org.emboss.jemboss.programs
Class RunEmbossApplication2

java.lang.Object
  org.emboss.jemboss.programs.RunEmbossApplication2

public class RunEmbossApplication2

extends java.lang.Object

RunEmbossApplication2 class used to run an EMBOSS process this reads stdout and stderr in separate threads.

Nested Class Summary

(package private) class	RunEmbossApplication2.StderrHandler
(package private) class	RunEmbossApplication2.StdoutHandler

Field Summary

private java.lang.Process	p running process
private java.io.File	project running directory
private java.lang.String	status process status
private java.lang.StringBuffer	stderr standard error
private RunEmbossApplication2.StderrHandler	stderrh
private java.lang.StringBuffer	stdout standard out
private RunEmbossApplication2.StdoutHandler	stdouth
private javax.swing.JTextArea	textArea

Constructor Summary

RunEmbossApplication2(java.lang.String embossCommand, java.lang.String[] envp, java.io.File project)

RunEmbossApplication2(java.lang.String embossCommand, java.lang.String[] envp, java.io.File project, javax.swing.JTextArea textArea)

Method Summary

java.lang.Process	getProcess()
java.lang.String	getProcessStderr()
java.lang.String	getProcessStdout()
java.lang.String	getStatus()
private void	readProcessStderr() Read in the process stderr.
private void	readProcessStdout() Read in the process stdout.
void	waitFor() Wait for the process to end
private void	writeStdout() This method can be called after the process has completed to write the stdout to the project directory.

Methods inherited from class java.lang.Object

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

Field Detail

p

private java.lang.Process p

running process

stdout

private java.lang.StringBuffer stdout

standard out

stderr

private java.lang.StringBuffer stderr

standard error

project

private java.io.File project

running directory

status

private java.lang.String status

process status

stdouth

private RunEmbossApplication2.StdoutHandler stdouth

stderrh

private RunEmbossApplication2.StderrHandler stderrh

textArea

private javax.swing.JTextArea textArea

Constructor Detail

RunEmbossApplication2

public RunEmbossApplication2(java.lang.String embossCommand,
                             java.lang.String[] envp,
                             java.io.File project)

Parameters:

embossCommand - emboss command to run

envp - environment

project - running directory

RunEmbossApplication2

public RunEmbossApplication2(java.lang.String embossCommand,
                             java.lang.String[] envp,
                             java.io.File project,
                             javax.swing.JTextArea textArea)

Parameters:

embossCommand - emboss command to run

envp - environment

project - running directory

Method Detail

readProcessStderr

private void readProcessStderr()

Read in the process stderr.

readProcessStdout

private void readProcessStdout()

Read in the process stdout.

writeStdout

private void writeStdout()

This method can be called after the process has completed to write the stdout to the project directory.

getProcessStdout

public java.lang.String getProcessStdout()

Returns:

standard out

getProcessStderr

public java.lang.String getProcessStderr()

Returns:

stderr

waitFor

public void waitFor()

Wait for the process to end

getProcess

public java.lang.Process getProcess()

Returns:

process

getStatus

public java.lang.String getStatus()

Returns:

status