bin/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.decorateAsClass (function () {
   4 this.mappings = null;
   5 Clazz.instantialize (this, arguments);
   6 }, jalview.workers, "ComplementConsensusThread", jalview.workers.ConsensusThread);
   7 Clazz.overrideMethod (c$, "getNewWorker",
   8 function () {
   9 return  new jalview.workers.ComplementConsensusThread (this.alignViewport, this.ap);
  10 });
  11 Clazz.overrideMethod (c$, "getConsensusAnnotation",
  12 function () {
  13 return this.alignViewport.getComplementConsensusAnnotation ();
  14 });
  15 Clazz.overrideMethod (c$, "getViewportConsensus",
  16 function () {
  17 return this.alignViewport.getComplementConsensusHash ();
  18 });
  19 Clazz.defineMethod (c$, "initializeCalc",
  20 function () {
  21 this.mappings = this.alignment.getCodonFrames ();
  22 return (this.mappings != null && !this.mappings.isEmpty () && Clazz.superCall (this, jalview.workers.ComplementConsensusThread, "initializeCalc", []));
  23 });
  24 Clazz.overrideMethod (c$, "computeConsensus",
  25 function () {
  26 for (var i = 0; i < 3; i++) {
  27 try {
  28 jalview.analysis.AAFrequency.calculateCdna (this.alignment, this.mappings, this.hconsensus, this.iFirst, this.iLast);
  29 break;
  30 } catch (e) {
  31 if (Clazz.exceptionOf (e, java.util.ConcurrentModificationException)) {
  32 } else {
  33 throw e;
  34 }
  35 }
  36 }
  37 });
  38 Clazz.overrideMethod (c$, "finalizeCalc",
  39 function () {
  40 this.alignViewport.setComplementConsensusHash (this.hconsensus);
  41 });
  42 Clazz.overrideMethod (c$, "deriveConsensus",
  43 function (consensusAnnotation, consensusData) {
  44 jalview.analysis.AAFrequency.completeCdnaConsensus (consensusAnnotation, consensusData, this.alignViewport.isShowSequenceLogo (), this.getSequences ().length);
  45 }, "jalview.datamodel.AlignmentAnnotation,~A");
  46 });