site/j2s/jalview/workers/ComplementConsensusThread.js

   1 Clazz.declarePackage ("jalview.workers");
   2 Clazz.load (["jalview.workers.ConsensusThread"], "jalview.workers.ComplementConsensusThread", ["jalview.analysis.AAFrequency"], function () {
   3 c$ = Clazz.declareType (jalview.workers, "ComplementConsensusThread", jalview.workers.ConsensusThread);
   4 Clazz.overrideMethod (c$, "getConsensusAnnotation",
   5 function () {
   6 return this.alignViewport.getComplementConsensusAnnotation ();
   7 });
   8 Clazz.overrideMethod (c$, "getViewportConsensus",
   9 function () {
  10 return this.alignViewport.getComplementConsensusHash ();
  11 });
  12 Clazz.overrideMethod (c$, "computeConsensus",
  13 function (alignment) {
  14 var hconsensus =  new Array (alignment.getWidth ());
  15 var aseqs = this.getSequences ();
  16 for (var i = 0; i < 3; i++) {
  17 try {
  18 jalview.analysis.AAFrequency.calculateCdna (alignment, hconsensus);
  19 break;
  20 } catch (e) {
  21 if (Clazz.exceptionOf (e, java.util.ConcurrentModificationException)) {
  22 } else {
  23 throw e;
  24 }
  25 }
  26 }
  27 this.alignViewport.setComplementConsensusHash (hconsensus);
  28 }, "jalview.datamodel.AlignmentI");
  29 Clazz.overrideMethod (c$, "deriveConsensus",
  30 function (consensusAnnotation, consensusData) {
  31 jalview.analysis.AAFrequency.completeCdnaConsensus (consensusAnnotation, consensusData, this.alignViewport.isShowSequenceLogo (), this.getSequences ().length);
  32 }, "jalview.datamodel.AlignmentAnnotation,~A");
  33 });