-Clazz.declarePackage ("jalview.javascript");\r
-Clazz.load (["jalview.javascript.JSFunctionExec", "$.JsCallBack", "jalview.structure.StructureListener"], "jalview.javascript.MouseOverStructureListener", ["jalview.api.AlignmentViewPanel", "jalview.appletgui.FeatureRenderer", "jalview.ext.jmol.JmolCommands", "jalview.structure.StructureSelectionManager", "java.net.URL", "java.util.ArrayList"], function () {\r
-c$ = Clazz.decorateAsClass (function () {\r
-this._listenerfn = null;\r
-this.modelSet = null;\r
-Clazz.instantialize (this, arguments);\r
-}, jalview.javascript, "MouseOverStructureListener", jalview.javascript.JSFunctionExec, [jalview.javascript.JsCallBack, jalview.structure.StructureListener]);\r
-Clazz.makeConstructor (c$, \r
-function (jalviewLite, listener, modelList) {\r
-Clazz.superConstructor (this, jalview.javascript.MouseOverStructureListener, [jalviewLite]);\r
-this._listenerfn = listener;\r
-this.modelSet = modelList;\r
-if (this.modelSet != null) {\r
-for (var i = 0; i < this.modelSet.length; i++) {\r
-try {\r
-if ( new java.net.URL (this.modelSet[i]).openConnection () != null) {\r
-continue;\r
-}} catch (x) {\r
-if (Clazz.exceptionOf (x, Exception)) {\r
-} else {\r
-throw x;\r
-}\r
-}\r
-;try {\r
-var db = this.jvlite.getDocumentBase ().toString ();\r
-db = db.substring (0, db.lastIndexOf ("/"));\r
-if ( new java.net.URL (db + "/" + this.modelSet[i]).openConnection () != null) {\r
-this.modelSet[i] = db + "/" + this.modelSet[i];\r
-continue;\r
-}} catch (x) {\r
-if (Clazz.exceptionOf (x, Exception)) {\r
-} else {\r
-throw x;\r
-}\r
-}\r
-;try {\r
-if ( new java.net.URL (this.jvlite.getCodeBase () + this.modelSet[i]).openConnection () != null) {\r
-this.modelSet[i] = this.jvlite.getCodeBase () + this.modelSet[i];\r
-continue;\r
-}} catch (x) {\r
-if (Clazz.exceptionOf (x, Exception)) {\r
-} else {\r
-throw x;\r
-}\r
-}\r
-;}\r
-}}, "jalview.bin.JalviewLite,~S,~A");\r
-Clazz.overrideMethod (c$, "getPdbFile", \r
-function () {\r
-return this.modelSet;\r
-});\r
-Clazz.defineMethod (c$, "mouseOverStructure", \r
-function (atomIndex, strInfo) {\r
-}, "~N,~S");\r
-Clazz.overrideMethod (c$, "highlightAtoms", \r
-function (atoms) {\r
-for (var atom, $atom = atoms.iterator (); $atom.hasNext () && ((atom = $atom.next ()) || true);) {\r
-try {\r
-this.executeJavascriptFunction (this._listenerfn, Clazz.newArray (-1, ["mouseover", "" + atom.getPdbFile (), "" + atom.getChain (), "" + (atom.getPdbResNum ()), "" + atom.getAtomIndex ()]));\r
-} catch (ex) {\r
-if (Clazz.exceptionOf (ex, Exception)) {\r
-System.err.println ("Couldn't execute callback with " + this._listenerfn + " for atomSpec: " + atom);\r
-ex.printStackTrace ();\r
-} else {\r
-throw ex;\r
-}\r
-}\r
-}\r
-}, "java.util.List");\r
-Clazz.overrideMethod (c$, "updateColours", \r
-function (srce) {\r
-var source = srce;\r
-var ssm = jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.jvlite);\r
-if (Clazz.instanceOf (source, jalview.api.AlignmentViewPanel)) {\r
-var sequence = new Array (this.modelSet.length);\r
-for (var m = 0; m < this.modelSet.length; m++) {\r
-var sm = ssm.getMapping (this.modelSet[m]);\r
-if (sm != null && sm.length > 0) {\r
-sequence[m] = new Array (sm.length);\r
-for (var i = 0; i < sm.length; i++) {\r
-sequence[m][i] = sm[i].getSequence ();\r
-}\r
-} else {\r
-sequence[m] = new Array (0);\r
-}}\r
-var sr = (source).getSequenceRenderer ();\r
-var fr = (source).av.isShowSequenceFeatures () ? new jalview.appletgui.FeatureRenderer ((source).av) : null;\r
-if (fr != null) {\r
-(fr).transferSettings ((source).getFeatureRenderer ());\r
-};var ccomands = new java.util.ArrayList ();\r
-var pdbfn = new java.util.ArrayList ();\r
-var colcommands = jalview.ext.jmol.JmolCommands.getColourBySequenceCommand (ssm, this.modelSet, sequence, sr, fr, (source).getAlignment ());\r
-if (colcommands == null) {\r
-return;\r
-}var sz = 0;\r
-for (var ccset, $ccset = 0, $$ccset = colcommands; $ccset < $$ccset.length && ((ccset = $$ccset[$ccset]) || true); $ccset++) {\r
-sz += ccset.commands.length;\r
-ccomands.add (ccset.commands);\r
-pdbfn.add (ccset.mapping);\r
-}\r
-var mclass;\r
-var mhandle;\r
-var ccomandset = new Array (sz);\r
-sz = 0;\r
-for (var ccset, $ccset = ccomands.iterator (); $ccset.hasNext () && ((ccset = $ccset.next ()) || true);) {\r
-System.arraycopy (ccset, 0, ccomandset, sz, ccset.length);\r
-sz += ccset.length;\r
-}\r
-if (this.jvlite.isJsMessageSetChanged (mclass = "colourstruct", mhandle = (source).av.getViewId (), ccomandset)) {\r
-this.jvlite.setJsMessageSet (mclass, mhandle, ccomandset);\r
-var st = Clazz.newArray (-1, ["colourstruct", "" + (source).av.getViewId (), "" + ccomandset.length, this.jvlite.arrayToSeparatorList (pdbfn.toArray ( new Array (pdbfn.size ())))]);\r
-try {\r
-this.executeJavascriptFunction (true, this._listenerfn, st);\r
-} catch (ex) {\r
-if (Clazz.exceptionOf (ex, Exception)) {\r
-System.err.println ("Couldn't execute callback with " + this._listenerfn + " using args { " + st[0] + ", " + st[1] + ", " + st[2] + "," + st[3] + "}");\r
-ex.printStackTrace ();\r
-} else {\r
-throw ex;\r
-}\r
-}\r
-}}}, "~O");\r
-Clazz.overrideMethod (c$, "getAlignFrame", \r
-function () {\r
-return null;\r
-});\r
-Clazz.overrideMethod (c$, "getListenerFunction", \r
-function () {\r
-return this._listenerfn;\r
-});\r
-Clazz.defineMethod (c$, "finalise", \r
-function () {\r
-this.jvlite = null;\r
-Clazz.superCall (this, jalview.javascript.MouseOverStructureListener, "finalize", []);\r
-});\r
-Clazz.overrideMethod (c$, "releaseReferences", \r
-function (svl) {\r
-}, "~O");\r
-Clazz.overrideMethod (c$, "isListeningFor", \r
-function (seq) {\r
-return true;\r
-}, "jalview.datamodel.SequenceI");\r
-});\r
+Clazz.declarePackage ("jalview.javascript");
+Clazz.load (["jalview.javascript.JSFunctionExec", "$.JsCallBack", "jalview.structure.StructureListener"], "jalview.javascript.MouseOverStructureListener", ["jalview.api.AlignmentViewPanel", "jalview.appletgui.FeatureRenderer", "jalview.ext.jmol.JmolCommands", "jalview.structure.StructureSelectionManager", "java.net.URL", "java.util.ArrayList"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this._listenerfn = null;
+this.modelSet = null;
+Clazz.instantialize (this, arguments);
+}, jalview.javascript, "MouseOverStructureListener", jalview.javascript.JSFunctionExec, [jalview.javascript.JsCallBack, jalview.structure.StructureListener]);
+Clazz.makeConstructor (c$,
+function (jalviewLite, listener, modelList) {
+Clazz.superConstructor (this, jalview.javascript.MouseOverStructureListener, [jalviewLite]);
+this._listenerfn = listener;
+this.modelSet = modelList;
+if (this.modelSet != null) {
+for (var i = 0; i < this.modelSet.length; i++) {
+try {
+if ( new java.net.URL (this.modelSet[i]).openConnection () != null) {
+continue;
+}} catch (x) {
+if (Clazz.exceptionOf (x, Exception)) {
+} else {
+throw x;
+}
+}
+;try {
+var db = this.jvlite.getDocumentBase ().toString ();
+db = db.substring (0, db.lastIndexOf ("/"));
+if ( new java.net.URL (db + "/" + this.modelSet[i]).openConnection () != null) {
+this.modelSet[i] = db + "/" + this.modelSet[i];
+continue;
+}} catch (x) {
+if (Clazz.exceptionOf (x, Exception)) {
+} else {
+throw x;
+}
+}
+;try {
+if ( new java.net.URL (this.jvlite.getCodeBase () + this.modelSet[i]).openConnection () != null) {
+this.modelSet[i] = this.jvlite.getCodeBase () + this.modelSet[i];
+continue;
+}} catch (x) {
+if (Clazz.exceptionOf (x, Exception)) {
+} else {
+throw x;
+}
+}
+;}
+}}, "jalview.bin.JalviewLite,~S,~A");
+Clazz.overrideMethod (c$, "getPdbFile",
+function () {
+return this.modelSet;
+});
+Clazz.defineMethod (c$, "mouseOverStructure",
+function (atomIndex, strInfo) {
+}, "~N,~S");
+Clazz.overrideMethod (c$, "highlightAtoms",
+function (atoms) {
+for (var atom, $atom = atoms.iterator (); $atom.hasNext () && ((atom = $atom.next ()) || true);) {
+try {
+this.executeJavascriptFunction (this._listenerfn, Clazz.newArray (-1, ["mouseover", "" + atom.getPdbFile (), "" + atom.getChain (), "" + (atom.getPdbResNum ()), "" + atom.getAtomIndex ()]));
+} catch (ex) {
+if (Clazz.exceptionOf (ex, Exception)) {
+System.err.println ("Couldn't execute callback with " + this._listenerfn + " for atomSpec: " + atom);
+ex.printStackTrace ();
+} else {
+throw ex;
+}
+}
+}
+}, "java.util.List");
+Clazz.overrideMethod (c$, "updateColours",
+function (srce) {
+var source = srce;
+var ssm = jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.jvlite);
+if (Clazz.instanceOf (source, jalview.api.AlignmentViewPanel)) {
+var sequence = new Array (this.modelSet.length);
+for (var m = 0; m < this.modelSet.length; m++) {
+var sm = ssm.getMapping (this.modelSet[m]);
+if (sm != null && sm.length > 0) {
+sequence[m] = new Array (sm.length);
+for (var i = 0; i < sm.length; i++) {
+sequence[m][i] = sm[i].getSequence ();
+}
+} else {
+sequence[m] = new Array (0);
+}}
+var sr = (source).getSequenceRenderer ();
+var fr = (source).av.isShowSequenceFeatures () ? new jalview.appletgui.FeatureRenderer ((source).av) : null;
+if (fr != null) {
+(fr).transferSettings ((source).getFeatureRenderer ());
+};var ccomands = new java.util.ArrayList ();
+var pdbfn = new java.util.ArrayList ();
+var colcommands = jalview.ext.jmol.JmolCommands.getColourBySequenceCommand (ssm, this.modelSet, sequence, sr, fr, (source).getAlignment ());
+if (colcommands == null) {
+return;
+}var sz = 0;
+for (var ccset, $ccset = 0, $$ccset = colcommands; $ccset < $$ccset.length && ((ccset = $$ccset[$ccset]) || true); $ccset++) {
+sz += ccset.commands.length;
+ccomands.add (ccset.commands);
+pdbfn.add (ccset.mapping);
+}
+var mclass;
+var mhandle;
+var ccomandset = new Array (sz);
+sz = 0;
+for (var ccset, $ccset = ccomands.iterator (); $ccset.hasNext () && ((ccset = $ccset.next ()) || true);) {
+System.arraycopy (ccset, 0, ccomandset, sz, ccset.length);
+sz += ccset.length;
+}
+if (this.jvlite.isJsMessageSetChanged (mclass = "colourstruct", mhandle = (source).av.getViewId (), ccomandset)) {
+this.jvlite.setJsMessageSet (mclass, mhandle, ccomandset);
+var st = Clazz.newArray (-1, ["colourstruct", "" + (source).av.getViewId (), "" + ccomandset.length, this.jvlite.arrayToSeparatorList (pdbfn.toArray ( new Array (pdbfn.size ())))]);
+try {
+this.executeJavascriptFunction (true, this._listenerfn, st);
+} catch (ex) {
+if (Clazz.exceptionOf (ex, Exception)) {
+System.err.println ("Couldn't execute callback with " + this._listenerfn + " using args { " + st[0] + ", " + st[1] + ", " + st[2] + "," + st[3] + "}");
+ex.printStackTrace ();
+} else {
+throw ex;
+}
+}
+}}}, "~O");
+Clazz.overrideMethod (c$, "getAlignFrame",
+function () {
+return null;
+});
+Clazz.overrideMethod (c$, "getListenerFunction",
+function () {
+return this._listenerfn;
+});
+Clazz.defineMethod (c$, "finalise",
+function () {
+this.jvlite = null;
+Clazz.superCall (this, jalview.javascript.MouseOverStructureListener, "finalize", []);
+});
+Clazz.overrideMethod (c$, "releaseReferences",
+function (svl) {
+}, "~O");
+Clazz.overrideMethod (c$, "isListeningFor",
+function (seq) {
+return true;
+}, "jalview.datamodel.SequenceI");
+});
git://source.jalview.org / jalviewjs.git / blobdiff