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

java.lang.Object
  extended by org.biojava.bio.structure.align.gui.AlignmentCalc
All Implemented Interfaces:
Runnable, AlignmentCalculationRunnable

public class AlignmentCalc
extends 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
static Logger logger
           
 
Constructor Summary
AlignmentCalc(AlignmentGui parent, Structure s1, Structure s2, String name1, String name2)
          requests an alignment of pdb1 vs pdb 2.
 
Method Summary
 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 Logger logger
Constructor Detail

AlignmentCalc

public AlignmentCalc(AlignmentGui parent,
                     Structure s1,
                     Structure s2,
                     String name1,
                     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 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