import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.ColourMenuHelper.ColourChangeListener;
-import jalview.io.FileFormat;
import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.FormatAdapter;
import jalview.io.SequenceAnnotationReport;
-import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemes;
import jalview.schemes.PIDColourScheme;
-import jalview.schemes.ResidueColourScheme;
import jalview.util.GroupUrlLink;
import jalview.util.GroupUrlLink.UrlStringTooLongException;
import jalview.util.MessageManager;
protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
+ protected JMenuItem modifyPID = new JMenuItem();
+
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+ protected JMenuItem modifyConservation = new JMenuItem();
+
AlignmentPanel ap;
JMenu sequenceMenu = new JMenu();
this.ap = ap;
sequence = seq;
- for (String ff : FileFormat.getWritableFormats(true))
+ for (String ff : FileFormats.getInstance().getWritableFormats(true))
{
JMenuItem item = new JMenuItem(ff);
add(menuItem);
}
-
}
SequenceGroup sg = ap.av.getSelectionGroup();
groupName.setText(MessageManager
.getString("label.edit_name_and_description_current_group"));
- ColourMenuHelper.setColourSelected(colourMenu, sg.cs);
+ ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
- if (sg.cs != null && sg.cs.conservationApplied())
+ conservationMenuItem.setEnabled(!sg.isNucleotide());
+
+ if (sg.cs != null)
{
- conservationMenuItem.setSelected(true);
+ if (sg.cs.conservationApplied())
+ {
+ conservationMenuItem.setSelected(true);
+ }
+ if (sg.cs.getThreshold() > 0)
+ {
+ abovePIDColour.setSelected(true);
+ }
}
+ modifyConservation.setEnabled(conservationMenuItem.isSelected());
+ modifyPID.setEnabled(abovePIDColour.isSelected());
displayNonconserved.setSelected(sg.getShowNonconserved());
showText.setSelected(sg.getDisplayText());
showColourText.setSelected(sg.getColourText());
}
-
-
/**
* Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
* "All" is added first, followed by a separator. Then add any annotation
sequenceSelectionDetails_actionPerformed();
}
});
+
unGroupMenuItem
.setText(MessageManager.getString("action.remove_group"));
unGroupMenuItem.addActionListener(new ActionListener()
});
createGroupMenuItem.setText(MessageManager
.getString("action.create_group"));
- createGroupMenuItem
-.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- createGroupMenuItem_actionPerformed();
- }
- });
+ createGroupMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createGroupMenuItem_actionPerformed();
+ }
+ });
outline.setText(MessageManager.getString("action.border_colour"));
outline.addActionListener(new ActionListener()
hideInsertions_actionPerformed(e);
}
});
- /*
- * annotationMenuItem.setText("By Annotation");
- * annotationMenuItem.addActionListener(new ActionListener() { public void
- * actionPerformed(ActionEvent actionEvent) {
- * annotationMenuItem_actionPerformed(actionEvent); } });
- */
+
groupMenu.add(sequenceSelDetails);
add(groupMenu);
add(sequenceMenu);
jMenu1.add(outline);
jMenu1.add(displayNonconserved);
}
-
+
/**
* Constructs the entries for the colour menu
*/
textColour_actionPerformed();
}
});
+
abovePIDColour.setText(MessageManager
.getString("label.above_identity_threshold"));
abovePIDColour.addActionListener(new ActionListener()
@Override
public void actionPerformed(ActionEvent e)
{
- abovePIDColour_actionPerformed();
+ abovePIDColour_actionPerformed(abovePIDColour.isSelected());
+ }
+ });
+
+ modifyPID.setText(MessageManager
+ .getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyPID_actionPerformed();
}
});
@Override
public void actionPerformed(ActionEvent e)
{
- conservationMenuItem_actionPerformed();
+ conservationMenuItem_actionPerformed(conservationMenuItem
+ .isSelected());
+ }
+ });
+
+ modifyConservation.setText(MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyConservation_actionPerformed();
}
});
}
*/
protected void buildColourMenu()
{
- SequenceGroup sg = getGroup();
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null)
+ {
+ /*
+ * popup menu with no sequence group scope
+ */
+ return;
+ }
colourMenu.removeAll();
colourMenu.add(textColour);
colourMenu.addSeparator();
- ColourMenuHelper.addMenuItems(colourMenu, this, sg);
+ ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
+ colourMenu.add(modifyConservation);
colourMenu.add(abovePIDColour);
+ colourMenu.add(modifyPID);
+ }
+
+ protected void modifyConservation_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs != null)
+ {
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+ SliderPanel.showConservationSlider();
+ }
+ }
+
+ protected void modifyPID_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs != null)
+ {
+ // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+ // .getName());
+ // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
+ SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+ .getName());
+ SliderPanel.showPIDSlider();
+ }
}
/**
/**
* DOCUMENT ME!
*
+ * @param selected
+ *
* @param e
* DOCUMENT ME!
*/
- protected void abovePIDColour_actionPerformed()
+ public void abovePIDColour_actionPerformed(boolean selected)
{
SequenceGroup sg = getGroup();
if (sg.cs == null)
return;
}
- if (abovePIDColour.isSelected())
+ if (selected)
{
sg.cs.setConsensus(AAFrequency.calculate(
sg.getSequences(ap.av.getHiddenRepSequences()),
sg.getStartRes(), sg.getEndRes() + 1));
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+ int threshold = SliderPanel.setPIDSliderSource(ap,
+ sg.getGroupColourScheme(), getGroup()
.getName());
sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
// remove PIDColouring
{
sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+ SliderPanel.hidePIDSlider();
}
+ modifyPID.setEnabled(selected);
refresh();
}
* @param e
* DOCUMENT ME!
*/
- protected void conservationMenuItem_actionPerformed()
+ public void conservationMenuItem_actionPerformed(boolean selected)
{
SequenceGroup sg = getGroup();
if (sg.cs == null)
return;
}
- if (conservationMenuItem.isSelected())
+ if (selected)
{
// JBPNote: Conservation name shouldn't be i18n translated
Conservation c = new Conservation("Group", sg.getSequences(ap.av
c.calculate();
c.verdict(false, ap.av.getConsPercGaps());
-
sg.cs.setConservation(c);
- SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+ SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
+ sg.getName());
SliderPanel.showConservationSlider();
}
else
// remove ConservationColouring
{
sg.cs.setConservation(null);
+ SliderPanel.hideConservationSlider();
}
-
- refresh();
- }
-
- public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
- {
- SequenceGroup sg = getGroup();
- if (sg == null)
- {
- return;
- }
-
- AnnotationColourGradient acg = new AnnotationColourGradient(
- sequence.getAnnotation()[0], null,
- AnnotationColourGradient.NO_THRESHOLD);
-
- acg.setPredefinedColours(true);
- sg.cs = acg;
+ modifyConservation.setEnabled(selected);
refresh();
}
// or we simply trust the user wants
// wysiwig behaviour
- FileFormatI fileFormat = FileFormat.forName(e.getActionCommand());
+ FileFormatI fileFormat = FileFormats.getInstance().forName(e.getActionCommand());
cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
}
/**
* Action on user selecting an item from the colour menu (that does not have
* its bespoke action handler)
+ *
+ * @return
*/
@Override
public void changeColour_actionPerformed(String colourSchemeName)
{
SequenceGroup sg = getGroup();
- if (ResidueColourScheme.USER_DEFINED.equals(colourSchemeName))
- {
- /*
- * open a panel to load or configure a user-defined colour scheme
- */
- new UserDefinedColours(ap, sg);
- }
- else
+ /*
+ * switch to the chosen colour scheme (or null for None)
+ */
+ ColourSchemeI colourScheme = ColourSchemes.getInstance()
+ .getColourScheme(colourSchemeName, sg,
+ ap.av.getHiddenRepSequences());
+ sg.setColourScheme(colourScheme);
+ if (colourScheme instanceof Blosum62ColourScheme
+ || colourScheme instanceof PIDColourScheme)
{
- /*
- * switch to the chosen colour scheme (or null for None)
- */
- sg.cs = ColourSchemes.getInstance().getColourScheme(colourSchemeName,
- sg, ap.av.getHiddenRepSequences());
- if (sg.cs instanceof Blosum62ColourScheme
- || sg.cs instanceof PIDColourScheme)
- {
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(ap.av.getHiddenRepSequences()),
- sg.getStartRes(), sg.getEndRes() + 1));
- }
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
}
refresh();