Merge branch 'master' of https://source.jalview.org/git/jalviewjs.git

[jalviewjs.git] / site / j2s / jalview / workers / ComplementConsensusThread.js

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