+
+ public void appendText(String text)
+ {
+ textarea.append(text);
+ }
+
+ @Override
+ public void save_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+
+ chooser.setAcceptAllFileFilterUsed(false);
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(MessageManager
+ .getString("label.save_text_to_file"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ try
+ {
+ java.io.PrintWriter out = new java.io.PrintWriter(
+ new java.io.FileWriter(chooser.getSelectedFile()));
+
+ out.print(getText());
+ out.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void copyItem_actionPerformed(ActionEvent e)
+ {
+ textarea.getSelectedText();
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+ c.setContents(new StringSelection(textarea.getSelectedText()), null);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void pasteMenu_actionPerformed(ActionEvent e)
+ {
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
+ Transferable contents = c.getContents(this);
+
+ if (contents == null)
+ {
+ return;
+ }
+
+ try
+ {
+ textarea.append((String) contents
+ .getTransferData(DataFlavor.stringFlavor));
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void ok_actionPerformed(ActionEvent e)
+ {
+ String text = getText();
+ if (text.trim().length() < 1)
+ {
+ return;
+ }
+
+ FileFormatI format = null;
+ try
+ {
+ format = new IdentifyFile().identify(text, DataSourceType.PASTE);
+ } catch (FileFormatException e1)
+ {
+ // leave as null
+ }
+ if (format == null)
+ {
+ System.err.println(MessageManager
+ .getString("label.couldnt_read_data"));
+ if (!Jalview.isHeadlessMode())
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ AppletFormatAdapter.SUPPORTED_FORMATS,
+ MessageManager.getString("label.couldnt_read_data"),
+ JOptionPane.WARNING_MESSAGE);
+ }
+ return;
+ }
+
+ // TODO: identify feature, annotation or tree file and parse appropriately.
+ AlignmentI al = null;
+
+ try
+ {
+ FormatAdapter fa = new FormatAdapter(alignpanel);
+ al = fa.readFile(getText(), DataSourceType.PASTE, format);
+ source = fa.getAlignFile();
+
+ } catch (java.io.IOException ex)
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.couldnt_read_pasted_text", new String[]
+ { ex.toString() }), MessageManager
+ .getString("label.error_parsing_text"),
+ JOptionPane.WARNING_MESSAGE);
+ }
+
+ if (al != null && al.hasValidSequence())
+ {
+ String title = MessageManager.formatMessage(
+ "label.input_cut_paste_params",
+ new String[] { format.toString() });
+ FeatureSettingsModelI proxyColourScheme = source
+ .getFeatureColourScheme();
+
+ /*
+ * if the view panel was closed its alignment is nulled
+ * and this is an orphaned cut and paste window
+ */
+ if (viewport != null && viewport.getAlignment() != null)
+ {
+ if (proxyColourScheme != null)
+ {
+ viewport.applyFeaturesStyle(proxyColourScheme);
+ }
+ ((AlignViewport) viewport).addAlignment(al, title);
+ }
+ else
+ {
+
+ AlignFrame af;
+ if (source instanceof ComplexAlignFile)
+ {
+ ColumnSelection colSel = ((ComplexAlignFile) source)
+ .getColumnSelection();
+ SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
+ .getHiddenSequences();
+ boolean showSeqFeatures = ((ComplexAlignFile) source)
+ .isShowSeqFeatures();
+ String colourSchemeName = ((ComplexAlignFile) source)
+ .getGlobalColourScheme();
+ FeaturesDisplayedI fd = ((ComplexAlignFile) source)
+ .getDisplayedFeatures();
+ af = new AlignFrame(al, hiddenSeqs, colSel,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ af.getViewport().setShowSequenceFeatures(showSeqFeatures);
+ af.getViewport().setFeaturesDisplayed(fd);
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ colourSchemeName, al);
+ if (cs != null)
+ {
+ af.changeColour(cs);
+ }
+ }
+ else
+ {
+ af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ if (source instanceof FeaturesSourceI)
+ {
+ af.getViewport().setShowSequenceFeatures(true);
+ }
+ }
+ if (proxyColourScheme != null)
+ {
+ af.getViewport().applyFeaturesStyle(proxyColourScheme);
+ }
+ af.currentFileFormat = format;
+ Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ af.statusBar.setText(MessageManager
+ .getString("label.successfully_pasted_alignment_file"));
+
+ try
+ {
+ af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
+ false));
+ } catch (Exception ex)
+ {
+ }
+ }
+ }
+ else
+ {
+ System.err.println(MessageManager
+ .getString("label.couldnt_read_data"));
+ if (!Jalview.isHeadlessMode())
+ {
+ javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ AppletFormatAdapter.SUPPORTED_FORMATS,
+ MessageManager.getString("label.couldnt_read_data"),
+ JOptionPane.WARNING_MESSAGE);
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void cancel_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ this.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ @Override
+ public void textarea_mousePressed(MouseEvent e)
+ {
+ if (e.isPopupTrigger())
+ {
+ JPopupMenu popup = new JPopupMenu(
+ MessageManager.getString("action.edit"));
+ JMenuItem item = new JMenuItem(
+ MessageManager.getString("action.copy"));
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ copyItem_actionPerformed(e);
+ }
+ });
+ popup.add(item);
+ item = new JMenuItem(MessageManager.getString("action.paste"));
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ pasteMenu_actionPerformed(e);
+ }
+ });
+ popup.add(item);
+ popup.show(this, e.getX() + 10, e.getY() + textarea.getY() + 40);
+
+ }
+ }
+