org.strbio.local
Class Malfe

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

public class Malfe
extends Minarea

Class to run new minarea front end malfe.

 Version 1.1, 9/8/99 - fixed to adapt to new MinareaResults class
 Version 1.0, 11/5/98 - original version
 

Version:

1.1, 9/8/99

Author:

JMC

See Also:

Protein

Field Summary

Fields inherited from class org.strbio.local.Program

processError, processInput, processOutput, PROGRAM_NAME

Constructor Summary

Malfe()

Method Summary

void	clean(java.lang.String args) malfe doesn't leave stuff lying around.
java.lang.String	programName() What's the name of this program?
MinareaResults	runOnProteins(Protein a, Protein b) Return a set of results, including alignment.

Methods inherited from class org.strbio.local.Program

exists, run, runBackground, runSilent, setError, setInput, setOutput, setProgramName

Methods inherited from class java.lang.Object

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

Constructor Detail

Malfe

public Malfe()

Method Detail

programName

public final java.lang.String programName()

Description copied from class: Program

What's the name of this program?

Overrides:

programName in class Minarea

runOnProteins

public MinareaResults runOnProteins(Protein a,
                                    Protein b)

Return a set of results, including alignment. The second protein will be transformed onto the first. Alignment Vector returned will be for a aligned to b.

Overrides:

runOnProteins in class Minarea

clean

public void clean(java.lang.String args)

malfe doesn't leave stuff lying around.

Overrides:

clean in class Minarea

Parameters:

args - the command file passed by -i to minarea. It also gets deleted.