org.biojava.bio.structure.align.gui

Class AlignmentCalc

java.lang.Object

org.biojava.bio.structure.align.gui.AlignmentCalc

All Implemented Interfaces:

java.lang.Runnable, AlignmentCalculationRunnable

public class AlignmentCalc
extends java.lang.Object
implements AlignmentCalculationRunnable

A class that obtains two structures via DAS and aligns them This is done in a separate thread. It is possible to register Event listeners to get notification of when the download has finished.

Since:

1.7

Version:

%I% %G%

Author:

Andreas Prlic

Field Summary

Fields

Modifier and Type	Field and Description
static java.util.logging.Logger	logger

Constructor Summary

Constructors

Constructor and Description
AlignmentCalc(AlignmentGui parent, Structure s1, Structure s2, java.lang.String name1, java.lang.String name2) requests an alignment of pdb1 vs pdb 2.

Method Summary

Methods

Modifier and Type	Method and Description
void	cleanup()
void	interrupt() stops what is currently happening and does not continue
void	run()
void	setNrCPUs(int useNrCPUs) does not do anything here...

Methods inherited from class java.lang.Object

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

Field Detail

logger

public static java.util.logging.Logger logger

Constructor Detail

AlignmentCalc

public AlignmentCalc(AlignmentGui parent,
             Structure s1,
             Structure s2,
             java.lang.String name1,
             java.lang.String name2)

requests an alignment of pdb1 vs pdb 2. Chain 1 and chain2 are optional. If they are empty strings, they are ignored

Parameters:

parent - the alignment gui frame that interacts with this class

s1 - structure 1

s2 - structure 2

Method Detail

run

public void run()

Specified by:

run in interface java.lang.Runnable

interrupt

public void interrupt()

stops what is currently happening and does not continue

Specified by:

interrupt in interface AlignmentCalculationRunnable

cleanup

public void cleanup()

Specified by:

cleanup in interface AlignmentCalculationRunnable

setNrCPUs

public void setNrCPUs(int useNrCPUs)

does not do anything here...

Specified by:

setNrCPUs in interface AlignmentCalculationRunnable