-Clazz.declarePackage ("jalview.appletgui");
-Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "awt2swing.Button", "$.Checkbox", "$.Label", "$.TextField", "java.awt.GridLayout"], "jalview.appletgui.Finder", ["awt2swing.Frame", "jalview.analysis.Finder", "jalview.bin.JalviewLite", "jalview.datamodel.SequenceFeature", "jalview.util.MessageManager", "java.awt.Font", "$.Rectangle", "java.awt.event.KeyAdapter", "$.WindowAdapter"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.av = null;
-this.ap = null;
-this.frame = null;
-this.searchResults = null;
-this.seqIndex = 0;
-this.resIndex = -1;
-this.jLabel1 = null;
-this.textfield = null;
-this.findAll = null;
-this.findNext = null;
-this.actionsPanel = null;
-this.gridLayout1 = null;
-this.createNewGroup = null;
-this.caseSensitive = null;
-this.searchDescription = null;
-Clazz.instantialize (this, arguments);
-}, jalview.appletgui, "Finder", awt2swing.Panel, java.awt.event.ActionListener);
-Clazz.prepareFields (c$, function () {
-this.jLabel1 = new awt2swing.Label ();
-this.textfield = new awt2swing.TextField ();
-this.findAll = new awt2swing.Button ();
-this.findNext = new awt2swing.Button ();
-this.actionsPanel = new awt2swing.Panel ();
-this.gridLayout1 = new java.awt.GridLayout ();
-this.createNewGroup = new awt2swing.Button ();
-this.caseSensitive = new awt2swing.Checkbox ();
-this.searchDescription = new awt2swing.Checkbox ();
-});
-Clazz.makeConstructor (c$,
-function (ap) {
-Clazz.superConstructor (this, jalview.appletgui.Finder, []);
-try {
-this.jbInit ();
-} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-e.printStackTrace ();
-} else {
-throw e;
-}
-}
-this.av = ap.av;
-this.ap = ap;
-this.frame = new awt2swing.Frame ();
-this.frame.add (this);
-jalview.bin.JalviewLite.addFrame (this.frame, jalview.util.MessageManager.getString ("action.find"), 340, 120);
-this.frame.repaint ();
-this.frame.addWindowListener (((Clazz.isClassDefined ("jalview.appletgui.Finder$1") ? 0 : jalview.appletgui.Finder.$Finder$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.Finder$1, this, Clazz.cloneFinals ("ap", ap))));
-this.textfield.requestFocus ();
-}, "jalview.appletgui.AlignmentPanel");
-Clazz.overrideMethod (c$, "actionPerformed",
-function (evt) {
-if (evt.getSource () === this.textfield) {
-this.doSearch (false);
-} else if (evt.getSource () === this.findNext) {
-this.doSearch (false);
-} else if (evt.getSource () === this.findAll) {
-this.resIndex = -1;
-this.seqIndex = 0;
-this.doSearch (true);
-} else if (evt.getSource () === this.createNewGroup) {
-this.createNewGroup_actionPerformed ();
-}}, "java.awt.event.ActionEvent");
-Clazz.defineMethod (c$, "createNewGroup_actionPerformed",
-function () {
-var seqs = new Array (this.searchResults.getSize ());
-var features = new Array (this.searchResults.getSize ());
-for (var i = 0; i < this.searchResults.getSize (); i++) {
-seqs[i] = this.searchResults.getResultSequence (i);
-features[i] = new jalview.datamodel.SequenceFeature (this.textfield.getText ().trim (), "Search Results", null, this.searchResults.getResultStart (i), this.searchResults.getResultEnd (i), "Search Results");
-}
-if (this.ap.seqPanel.seqCanvas.getFeatureRenderer ().amendFeatures (seqs, features, true, this.ap)) {
-this.ap.alignFrame.sequenceFeatures.setState (true);
-this.av.setShowSequenceFeatures (true);
-this.ap.highlightSearchResults (null);
-}});
-Clazz.defineMethod (c$, "doSearch",
-function (findAll) {
-if (this.ap.av.applet.currentAlignFrame != null) {
-this.ap = this.ap.av.applet.currentAlignFrame.alignPanel;
-this.av = this.ap.av;
-}this.createNewGroup.setEnabled (false);
-var finder = new jalview.analysis.Finder (this.av.getAlignment (), this.av.getSelectionGroup (), this.seqIndex, this.resIndex);
-finder.setCaseSensitive (this.caseSensitive.getState ());
-finder.setIncludeDescription (this.searchDescription.getState ());
-finder.setFindAll (findAll);
-var searchString = this.textfield.getText ();
-finder.find (searchString);
-this.seqIndex = finder.getSeqIndex ();
-this.resIndex = finder.getResIndex ();
-this.searchResults = finder.getSearchResults ();
-var idMatch = finder.getIdMatch ();
-var haveResults = false;
-if ((idMatch.size () > 0)) {
-haveResults = true;
-this.ap.idPanel.highlightSearchResults (idMatch);
-} else {
-this.ap.idPanel.highlightSearchResults (null);
-}if (this.searchResults.getSize () > 0) {
-haveResults = true;
-this.createNewGroup.setEnabled (true);
-} else {
-this.searchResults = null;
-}this.ap.highlightSearchResults (this.searchResults);
-if (!haveResults) {
-this.ap.alignFrame.setStatus (jalview.util.MessageManager.getString ("label.finished_searching"));
-this.resIndex = -1;
-this.seqIndex = 0;
-} else {
-if (findAll) {
-var message = (idMatch.size () > 0) ? "" + idMatch.size () + " IDs" : "";
-if (idMatch.size () > 0 && this.searchResults != null && this.searchResults.getSize () > 0) {
-message += " and ";
-}if (this.searchResults != null) {
-message += this.searchResults.getSize () + " subsequence matches.";
-}this.ap.alignFrame.setStatus (jalview.util.MessageManager.formatMessage ("label.search_results", Clazz.newArray (-1, [searchString, message])));
-} else {
-this.ap.alignFrame.setStatus (jalview.util.MessageManager.formatMessage ("label.found_match_for", Clazz.newArray (-1, [searchString])));
-}}}, "~B");
-Clazz.defineMethod (c$, "jbInit",
-($fz = function () {
-this.jLabel1.setFont ( new java.awt.Font ("Verdana", 0, 12));
-this.jLabel1.setText (jalview.util.MessageManager.getString ("action.find"));
-this.jLabel1.setBounds ( new java.awt.Rectangle (3, 30, 34, 15));
-this.setLayout (null);
-this.textfield.setFont ( new java.awt.Font ("Verdana", 0, 10));
-this.textfield.setText ("");
-this.textfield.setBounds ( new java.awt.Rectangle (40, 17, 133, 21));
-this.textfield.addKeyListener (((Clazz.isClassDefined ("jalview.appletgui.Finder$2") ? 0 : jalview.appletgui.Finder.$Finder$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.Finder$2, this, null)));
-this.textfield.addActionListener (this);
-this.findAll.setFont ( new java.awt.Font ("Verdana", 0, 10));
-this.findAll.setLabel (jalview.util.MessageManager.getString ("action.find_all"));
-this.findAll.addActionListener (this);
-this.findNext.setEnabled (false);
-this.findNext.setFont ( new java.awt.Font ("Verdana", 0, 10));
-this.findNext.setLabel (jalview.util.MessageManager.getString ("action.find_next"));
-this.findNext.addActionListener (this);
-this.actionsPanel.setBounds ( new java.awt.Rectangle (195, 5, 141, 64));
-this.actionsPanel.setLayout (this.gridLayout1);
-this.gridLayout1.setHgap (0);
-this.gridLayout1.setRows (3);
-this.gridLayout1.setVgap (2);
-this.createNewGroup.setEnabled (false);
-this.createNewGroup.setFont ( new java.awt.Font ("Verdana", 0, 10));
-this.createNewGroup.setLabel (jalview.util.MessageManager.getString ("label.new_feature"));
-this.createNewGroup.addActionListener (this);
-this.caseSensitive.setLabel (jalview.util.MessageManager.getString ("label.match_case"));
-this.caseSensitive.setBounds ( new java.awt.Rectangle (30, 39, 126, 23));
-this.searchDescription.setLabel (jalview.util.MessageManager.getString ("label.include_description"));
-this.searchDescription.setBounds ( new java.awt.Rectangle (30, 59, 170, 23));
-this.actionsPanel.add (this.findNext, null);
-this.actionsPanel.add (this.findAll, null);
-this.actionsPanel.add (this.createNewGroup, null);
-this.add (this.caseSensitive);
-this.add (this.textfield, null);
-this.add (this.jLabel1, null);
-this.add (this.actionsPanel, null);
-this.add (this.searchDescription);
-}, $fz.isPrivate = true, $fz));
-Clazz.defineMethod (c$, "textfield_keyTyped",
-function (e) {
-this.findNext.setEnabled (true);
-}, "java.awt.event.KeyEvent");
-c$.$Finder$1$ = function () {
-Clazz.pu$h ();
-c$ = Clazz.declareAnonymous (jalview.appletgui, "Finder$1", java.awt.event.WindowAdapter);
-Clazz.overrideMethod (c$, "windowClosing",
-function (evt) {
-this.f$.ap.highlightSearchResults (null);
-}, "java.awt.event.WindowEvent");
-c$ = Clazz.p0p ();
-};
-c$.$Finder$2$ = function () {
-Clazz.pu$h ();
-c$ = Clazz.declareAnonymous (jalview.appletgui, "Finder$2", java.awt.event.KeyAdapter);
-Clazz.overrideMethod (c$, "keyTyped",
-function (e) {
-this.b$["jalview.appletgui.Finder"].textfield_keyTyped (e);
-}, "java.awt.event.KeyEvent");
-c$ = Clazz.p0p ();
-};
-});
+Clazz.declarePackage ("jalview.appletgui");\r
+Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "awt2swing.Button", "$.Checkbox", "$.Label", "$.TextField", "java.awt.GridLayout"], "jalview.appletgui.Finder", ["awt2swing.Frame", "jalview.analysis.Finder", "jalview.bin.JalviewLite", "jalview.datamodel.SequenceFeature", "jalview.util.MessageManager", "java.awt.Font", "$.Rectangle", "java.awt.event.KeyAdapter", "$.WindowAdapter"], function () {\r
+c$ = Clazz.decorateAsClass (function () {\r
+this.av = null;\r
+this.ap = null;\r
+this.frame = null;\r
+this.searchResults = null;\r
+this.seqIndex = 0;\r
+this.resIndex = -1;\r
+this.jLabel1 = null;\r
+this.textfield = null;\r
+this.findAll = null;\r
+this.findNext = null;\r
+this.actionsPanel = null;\r
+this.gridLayout1 = null;\r
+this.createNewGroup = null;\r
+this.caseSensitive = null;\r
+this.searchDescription = null;\r
+Clazz.instantialize (this, arguments);\r
+}, jalview.appletgui, "Finder", awt2swing.Panel, java.awt.event.ActionListener);\r
+Clazz.prepareFields (c$, function () {\r
+this.jLabel1 = new awt2swing.Label ();\r
+this.textfield = new awt2swing.TextField ();\r
+this.findAll = new awt2swing.Button ();\r
+this.findNext = new awt2swing.Button ();\r
+this.actionsPanel = new awt2swing.Panel ();\r
+this.gridLayout1 = new java.awt.GridLayout ();\r
+this.createNewGroup = new awt2swing.Button ();\r
+this.caseSensitive = new awt2swing.Checkbox ();\r
+this.searchDescription = new awt2swing.Checkbox ();\r
+});\r
+Clazz.makeConstructor (c$, \r
+function (ap) {\r
+Clazz.superConstructor (this, jalview.appletgui.Finder, []);\r
+try {\r
+this.jbInit ();\r
+} catch (e) {\r
+if (Clazz.exceptionOf (e, Exception)) {\r
+e.printStackTrace ();\r
+} else {\r
+throw e;\r
+}\r
+}\r
+this.av = ap.av;\r
+this.ap = ap;\r
+this.frame = new awt2swing.Frame ();\r
+this.frame.add (this);\r
+jalview.bin.JalviewLite.addFrame (this.frame, jalview.util.MessageManager.getString ("action.find"), 340, 120);\r
+this.frame.repaint ();\r
+this.frame.addWindowListener (((Clazz.isClassDefined ("jalview.appletgui.Finder$1") ? 0 : jalview.appletgui.Finder.$Finder$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.Finder$1, this, Clazz.cloneFinals ("ap", ap))));\r
+this.textfield.requestFocus ();\r
+}, "jalview.appletgui.AlignmentPanel");\r
+Clazz.overrideMethod (c$, "actionPerformed", \r
+function (evt) {\r
+if (evt.getSource () === this.textfield) {\r
+this.doSearch (false);\r
+} else if (evt.getSource () === this.findNext) {\r
+this.doSearch (false);\r
+} else if (evt.getSource () === this.findAll) {\r
+this.resIndex = -1;\r
+this.seqIndex = 0;\r
+this.doSearch (true);\r
+} else if (evt.getSource () === this.createNewGroup) {\r
+this.createNewGroup_actionPerformed ();\r
+}}, "java.awt.event.ActionEvent");\r
+Clazz.defineMethod (c$, "createNewGroup_actionPerformed", \r
+function () {\r
+var seqs = new Array (this.searchResults.getSize ());\r
+var features = new Array (this.searchResults.getSize ());\r
+for (var i = 0; i < this.searchResults.getSize (); i++) {\r
+seqs[i] = this.searchResults.getResultSequence (i);\r
+features[i] = new jalview.datamodel.SequenceFeature (this.textfield.getText ().trim (), "Search Results", null, this.searchResults.getResultStart (i), this.searchResults.getResultEnd (i), "Search Results");\r
+}\r
+if (this.ap.seqPanel.seqCanvas.getFeatureRenderer ().amendFeatures (seqs, features, true, this.ap)) {\r
+this.ap.alignFrame.sequenceFeatures.setState (true);\r
+this.av.setShowSequenceFeatures (true);\r
+this.ap.highlightSearchResults (null);\r
+}});\r
+Clazz.defineMethod (c$, "doSearch", \r
+function (findAll) {\r
+if (this.ap.av.applet.currentAlignFrame != null) {\r
+this.ap = this.ap.av.applet.currentAlignFrame.alignPanel;\r
+this.av = this.ap.av;\r
+}this.createNewGroup.setEnabled (false);\r
+var finder = new jalview.analysis.Finder (this.av.getAlignment (), this.av.getSelectionGroup (), this.seqIndex, this.resIndex);\r
+finder.setCaseSensitive (this.caseSensitive.getState ());\r
+finder.setIncludeDescription (this.searchDescription.getState ());\r
+finder.setFindAll (findAll);\r
+var searchString = this.textfield.getText ();\r
+finder.find (searchString);\r
+this.seqIndex = finder.getSeqIndex ();\r
+this.resIndex = finder.getResIndex ();\r
+this.searchResults = finder.getSearchResults ();\r
+var idMatch = finder.getIdMatch ();\r
+var haveResults = false;\r
+if ((idMatch.size () > 0)) {\r
+haveResults = true;\r
+this.ap.idPanel.highlightSearchResults (idMatch);\r
+} else {\r
+this.ap.idPanel.highlightSearchResults (null);\r
+}if (this.searchResults.getSize () > 0) {\r
+haveResults = true;\r
+this.createNewGroup.setEnabled (true);\r
+} else {\r
+this.searchResults = null;\r
+}this.ap.highlightSearchResults (this.searchResults);\r
+if (!haveResults) {\r
+this.ap.alignFrame.setStatus (jalview.util.MessageManager.getString ("label.finished_searching"));\r
+this.resIndex = -1;\r
+this.seqIndex = 0;\r
+} else {\r
+if (findAll) {\r
+var message = (idMatch.size () > 0) ? "" + idMatch.size () + " IDs" : "";\r
+if (idMatch.size () > 0 && this.searchResults != null && this.searchResults.getSize () > 0) {\r
+message += " and ";\r
+}if (this.searchResults != null) {\r
+message += this.searchResults.getSize () + " subsequence matches.";\r
+}this.ap.alignFrame.setStatus (jalview.util.MessageManager.formatMessage ("label.search_results", Clazz.newArray (-1, [searchString, message])));\r
+} else {\r
+this.ap.alignFrame.setStatus (jalview.util.MessageManager.formatMessage ("label.found_match_for", Clazz.newArray (-1, [searchString])));\r
+}}}, "~B");\r
+Clazz.defineMethod (c$, "jbInit", \r
+($fz = function () {\r
+this.jLabel1.setFont ( new java.awt.Font ("Verdana", 0, 12));\r
+this.jLabel1.setText (jalview.util.MessageManager.getString ("action.find"));\r
+this.jLabel1.setBounds ( new java.awt.Rectangle (3, 30, 34, 15));\r
+this.setLayout (null);\r
+this.textfield.setFont ( new java.awt.Font ("Verdana", 0, 10));\r
+this.textfield.setText ("");\r
+this.textfield.setBounds ( new java.awt.Rectangle (40, 17, 133, 21));\r
+this.textfield.addKeyListener (((Clazz.isClassDefined ("jalview.appletgui.Finder$2") ? 0 : jalview.appletgui.Finder.$Finder$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.Finder$2, this, null)));\r
+this.textfield.addActionListener (this);\r
+this.findAll.setFont ( new java.awt.Font ("Verdana", 0, 10));\r
+this.findAll.setLabel (jalview.util.MessageManager.getString ("action.find_all"));\r
+this.findAll.addActionListener (this);\r
+this.findNext.setEnabled (false);\r
+this.findNext.setFont ( new java.awt.Font ("Verdana", 0, 10));\r
+this.findNext.setLabel (jalview.util.MessageManager.getString ("action.find_next"));\r
+this.findNext.addActionListener (this);\r
+this.actionsPanel.setBounds ( new java.awt.Rectangle (195, 5, 141, 64));\r
+this.actionsPanel.setLayout (this.gridLayout1);\r
+this.gridLayout1.setHgap (0);\r
+this.gridLayout1.setRows (3);\r
+this.gridLayout1.setVgap (2);\r
+this.createNewGroup.setEnabled (false);\r
+this.createNewGroup.setFont ( new java.awt.Font ("Verdana", 0, 10));\r
+this.createNewGroup.setLabel (jalview.util.MessageManager.getString ("label.new_feature"));\r
+this.createNewGroup.addActionListener (this);\r
+this.caseSensitive.setLabel (jalview.util.MessageManager.getString ("label.match_case"));\r
+this.caseSensitive.setBounds ( new java.awt.Rectangle (30, 39, 126, 23));\r
+this.searchDescription.setLabel (jalview.util.MessageManager.getString ("label.include_description"));\r
+this.searchDescription.setBounds ( new java.awt.Rectangle (30, 59, 170, 23));\r
+this.actionsPanel.add (this.findNext, null);\r
+this.actionsPanel.add (this.findAll, null);\r
+this.actionsPanel.add (this.createNewGroup, null);\r
+this.add (this.caseSensitive);\r
+this.add (this.textfield, null);\r
+this.add (this.jLabel1, null);\r
+this.add (this.actionsPanel, null);\r
+this.add (this.searchDescription);\r
+}, $fz.isPrivate = true, $fz));\r
+Clazz.defineMethod (c$, "textfield_keyTyped", \r
+function (e) {\r
+this.findNext.setEnabled (true);\r
+}, "java.awt.event.KeyEvent");\r
+c$.$Finder$1$ = function () {\r
+Clazz.pu$h ();\r
+c$ = Clazz.declareAnonymous (jalview.appletgui, "Finder$1", java.awt.event.WindowAdapter);\r
+Clazz.overrideMethod (c$, "windowClosing", \r
+function (evt) {\r
+this.f$.ap.highlightSearchResults (null);\r
+}, "java.awt.event.WindowEvent");\r
+c$ = Clazz.p0p ();\r
+};\r
+c$.$Finder$2$ = function () {\r
+Clazz.pu$h ();\r
+c$ = Clazz.declareAnonymous (jalview.appletgui, "Finder$2", java.awt.event.KeyAdapter);\r
+Clazz.overrideMethod (c$, "keyTyped", \r
+function (e) {\r
+this.b$["jalview.appletgui.Finder"].textfield_keyTyped (e);\r
+}, "java.awt.event.KeyEvent");\r
+c$ = Clazz.p0p ();\r
+};\r
+});\r
git://source.jalview.org / jalviewjs.git / blobdiff