case KeyEvent.VK_PAGE_UP:
if (viewport.getWrapAlignment())
{
- alignPanel.scrollUp(true);
+ vpRanges.scrollUp(true);
}
else
{
- alignPanel.setScrollValues(vpRanges.getStartRes(),
- 2 * vpRanges.getStartSeq() - vpRanges.getEndSeq());
+ vpRanges.pageUp();
}
break;
case KeyEvent.VK_PAGE_DOWN:
if (viewport.getWrapAlignment())
{
- alignPanel.scrollUp(false);
+ vpRanges.scrollUp(false);
}
else
{
- alignPanel.setScrollValues(vpRanges.getStartRes(),
- vpRanges.getEndSeq());
+ vpRanges.pageDown();
}
break;
}
alignmentStartEnd = alignmentToExport
.getVisibleStartAndEndIndex(viewport.getAlignment()
.getHiddenColumns()
- .getListOfCols());
+ .getHiddenRegions());
AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
omitHidden, alignmentStartEnd, settings);
return ed;
int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
.getSelectionGroup().getEndRes();
for (int[] region : viewport.getAlignment().getHiddenColumns()
- .getListOfCols())
+ .getHiddenRegions())
{
if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
{
frame.setContentPane(overview);
Desktop.addInternalFrame(frame, MessageManager.formatMessage(
"label.overview_params", new Object[] { this.getTitle() }),
- frame.getWidth(), frame.getHeight());
+ true, frame.getWidth(), frame.getHeight(), true, true);
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
* 'User Defined' opens a panel to configure or load a
* user-defined colour scheme
*/
- if (ResidueColourScheme.USER_DEFINED.equals(name))
+ if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
{
new UserDefinedColours(alignPanel);
return;
if (viewport.getSelectionGroup() != null
&& viewport.getSelectionGroup().getSize() > 0)
{
- if (viewport.getSelectionGroup().getSize() < 3)
- {
- JvOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager
- .getString("label.you_need_more_two_sequences_selected_build_tree"),
- MessageManager
- .getString("label.not_enough_sequences"),
- JvOptionPane.WARNING_MESSAGE);
- return;
- }
-
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */