X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fappletgui%2FFinder.js;h=372bcb8075931052f1b03e117ebc927641da647c;hp=76128f9a3e88a1785842b6900073b90f85af29fa;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6

diff --git a/site/j2s/jalview/appletgui/Finder.js b/site/j2s/jalview/appletgui/Finder.js
index 76128f9..372bcb8 100644
--- a/site/j2s/jalview/appletgui/Finder.js
+++ b/site/j2s/jalview/appletgui/Finder.js
@@ -1,184 +1,184 @@
-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", 
- 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$2, this, null)));
-this.textfield.addActionListener (this);
-this.findAll.setFont ( new java.awt.Font ("Verdana", 0, 10));
-this.findAll.setLabel (jalview.util.MessageManager.getString ("action.find_all"));
-this.findAll.addActionListener (this);
-this.findNext.setEnabled (false);
-this.findNext.setFont ( new java.awt.Font ("Verdana", 0, 10));
-this.findNext.setLabel (jalview.util.MessageManager.getString ("action.find_next"));
-this.findNext.addActionListener (this);
-this.actionsPanel.setBounds ( new java.awt.Rectangle (195, 5, 141, 64));
-this.actionsPanel.setLayout (this.gridLayout1);
-this.gridLayout1.setHgap (0);
-this.gridLayout1.setRows (3);
-this.gridLayout1.setVgap (2);
-this.createNewGroup.setEnabled (false);
-this.createNewGroup.setFont ( new java.awt.Font ("Verdana", 0, 10));
-this.createNewGroup.setLabel (jalview.util.MessageManager.getString ("label.new_feature"));
-this.createNewGroup.addActionListener (this);
-this.caseSensitive.setLabel (jalview.util.MessageManager.getString ("label.match_case"));
-this.caseSensitive.setBounds ( new java.awt.Rectangle (30, 39, 126, 23));
-this.searchDescription.setLabel (jalview.util.MessageManager.getString ("label.include_description"));
-this.searchDescription.setBounds ( new java.awt.Rectangle (30, 59, 170, 23));
-this.actionsPanel.add (this.findNext, null);
-this.actionsPanel.add (this.findAll, null);
-this.actionsPanel.add (this.createNewGroup, null);
-this.add (this.caseSensitive);
-this.add (this.textfield, null);
-this.add (this.jLabel1, null);
-this.add (this.actionsPanel, null);
-this.add (this.searchDescription);
-});
-Clazz.defineMethod (c$, "textfield_keyTyped", 
-function (e) {
-this.findNext.setEnabled (true);
-}, "java.awt.event.KeyEvent");
-c$.$Finder$1$ = function () {
-Clazz.pu$h(self.c$);
-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$h(self.c$);
-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");
+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", 
+ 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$2, this, null)));
+this.textfield.addActionListener (this);
+this.findAll.setFont ( new java.awt.Font ("Verdana", 0, 10));
+this.findAll.setLabel (jalview.util.MessageManager.getString ("action.find_all"));
+this.findAll.addActionListener (this);
+this.findNext.setEnabled (false);
+this.findNext.setFont ( new java.awt.Font ("Verdana", 0, 10));
+this.findNext.setLabel (jalview.util.MessageManager.getString ("action.find_next"));
+this.findNext.addActionListener (this);
+this.actionsPanel.setBounds ( new java.awt.Rectangle (195, 5, 141, 64));
+this.actionsPanel.setLayout (this.gridLayout1);
+this.gridLayout1.setHgap (0);
+this.gridLayout1.setRows (3);
+this.gridLayout1.setVgap (2);
+this.createNewGroup.setEnabled (false);
+this.createNewGroup.setFont ( new java.awt.Font ("Verdana", 0, 10));
+this.createNewGroup.setLabel (jalview.util.MessageManager.getString ("label.new_feature"));
+this.createNewGroup.addActionListener (this);
+this.caseSensitive.setLabel (jalview.util.MessageManager.getString ("label.match_case"));
+this.caseSensitive.setBounds ( new java.awt.Rectangle (30, 39, 126, 23));
+this.searchDescription.setLabel (jalview.util.MessageManager.getString ("label.include_description"));
+this.searchDescription.setBounds ( new java.awt.Rectangle (30, 59, 170, 23));
+this.actionsPanel.add (this.findNext, null);
+this.actionsPanel.add (this.findAll, null);
+this.actionsPanel.add (this.createNewGroup, null);
+this.add (this.caseSensitive);
+this.add (this.textfield, null);
+this.add (this.jLabel1, null);
+this.add (this.actionsPanel, null);
+this.add (this.searchDescription);
+});
+Clazz.defineMethod (c$, "textfield_keyTyped", 
+function (e) {
+this.findNext.setEnabled (true);
+}, "java.awt.event.KeyEvent");
+c$.$Finder$1$ = function () {
+Clazz.pu$h(self.c$);
+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$h(self.c$);
+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 ();
+};
+});