-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$, "run1",
-function (state) {
-}, "~N");
-});
+Clazz.declarePackage ("jalview.workers");\r
+Clazz.load (["jalview.api.AlignCalcWorkerI", "jalview.workers.AlignCalcWorker"], "jalview.workers.StrucConsensusThread", ["jalview.analysis.StructureFrequency", "java.lang.Thread"], function () {\r
+c$ = Clazz.decorateAsClass (function () {\r
+this.strucConsensus = null;\r
+this.hStrucConsensus = null;\r
+this.nseq = -1;\r
+Clazz.instantialize (this, arguments);\r
+}, jalview.workers, "StrucConsensusThread", jalview.workers.AlignCalcWorker, jalview.api.AlignCalcWorkerI);\r
+Clazz.overrideMethod (c$, "getNewWorker", \r
+function () {\r
+return new jalview.workers.StrucConsensusThread (this.alignViewport, this.ap);\r
+});\r
+Clazz.overrideMethod (c$, "run", \r
+function () {\r
+try {\r
+if (this.calcMan.isPending (this)) {\r
+return;\r
+}this.calcMan.notifyStart (this);\r
+while (!this.calcMan.notifyWorking (this)) {\r
+try {\r
+if (this.ap != null) {\r
+}Thread.sleep (200);\r
+} catch (ex) {\r
+if (Clazz.exceptionOf (ex, Exception)) {\r
+ex.printStackTrace ();\r
+} else {\r
+throw ex;\r
+}\r
+}\r
+}\r
+if (this.alignViewport.isClosed ()) {\r
+this.abortAndDestroy ();\r
+return;\r
+}var alignment = this.alignViewport.getAlignment ();\r
+var aWidth = -1;\r
+if (alignment == null || (aWidth = alignment.getWidth ()) < 0) {\r
+this.calcMan.workerComplete (this);\r
+return;\r
+}this.strucConsensus = this.alignViewport.getAlignmentStrucConsensusAnnotation ();\r
+this.hStrucConsensus = this.alignViewport.getRnaStructureConsensusHash ();\r
+this.strucConsensus.annotations = null;\r
+this.strucConsensus.annotations = new Array (aWidth);\r
+this.hStrucConsensus = new Array (aWidth);\r
+var aa = this.alignViewport.getAlignment ().getAlignmentAnnotation ();\r
+var rnaStruc = null;\r
+for (var i = 0; i < aa.length; i++) {\r
+if (aa[i].getRNAStruc () != null && aa[i].isValidStruc ()) {\r
+rnaStruc = aa[i];\r
+break;\r
+}}\r
+if (rnaStruc == null || !rnaStruc.isValidStruc ()) {\r
+this.calcMan.workerComplete (this);\r
+return;\r
+}try {\r
+var arr = alignment.getSequencesArray ();\r
+this.nseq = arr.length;\r
+jalview.analysis.StructureFrequency.calculate (arr, 0, alignment.getWidth (), this.hStrucConsensus, true, rnaStruc);\r
+} catch (x) {\r
+if (Clazz.exceptionOf (x, ArrayIndexOutOfBoundsException)) {\r
+this.calcMan.workerComplete (this);\r
+return;\r
+} else {\r
+throw x;\r
+}\r
+}\r
+this.alignViewport.setRnaStructureConsensusHash (this.hStrucConsensus);\r
+this.updateResultAnnotation (true);\r
+if (this.alignViewport.getGlobalColourScheme () != null) {\r
+this.alignViewport.getGlobalColourScheme ().setConsensus (this.hStrucConsensus);\r
+}} catch (error) {\r
+if (Clazz.exceptionOf (error, OutOfMemoryError)) {\r
+this.calcMan.workerCannotRun (this);\r
+this.ap.raiseOOMWarning ("calculating RNA structure consensus", error);\r
+} else {\r
+throw error;\r
+}\r
+} finally {\r
+this.calcMan.workerComplete (this);\r
+if (this.ap != null) {\r
+this.ap.paintAlignment (true);\r
+}}\r
+});\r
+Clazz.overrideMethod (c$, "updateAnnotation", \r
+function () {\r
+this.updateResultAnnotation (false);\r
+});\r
+Clazz.defineMethod (c$, "updateResultAnnotation", \r
+function (immediate) {\r
+if (immediate || !this.calcMan.isWorking (this) && this.strucConsensus != null && this.hStrucConsensus != null) {\r
+jalview.analysis.StructureFrequency.completeConsensus (this.strucConsensus, this.hStrucConsensus, 0, this.hStrucConsensus.length, this.alignViewport.isIgnoreGapsConsensus (), this.alignViewport.isShowSequenceLogo (), this.nseq);\r
+}}, "~B");\r
+Clazz.overrideMethod (c$, "run1", \r
+function (state) {\r
+}, "~N");\r
+});\r
git://source.jalview.org / jalviewjs.git / blobdiff