X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fworkers%2FConsensusThread.js;h=089a18e2f77c982b0c2aa5904fce6df8b12d359b;hp=3f62035da13c6a9437a479e96b2da3d567e389f8;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/j2s/jalview/workers/ConsensusThread.js b/site/j2s/jalview/workers/ConsensusThread.js
index 3f62035..089a18e 100644
--- a/site/j2s/jalview/workers/ConsensusThread.js
+++ b/site/j2s/jalview/workers/ConsensusThread.js
@@ -1,149 +1,149 @@
-Clazz.declarePackage ("jalview.workers");
-Clazz.load (["jalview.api.AlignCalcWorkerI", "jalview.workers.AlignCalcWorker"], "jalview.workers.ConsensusThread", ["jalview.analysis.AAFrequency"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.hconsensus = null;
-this.aseqs = null;
-Clazz.instantialize (this, arguments);
-}, jalview.workers, "ConsensusThread", jalview.workers.AlignCalcWorker, jalview.api.AlignCalcWorkerI);
-Clazz.overrideMethod (c$, "getNewWorker", 
-function () {
-return  new jalview.workers.ConsensusThread (this.alignViewport, this.ap);
-});
-Clazz.overrideMethod (c$, "run1", 
-function (state) {
-while (!Thread.interrupted ()) {
-if (this.alignViewport.isClosed ()) {
-this.abortAndDestroy ();
-return;
-}try {
-switch (state) {
-case 0:
-if (this.calcMan.isPending (this)) return;
-this.calcMan.notifyStart (this);
-var consensus = this.getConsensusAnnotation ();
-if (consensus == null || this.calcMan.isPending (this)) {
-this.calcMan.workerComplete (this);
-return;
-}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;
-}this.alignment = this.alignViewport.getAlignment ();
-this.aWidth = -1;
-if (this.alignment == null || (this.aWidth = this.alignment.getWidth ()) < 0) {
-state = 2;
-}this.eraseConsensus (this.aWidth);
-state = (this.initializeCalc () ? 4 : 2);
-break;
-case 4:
-this.iFirst = this.iLast;
-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.finalizeCalc ();
-this.updateAlignment ();
-this.notifyDone ();
-return;
-}
-} catch (e$$) {
-if (Clazz.exceptionOf (e$$, OutOfMemoryError)) {
-var error = e$$;
-{
-this.calcMan.workerCannotRun (this);
-this.ap.raiseOOMWarning ("calculating consensus", error);
-}
-} else {
-var e = e$$;
-{
-System.out.println ("Error in ConsensusThread: " + e);
-e.printStackTrace ();
-this.calcMan.workerComplete (this);
-}
-}
-}
-}
-}, "~N");
-Clazz.defineMethod (c$, "initializeCalc", 
-function () {
-this.iLast = 0;
-this.hconsensus =  new Array (this.aWidth);
-this.aseqs = this.getSequences ();
-return true;
-});
-Clazz.defineMethod (c$, "computeConsensus", 
-function () {
-this.started = System.currentTimeMillis ();
-jalview.analysis.AAFrequency.calculate (this.aseqs, this.iFirst, this.iLast, this.hconsensus, true);
-if (System.currentTimeMillis () - this.started < 500) this.nPer *= 2;
-});
-Clazz.defineMethod (c$, "finalizeCalc", 
-function () {
-this.alignViewport.setSequenceConsensusHash (this.hconsensus);
-});
-Clazz.defineMethod (c$, "updateAlignment", 
-function () {
-this.setColourSchemeConsensus (this.hconsensus);
-this.updateResultAnnotation (true);
-});
-Clazz.defineMethod (c$, "eraseConsensus", 
-function (aWidth) {
-var consensus = this.getConsensusAnnotation ();
-consensus.annotations =  new Array (aWidth);
-}, "~N");
-Clazz.defineMethod (c$, "getSequences", 
-function () {
-return this.alignViewport.getAlignment ().getSequencesArray ();
-});
-Clazz.defineMethod (c$, "setColourSchemeConsensus", 
-function (hconsensus) {
-var globalColourScheme = this.alignViewport.getGlobalColourScheme ();
-if (globalColourScheme != null) {
-globalColourScheme.setConsensus (hconsensus);
-}}, "~A");
-Clazz.defineMethod (c$, "getConsensusAnnotation", 
-function () {
-return this.alignViewport.getAlignmentConsensusAnnotation ();
-});
-Clazz.overrideMethod (c$, "updateAnnotation", 
-function () {
-this.updateResultAnnotation (false);
-});
-Clazz.defineMethod (c$, "updateResultAnnotation", 
-function (immediate) {
-var consensus = this.getConsensusAnnotation ();
-var hconsensus = this.getViewportConsensus ();
-if (immediate || !this.calcMan.isWorking (this) && consensus != null && hconsensus != null) {
-this.deriveConsensus (consensus, hconsensus);
-}}, "~B");
-Clazz.defineMethod (c$, "deriveConsensus", 
-function (consensusAnnotation, consensusData) {
-var nseq = this.getSequences ().length;
-jalview.analysis.AAFrequency.completeConsensus (consensusAnnotation, consensusData, 0, consensusData.length, this.alignViewport.isIgnoreGapsConsensus (), this.alignViewport.isShowSequenceLogo (), nseq);
-}, "jalview.datamodel.AlignmentAnnotation,~A");
-Clazz.defineMethod (c$, "getViewportConsensus", 
-function () {
-return this.alignViewport.getSequenceConsensusHash ();
-});
-});
+Clazz.declarePackage ("jalview.workers");
+Clazz.load (["jalview.api.AlignCalcWorkerI", "jalview.workers.AlignCalcWorker"], "jalview.workers.ConsensusThread", ["jalview.analysis.AAFrequency"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.hconsensus = null;
+this.aseqs = null;
+Clazz.instantialize (this, arguments);
+}, jalview.workers, "ConsensusThread", jalview.workers.AlignCalcWorker, jalview.api.AlignCalcWorkerI);
+Clazz.overrideMethod (c$, "getNewWorker", 
+function () {
+return  new jalview.workers.ConsensusThread (this.alignViewport, this.ap);
+});
+Clazz.overrideMethod (c$, "run1", 
+function (state) {
+while (!Thread.interrupted ()) {
+if (this.alignViewport.isClosed ()) {
+this.abortAndDestroy ();
+return;
+}try {
+switch (state) {
+case 0:
+if (this.calcMan.isPending (this)) return;
+this.calcMan.notifyStart (this);
+var consensus = this.getConsensusAnnotation ();
+if (consensus == null || this.calcMan.isPending (this)) {
+this.calcMan.workerComplete (this);
+return;
+}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;
+}this.alignment = this.alignViewport.getAlignment ();
+this.aWidth = -1;
+if (this.alignment == null || (this.aWidth = this.alignment.getWidth ()) < 0) {
+state = 2;
+}this.eraseConsensus (this.aWidth);
+state = (this.initializeCalc () ? 4 : 2);
+break;
+case 4:
+this.iFirst = this.iLast;
+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.finalizeCalc ();
+this.updateAlignment ();
+this.notifyDone ();
+return;
+}
+} catch (e$$) {
+if (Clazz.exceptionOf (e$$, OutOfMemoryError)) {
+var error = e$$;
+{
+this.calcMan.workerCannotRun (this);
+this.ap.raiseOOMWarning ("calculating consensus", error);
+}
+} else {
+var e = e$$;
+{
+System.out.println ("Error in ConsensusThread: " + e);
+e.printStackTrace ();
+this.calcMan.workerComplete (this);
+}
+}
+}
+}
+}, "~N");
+Clazz.defineMethod (c$, "initializeCalc", 
+function () {
+this.iLast = 0;
+this.hconsensus =  new Array (this.aWidth);
+this.aseqs = this.getSequences ();
+return true;
+});
+Clazz.defineMethod (c$, "computeConsensus", 
+function () {
+this.started = System.currentTimeMillis ();
+jalview.analysis.AAFrequency.calculate (this.aseqs, this.iFirst, this.iLast, this.hconsensus, true);
+if (System.currentTimeMillis () - this.started < 500) this.nPer *= 2;
+});
+Clazz.defineMethod (c$, "finalizeCalc", 
+function () {
+this.alignViewport.setSequenceConsensusHash (this.hconsensus);
+});
+Clazz.defineMethod (c$, "updateAlignment", 
+function () {
+this.setColourSchemeConsensus (this.hconsensus);
+this.updateResultAnnotation (true);
+});
+Clazz.defineMethod (c$, "eraseConsensus", 
+function (aWidth) {
+var consensus = this.getConsensusAnnotation ();
+consensus.annotations =  new Array (aWidth);
+}, "~N");
+Clazz.defineMethod (c$, "getSequences", 
+function () {
+return this.alignViewport.getAlignment ().getSequencesArray ();
+});
+Clazz.defineMethod (c$, "setColourSchemeConsensus", 
+function (hconsensus) {
+var globalColourScheme = this.alignViewport.getGlobalColourScheme ();
+if (globalColourScheme != null) {
+globalColourScheme.setConsensus (hconsensus);
+}}, "~A");
+Clazz.defineMethod (c$, "getConsensusAnnotation", 
+function () {
+return this.alignViewport.getAlignmentConsensusAnnotation ();
+});
+Clazz.overrideMethod (c$, "updateAnnotation", 
+function () {
+this.updateResultAnnotation (false);
+});
+Clazz.defineMethod (c$, "updateResultAnnotation", 
+function (immediate) {
+var consensus = this.getConsensusAnnotation ();
+var hconsensus = this.getViewportConsensus ();
+if (immediate || !this.calcMan.isWorking (this) && consensus != null && hconsensus != null) {
+this.deriveConsensus (consensus, hconsensus);
+}}, "~B");
+Clazz.defineMethod (c$, "deriveConsensus", 
+function (consensusAnnotation, consensusData) {
+var nseq = this.getSequences ().length;
+jalview.analysis.AAFrequency.completeConsensus (consensusAnnotation, consensusData, 0, consensusData.length, this.alignViewport.isIgnoreGapsConsensus (), this.alignViewport.isShowSequenceLogo (), nseq);
+}, "jalview.datamodel.AlignmentAnnotation,~A");
+Clazz.defineMethod (c$, "getViewportConsensus", 
+function () {
+return this.alignViewport.getSequenceConsensusHash ();
+});
+});