src/jalview/workers/ComplementConsensusThread.java

   1 package jalview.workers;
   2
   3 import java.util.ConcurrentModificationException;
   4 import java.util.Hashtable;
   5 import java.util.Set;
   6
   7 import jalview.analysis.AAFrequency;
   8 import jalview.api.AlignCalcWorkerI;
   9 import jalview.api.AlignViewportI;
  10 import jalview.api.AlignmentViewPanel;
  11 import jalview.datamodel.AlignedCodonFrame;
  12 import jalview.datamodel.AlignmentAnnotation;
  13
  14 /**
  15  * A thread to recompute the consensus of the cDNA complement for a linked
  16  * protein alignment.
  17  *
  18  * @author gmcarstairs
  19  *
  20  */
  21 public class ComplementConsensusThread extends ConsensusThread
  22 {
  23
  24   private Set<AlignedCodonFrame> mappings;
  25
  26
  27         @Override
  28         public AlignCalcWorkerI getNewWorker() {
  29                 return new ComplementConsensusThread(alignViewport, ap);
  30         }
  31
  32         public ComplementConsensusThread(AlignViewportI alignViewport,
  33           AlignmentViewPanel alignPanel)
  34   {
  35     super(alignViewport, alignPanel);
  36   }
  37
  38   @Override
  39   protected AlignmentAnnotation getConsensusAnnotation()
  40   {
  41     return alignViewport.getComplementConsensusAnnotation();
  42   }
  43
  44   @Override
  45   protected Hashtable[] getViewportConsensus()
  46   {
  47     return alignViewport.getComplementConsensusHash();
  48   }
  49
  50   @Override
  51         protected boolean initializeCalc() {
  52     mappings = alignment.getCodonFrames();
  53     return (mappings != null && !mappings.isEmpty() && super.initializeCalc());
  54         }
  55
  56   /**
  57    * Calculate the cDNA consensus and store it on the Viewport
  58    */
  59   @Override
  60   protected void computeConsensus()
  61   {
  62     /*
  63      * Allow 3 tries at this, since this thread can start up while we are still
  64      * modifying protein-codon mappings on the alignment
  65      */
  66     for (int i = 0; i < 3; i++)
  67     {
  68       try
  69       {
  70         AAFrequency.calculateCdna(alignment, mappings, hconsensus, iFirst, iLast);
  71         break;
  72       } catch (ConcurrentModificationException e)
  73       {
  74         // try again
  75       }
  76     }
  77   }
  78
  79
  80         protected void finalizeCalc() {
  81           alignViewport.setComplementConsensusHash(hconsensus);
  82         }
  83
  84
  85         /**
  86    * Convert the computed consensus data into the desired annotation for
  87    * display.
  88    *
  89    * @param consensusAnnotation
  90    *          the annotation to be populated
  91    * @param consensusData
  92    *          the computed consensus data
  93    */
  94   @Override
  95   protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
  96           Hashtable[] consensusData)
  97   {
  98     AAFrequency.completeCdnaConsensus(consensusAnnotation, consensusData,
  99             alignViewport.isShowSequenceLogo(), getSequences().length);
 100   }
 101
 102 }