X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fworkers%2FAlignCalcManager.js;fp=site%2Fj2s%2Fjalview%2Fworkers%2FAlignCalcManager.js;h=39105f89a3e6fbe9c395a21a2c67c506cedfc034;hp=7f25a9c460d7ebc11f5bd7394ce7b21adf822ed0;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/j2s/jalview/workers/AlignCalcManager.js b/site/j2s/jalview/workers/AlignCalcManager.js
index 7f25a9c..39105f8 100644
--- a/site/j2s/jalview/workers/AlignCalcManager.js
+++ b/site/j2s/jalview/workers/AlignCalcManager.js
@@ -1,192 +1,192 @@
-Clazz.declarePackage ("jalview.workers");
-Clazz.load (["jalview.api.AlignCalcManagerI", "java.util.ArrayList", "$.Collections", "$.HashSet", "$.Hashtable"], "jalview.workers.AlignCalcManager", null, function () {
-c$ = Clazz.decorateAsClass (function () {
-this.restartable = null;
-this.blackList = null;
-this.inProgress = null;
-this.updating = null;
-this.canUpdate = null;
-Clazz.instantialize (this, arguments);
-}, jalview.workers, "AlignCalcManager", null, jalview.api.AlignCalcManagerI);
-Clazz.prepareFields (c$, function () {
-this.restartable = java.util.Collections.synchronizedList ( new java.util.ArrayList ());
-this.blackList = java.util.Collections.synchronizedList ( new java.util.ArrayList ());
-this.inProgress = java.util.Collections.synchronizedMap ( new java.util.Hashtable ());
-this.updating = java.util.Collections.synchronizedMap ( new java.util.Hashtable ());
-this.canUpdate =  new java.util.HashSet ();
-});
-Clazz.overrideMethod (c$, "notifyStart", 
-function (worker) {
-{
-var upd = this.updating.get (worker.getClass ());
-if (upd == null) {
-this.updating.put (worker.getClass (), upd = java.util.Collections.synchronizedList ( new java.util.ArrayList ()));
-}{
-upd.add (worker);
-}}}, "jalview.api.AlignCalcWorkerI");
-Clazz.overrideMethod (c$, "alreadyDoing", 
-function (worker) {
-{
-return this.inProgress.containsKey (worker.getClass ());
-}}, "jalview.api.AlignCalcWorkerI");
-Clazz.overrideMethod (c$, "isPending", 
-function (workingClass) {
-var upd;
-{
-upd = this.updating.get (workingClass.getClass ());
-if (upd == null) {
-return false;
-}{
-if (upd.size () > 1) {
-return true;
-}}return false;
-}}, "jalview.api.AlignCalcWorkerI");
-Clazz.defineMethod (c$, "numberLive", 
-function (worker) {
-{
-var upd = this.updating.get (worker.getClass ());
-if (upd == null) {
-return 0;
-};return upd.size ();
-}}, "jalview.api.AlignCalcWorkerI");
-Clazz.overrideMethod (c$, "notifyWorking", 
-function (worker) {
-{
-if (this.inProgress.get (worker.getClass ()) != null) {
-if (false) {
-System.err.println ("Warning: Multiple workers are running of type " + worker.getClass ());
-}return false;
-}this.inProgress.put (worker.getClass (), worker);
-}return true;
-}, "jalview.api.AlignCalcWorkerI");
-Clazz.overrideMethod (c$, "workerComplete", 
-function (worker) {
-{
-this.inProgress.remove (worker.getClass ());
-var upd = this.updating.get (worker.getClass ());
-if (upd != null) {
-{
-upd.remove (worker);
-}this.canUpdate.add (worker);
-}}}, "jalview.api.AlignCalcWorkerI");
-Clazz.overrideMethod (c$, "workerCannotRun", 
-function (worker) {
-{
-this.blackList.add (worker.getClass ());
-}}, "jalview.api.AlignCalcWorkerI");
-Clazz.defineMethod (c$, "isBlackListed", 
-function (workerType) {
-{
-return this.blackList.contains (workerType);
-}}, "Class");
-Clazz.overrideMethod (c$, "startWorker", 
-function (worker) {
-var workerAsThread = worker;
-if (workerAsThread.isAlive ()) {
-workerAsThread.interrupt ();
-worker = worker.getNewWorker ();
-}worker.setName (worker.getClass ().getName ());
-worker.start ();
-}, "jalview.api.AlignCalcWorkerI");
-Clazz.defineMethod (c$, "isWorking", 
-function (worker) {
-{
-return worker != null && this.inProgress.get (worker.getClass ()) === worker;
-}}, "jalview.api.AlignCalcWorkerI");
-Clazz.defineMethod (c$, "isWorking", 
-function () {
-{
-return this.inProgress.size () > 0;
-}});
-Clazz.overrideMethod (c$, "registerWorker", 
-function (worker) {
-{
-if (!this.restartable.contains (worker)) {
-this.restartable.add (worker);
-}this.startWorker (worker);
-}}, "jalview.api.AlignCalcWorkerI");
-Clazz.overrideMethod (c$, "restartWorkers", 
-function () {
-{
-for (var worker, $worker = this.restartable.iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) {
-this.startWorker (worker);
-}
-}});
-Clazz.overrideMethod (c$, "workingInvolvedWith", 
-function (alignmentAnnotation) {
-{
-for (var worker, $worker = this.inProgress.values ().iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) {
-if (worker.involves (alignmentAnnotation)) {
-return true;
-}}
-}{
-for (var workers, $workers = this.updating.values ().iterator (); $workers.hasNext () && ((workers = $workers.next ()) || true);) {
-for (var worker, $worker = workers.iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) {
-if (worker.involves (alignmentAnnotation)) {
-return true;
-}}
-}
-}return false;
-}, "jalview.datamodel.AlignmentAnnotation");
-Clazz.overrideMethod (c$, "updateAnnotationFor", 
-function (workerClass) {
-var workers;
-{
-workers = this.canUpdate.toArray ( new Array (0));
-}for (var worker, $worker = 0, $$worker = workers; $worker < $$worker.length && ((worker = $$worker[$worker]) || true); $worker++) {
-if (workerClass.equals (worker.getClass ())) {
-worker.updateAnnotation ();
-}}
-}, "Class");
-Clazz.overrideMethod (c$, "getRegisteredWorkersOfClass", 
-function (workerClass) {
-var workingClass =  new java.util.ArrayList ();
-var workers;
-{
-workers = this.canUpdate.toArray ( new Array (this.canUpdate.size ()));
-}for (var worker, $worker = 0, $$worker = workers; $worker < $$worker.length && ((worker = $$worker[$worker]) || true); $worker++) {
-if (workerClass.equals (worker.getClass ())) {
-workingClass.add (worker);
-}}
-return (workingClass.size () == 0) ? null : workingClass;
-}, "Class");
-Clazz.overrideMethod (c$, "startRegisteredWorkersOfClass", 
-function (workerClass) {
-var workers = this.getRegisteredWorkersOfClass (workerClass);
-if (workers == null) {
-return false;
-}for (var worker, $worker = workers.iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) {
-if (!this.isPending (worker)) {
-this.startWorker (worker);
-} else {
-System.err.println ("Pending exists for " + workerClass);
-}}
-return true;
-}, "Class");
-Clazz.overrideMethod (c$, "workerMayRun", 
-function (worker) {
-{
-if (this.blackList.contains (worker.getClass ())) {
-this.blackList.remove (worker.getClass ());
-}}}, "jalview.api.AlignCalcWorkerI");
-Clazz.overrideMethod (c$, "removeRegisteredWorkersOfClass", 
-function (typeToRemove) {
-var workers = this.getRegisteredWorkersOfClass (typeToRemove);
-var removable =  new java.util.ArrayList ();
-var toremovannot =  new java.util.HashSet ();
-{
-for (var worker, $worker = this.restartable.iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) {
-if (typeToRemove.equals (worker.getClass ())) {
-removable.add (worker);
-toremovannot.add (worker);
-}}
-this.restartable.removeAll (removable);
-}{
-for (var worker, $worker = this.canUpdate.iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) {
-if (typeToRemove.equals (worker.getClass ())) {
-removable.add (worker);
-toremovannot.add (worker);
-}}
-this.canUpdate.removeAll (removable);
-}}, "Class");
-});
+Clazz.declarePackage ("jalview.workers");
+Clazz.load (["jalview.api.AlignCalcManagerI", "java.util.ArrayList", "$.Collections", "$.HashSet", "$.Hashtable"], "jalview.workers.AlignCalcManager", null, function () {
+c$ = Clazz.decorateAsClass (function () {
+this.restartable = null;
+this.blackList = null;
+this.inProgress = null;
+this.updating = null;
+this.canUpdate = null;
+Clazz.instantialize (this, arguments);
+}, jalview.workers, "AlignCalcManager", null, jalview.api.AlignCalcManagerI);
+Clazz.prepareFields (c$, function () {
+this.restartable = java.util.Collections.synchronizedList ( new java.util.ArrayList ());
+this.blackList = java.util.Collections.synchronizedList ( new java.util.ArrayList ());
+this.inProgress = java.util.Collections.synchronizedMap ( new java.util.Hashtable ());
+this.updating = java.util.Collections.synchronizedMap ( new java.util.Hashtable ());
+this.canUpdate =  new java.util.HashSet ();
+});
+Clazz.overrideMethod (c$, "notifyStart", 
+function (worker) {
+{
+var upd = this.updating.get (worker.getClass ());
+if (upd == null) {
+this.updating.put (worker.getClass (), upd = java.util.Collections.synchronizedList ( new java.util.ArrayList ()));
+}{
+upd.add (worker);
+}}}, "jalview.api.AlignCalcWorkerI");
+Clazz.overrideMethod (c$, "alreadyDoing", 
+function (worker) {
+{
+return this.inProgress.containsKey (worker.getClass ());
+}}, "jalview.api.AlignCalcWorkerI");
+Clazz.overrideMethod (c$, "isPending", 
+function (workingClass) {
+var upd;
+{
+upd = this.updating.get (workingClass.getClass ());
+if (upd == null) {
+return false;
+}{
+if (upd.size () > 1) {
+return true;
+}}return false;
+}}, "jalview.api.AlignCalcWorkerI");
+Clazz.defineMethod (c$, "numberLive", 
+function (worker) {
+{
+var upd = this.updating.get (worker.getClass ());
+if (upd == null) {
+return 0;
+};return upd.size ();
+}}, "jalview.api.AlignCalcWorkerI");
+Clazz.overrideMethod (c$, "notifyWorking", 
+function (worker) {
+{
+if (this.inProgress.get (worker.getClass ()) != null) {
+if (false) {
+System.err.println ("Warning: Multiple workers are running of type " + worker.getClass ());
+}return false;
+}this.inProgress.put (worker.getClass (), worker);
+}return true;
+}, "jalview.api.AlignCalcWorkerI");
+Clazz.overrideMethod (c$, "workerComplete", 
+function (worker) {
+{
+this.inProgress.remove (worker.getClass ());
+var upd = this.updating.get (worker.getClass ());
+if (upd != null) {
+{
+upd.remove (worker);
+}this.canUpdate.add (worker);
+}}}, "jalview.api.AlignCalcWorkerI");
+Clazz.overrideMethod (c$, "workerCannotRun", 
+function (worker) {
+{
+this.blackList.add (worker.getClass ());
+}}, "jalview.api.AlignCalcWorkerI");
+Clazz.defineMethod (c$, "isBlackListed", 
+function (workerType) {
+{
+return this.blackList.contains (workerType);
+}}, "Class");
+Clazz.overrideMethod (c$, "startWorker", 
+function (worker) {
+var workerAsThread = worker;
+if (workerAsThread.isAlive ()) {
+workerAsThread.interrupt ();
+worker = worker.getNewWorker ();
+}worker.setName (worker.getClass ().getName ());
+worker.start ();
+}, "jalview.api.AlignCalcWorkerI");
+Clazz.defineMethod (c$, "isWorking", 
+function (worker) {
+{
+return worker != null && this.inProgress.get (worker.getClass ()) === worker;
+}}, "jalview.api.AlignCalcWorkerI");
+Clazz.defineMethod (c$, "isWorking", 
+function () {
+{
+return this.inProgress.size () > 0;
+}});
+Clazz.overrideMethod (c$, "registerWorker", 
+function (worker) {
+{
+if (!this.restartable.contains (worker)) {
+this.restartable.add (worker);
+}this.startWorker (worker);
+}}, "jalview.api.AlignCalcWorkerI");
+Clazz.overrideMethod (c$, "restartWorkers", 
+function () {
+{
+for (var worker, $worker = this.restartable.iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) {
+this.startWorker (worker);
+}
+}});
+Clazz.overrideMethod (c$, "workingInvolvedWith", 
+function (alignmentAnnotation) {
+{
+for (var worker, $worker = this.inProgress.values ().iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) {
+if (worker.involves (alignmentAnnotation)) {
+return true;
+}}
+}{
+for (var workers, $workers = this.updating.values ().iterator (); $workers.hasNext () && ((workers = $workers.next ()) || true);) {
+for (var worker, $worker = workers.iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) {
+if (worker.involves (alignmentAnnotation)) {
+return true;
+}}
+}
+}return false;
+}, "jalview.datamodel.AlignmentAnnotation");
+Clazz.overrideMethod (c$, "updateAnnotationFor", 
+function (workerClass) {
+var workers;
+{
+workers = this.canUpdate.toArray ( new Array (0));
+}for (var worker, $worker = 0, $$worker = workers; $worker < $$worker.length && ((worker = $$worker[$worker]) || true); $worker++) {
+if (workerClass.equals (worker.getClass ())) {
+worker.updateAnnotation ();
+}}
+}, "Class");
+Clazz.overrideMethod (c$, "getRegisteredWorkersOfClass", 
+function (workerClass) {
+var workingClass =  new java.util.ArrayList ();
+var workers;
+{
+workers = this.canUpdate.toArray ( new Array (this.canUpdate.size ()));
+}for (var worker, $worker = 0, $$worker = workers; $worker < $$worker.length && ((worker = $$worker[$worker]) || true); $worker++) {
+if (workerClass.equals (worker.getClass ())) {
+workingClass.add (worker);
+}}
+return (workingClass.size () == 0) ? null : workingClass;
+}, "Class");
+Clazz.overrideMethod (c$, "startRegisteredWorkersOfClass", 
+function (workerClass) {
+var workers = this.getRegisteredWorkersOfClass (workerClass);
+if (workers == null) {
+return false;
+}for (var worker, $worker = workers.iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) {
+if (!this.isPending (worker)) {
+this.startWorker (worker);
+} else {
+System.err.println ("Pending exists for " + workerClass);
+}}
+return true;
+}, "Class");
+Clazz.overrideMethod (c$, "workerMayRun", 
+function (worker) {
+{
+if (this.blackList.contains (worker.getClass ())) {
+this.blackList.remove (worker.getClass ());
+}}}, "jalview.api.AlignCalcWorkerI");
+Clazz.overrideMethod (c$, "removeRegisteredWorkersOfClass", 
+function (typeToRemove) {
+var workers = this.getRegisteredWorkersOfClass (typeToRemove);
+var removable =  new java.util.ArrayList ();
+var toremovannot =  new java.util.HashSet ();
+{
+for (var worker, $worker = this.restartable.iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) {
+if (typeToRemove.equals (worker.getClass ())) {
+removable.add (worker);
+toremovannot.add (worker);
+}}
+this.restartable.removeAll (removable);
+}{
+for (var worker, $worker = this.canUpdate.iterator (); $worker.hasNext () && ((worker = $worker.next ()) || true);) {
+if (typeToRemove.equals (worker.getClass ())) {
+removable.add (worker);
+toremovannot.add (worker);
+}}
+this.canUpdate.removeAll (removable);
+}}, "Class");
+});