* operation that affects the data in the current view (selection changed,
* etc) to update the menus to reflect the new state.
*/
+ @Override
public void setMenusForViewport()
{
setMenusFromViewport(viewport);
alignPanel.makeEPS(f);
}
+ @Override
public void createSVG(File f)
{
alignPanel.makeSVG(f);
}
}
+ @Override
public void addHistoryItem(CommandI command)
{
if (command.getSize() > 0)
*/
if (sg.getSize() == viewport.getAlignment().getHeight())
{
- int confirm = JOptionPane.showConfirmDialog(this,
- MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
- MessageManager.getString("label.delete_all"), // $NON-NLS-1$
- JOptionPane.OK_CANCEL_OPTION);
-
- if (confirm == JOptionPane.CANCEL_OPTION
- || confirm == JOptionPane.CLOSED_OPTION)
+ boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
+ .getAlignment().getWidth()) ? true : false;
+ if (isEntireAlignWidth)
{
- return;
+ int confirm = JOptionPane.showConfirmDialog(this,
+ MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
+ MessageManager.getString("label.delete_all"), // $NON-NLS-1$
+ JOptionPane.OK_CANCEL_OPTION);
+
+ if (confirm == JOptionPane.CANCEL_OPTION
+ || confirm == JOptionPane.CLOSED_OPTION)
+ {
+ return;
+ }
}
viewport.getColumnSelection().removeElements(sg.getStartRes(),
sg.getEndRes() + 1);
}
-
SequenceI[] cut = sg.getSequences()
.toArray(new SequenceI[sg.getSize()]);
* @param cs
* DOCUMENT ME!
*/
+ @Override
public void changeColour(ColourSchemeI cs)
{
// TODO: pull up to controller method
cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
cs, "Background"));
}
+ if (cs instanceof TCoffeeColourScheme)
+ {
+ tcoffeeColour.setEnabled(true);
+ tcoffeeColour.setSelected(true);
+ }
}
viewport.setGlobalColourScheme(cs);
@Override
public void run()
{
+ boolean isNuclueotide = alignPanel.alignFrame
+ .getViewport().getAlignment()
+ .isNucleotide();
new jalview.ws.DBRefFetcher(alignPanel.av
- .getSequenceSelection(), alignPanel.alignFrame)
+ .getSequenceSelection(),
+ alignPanel.alignFrame, null,
+ alignPanel.alignFrame.featureSettings,
+ isNuclueotide)
.fetchDBRefs(false);
}
}).start();
@Override
public void run()
{
+ boolean isNuclueotide = alignPanel.alignFrame
+ .getViewport().getAlignment()
+ .isNucleotide();
new jalview.ws.DBRefFetcher(alignPanel.av
.getSequenceSelection(),
- alignPanel.alignFrame, dassource)
+ alignPanel.alignFrame, dassource,
+ alignPanel.alignFrame.featureSettings,
+ isNuclueotide)
.fetchDBRefs(false);
}
}).start();
@Override
public void run()
{
+ boolean isNuclueotide = alignPanel.alignFrame
+ .getViewport().getAlignment()
+ .isNucleotide();
new jalview.ws.DBRefFetcher(alignPanel.av
.getSequenceSelection(),
- alignPanel.alignFrame, dassource)
+ alignPanel.alignFrame, dassource,
+ alignPanel.alignFrame.featureSettings,
+ isNuclueotide)
.fetchDBRefs(false);
}
}).start();
@Override
public void run()
{
+ boolean isNuclueotide = alignPanel.alignFrame
+ .getViewport().getAlignment()
+ .isNucleotide();
new jalview.ws.DBRefFetcher(alignPanel.av
.getSequenceSelection(),
- alignPanel.alignFrame, dassrc)
+ alignPanel.alignFrame, dassrc,
+ alignPanel.alignFrame.featureSettings,
+ isNuclueotide)
.fetchDBRefs(false);
}
}).start();
viewport.firePropertyChange("alignment", null, al);
}
+ @Override
public void setShowSeqFeatures(boolean b)
{
showSeqFeatures.setSelected(b);