X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fappletgui%2FCutAndPasteTransfer.js;h=4030094069ab61181e6517a0417d179c792bdf85;hp=c1e339af043e57470fafa347f26ea9bbeaaefdf3;hb=7301a2415adab88038b291fc54caeeb3a5a47a44;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/appletgui/CutAndPasteTransfer.js b/bin/jalview/appletgui/CutAndPasteTransfer.js
index c1e339a..4030094 100644
--- a/bin/jalview/appletgui/CutAndPasteTransfer.js
+++ b/bin/jalview/appletgui/CutAndPasteTransfer.js
@@ -1,264 +1,264 @@
-Clazz.declarePackage ("jalview.appletgui");
-Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "$.MouseListener", "awt2swing.Button", "$.TextArea", "java.awt.BorderLayout"], "jalview.appletgui.CutAndPasteTransfer", ["awt2swing.Frame", "$.Label", "jalview.analysis.AlignmentUtils", "jalview.api.ComplexAlignFile", "jalview.appletgui.AlignFrame", "$.AppletJmol", "$.JVDialog", "$.SplitFrame", "jalview.datamodel.PDBEntry", "jalview.io.AnnotationFile", "$.AppletFormatAdapter", "$.IdentifyFile", "$.NewickFile", "jalview.jsdev.GenericFileAdapter", "jalview.schemes.TCoffeeColourScheme", "jalview.util.MessageManager", "java.awt.Font"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.pdbImport = false;
-this.treeImport = false;
-this.annotationImport = false;
-this.seq = null;
-this.alignFrame = null;
-this.source = null;
-this.textarea = null;
-this.accept = null;
-this.addSequences = null;
-this.$cancel = null;
-this.buttonPanel = null;
-this.borderLayout1 = null;
-Clazz.instantialize (this, arguments);
-}, jalview.appletgui, "CutAndPasteTransfer", awt2swing.Panel, [java.awt.event.ActionListener, java.awt.event.MouseListener]);
-Clazz.prepareFields (c$, function () {
-this.textarea =  new awt2swing.TextArea ();
-this.accept =  new awt2swing.Button ("New Window");
-this.addSequences =  new awt2swing.Button ("Add to Current Alignment");
-this.$cancel =  new awt2swing.Button ("Close");
-this.buttonPanel =  new awt2swing.Panel ();
-this.borderLayout1 =  new java.awt.BorderLayout ();
-});
-Clazz.makeConstructor (c$, 
-function (forImport, alignFrame) {
-Clazz.superConstructor (this, jalview.appletgui.CutAndPasteTransfer, []);
-try {
-this.jbInit ();
-} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-e.printStackTrace ();
-} else {
-throw e;
-}
-}
-this.alignFrame = alignFrame;
-if (!forImport) {
-this.buttonPanel.setVisible (false);
-}}, "~B,jalview.appletgui.AlignFrame");
-Clazz.defineMethod (c$, "getText", 
-function () {
-return this.textarea.getText ();
-});
-Clazz.defineMethod (c$, "setText", 
-function (text) {
-this.textarea.setText (text);
-}, "~S");
-Clazz.defineMethod (c$, "setPDBImport", 
-function (seq) {
-this.seq = seq;
-this.accept.setLabel (jalview.util.MessageManager.getString ("action.accept"));
-this.addSequences.setVisible (false);
-this.pdbImport = true;
-}, "jalview.datamodel.SequenceI");
-Clazz.defineMethod (c$, "setTreeImport", 
-function () {
-this.treeImport = true;
-this.accept.setLabel (jalview.util.MessageManager.getString ("action.accept"));
-this.addSequences.setVisible (false);
-});
-Clazz.defineMethod (c$, "setAnnotationImport", 
-function () {
-this.annotationImport = true;
-this.accept.setLabel (jalview.util.MessageManager.getString ("action.accept"));
-this.addSequences.setVisible (false);
-});
-Clazz.overrideMethod (c$, "actionPerformed", 
-function (evt) {
-if (evt.getSource () === this.accept) {
-this.ok (true);
-} else if (evt.getSource () === this.addSequences) {
-this.ok (false);
-} else if (evt.getSource () === this.$cancel) {
-this.cancel ();
-}}, "java.awt.event.ActionEvent");
-Clazz.defineMethod (c$, "ok", 
-function (newWindow) {
-var text = this.getText ();
-var length = text.length;
-this.textarea.append ("\n");
-if (this.textarea.getText ().length == length) {
-var warning = "\n\n#################################################\nWARNING!! THIS IS THE MAXIMUM SIZE OF TEXTAREA!!\n\nCAN\'T INPUT FULL ALIGNMENT\n\nYOU MUST DELETE THIS WARNING TO CONTINUE\n\nMAKE SURE LAST SEQUENCE PASTED IS COMPLETE\n#################################################\n";
-this.textarea.setText (text.substring (0, text.length - warning.length) + warning);
-this.textarea.setCaretPosition (text.length);
-}if (this.pdbImport) {
-this.openPdbViewer (text);
-} else if (this.treeImport) {
-if (!this.loadTree ()) {
-return;
-}} else if (this.annotationImport) {
-this.loadAnnotations ();
-} else if (this.alignFrame != null) {
-this.loadAlignment (text, newWindow, this.alignFrame.getAlignViewport ());
-}if (Clazz.instanceOf (this.getParent (), awt2swing.Frame)) {
-(this.getParent ()).setVisible (false);
-} else {
-(this.getParent ()).setVisible (false);
-}}, "~B");
-Clazz.defineMethod (c$, "loadTree", 
-function () {
-try {
-var fin =  new jalview.io.NewickFile (this.textarea.getText (), "Paste");
-fin.parse ();
-if (fin.getTree () != null) {
-this.alignFrame.loadTree (fin, "Pasted tree file");
-return true;
-}} catch (ex) {
-if (Clazz.exceptionOf (ex, Exception)) {
-this.textarea.setText (jalview.util.MessageManager.formatMessage ("label.could_not_parse_newick_file",  Clazz.newArray (-1, [ex.getMessage ()])));
-return false;
-} else {
-throw ex;
-}
-}
-return false;
-});
-Clazz.defineMethod (c$, "loadAlignment", 
-function (text, newWindow, viewport) {
-var al = null;
-var format =  new jalview.io.IdentifyFile ().Identify (text, jalview.io.AppletFormatAdapter.PASTE);
-var afa =  new jalview.io.AppletFormatAdapter (this.alignFrame.alignPanel);
-try {
-al = afa.readFile (text, jalview.io.AppletFormatAdapter.PASTE, format);
-this.source = afa.getAlignFile ();
-} catch (ex) {
-if (Clazz.exceptionOf (ex, java.io.IOException)) {
-ex.printStackTrace ();
-} else {
-throw ex;
-}
-}
-if (al != null) {
-al.setDataset (null);
-var allowSplitFrame = this.alignFrame.viewport.applet.getDefaultParameter ("enableSplitFrame", false);
-if (allowSplitFrame && this.openSplitFrame (al, format)) {
-return;
-}if (newWindow) {
-var af;
-if (Clazz.instanceOf (this.source, jalview.api.ComplexAlignFile)) {
-var colSel = (this.source).getColumnSelection ();
-var hiddenSeqs = (this.source).getHiddenSequences ();
-var showSeqFeatures = (this.source).isShowSeqFeatures ();
-var cs = (this.source).getColourScheme ();
-af =  new jalview.appletgui.AlignFrame (al, hiddenSeqs, colSel, this.alignFrame.viewport.applet, "Cut & Paste input - " + format, false);
-af.getAlignViewport ().setShowSequenceFeatures (showSeqFeatures);
-af.changeColour (cs);
-} else {
-af =  new jalview.appletgui.AlignFrame (al, this.alignFrame.viewport.applet, "Cut & Paste input - " + format, false);
-}af.setStatus (jalview.util.MessageManager.getString ("label.successfully_pasted_annotation_to_alignment"));
-} else {
-this.alignFrame.addSequences (al.getSequencesArray ());
-this.alignFrame.setStatus (jalview.util.MessageManager.getString ("label.successfully_pasted_alignment_file"));
-}}}, "~S,~B,jalview.appletgui.AlignViewport");
-Clazz.defineMethod (c$, "openSplitFrame", 
-function (al, format) {
-var thisAlignment = this.alignFrame.getAlignViewport ().getAlignment ();
-if (thisAlignment.isNucleotide () == al.isNucleotide ()) {
-return false;
-}var protein = thisAlignment.isNucleotide () ? al : thisAlignment;
-var dna = thisAlignment.isNucleotide () ? thisAlignment : al;
-var mapped = jalview.analysis.AlignmentUtils.mapProteinToCdna (protein, dna);
-if (!mapped) {
-return false;
-}var title = jalview.util.MessageManager.getString ("label.open_split_window");
-var dialog =  new jalview.appletgui.JVDialog (this.getParent (), title, true, 100, 400);
-dialog.ok.setLabel (jalview.util.MessageManager.getString ("action.yes"));
-dialog.cancel.setLabel (jalview.util.MessageManager.getString ("action.no"));
-var question =  new awt2swing.Panel ( new java.awt.BorderLayout ());
-var text = jalview.util.MessageManager.getString ("label.open_split_window?");
-question.add ( new awt2swing.Label (text, 0), "Center");
-dialog.setMainPanel (question);
-dialog.setVisible (true);
-dialog.toFront ();
-if (!dialog.accept) {
-return false;
-}var applet = this.alignFrame.viewport.applet;
-var copyFrame =  new jalview.appletgui.AlignFrame (this.alignFrame.viewport.getAlignment (), applet, this.alignFrame.getTitle (), false, false);
-var newFrame =  new jalview.appletgui.AlignFrame (al, this.alignFrame.viewport.applet, "Cut & Paste input - " + format, false, false);
-var dnaFrame = al.isNucleotide () ? newFrame : copyFrame;
-var proteinFrame = al.isNucleotide () ? copyFrame : newFrame;
-var sf =  new jalview.appletgui.SplitFrame (dnaFrame, proteinFrame);
-sf.addToDisplay (false, applet);
-return true;
-}, "jalview.datamodel.AlignmentI,~S");
-Clazz.defineMethod (c$, "loadAnnotations", 
-function () {
-var tcf = null;
-try {
-tcf = jalview.jsdev.GenericFileAdapter.getFile ("TCoffeeScoreFile", [this.textarea.getText (), jalview.io.AppletFormatAdapter.PASTE]);
-if (tcf.isValid ()) {
-if (tcf.annotateAlignment (this.alignFrame.viewport.getAlignment (), true)) {
-this.alignFrame.tcoffeeColour.setEnabled (true);
-this.alignFrame.alignPanel.fontChanged ();
-this.alignFrame.changeColour ( new jalview.schemes.TCoffeeColourScheme (this.alignFrame.viewport.getAlignment ()));
-this.alignFrame.setStatus (jalview.util.MessageManager.getString ("label.successfully_pasted_tcoffee_scores_to_alignment"));
-} else {
-this.alignFrame.setStatus (jalview.util.MessageManager.formatMessage ("label.failed_add_tcoffee_scores",  Clazz.newArray (-1, [(tcf.getWarningMessage () != null ? tcf.getWarningMessage () : "")])));
-}} else {
-tcf = null;
-}} catch (x) {
-if (Clazz.exceptionOf (x, Exception)) {
-tcf = null;
-} else {
-throw x;
-}
-}
-if (tcf == null) {
-if ( new jalview.io.AnnotationFile ().annotateAlignmentView (this.alignFrame.viewport, this.textarea.getText (), jalview.io.AppletFormatAdapter.PASTE)) {
-this.alignFrame.alignPanel.fontChanged ();
-this.alignFrame.alignPanel.setScrollValues (0, 0);
-this.alignFrame.setStatus (jalview.util.MessageManager.getString ("label.successfully_pasted_annotation_to_alignment"));
-} else {
-if (!this.alignFrame.parseFeaturesFile (this.textarea.getText (), jalview.io.AppletFormatAdapter.PASTE)) {
-this.alignFrame.setStatus (jalview.util.MessageManager.getString ("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file"));
-}}}});
-Clazz.defineMethod (c$, "openPdbViewer", 
-function (text) {
-var pdb =  new jalview.datamodel.PDBEntry ();
-pdb.setFile (text);
- new jalview.appletgui.AppletJmol (pdb,  Clazz.newArray (-1, [this.seq]), null, this.alignFrame.alignPanel, jalview.io.AppletFormatAdapter.PASTE);
-}, "~S");
-Clazz.defineMethod (c$, "cancel", 
-function () {
-this.textarea.setText ("");
-if (Clazz.instanceOf (this.getParent (), awt2swing.Frame)) {
-(this.getParent ()).setVisible (false);
-} else {
-(this.getParent ()).setVisible (false);
-}});
-Clazz.defineMethod (c$, "jbInit", 
-($fz = function () {
-this.textarea.setFont ( new java.awt.Font ("Monospaced", 0, 10));
-this.textarea.setText (jalview.util.MessageManager.getString ("label.paste_your_alignment_file"));
-this.textarea.addMouseListener (this);
-this.setLayout (this.borderLayout1);
-this.accept.addActionListener (this);
-this.addSequences.addActionListener (this);
-this.$cancel.addActionListener (this);
-this.add (this.buttonPanel, "South");
-this.buttonPanel.add (this.accept, null);
-this.buttonPanel.add (this.addSequences);
-this.buttonPanel.add (this.$cancel, null);
-this.add (this.textarea, "Center");
-}, $fz.isPrivate = true, $fz));
-Clazz.overrideMethod (c$, "mousePressed", 
-function (evt) {
-if (this.textarea.getText ().startsWith (jalview.util.MessageManager.getString ("label.paste_your"))) {
-this.textarea.setText ("");
-}}, "java.awt.event.MouseEvent");
-Clazz.overrideMethod (c$, "mouseReleased", 
-function (evt) {
-}, "java.awt.event.MouseEvent");
-Clazz.overrideMethod (c$, "mouseClicked", 
-function (evt) {
-}, "java.awt.event.MouseEvent");
-Clazz.overrideMethod (c$, "mouseEntered", 
-function (evt) {
-}, "java.awt.event.MouseEvent");
-Clazz.overrideMethod (c$, "mouseExited", 
-function (evt) {
-}, "java.awt.event.MouseEvent");
-});
+Clazz.declarePackage ("jalview.appletgui");
+Clazz.load (["awt2swing.Panel", "java.awt.event.ActionListener", "$.MouseListener", "awt2swing.Button", "$.TextArea", "java.awt.BorderLayout"], "jalview.appletgui.CutAndPasteTransfer", ["awt2swing.Frame", "$.Label", "jalview.analysis.AlignmentUtils", "jalview.api.ComplexAlignFile", "jalview.appletgui.AlignFrame", "$.AppletJmol", "$.JVDialog", "$.SplitFrame", "jalview.datamodel.PDBEntry", "jalview.io.AnnotationFile", "$.AppletFormatAdapter", "$.IdentifyFile", "$.NewickFile", "jalview.jsdev.GenericFileAdapter", "jalview.schemes.TCoffeeColourScheme", "jalview.util.MessageManager", "java.awt.Font"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.pdbImport = false;
+this.treeImport = false;
+this.annotationImport = false;
+this.seq = null;
+this.alignFrame = null;
+this.source = null;
+this.textarea = null;
+this.accept = null;
+this.addSequences = null;
+this.$cancel = null;
+this.buttonPanel = null;
+this.borderLayout1 = null;
+Clazz.instantialize (this, arguments);
+}, jalview.appletgui, "CutAndPasteTransfer", awt2swing.Panel, [java.awt.event.ActionListener, java.awt.event.MouseListener]);
+Clazz.prepareFields (c$, function () {
+this.textarea =  new awt2swing.TextArea ();
+this.accept =  new awt2swing.Button ("New Window");
+this.addSequences =  new awt2swing.Button ("Add to Current Alignment");
+this.$cancel =  new awt2swing.Button ("Close");
+this.buttonPanel =  new awt2swing.Panel ();
+this.borderLayout1 =  new java.awt.BorderLayout ();
+});
+Clazz.makeConstructor (c$, 
+function (forImport, alignFrame) {
+Clazz.superConstructor (this, jalview.appletgui.CutAndPasteTransfer, []);
+try {
+this.jbInit ();
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+e.printStackTrace ();
+} else {
+throw e;
+}
+}
+this.alignFrame = alignFrame;
+if (!forImport) {
+this.buttonPanel.setVisible (false);
+}}, "~B,jalview.appletgui.AlignFrame");
+Clazz.defineMethod (c$, "getText", 
+function () {
+return this.textarea.getText ();
+});
+Clazz.defineMethod (c$, "setText", 
+function (text) {
+this.textarea.setText (text);
+}, "~S");
+Clazz.defineMethod (c$, "setPDBImport", 
+function (seq) {
+this.seq = seq;
+this.accept.setLabel (jalview.util.MessageManager.getString ("action.accept"));
+this.addSequences.setVisible (false);
+this.pdbImport = true;
+}, "jalview.datamodel.SequenceI");
+Clazz.defineMethod (c$, "setTreeImport", 
+function () {
+this.treeImport = true;
+this.accept.setLabel (jalview.util.MessageManager.getString ("action.accept"));
+this.addSequences.setVisible (false);
+});
+Clazz.defineMethod (c$, "setAnnotationImport", 
+function () {
+this.annotationImport = true;
+this.accept.setLabel (jalview.util.MessageManager.getString ("action.accept"));
+this.addSequences.setVisible (false);
+});
+Clazz.overrideMethod (c$, "actionPerformed", 
+function (evt) {
+if (evt.getSource () === this.accept) {
+this.ok (true);
+} else if (evt.getSource () === this.addSequences) {
+this.ok (false);
+} else if (evt.getSource () === this.$cancel) {
+this.cancel ();
+}}, "java.awt.event.ActionEvent");
+Clazz.defineMethod (c$, "ok", 
+function (newWindow) {
+var text = this.getText ();
+var length = text.length;
+this.textarea.append ("\n");
+if (this.textarea.getText ().length == length) {
+var warning = "\n\n#################################################\nWARNING!! THIS IS THE MAXIMUM SIZE OF TEXTAREA!!\n\nCAN\'T INPUT FULL ALIGNMENT\n\nYOU MUST DELETE THIS WARNING TO CONTINUE\n\nMAKE SURE LAST SEQUENCE PASTED IS COMPLETE\n#################################################\n";
+this.textarea.setText (text.substring (0, text.length - warning.length) + warning);
+this.textarea.setCaretPosition (text.length);
+}if (this.pdbImport) {
+this.openPdbViewer (text);
+} else if (this.treeImport) {
+if (!this.loadTree ()) {
+return;
+}} else if (this.annotationImport) {
+this.loadAnnotations ();
+} else if (this.alignFrame != null) {
+this.loadAlignment (text, newWindow, this.alignFrame.getAlignViewport ());
+}if (Clazz.instanceOf (this.getParent (), awt2swing.Frame)) {
+(this.getParent ()).setVisible (false);
+} else {
+(this.getParent ()).setVisible (false);
+}}, "~B");
+Clazz.defineMethod (c$, "loadTree", 
+function () {
+try {
+var fin =  new jalview.io.NewickFile (this.textarea.getText (), "Paste");
+fin.parse ();
+if (fin.getTree () != null) {
+this.alignFrame.loadTree (fin, "Pasted tree file");
+return true;
+}} catch (ex) {
+if (Clazz.exceptionOf (ex, Exception)) {
+this.textarea.setText (jalview.util.MessageManager.formatMessage ("label.could_not_parse_newick_file",  Clazz.newArray (-1, [ex.getMessage ()])));
+return false;
+} else {
+throw ex;
+}
+}
+return false;
+});
+Clazz.defineMethod (c$, "loadAlignment", 
+function (text, newWindow, viewport) {
+var al = null;
+var format =  new jalview.io.IdentifyFile ().Identify (text, jalview.io.AppletFormatAdapter.PASTE);
+var afa =  new jalview.io.AppletFormatAdapter (this.alignFrame.alignPanel);
+try {
+al = afa.readFile (text, jalview.io.AppletFormatAdapter.PASTE, format);
+this.source = afa.getAlignFile ();
+} catch (ex) {
+if (Clazz.exceptionOf (ex, java.io.IOException)) {
+ex.printStackTrace ();
+} else {
+throw ex;
+}
+}
+if (al != null) {
+al.setDataset (null);
+var allowSplitFrame = this.alignFrame.viewport.applet.getDefaultParameter ("enableSplitFrame", false);
+if (allowSplitFrame && this.openSplitFrame (al, format)) {
+return;
+}if (newWindow) {
+var af;
+if (Clazz.instanceOf (this.source, jalview.api.ComplexAlignFile)) {
+var colSel = (this.source).getColumnSelection ();
+var hiddenSeqs = (this.source).getHiddenSequences ();
+var showSeqFeatures = (this.source).isShowSeqFeatures ();
+var cs = (this.source).getColourScheme ();
+af =  new jalview.appletgui.AlignFrame (al, hiddenSeqs, colSel, this.alignFrame.viewport.applet, "Cut & Paste input - " + format, false);
+af.getAlignViewport ().setShowSequenceFeatures (showSeqFeatures);
+af.changeColour (cs);
+} else {
+af =  new jalview.appletgui.AlignFrame (al, this.alignFrame.viewport.applet, "Cut & Paste input - " + format, false);
+}af.setStatus (jalview.util.MessageManager.getString ("label.successfully_pasted_annotation_to_alignment"));
+} else {
+this.alignFrame.addSequences (al.getSequencesArray ());
+this.alignFrame.setStatus (jalview.util.MessageManager.getString ("label.successfully_pasted_alignment_file"));
+}}}, "~S,~B,jalview.appletgui.AlignViewport");
+Clazz.defineMethod (c$, "openSplitFrame", 
+function (al, format) {
+var thisAlignment = this.alignFrame.getAlignViewport ().getAlignment ();
+if (thisAlignment.isNucleotide () == al.isNucleotide ()) {
+return false;
+}var protein = thisAlignment.isNucleotide () ? al : thisAlignment;
+var dna = thisAlignment.isNucleotide () ? thisAlignment : al;
+var mapped = jalview.analysis.AlignmentUtils.mapProteinToCdna (protein, dna);
+if (!mapped) {
+return false;
+}var title = jalview.util.MessageManager.getString ("label.open_split_window");
+var dialog =  new jalview.appletgui.JVDialog (this.getParent (), title, true, 100, 400);
+dialog.ok.setLabel (jalview.util.MessageManager.getString ("action.yes"));
+dialog.cancel.setLabel (jalview.util.MessageManager.getString ("action.no"));
+var question =  new awt2swing.Panel ( new java.awt.BorderLayout ());
+var text = jalview.util.MessageManager.getString ("label.open_split_window?");
+question.add ( new awt2swing.Label (text, 0), "Center");
+dialog.setMainPanel (question);
+dialog.setVisible (true);
+dialog.toFront ();
+if (!dialog.accept) {
+return false;
+}var applet = this.alignFrame.viewport.applet;
+var copyFrame =  new jalview.appletgui.AlignFrame (this.alignFrame.viewport.getAlignment (), applet, this.alignFrame.getTitle (), false, false);
+var newFrame =  new jalview.appletgui.AlignFrame (al, this.alignFrame.viewport.applet, "Cut & Paste input - " + format, false, false);
+var dnaFrame = al.isNucleotide () ? newFrame : copyFrame;
+var proteinFrame = al.isNucleotide () ? copyFrame : newFrame;
+var sf =  new jalview.appletgui.SplitFrame (dnaFrame, proteinFrame);
+sf.addToDisplay (false, applet);
+return true;
+}, "jalview.datamodel.AlignmentI,~S");
+Clazz.defineMethod (c$, "loadAnnotations", 
+function () {
+var tcf = null;
+try {
+tcf = jalview.jsdev.GenericFileAdapter.getFile ("TCoffeeScoreFile", [this.textarea.getText (), jalview.io.AppletFormatAdapter.PASTE]);
+if (tcf.isValid ()) {
+if (tcf.annotateAlignment (this.alignFrame.viewport.getAlignment (), true)) {
+this.alignFrame.tcoffeeColour.setEnabled (true);
+this.alignFrame.alignPanel.fontChanged ();
+this.alignFrame.changeColour ( new jalview.schemes.TCoffeeColourScheme (this.alignFrame.viewport.getAlignment ()));
+this.alignFrame.setStatus (jalview.util.MessageManager.getString ("label.successfully_pasted_tcoffee_scores_to_alignment"));
+} else {
+this.alignFrame.setStatus (jalview.util.MessageManager.formatMessage ("label.failed_add_tcoffee_scores",  Clazz.newArray (-1, [(tcf.getWarningMessage () != null ? tcf.getWarningMessage () : "")])));
+}} else {
+tcf = null;
+}} catch (x) {
+if (Clazz.exceptionOf (x, Exception)) {
+tcf = null;
+} else {
+throw x;
+}
+}
+if (tcf == null) {
+if ( new jalview.io.AnnotationFile ().annotateAlignmentView (this.alignFrame.viewport, this.textarea.getText (), jalview.io.AppletFormatAdapter.PASTE)) {
+this.alignFrame.alignPanel.fontChanged ();
+this.alignFrame.alignPanel.setScrollValues (0, 0);
+this.alignFrame.setStatus (jalview.util.MessageManager.getString ("label.successfully_pasted_annotation_to_alignment"));
+} else {
+if (!this.alignFrame.parseFeaturesFile (this.textarea.getText (), jalview.io.AppletFormatAdapter.PASTE)) {
+this.alignFrame.setStatus (jalview.util.MessageManager.getString ("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file"));
+}}}});
+Clazz.defineMethod (c$, "openPdbViewer", 
+function (text) {
+var pdb =  new jalview.datamodel.PDBEntry ();
+pdb.setFile (text);
+ new jalview.appletgui.AppletJmol (pdb,  Clazz.newArray (-1, [this.seq]), null, this.alignFrame.alignPanel, jalview.io.AppletFormatAdapter.PASTE);
+}, "~S");
+Clazz.defineMethod (c$, "cancel", 
+function () {
+this.textarea.setText ("");
+if (Clazz.instanceOf (this.getParent (), awt2swing.Frame)) {
+(this.getParent ()).setVisible (false);
+} else {
+(this.getParent ()).setVisible (false);
+}});
+Clazz.defineMethod (c$, "jbInit", 
+($fz = function () {
+this.textarea.setFont ( new java.awt.Font ("Monospaced", 0, 10));
+this.textarea.setText (jalview.util.MessageManager.getString ("label.paste_your_alignment_file"));
+this.textarea.addMouseListener (this);
+this.setLayout (this.borderLayout1);
+this.accept.addActionListener (this);
+this.addSequences.addActionListener (this);
+this.$cancel.addActionListener (this);
+this.add (this.buttonPanel, "South");
+this.buttonPanel.add (this.accept, null);
+this.buttonPanel.add (this.addSequences);
+this.buttonPanel.add (this.$cancel, null);
+this.add (this.textarea, "Center");
+}, $fz.isPrivate = true, $fz));
+Clazz.overrideMethod (c$, "mousePressed", 
+function (evt) {
+if (this.textarea.getText ().startsWith (jalview.util.MessageManager.getString ("label.paste_your"))) {
+this.textarea.setText ("");
+}}, "java.awt.event.MouseEvent");
+Clazz.overrideMethod (c$, "mouseReleased", 
+function (evt) {
+}, "java.awt.event.MouseEvent");
+Clazz.overrideMethod (c$, "mouseClicked", 
+function (evt) {
+}, "java.awt.event.MouseEvent");
+Clazz.overrideMethod (c$, "mouseEntered", 
+function (evt) {
+}, "java.awt.event.MouseEvent");
+Clazz.overrideMethod (c$, "mouseExited", 
+function (evt) {
+}, "java.awt.event.MouseEvent");
+});