-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");
-});
+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
git://source.jalview.org / jalviewjs.git / blobdiff