src/jalview/workers/ComplementConsensusThread.java

   1 package jalview.workers;
   2
   3 import jalview.analysis.AAFrequency;
   4 import jalview.api.AlignViewportI;
   5 import jalview.api.AlignmentViewPanel;
   6 import jalview.datamodel.AlignmentAnnotation;
   7 import jalview.datamodel.AlignmentI;
   8 import jalview.datamodel.SequenceI;
   9
  10 import java.util.Hashtable;
  11
  12 /**
  13  * A thread to recompute the consensus of the cDNA complement for a linked
  14  * protein alignment.
  15  *
  16  * @author gmcarstairs
  17  *
  18  */
  19 public class ComplementConsensusThread extends ConsensusThread
  20 {
  21
  22   public ComplementConsensusThread(AlignViewportI alignViewport,
  23           AlignmentViewPanel alignPanel)
  24   {
  25     super(alignViewport, alignPanel);
  26   }
  27
  28   @Override
  29   protected AlignmentAnnotation getConsensusAnnotation()
  30   {
  31     return alignViewport.getComplementConsensusAnnotation();
  32   }
  33
  34   @Override
  35   protected Hashtable[] getViewportConsensus()
  36   {
  37     return alignViewport.getComplementConsensusHash();
  38   }
  39
  40   @Override
  41   protected void computeConsensus(AlignmentI alignment)
  42   {
  43     Hashtable[] hconsensus = new Hashtable[alignment.getWidth()];
  44
  45     SequenceI[] aseqs = getSequences();
  46     AAFrequency.calculateCdna(alignment, hconsensus);
  47
  48     alignViewport.setComplementConsensusHash(hconsensus);
  49   }
  50
  51   /**
  52    * Convert the computed consensus data into the desired annotation for
  53    * display.
  54    *
  55    * @param consensusAnnotation
  56    *          the annotation to be populated
  57    * @param consensusData
  58    *          the computed consensus data
  59    */
  60   @Override
  61   protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
  62           Hashtable[] consensusData)
  63   {
  64     AAFrequency.completeCdnaConsensus(consensusAnnotation, consensusData,
  65             alignViewport.isShowSequenceLogo(), getSequences().length);
  66   }
  67
  68 }