X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fworkers%2FConservationThread.js;h=072fbdcdb305aa58d7b834ce00f77158d1dfbaea;hp=83e54e71f011d4e46a0d641c39e6190b2696dfd3;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6

diff --git a/site/j2s/jalview/workers/ConservationThread.js b/site/j2s/jalview/workers/ConservationThread.js
index 83e54e7..072fbdc 100644
--- a/site/j2s/jalview/workers/ConservationThread.js
+++ b/site/j2s/jalview/workers/ConservationThread.js
@@ -1,108 +1,108 @@
-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$, "updateAnnotation", 
-function () {
-this.updateResultAnnotation (false);
-});
-});
+Clazz.declarePackage ("jalview.workers");
+Clazz.load (["jalview.api.AlignCalcWorkerI", "jalview.workers.AlignCalcWorker"], "jalview.workers.ConservationThread", ["jalview.analysis.Conservation", "jalview.schemes.ResidueProperties", "java.util.ArrayList"], function () {
+c$ = 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);
+});
+});