X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fworkers%2FStrucConsensusThread.js;h=dbe6d50a176bc520dfc219e7a00e0fc3a5186a82;hp=4010f84a002518c99ce3d0a32a69d3d6aefa43b8;hb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/workers/StrucConsensusThread.js b/bin/jalview/workers/StrucConsensusThread.js
index 4010f84..dbe6d50 100644
--- a/bin/jalview/workers/StrucConsensusThread.js
+++ b/bin/jalview/workers/StrucConsensusThread.js
@@ -1,95 +1,95 @@
-Clazz.declarePackage ("jalview.workers");
-Clazz.load (["jalview.api.AlignCalcWorkerI", "jalview.workers.AlignCalcWorker"], "jalview.workers.StrucConsensusThread", ["jalview.analysis.StructureFrequency", "java.lang.Thread"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.strucConsensus = null;
-this.hStrucConsensus = null;
-this.nseq = -1;
-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)) {
-return;
-}this.calcMan.notifyStart (this);
-while (!this.calcMan.notifyWorking (this)) {
-try {
-if (this.ap != null) {
-}Thread.sleep (200);
-} catch (ex) {
-if (Clazz.exceptionOf (ex, Exception)) {
-ex.printStackTrace ();
-} else {
-throw ex;
-}
-}
-}
-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;
-}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];
-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)) {
-this.calcMan.workerComplete (this);
-return;
-} else {
-throw x;
-}
-}
-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.calcMan.workerCannotRun (this);
-this.ap.raiseOOMWarning ("calculating RNA structure consensus", error);
-} else {
-throw error;
-}
-} finally {
-this.calcMan.workerComplete (this);
-if (this.ap != null) {
-this.ap.paintAlignment (true);
-}}
-});
-Clazz.overrideMethod (c$, "updateAnnotation", 
-function () {
-this.updateResultAnnotation (false);
-});
-Clazz.defineMethod (c$, "updateResultAnnotation", 
-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$, "run1", 
-function (state) {
-}, "~N");
-});
+Clazz.declarePackage ("jalview.workers");
+Clazz.load (["jalview.api.AlignCalcWorkerI", "jalview.workers.AlignCalcWorker"], "jalview.workers.StrucConsensusThread", ["jalview.analysis.StructureFrequency", "java.lang.Thread"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.strucConsensus = null;
+this.hStrucConsensus = null;
+this.nseq = -1;
+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)) {
+return;
+}this.calcMan.notifyStart (this);
+while (!this.calcMan.notifyWorking (this)) {
+try {
+if (this.ap != null) {
+}Thread.sleep (200);
+} catch (ex) {
+if (Clazz.exceptionOf (ex, Exception)) {
+ex.printStackTrace ();
+} else {
+throw ex;
+}
+}
+}
+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;
+}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];
+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)) {
+this.calcMan.workerComplete (this);
+return;
+} else {
+throw x;
+}
+}
+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.calcMan.workerCannotRun (this);
+this.ap.raiseOOMWarning ("calculating RNA structure consensus", error);
+} else {
+throw error;
+}
+} finally {
+this.calcMan.workerComplete (this);
+if (this.ap != null) {
+this.ap.paintAlignment (true);
+}}
+});
+Clazz.overrideMethod (c$, "updateAnnotation", 
+function () {
+this.updateResultAnnotation (false);
+});
+Clazz.defineMethod (c$, "updateResultAnnotation", 
+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");
+});