org.strbio.mol.lib
Class JMCThreadMethod

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

All Implemented Interfaces:

ThreadMethod

public class JMCThreadMethod
extends java.lang.Object
implements ThreadMethod

JMC's global threading method.

  Version 1.1, 2/17/00 - simplified method for single proteins
  Version 1.0, 7/9/99 - original version
  

Version:

1.1, 2/17/00

Author:

JMC

Field Summary

protected PSIBlast	blast
protected FoldLibrary	library

Constructor Summary

JMCThreadMethod()
Use the default fold library.

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

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

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

Method Summary

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

blast

protected PSIBlast blast

Constructor Detail

JMCThreadMethod

public JMCThreadMethod()

Use the default fold library.

JMCThreadMethod

public JMCThreadMethod(FoldLibrary lib)

Use a user-specified fold library.

JMCThreadMethod

public JMCThreadMethod(PSIBlast b)

Use a user-specified psiblast method

JMCThreadMethod

public JMCThreadMethod(FoldLibrary lib,
                       PSIBlast b)

Use a user-specified library and psiblast method

Method Detail

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