java.lang.Object

org.biojava.nbio.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

Constructor Summary

Constructors

Constructor

Description

AlignmentCalc(AlignmentGui parent, Structure s1, Structure s2, String name1, String name2)

requests an alignment of pdb1 vs pdb 2.
Method Summary

Modifier and Type

Method

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

Constructor Details
- 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 Details
- 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

Class AlignmentCalc

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

AlignmentCalc

Method Details

run

interrupt

cleanup

setNrCPUs