1 Clazz.declarePackage ("jalview.workers");
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2 Clazz.load (["jalview.workers.ConsensusThread"], "jalview.workers.ComplementConsensusThread", ["jalview.analysis.AAFrequency"], function () {
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3 c$ = Clazz.decorateAsClass (function () {
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4 this.mappings = null;
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5 Clazz.instantialize (this, arguments);
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6 }, jalview.workers, "ComplementConsensusThread", jalview.workers.ConsensusThread);
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7 Clazz.overrideMethod (c$, "getNewWorker",
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9 return new jalview.workers.ComplementConsensusThread (this.alignViewport, this.ap);
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11 Clazz.overrideMethod (c$, "getConsensusAnnotation",
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13 return this.alignViewport.getComplementConsensusAnnotation ();
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15 Clazz.overrideMethod (c$, "getViewportConsensus",
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17 return this.alignViewport.getComplementConsensusHash ();
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19 Clazz.defineMethod (c$, "initializeCalc",
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21 this.mappings = this.alignment.getCodonFrames ();
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22 return (this.mappings != null && !this.mappings.isEmpty () && Clazz.superCall (this, jalview.workers.ComplementConsensusThread, "initializeCalc", []));
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24 Clazz.overrideMethod (c$, "computeConsensus",
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26 for (var i = 0; i < 3; i++) {
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28 jalview.analysis.AAFrequency.calculateCdna (this.alignment, this.mappings, this.hconsensus, this.iFirst, this.iLast);
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31 if (Clazz.exceptionOf (e, java.util.ConcurrentModificationException)) {
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38 Clazz.overrideMethod (c$, "finalizeCalc",
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40 this.alignViewport.setComplementConsensusHash (this.hconsensus);
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42 Clazz.overrideMethod (c$, "deriveConsensus",
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43 function (consensusAnnotation, consensusData) {
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44 jalview.analysis.AAFrequency.completeCdnaConsensus (consensusAnnotation, consensusData, this.alignViewport.isShowSequenceLogo (), this.getSequences ().length);
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45 }, "jalview.datamodel.AlignmentAnnotation,~A");
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