import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceI;
+import jalview.io.AlignmentFileReaderI;
import jalview.io.AppletFormatAdapter;
-import jalview.io.FileParse;
+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 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;
- FileParse 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();
return;
}
- String format = new IdentifyFile().identify(text, "Paste");
- if (format == null || format.equalsIgnoreCase("EMPTY DATA FILE"))
+ 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())
{
- 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);
}
return;
}
// TODO: identify feature, annotation or tree file and parse appropriately.
AlignmentI al = null;
- if (FormatAdapter.isValidFormat(format))
+ try
{
- try
- {
- FormatAdapter fa = new FormatAdapter(alignpanel);
- al = fa.readFile(getText(), "Paste", format);
- source = fa.getAlignFile();
+ 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);
- }
+ } catch (IOException ex)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.couldnt_read_pasted_text", new String[]
+ { ex.toString() }), MessageManager
+ .getString("label.error_parsing_text"),
+ JvOptionPane.WARNING_MESSAGE);
}
if (al != null && al.hasValidSequence())
{
String title = MessageManager.formatMessage(
- "label.input_cut_paste_params", new String[] { format });
+ "label.input_cut_paste_params",
+ new String[] { format.getName() });
FeatureSettingsModelI proxyColourScheme = source
.getFeatureColourScheme();
.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(