org.strbio.local
Class Minarea

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

Direct Known Subclasses:

Malfe

public class Minarea
extends Program

Class to run minarea.

 Version 1.32, 9/1/99 - split off Results into org.strbio.mol.lib.MinareaResults
 Version 1.31, 11/10/98 - renamed rms to notRMS, since it isn't.
 Version 1.3, 11/5/98 - added runOnProteins method, added
   Alignment to Results class
 Version 1.21, 10/28/98 - added makeInverseTransform to Results class
 Version 1.2, 10/19/98 - added Results class
 Version 1.1, 10/2/98 - now runs nw_minarea to avoid RMS bug
   in minarea
 Version 1.0, 4/14/98 - original version
 

Version:

1.32, 9/1/99

Author:

JMC

See Also:

Protein

Field Summary

Fields inherited from class org.strbio.local.Program

processError, processInput, processOutput, PROGRAM_NAME

Constructor Summary

Minarea()

Method Summary

void	clean(java.lang.String args) Clean files left around by minarea.
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

Minarea

public Minarea()

Method Detail

programName

public java.lang.String programName()

Description copied from class: Program

What's the name of this program?

Overrides:

programName in class Program

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 returned will be for a aligned to b.

clean

public void clean(java.lang.String args)

Clean files left around by minarea. Warning... this deletes a lot of files, including some (data1, data2, check) seemingly not related to minarea.

Overrides:

clean in class Program

Parameters:

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