org.strbio.local
Class ClustalW

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

public class ClustalW
extends Program

Class to run clustalw

 Version 1.0, 8/21/01 - original version
 

Version:

1.0, 8/21/01

Author:

JMC

See Also:

Protein

Field Summary

Fields inherited from class org.strbio.local.Program

processError, processInput, processOutput, PROGRAM_NAME

Constructor Summary

ClustalW()

Method Summary

Profile	getProfile(java.lang.String raw) return the profile stored in the raw clustal output
java.lang.String	programName() What's the name of this program?
java.lang.String	runOnProteinSet(ProteinSet p) return a string containing the raw output (aln file) from running clustalw on a protein set

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

ClustalW

public ClustalW()

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

runOnProteinSet

public final java.lang.String runOnProteinSet(ProteinSet p)

return a string containing the raw output (aln file) from running clustalw on a protein set

getProfile

public final Profile getProfile(java.lang.String raw)

return the profile stored in the raw clustal output