import jalview.api.FeaturesSourceI;
import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
-import jalview.io.AlignmentFileI;
+import jalview.io.AlignmentFileReaderI;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
import jalview.io.FileFormatException;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.MouseEvent;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.JPopupMenu;
import javax.swing.SwingUtilities;
AlignViewportI viewport;
- AlignmentFileI source = null;
+ AlignmentFileReaderI source = null;
public CutAndPasteTransfer()
{
{
try
{
- java.io.PrintWriter out = new java.io.PrintWriter(
- new java.io.FileWriter(chooser.getSelectedFile()));
+ PrintWriter out = new PrintWriter(new FileWriter(
+ chooser.getSelectedFile()));
out.print(getText());
out.close();
.getString("label.couldnt_read_data"));
if (!Jalview.isHeadlessMode())
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- AppletFormatAdapter.SUPPORTED_FORMATS,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ AppletFormatAdapter.getSupportedFormats(),
MessageManager.getString("label.couldnt_read_data"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
return;
}
al = fa.readFile(getText(), DataSourceType.PASTE, format);
source = fa.getAlignFile();
- } catch (java.io.IOException ex)
+ } catch (IOException ex)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.couldnt_read_pasted_text", new String[]
{ ex.toString() }), MessageManager
.getString("label.error_parsing_text"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
if (al != null && al.hasValidSequence())
{
String title = MessageManager.formatMessage(
"label.input_cut_paste_params",
- new String[] { format.getShortDescription() });
+ new String[] { format.getName() });
FeatureSettingsModelI proxyColourScheme = source
.getFeatureColourScheme();
AlignFrame af;
if (source instanceof ComplexAlignFile)
{
- ColumnSelection colSel = ((ComplexAlignFile) source)
- .getColumnSelection();
+ HiddenColumns hidden = ((ComplexAlignFile) source)
+ .getHiddenColumns();
SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
.getHiddenSequences();
boolean showSeqFeatures = ((ComplexAlignFile) source)
.getGlobalColourScheme();
FeaturesDisplayedI fd = ((ComplexAlignFile) source)
.getDisplayedFeatures();
- af = new AlignFrame(al, hiddenSeqs, colSel,
+ af = new AlignFrame(al, hiddenSeqs, hidden,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
af.getViewport().setShowSequenceFeatures(showSeqFeatures);
af.getViewport().setFeaturesDisplayed(fd);
+ af.setMenusForViewport();
ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
colourSchemeName, al);
if (cs != null)
.getString("label.couldnt_read_data"));
if (!Jalview.isHeadlessMode())
{
- javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
- AppletFormatAdapter.SUPPORTED_FORMATS,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ AppletFormatAdapter.getSupportedFormats(),
MessageManager.getString("label.couldnt_read_data"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
}
}
@Override
public void textarea_mousePressed(MouseEvent e)
{
+ /*
+ * isPopupTrigger is checked in mousePressed on Mac,
+ * in mouseReleased on Windows
+ */
if (e.isPopupTrigger())
{
JPopupMenu popup = new JPopupMenu(