X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fworkers%2FComplementConsensusThread.js;h=17ece7fc23cae2ec0348325bc192856171692c60;hp=641c3baa73cde4ea5b8d424bf9ee68d6530247fb;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/j2s/jalview/workers/ComplementConsensusThread.js b/site/j2s/jalview/workers/ComplementConsensusThread.js
index 641c3ba..17ece7f 100644
--- a/site/j2s/jalview/workers/ComplementConsensusThread.js
+++ b/site/j2s/jalview/workers/ComplementConsensusThread.js
@@ -1,46 +1,46 @@
-Clazz.declarePackage ("jalview.workers");
-Clazz.load (["jalview.workers.ConsensusThread"], "jalview.workers.ComplementConsensusThread", ["jalview.analysis.AAFrequency"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.mappings = null;
-Clazz.instantialize (this, arguments);
-}, jalview.workers, "ComplementConsensusThread", jalview.workers.ConsensusThread);
-Clazz.overrideMethod (c$, "getNewWorker", 
-function () {
-return  new jalview.workers.ComplementConsensusThread (this.alignViewport, this.ap);
-});
-Clazz.overrideMethod (c$, "getConsensusAnnotation", 
-function () {
-return this.alignViewport.getComplementConsensusAnnotation ();
-});
-Clazz.overrideMethod (c$, "getViewportConsensus", 
-function () {
-return this.alignViewport.getComplementConsensusHash ();
-});
-Clazz.defineMethod (c$, "initializeCalc", 
-function () {
-this.mappings = this.alignment.getCodonFrames ();
-return (this.mappings != null && !this.mappings.isEmpty () && Clazz.superCall (this, jalview.workers.ComplementConsensusThread, "initializeCalc", []));
-});
-Clazz.overrideMethod (c$, "computeConsensus", 
-function () {
-for (var i = 0; i < 3; i++) {
-try {
-jalview.analysis.AAFrequency.calculateCdna (this.alignment, this.mappings, this.hconsensus, this.iFirst, this.iLast);
-break;
-} catch (e) {
-if (Clazz.exceptionOf (e, java.util.ConcurrentModificationException)) {
-} else {
-throw e;
-}
-}
-}
-});
-Clazz.overrideMethod (c$, "finalizeCalc", 
-function () {
-this.alignViewport.setComplementConsensusHash (this.hconsensus);
-});
-Clazz.overrideMethod (c$, "deriveConsensus", 
-function (consensusAnnotation, consensusData) {
-jalview.analysis.AAFrequency.completeCdnaConsensus (consensusAnnotation, consensusData, this.alignViewport.isShowSequenceLogo (), this.getSequences ().length);
-}, "jalview.datamodel.AlignmentAnnotation,~A");
-});
+Clazz.declarePackage ("jalview.workers");
+Clazz.load (["jalview.workers.ConsensusThread"], "jalview.workers.ComplementConsensusThread", ["jalview.analysis.AAFrequency"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.mappings = null;
+Clazz.instantialize (this, arguments);
+}, jalview.workers, "ComplementConsensusThread", jalview.workers.ConsensusThread);
+Clazz.overrideMethod (c$, "getNewWorker", 
+function () {
+return  new jalview.workers.ComplementConsensusThread (this.alignViewport, this.ap);
+});
+Clazz.overrideMethod (c$, "getConsensusAnnotation", 
+function () {
+return this.alignViewport.getComplementConsensusAnnotation ();
+});
+Clazz.overrideMethod (c$, "getViewportConsensus", 
+function () {
+return this.alignViewport.getComplementConsensusHash ();
+});
+Clazz.defineMethod (c$, "initializeCalc", 
+function () {
+this.mappings = this.alignment.getCodonFrames ();
+return (this.mappings != null && !this.mappings.isEmpty () && Clazz.superCall (this, jalview.workers.ComplementConsensusThread, "initializeCalc", []));
+});
+Clazz.overrideMethod (c$, "computeConsensus", 
+function () {
+for (var i = 0; i < 3; i++) {
+try {
+jalview.analysis.AAFrequency.calculateCdna (this.alignment, this.mappings, this.hconsensus, this.iFirst, this.iLast);
+break;
+} catch (e) {
+if (Clazz.exceptionOf (e, java.util.ConcurrentModificationException)) {
+} else {
+throw e;
+}
+}
+}
+});
+Clazz.overrideMethod (c$, "finalizeCalc", 
+function () {
+this.alignViewport.setComplementConsensusHash (this.hconsensus);
+});
+Clazz.overrideMethod (c$, "deriveConsensus", 
+function (consensusAnnotation, consensusData) {
+jalview.analysis.AAFrequency.completeCdnaConsensus (consensusAnnotation, consensusData, this.alignViewport.isShowSequenceLogo (), this.getSequences ().length);
+}, "jalview.datamodel.AlignmentAnnotation,~A");
+});