org.strbio.local
Class Program

java.lang.Object
  org.strbio.local.Program

Direct Known Subclasses:

Access, BlastPAdapter, ClustalW, DSSP, Ls, MaxSub, Melting, Mfold, Minarea, Modeller, Muscle, Primer3, VarTom

public class Program
extends java.lang.Object

Class to run a program on the local system.

 Version 2.01, 6/14/06 - fixed comments, removed debugging messages
 Version 2.0, 10/3/02 - works with more modern Java, doesn't
   require a new class for each program that's run.
 Version 1.0, 4/22/98 - original version
 

Version:

2.01, 6/14/06

Author:

JMC

Field Summary

java.io.OutputStream	processError Stream for program to write error to; default System.err.
java.io.InputStream	processInput Stream for program to take input from; default none.
java.io.OutputStream	processOutput Stream for program to write output to; default System.out.
java.lang.String	PROGRAM_NAME What's the name of this program?

Constructor Summary

Program()
Default constructor doesn't know program name; must setProgramName to work

Program(java.lang.String programName)
constructor with program name

Method Summary

void	clean(java.lang.String args) Clean up files left around after running the program with a given argument string.
boolean	exists() Can we run the program on this system?
java.lang.String	programName() What's the name of this program?
void	run(java.lang.String args) Run program with specified arguments, in foreground; both stdout and stdin are redirected to the
java.lang.Process	runBackground(java.lang.String args) Run program with specified arguments, in background, quietly.
void	runSilent(java.lang.String args) Run program with specified arguments, quietly.
void	setError(java.io.OutputStream error) redirect process error to a given stream
void	setInput(java.io.InputStream input) redirect process input from a given stream
void	setOutput(java.io.OutputStream output) redirect process output to a given stream
void	setProgramName(java.lang.String s) Set the name of this program

Methods inherited from class java.lang.Object

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

Field Detail

processInput

public java.io.InputStream processInput

Stream for program to take input from; default none.

processOutput

public java.io.OutputStream processOutput

Stream for program to write output to; default System.out.

processError

public java.io.OutputStream processError

Stream for program to write error to; default System.err.

PROGRAM_NAME

public java.lang.String PROGRAM_NAME

What's the name of this program?

Constructor Detail

Program

public Program()

Default constructor doesn't know program name; must setProgramName to work

Program

public Program(java.lang.String programName)

constructor with program name

Method Detail

setInput

public void setInput(java.io.InputStream input)

redirect process input from a given stream

setOutput

public void setOutput(java.io.OutputStream output)

redirect process output to a given stream

setError

public void setError(java.io.OutputStream error)

redirect process error to a given stream

programName

public java.lang.String programName()

What's the name of this program?

setProgramName

public void setProgramName(java.lang.String s)

Set the name of this program

exists

public boolean exists()

Can we run the program on this system? This doesn't work in Java 1.1.

run

public void run(java.lang.String args)

Run program with specified arguments, in foreground; both stdout and stdin are redirected to the

runSilent

public void runSilent(java.lang.String args)

Run program with specified arguments, quietly.

runBackground

public java.lang.Process runBackground(java.lang.String args)
                                throws java.io.IOException

Run program with specified arguments, in background, quietly. Returns Process. You have to control the process, i.e. waitFor() it to finish or kill it when done with it.

Throws:

java.io.IOException

clean

public void clean(java.lang.String args)

Clean up files left around after running the program with a given argument string.