Field Detail

• cache

  protected AtomCache cache

Constructor Detail

• FarmJobRunnable

  public FarmJobRunnable​(FarmJobParameters params)

Method Detail

• addAlignmentProgressListener

  public void addAlignmentProgressListener​(AlignmentProgressListener listener)

• clearListeners

  public void clearListeners()

• getRandomUsername

  protected static java.lang.String getRandomUsername()

• run

  public void run()

  Specified by:

  run in interface java.lang.Runnable

• alignPair

  public java.lang.String alignPair​(java.lang.String name1,
                                    java.lang.String name2)
                             throws StructureException,
                                    java.io.IOException

  Throws:

  StructureException

  java.io.IOException

• alignPair

  public java.lang.String alignPair​(java.lang.String name1,
                                    java.lang.String name2,
                                    java.lang.String algorithmName)
                             throws StructureException,
                                    java.io.IOException

  Throws:

  StructureException

  java.io.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​(java.util.List<java.lang.String> results)

• terminate

  public void terminate()

  Send signal to terminate calculations

• isWaitForAlignments

  public boolean isWaitForAlignments()

• setWaitForAlignments

  public void setWaitForAlignments​(boolean waitForAlignments)