import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.ComplexAlignFile;
+import jalview.api.FeatureSettingsModelI;
import jalview.api.FeaturesDisplayedI;
+import jalview.api.FeaturesSourceI;
+import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceI;
-import jalview.io.FileParse;
+import jalview.io.AlignmentFileI;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
import jalview.io.IdentifyFile;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.jbgui.GCutAndPasteTransfer;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
AlignViewportI viewport;
- FileParse source = null;
+ AlignmentFileI source = null;
+
public CutAndPasteTransfer()
{
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
textarea.requestFocus();
textarea.append(text);
}
+ @Override
public void save_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
chooser.setAcceptAllFileFilterUsed(false);
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_text_to_file"));
+ chooser.setDialogTitle(MessageManager
+ .getString("label.save_text_to_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
* @param e
* DOCUMENT ME!
*/
+ @Override
public void copyItem_actionPerformed(ActionEvent e)
{
textarea.getSelectedText();
* @param e
* DOCUMENT ME!
*/
+ @Override
public void pasteMenu_actionPerformed(ActionEvent e)
{
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
* @param e
* DOCUMENT ME!
*/
+ @Override
public void ok_actionPerformed(ActionEvent e)
{
String text = getText();
return;
}
- String format = new IdentifyFile().Identify(text, "Paste");
- // TODO: identify feature, annotation or tree file and parse appropriately.
- AlignmentI al = null;
-
- if (FormatAdapter.isValidFormat(format))
+ FileFormatI format = null;
+ try
{
- try
- {
- FormatAdapter fa = new FormatAdapter(alignpanel);
- al = fa.readFile(getText(), "Paste", format);
- source = fa.getAlignFile();
-
- } catch (java.io.IOException ex)
+ 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,
- MessageManager.formatMessage(
- "label.couldnt_read_pasted_text", new String[]
- { ex.toString() }), MessageManager
- .getString("label.error_parsing_text"),
+ AppletFormatAdapter.SUPPORTED_FORMATS,
+ MessageManager.getString("label.couldnt_read_data"),
JOptionPane.WARNING_MESSAGE);
}
+ return;
}
- if (al != null)
+ // 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 });
- if (viewport != null)
+ "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
.getHiddenSequences();
boolean showSeqFeatures = ((ComplexAlignFile) source)
.isShowSeqFeatures();
- ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
+ String colourSchemeName = ((ComplexAlignFile) source)
+ .getGlobalColourScheme();
FeaturesDisplayedI fd = ((ComplexAlignFile) source)
.getDisplayedFeatures();
af = new AlignFrame(al, hiddenSeqs, colSel,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
af.getViewport().setShowSequenceFeatures(showSeqFeatures);
af.getViewport().setFeaturesDisplayed(fd);
- af.changeColour(cs);
+ 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);
}
}
}
+ 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
}
}
+ @Override
public void textarea_mousePressed(MouseEvent e)
{
- if (SwingUtilities.isRightMouseButton(e))
+ if (e.isPopupTrigger())
{
JPopupMenu popup = new JPopupMenu(
MessageManager.getString("action.edit"));
MessageManager.getString("action.copy"));
item.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
copyItem_actionPerformed(e);
item = new JMenuItem(MessageManager.getString("action.paste"));
item.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
pasteMenu_actionPerformed(e);
git://source.jalview.org / jalview.git / blobdiff