org.strbio.mol.lib
Class JMCThreadMethod2

java.lang.Object
  org.strbio.mol.lib.JMCThreadMethod2

All Implemented Interfaces:

ThreadMethod

public class JMCThreadMethod2
extends java.lang.Object
implements ThreadMethod

JMC's global threading method, based on a combination of methods.

  Version 1.1, 3/6/00 - better handling of extraLibrary
  Version 1.0, 2/17/00 - original version
  

Version:

1.1, 3/6/00

Author:

JMC

Field Summary

protected PSIBlast	blast
protected FoldLibrary	extraLibrary
protected boolean	includeOriginal
protected FoldLibrary	library

Constructor Summary

JMCThreadMethod2()
Use the default fold library.

JMCThreadMethod2(FoldLibrary lib)
Use a user-specified fold library.

JMCThreadMethod2(FoldLibrary baseLib, FoldLibrary extraLib, PSIBlast b)
Use a user-specified base library, extra library and psiblast method.

JMCThreadMethod2(FoldLibrary lib, PSIBlast b)
Use a user-specified library and psiblast method

JMCThreadMethod2(PSIBlast b)
Use a user-specified psiblast method

Method Summary

void	setBaseLibrary(FoldLibrary lib) Set a custom BASE fold library.
void	setOriginal(boolean use) Use the original fold library in addition to the other library?
ThreadResults	thread(Protein p, Printf outfile) Thread a given protein, returning a ThreadResults object.
ThreadResults[]	thread(ProteinSet ps, Printf outfile) Thread a given protein set, returning an array of ThreadResults objects.

Methods inherited from class java.lang.Object

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

Field Detail

library

protected FoldLibrary library

extraLibrary

protected FoldLibrary extraLibrary

includeOriginal

protected boolean includeOriginal

blast

protected PSIBlast blast

Constructor Detail

JMCThreadMethod2

public JMCThreadMethod2()

Use the default fold library.

JMCThreadMethod2

public JMCThreadMethod2(FoldLibrary lib)

Use a user-specified fold library.

JMCThreadMethod2

public JMCThreadMethod2(PSIBlast b)

Use a user-specified psiblast method

JMCThreadMethod2

public JMCThreadMethod2(FoldLibrary lib,
                        PSIBlast b)

Use a user-specified library and psiblast method

JMCThreadMethod2

public JMCThreadMethod2(FoldLibrary baseLib,
                        FoldLibrary extraLib,
                        PSIBlast b)

Use a user-specified base library, extra library and psiblast method. Since this can change calculated z scores, don't mess with the base library unless you know what you're doing.

Method Detail

setOriginal

public void setOriginal(boolean use)

Use the original fold library in addition to the other library?

setBaseLibrary

public void setBaseLibrary(FoldLibrary lib)

Set a custom BASE fold library. (not Extra library... use this only if you know what you're doing)

thread

public ThreadResults thread(Protein p,
                            Printf outfile)
                     throws java.io.IOException

Thread a given protein, returning a ThreadResults object.

Specified by:

thread in interface ThreadMethod

Throws:

java.io.IOException

thread

public ThreadResults[] thread(ProteinSet ps,
                              Printf outfile)
                       throws java.io.IOException

Thread a given protein set, returning an array of ThreadResults objects.

Specified by:

thread in interface ThreadMethod

Throws:

java.io.IOException