Initialize PhyML Task.

Method Summary

Modifier and Type	Method and Description
protected java.lang.String	doInBackground()
protected void	done()
java.lang.String	getCommand() Get complete command previously initialized in constructor, to string.
int	getCurrent() Get current value for display progress bar and/or monitor. It returns only the value that is greater than the previous one.
java.lang.String	getMessage() Get formated message of elapsed time since beginning of execution.
java.lang.String	getOutput() Get output resulting from terminated execution.
boolean	gotError() Verify if execution terminated with an error.
boolean	isdone() Verify if task has terminated.
void	stop() Stop PhyML execution.

Methods inherited from class javax.swing.SwingWorker

addPropertyChangeListener, cancel, execute, firePropertyChange, get, get, getProgress, getPropertyChangeSupport, getState, isCancelled, isDone, process, publish, removePropertyChangeListener, run, setProgress

Methods inherited from class java.lang.Object

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

Constructor Detail

PhyMLTask

public PhyMLTask(java.lang.String location,
                 java.lang.String seqfile,
                 java.lang.String[] options,
                 int pmlen)

Initialize PhyML Task. Build execution command using following parameters.

Parameters:

location - PhyML executable absolute path location.

seqfile - sequence absolute path file location.

options - user phyml options.

pmlen - maximum value of progress bar and/or monitor.

Method Detail

getCommand

public java.lang.String getCommand()

Get complete command previously initialized in constructor, to string.

Returns:

command.

doInBackground

protected java.lang.String doInBackground()

Specified by:

doInBackground in class javax.swing.SwingWorker<java.lang.String,java.lang.Void>

done

protected void done()

Overrides:

done in class javax.swing.SwingWorker<java.lang.String,java.lang.Void>

isdone

public boolean isdone()

Verify if task has terminated. While task not terminated performs operations on several values.

Returns:

true if task is done. false otherwise.

gotError

public boolean gotError()

Verify if execution terminated with an error.

Returns:

true if error occurred; false otherwise.

getCurrent

public int getCurrent()

Get current value for display progress bar and/or monitor.
It returns only the value that is greater than the previous one.

Returns:

display value.

getMessage

public java.lang.String getMessage()

Get formated message of elapsed time since beginning of execution.

Returns:

message.

getOutput

public java.lang.String getOutput()

Get output resulting from terminated execution.

Returns:

program output; null execution while not terminated.

stop

public void stop()

Stop PhyML execution.