X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fjavascript%2FMouseOverStructureListener.js;h=c897252b605373e18e9ef059156a673c67db95f9;hp=12d1e2f4179cc80324deae176638cfaa01605cf6;hb=7301a2415adab88038b291fc54caeeb3a5a47a44;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/javascript/MouseOverStructureListener.js b/bin/jalview/javascript/MouseOverStructureListener.js
index 12d1e2f..c897252 100644
--- a/bin/jalview/javascript/MouseOverStructureListener.js
+++ b/bin/jalview/javascript/MouseOverStructureListener.js
@@ -1,143 +1,143 @@
-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");
+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");
+});