src/jalview/workers/ComplementConsensusThread.java

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