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.AlignmentFileReaderI;
import jalview.io.AppletFormatAdapter;
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
{
- PrintWriter out = new PrintWriter(new FileWriter(
- chooser.getSelectedFile()));
+ PrintWriter out = new PrintWriter(
+ new FileWriter(chooser.getSelectedFile()));
out.print(getText());
out.close();
try
{
- textarea.append((String) contents
- .getTransferData(DataFlavor.stringFlavor));
+ textarea.append(
+ (String) contents.getTransferData(DataFlavor.stringFlavor));
} catch (Exception ex)
{
}
}
if (format == null)
{
- System.err.println(MessageManager
- .getString("label.couldnt_read_data"));
+ System.err
+ .println(MessageManager.getString("label.couldnt_read_data"));
if (!Jalview.isHeadlessMode())
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.couldnt_read_pasted_text", new String[]
- { ex.toString() }), MessageManager
- .getString("label.error_parsing_text"),
+ { 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.getName() });
+ String title = MessageManager
+ .formatMessage("label.input_cut_paste_params", 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)
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(
+ jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (Exception ex)
{
}
}
else
{
- System.err.println(MessageManager
- .getString("label.couldnt_read_data"));
+ System.err
+ .println(MessageManager.getString("label.couldnt_read_data"));
if (!Jalview.isHeadlessMode())
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop,