-Clazz.declarePackage ("jalview.workers");\r
-Clazz.load (["jalview.api.AlignCalcWorkerI", "jalview.workers.AlignCalcWorker"], "jalview.workers.ConservationThread", ["jalview.analysis.Conservation", "jalview.schemes.ResidueProperties", "java.util.ArrayList"], function () {\r
-c$ = Clazz.decorateAsClass (function () {\r
-this.ConsPercGaps = 25;\r
-this.cons = null;\r
-this.conservation = null;\r
-this.quality = null;\r
-Clazz.instantialize (this, arguments);\r
-}, jalview.workers, "ConservationThread", jalview.workers.AlignCalcWorker, jalview.api.AlignCalcWorkerI);\r
-Clazz.overrideMethod (c$, "getNewWorker", \r
-function () {\r
-return new jalview.workers.ConservationThread (this.alignViewport, this.ap);\r
-});\r
-Clazz.makeConstructor (c$, \r
-function (alignViewport, alignPanel) {\r
-Clazz.superConstructor (this, jalview.workers.ConservationThread, [alignViewport, alignPanel]);\r
-this.ConsPercGaps = alignViewport.getConsPercGaps ();\r
-}, "jalview.api.AlignViewportI,jalview.api.AlignmentViewPanel");\r
-Clazz.overrideMethod (c$, "run1", \r
-function (state) {\r
-while (!Thread.interrupted ()) {\r
-try {\r
-switch (state) {\r
-case 0:\r
-if (this.calcMan.isPending (this)) return;\r
-this.calcMan.notifyStart (this);\r
-state = 3;\r
-break;\r
-case 3:\r
-while (!this.calcMan.notifyWorking (this)) {\r
-if (this.ap != null) {\r
-this.ap.paintAlignment (false);\r
-}try {\r
-if (this.sleepAndReturn (200, state)) return;\r
-} catch (e) {\r
-if (Clazz.exceptionOf (e, InterruptedException)) {\r
-state = 2;\r
-break;\r
-} else {\r
-throw e;\r
-}\r
-}\r
-}\r
-if (this.alignViewport.isClosed ()) {\r
-this.abortAndDestroy ();\r
-state = 2;\r
-break;\r
-}var ourAnnot = new java.util.ArrayList ();\r
-this.alignment = this.alignViewport.getAlignment ();\r
-this.conservation = this.alignViewport.getAlignmentConservationAnnotation ();\r
-this.quality = this.alignViewport.getAlignmentQualityAnnot ();\r
-ourAnnot.add (this.conservation);\r
-ourAnnot.add (this.quality);\r
-this.ourAnnots = ourAnnot;\r
-this.ConsPercGaps = this.alignViewport.getConsPercGaps ();\r
-if (this.alignment == null || (this.aWidth = this.alignment.getWidth ()) < 0) {\r
-this.calcMan.workerComplete (this);\r
-return;\r
-}state = 4;\r
-break;\r
-case 4:\r
-this.iFirst = this.iLast;\r
-this.nPer = this.aWidth + 1;\r
-this.iLast = Math.min (this.iLast + this.nPer, this.aWidth);\r
-if (this.iLast == this.iFirst) {\r
-state = 2;\r
-} else {\r
-this.computeConsensus ();\r
-if (this.sleepAndReturn (0, state)) return;\r
-}break;\r
-case 2:\r
-this.updateResultAnnotation (true);\r
-this.notifyDone ();\r
-return;\r
-}\r
-} catch (e$$) {\r
-if (Clazz.exceptionOf (e$$, OutOfMemoryError)) {\r
-var error = e$$;\r
-{\r
-this.calcMan.workerCannotRun (this);\r
-this.ap.raiseOOMWarning ("calculating conservation", error);\r
-}\r
-} else {\r
-var e = e$$;\r
-{\r
-System.out.println ("Error in ConsensusThread: " + e);\r
-e.printStackTrace ();\r
-this.calcMan.workerComplete (this);\r
-}\r
-}\r
-}\r
-}\r
-}, "~N");\r
-Clazz.defineMethod (c$, "computeConsensus", \r
- function () {\r
-this.cons = jalview.analysis.Conservation.calculateConservation ("All", jalview.schemes.ResidueProperties.propHash, 3, this.alignment.getSequences (), 0, this.aWidth - 1, false, this.ConsPercGaps, this.quality != null);\r
-});\r
-Clazz.defineMethod (c$, "updateResultAnnotation", \r
- function (b) {\r
-if (b || !this.calcMan.isWorking (this) && this.cons != null && this.conservation != null && this.quality != null) {\r
-this.alignViewport.setConservation (this.cons);\r
-this.cons.completeAnnotations (this.conservation, this.quality, 0, this.aWidth);\r
-}}, "~B");\r
-Clazz.overrideMethod (c$, "updateAnnotation", \r
-function () {\r
-this.updateResultAnnotation (false);\r
-});\r
-});\r
+Clazz.declarePackage ("jalview.workers");
+Clazz.load (["jalview.api.AlignCalcWorkerI", "jalview.workers.AlignCalcWorker"], "jalview.workers.ConservationThread", ["jalview.analysis.Conservation", "jalview.schemes.ResidueProperties", "java.util.ArrayList"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.ConsPercGaps = 25;
+this.cons = null;
+this.conservation = null;
+this.quality = null;
+Clazz.instantialize (this, arguments);
+}, jalview.workers, "ConservationThread", jalview.workers.AlignCalcWorker, jalview.api.AlignCalcWorkerI);
+Clazz.overrideMethod (c$, "getNewWorker",
+function () {
+return new jalview.workers.ConservationThread (this.alignViewport, this.ap);
+});
+Clazz.makeConstructor (c$,
+function (alignViewport, alignPanel) {
+Clazz.superConstructor (this, jalview.workers.ConservationThread, [alignViewport, alignPanel]);
+this.ConsPercGaps = alignViewport.getConsPercGaps ();
+}, "jalview.api.AlignViewportI,jalview.api.AlignmentViewPanel");
+Clazz.overrideMethod (c$, "run1",
+function (state) {
+while (!Thread.interrupted ()) {
+try {
+switch (state) {
+case 0:
+if (this.calcMan.isPending (this)) return;
+this.calcMan.notifyStart (this);
+state = 3;
+break;
+case 3:
+while (!this.calcMan.notifyWorking (this)) {
+if (this.ap != null) {
+this.ap.paintAlignment (false);
+}try {
+if (this.sleepAndReturn (200, state)) return;
+} catch (e) {
+if (Clazz.exceptionOf (e, InterruptedException)) {
+state = 2;
+break;
+} else {
+throw e;
+}
+}
+}
+if (this.alignViewport.isClosed ()) {
+this.abortAndDestroy ();
+state = 2;
+break;
+}var ourAnnot = new java.util.ArrayList ();
+this.alignment = this.alignViewport.getAlignment ();
+this.conservation = this.alignViewport.getAlignmentConservationAnnotation ();
+this.quality = this.alignViewport.getAlignmentQualityAnnot ();
+ourAnnot.add (this.conservation);
+ourAnnot.add (this.quality);
+this.ourAnnots = ourAnnot;
+this.ConsPercGaps = this.alignViewport.getConsPercGaps ();
+if (this.alignment == null || (this.aWidth = this.alignment.getWidth ()) < 0) {
+this.calcMan.workerComplete (this);
+return;
+}state = 4;
+break;
+case 4:
+this.iFirst = this.iLast;
+this.nPer = this.aWidth + 1;
+this.iLast = Math.min (this.iLast + this.nPer, this.aWidth);
+if (this.iLast == this.iFirst) {
+state = 2;
+} else {
+this.computeConsensus ();
+if (this.sleepAndReturn (0, state)) return;
+}break;
+case 2:
+this.updateResultAnnotation (true);
+this.notifyDone ();
+return;
+}
+} catch (e$$) {
+if (Clazz.exceptionOf (e$$, OutOfMemoryError)) {
+var error = e$$;
+{
+this.calcMan.workerCannotRun (this);
+this.ap.raiseOOMWarning ("calculating conservation", error);
+}
+} else {
+var e = e$$;
+{
+System.out.println ("Error in ConsensusThread: " + e);
+e.printStackTrace ();
+this.calcMan.workerComplete (this);
+}
+}
+}
+}
+}, "~N");
+Clazz.defineMethod (c$, "computeConsensus",
+ function () {
+this.cons = jalview.analysis.Conservation.calculateConservation ("All", jalview.schemes.ResidueProperties.propHash, 3, this.alignment.getSequences (), 0, this.aWidth - 1, false, this.ConsPercGaps, this.quality != null);
+});
+Clazz.defineMethod (c$, "updateResultAnnotation",
+ function (b) {
+if (b || !this.calcMan.isWorking (this) && this.cons != null && this.conservation != null && this.quality != null) {
+this.alignViewport.setConservation (this.cons);
+this.cons.completeAnnotations (this.conservation, this.quality, 0, this.aWidth);
+}}, "~B");
+Clazz.overrideMethod (c$, "updateAnnotation",
+function () {
+this.updateResultAnnotation (false);
+});
+});
git://source.jalview.org / jalviewjs.git / blobdiff