X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fworkers%2FStrucConsensusThread.js;h=7908c3f36b6bb878b489e2afce54dcd15ac2290d;hp=4010f84a002518c99ce3d0a32a69d3d6aefa43b8;hb=7301a2415adab88038b291fc54caeeb3a5a47a44;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/site/j2s/jalview/workers/StrucConsensusThread.js b/site/j2s/jalview/workers/StrucConsensusThread.js
index 4010f84..7908c3f 100644
--- a/site/j2s/jalview/workers/StrucConsensusThread.js
+++ b/site/j2s/jalview/workers/StrucConsensusThread.js
@@ -1,85 +1,107 @@
 Clazz.declarePackage ("jalview.workers");
-Clazz.load (["jalview.api.AlignCalcWorkerI", "jalview.workers.AlignCalcWorker"], "jalview.workers.StrucConsensusThread", ["jalview.analysis.StructureFrequency", "java.lang.Thread"], function () {
+Clazz.load (["jalview.api.AlignCalcWorkerI", "jalview.workers.AlignCalcWorker"], "jalview.workers.StrucConsensusThread", ["jalview.analysis.StructureFrequency"], function () {
 c$ = Clazz.decorateAsClass (function () {
+this.rnaStruc = null;
 this.strucConsensus = null;
 this.hStrucConsensus = null;
 this.nseq = -1;
+this.aa = null;
+this.arr = null;
 Clazz.instantialize (this, arguments);
 }, jalview.workers, "StrucConsensusThread", jalview.workers.AlignCalcWorker, jalview.api.AlignCalcWorkerI);
 Clazz.overrideMethod (c$, "getNewWorker", 
 function () {
 return  new jalview.workers.StrucConsensusThread (this.alignViewport, this.ap);
 });
-Clazz.overrideMethod (c$, "run", 
-function () {
-try {
-if (this.calcMan.isPending (this)) {
+Clazz.overrideMethod (c$, "run1", 
+function (state) {
+if (this.alignViewport.isClosed ()) {
+this.abortAndDestroy ();
 return;
-}this.calcMan.notifyStart (this);
-while (!this.calcMan.notifyWorking (this)) {
+}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) {
-}Thread.sleep (200);
-} catch (ex) {
-if (Clazz.exceptionOf (ex, Exception)) {
-ex.printStackTrace ();
+this.ap.paintAlignment (false);
+}try {
+if (this.sleepAndReturn (200, state)) return;
+} catch (e) {
+if (Clazz.exceptionOf (e, InterruptedException)) {
+state = 2;
+break;
 } else {
-throw ex;
+throw e;
 }
 }
 }
 if (this.alignViewport.isClosed ()) {
 this.abortAndDestroy ();
-return;
-}var alignment = this.alignViewport.getAlignment ();
-var aWidth = -1;
-if (alignment == null || (aWidth = alignment.getWidth ()) < 0) {
-this.calcMan.workerComplete (this);
-return;
+state = 2;
+break;
+}this.alignment = this.alignViewport.getAlignment ();
+this.aWidth = -1;
+if (this.alignment == null || (this.aWidth = this.alignment.getWidth ()) < 0) {
+state = 2;
 }this.strucConsensus = this.alignViewport.getAlignmentStrucConsensusAnnotation ();
 this.hStrucConsensus = this.alignViewport.getRnaStructureConsensusHash ();
 this.strucConsensus.annotations = null;
-this.strucConsensus.annotations =  new Array (aWidth);
-this.hStrucConsensus =  new Array (aWidth);
-var aa = this.alignViewport.getAlignment ().getAlignmentAnnotation ();
-var rnaStruc = null;
-for (var i = 0; i < aa.length; i++) {
-if (aa[i].getRNAStruc () != null && aa[i].isValidStruc ()) {
-rnaStruc = aa[i];
+this.strucConsensus.annotations =  new Array (this.aWidth);
+this.hStrucConsensus =  new Array (this.aWidth);
+this.aa = this.alignViewport.getAlignment ().getAlignmentAnnotation ();
+for (var i = 0; i < this.aa.length; i++) {
+if (this.aa[i].getRNAStruc () != null && this.aa[i].isValidStruc ()) {
+this.rnaStruc = this.aa[i];
 break;
 }}
-if (rnaStruc == null || !rnaStruc.isValidStruc ()) {
-this.calcMan.workerComplete (this);
-return;
-}try {
-var arr = alignment.getSequencesArray ();
-this.nseq = arr.length;
-jalview.analysis.StructureFrequency.calculate (arr, 0, alignment.getWidth (), this.hStrucConsensus, true, rnaStruc);
-} catch (x) {
-if (Clazz.exceptionOf (x, ArrayIndexOutOfBoundsException)) {
+if (this.rnaStruc == null || !this.rnaStruc.isValidStruc ()) {
 this.calcMan.workerComplete (this);
 return;
+}this.arr = this.alignment.getSequencesArray ();
+this.nseq = this.arr.length;
+state = 4;
+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 {
-throw x;
-}
-}
+jalview.analysis.StructureFrequency.calculate (this.arr, 0, this.alignment.getWidth (), this.hStrucConsensus, true, this.rnaStruc);
+if (this.sleepAndReturn (0, state)) return;
+}break;
+case 2:
 this.alignViewport.setRnaStructureConsensusHash (this.hStrucConsensus);
 this.updateResultAnnotation (true);
 if (this.alignViewport.getGlobalColourScheme () != null) {
 this.alignViewport.getGlobalColourScheme ().setConsensus (this.hStrucConsensus);
-}} catch (error) {
-if (Clazz.exceptionOf (error, OutOfMemoryError)) {
+}this.notifyDone ();
+return;
+}
+} catch (e$$) {
+if (Clazz.exceptionOf (e$$, OutOfMemoryError)) {
+var error = e$$;
+{
 this.calcMan.workerCannotRun (this);
 this.ap.raiseOOMWarning ("calculating RNA structure consensus", error);
-} else {
-throw error;
 }
-} finally {
+} else {
+var e = e$$;
+{
+System.out.println ("Error in ConsensusThread: " + e);
+e.printStackTrace ();
 this.calcMan.workerComplete (this);
-if (this.ap != null) {
-this.ap.paintAlignment (true);
-}}
-});
+}
+}
+}
+}
+}, "~N");
 Clazz.overrideMethod (c$, "updateAnnotation", 
 function () {
 this.updateResultAnnotation (false);
@@ -89,7 +111,4 @@ function (immediate) {
 if (immediate || !this.calcMan.isWorking (this) && this.strucConsensus != null && this.hStrucConsensus != null) {
 jalview.analysis.StructureFrequency.completeConsensus (this.strucConsensus, this.hStrucConsensus, 0, this.hStrucConsensus.length, this.alignViewport.isIgnoreGapsConsensus (), this.alignViewport.isShowSequenceLogo (), this.nseq);
 }}, "~B");
-Clazz.overrideMethod (c$, "run1", 
-function (state) {
-}, "~N");
 });