*/
package jalview.gui;
+import jalview.bin.Cache;
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.HiddenColumns;
import jalview.datamodel.SequenceI;
-import jalview.io.FileParse;
+import jalview.io.AlignmentFileReaderI;
+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;
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()
{
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
textarea.requestFocus();
this.alignpanel = viewpanel;
if (alignpanel != null)
{
-
+ this.viewport = alignpanel.getAlignViewport();
}
- this.viewport = alignpanel.getAlignViewport();
if (viewport != null)
{
ok.setText(MessageManager.getString("action.add"));
textarea.append(text);
}
+ @Override
public void save_actionPerformed(ActionEvent e)
{
+ // TODO: JAL-3048 JalviewFileChooser - Save option
+
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
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);
{
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();
* @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();
try
{
- textarea.append((String) contents
- .getTransferData(DataFlavor.stringFlavor));
+ textarea.append(
+ (String) contents.getTransferData(DataFlavor.stringFlavor));
} catch (Exception ex)
{
}
* @param e
* DOCUMENT ME!
*/
+ @Override
public void ok_actionPerformed(ActionEvent e)
{
- String format = new IdentifyFile().Identify(getText(), "Paste");
+ 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())
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ AppletFormatAdapter.getSupportedFormats(),
+ MessageManager.getString("label.couldnt_read_data"),
+ 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)
+ if (al != null && al.hasValidSequence())
{
- String title = MessageManager.formatMessage(
- "label.input_cut_paste_params", new String[]
- { format });
- if (viewport != null)
+ String title = MessageManager
+ .formatMessage("label.input_cut_paste_params", new String[]
+ { format.getName() });
+ 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)
{
((AlignViewport) viewport).addAlignment(al, title);
+ viewport.applyFeaturesStyle(proxyColourScheme);
}
else
{
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)
.isShowSeqFeatures();
- ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
- af = new AlignFrame(al, hiddenSeqs, colSel,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
-
+ String colourSchemeName = ((ComplexAlignFile) source)
+ .getGlobalColourScheme();
+ FeaturesDisplayedI fd = ((ComplexAlignFile) source)
+ .getDisplayedFeatures();
+ af = new AlignFrame(al, hiddenSeqs, hidden,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
af.getViewport().setShowSequenceFeatures(showSeqFeatures);
- af.changeColour(cs);
+ af.getViewport().setFeaturesDisplayed(fd);
+ af.setMenusForViewport();
+ 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
+ af.setStatus(MessageManager
.getString("label.successfully_pasted_alignment_file"));
try
{
- af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
- false));
+ af.setMaximum(
+ Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (Exception ex)
{
}
}
}
+ else
+ {
+ System.err
+ .println(MessageManager.getString("label.couldnt_read_data"));
+ if (!Jalview.isHeadlessMode())
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ AppletFormatAdapter.getSupportedFormats(),
+ MessageManager.getString("label.couldnt_read_data"),
+ JvOptionPane.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))
+ /*
+ * isPopupTrigger is checked in mousePressed on Mac,
+ * in mouseReleased on Windows
+ */
+ 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