org.biojava.nbio.structure.align.client.FarmJobRunnable

public class FarmJobRunnable extends Object implements Runnable

Contains the single thread for a job that can run multiple alignments.

Field Details
- cache
  
  protected AtomCache cache
Constructor Details
- FarmJobRunnable
  
  public FarmJobRunnable(FarmJobParameters params)
Method Details
- addAlignmentProgressListener
  
  public void addAlignmentProgressListener(AlignmentProgressListener listener)
- clearListeners
  
  public void clearListeners()
- getRandomUsername
  
  protected static String getRandomUsername()
- run
  
  public void run()
  
  Specified by:
  
  run in interface Runnable
- alignPair
  
  public String alignPair(String name1, String name2) throws StructureException, IOException
  
  Throws:
  
  StructureException
  
  IOException
- alignPair
  
  public String alignPair(String name1, String name2, String algorithmName) throws StructureException, IOException
  
  Throws:
  
  StructureException
  
  IOException
- getAlignmentPairsFromServer
  
  protected PdbPairsMessage getAlignmentPairsFromServer()
  
  talk to centralized server and fetch all alignments to run.
  
  Returns:
  
  a list of pairs to align.
- sendResultsToServer
  
  protected void sendResultsToServer(List<String> results)
- terminate
  
  public void terminate()
  
  Send signal to terminate calculations
- isWaitForAlignments
  
  public boolean isWaitForAlignments()
- setWaitForAlignments
  
  public void setWaitForAlignments(boolean waitForAlignments)

Class FarmJobRunnable

Field Summary