org.strbio.local
Class Muscle

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

public class Muscle
extends Program

Class to run Muscle

 Verions 1.1, 3/30/07 - added ability to pass other options to muscle
 Version 1.0, 11/27/06 - original version, based on ClustalW
 

Version:

1.1, 3/30/07

Author:

JMC

Field Summary

Fields inherited from class org.strbio.local.Program

processError, processInput, processOutput, PROGRAM_NAME

Constructor Summary

Muscle()

Method Summary

java.lang.String	programName() What's the name of this program?
PolymerSet	runOnPolymerSet(PolymerSet p)
PolymerSet	runOnPolymerSet(PolymerSet p, java.lang.String options) return a protein set resulting from running muscle on a protein set, with optional options to Muscle

Methods inherited from class org.strbio.local.Program

clean, 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

Muscle

public Muscle()

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 Program

runOnPolymerSet

public final PolymerSet runOnPolymerSet(PolymerSet p,
                                        java.lang.String options)

return a protein set resulting from running muscle on a protein set, with optional options to Muscle

runOnPolymerSet

public final PolymerSet runOnPolymerSet(PolymerSet p)