import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
import jalview.io.SequenceAnnotationReport;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ClustalxColourScheme;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.JalviewColourScheme;
-import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.ColourSchemes;
import jalview.schemes.PIDColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TCoffeeColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.UserColourScheme;
-import jalview.schemes.ZappoColourScheme;
+import jalview.schemes.ResidueColourScheme;
import jalview.util.GroupUrlLink;
import jalview.util.GroupUrlLink.UrlStringTooLongException;
import jalview.util.MessageManager;
import jalview.util.UrlLink;
import java.awt.Color;
-import java.awt.Component;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.Arrays;
import java.util.TreeMap;
import java.util.Vector;
-import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JColorChooser;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.JPopupMenu;
-import javax.swing.JRadioButtonMenuItem;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision: 1.118 $
*/
-public class PopupMenu extends JPopupMenu
+public class PopupMenu extends JPopupMenu implements ColourChangeListener
{
JMenu groupMenu = new JMenu();
JMenuItem groupName = new JMenuItem();
- protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
-
protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
- protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
-
- // protected JRadioButtonMenuItem RNAInteractionColour;
-
- JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
-
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
AlignmentPanel ap;
groupName.setText(MessageManager
.getString("label.edit_name_and_description_current_group"));
- setColourSelected(sg.cs);
+ ColourMenuHelper.setColourSelected(colourMenu, sg.cs);
if (sg.cs != null && sg.cs.conservationApplied())
{
});
sequenceSelDetails.setText(MessageManager
.getString("label.sequence_details"));
- sequenceSelDetails
-.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- sequenceSelectionDetails_actionPerformed();
- }
- });
- PIDColour.setFocusPainted(false);
+ sequenceSelDetails.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceSelectionDetails_actionPerformed();
+ }
+ });
unGroupMenuItem
.setText(MessageManager.getString("action.remove_group"));
unGroupMenuItem.addActionListener(new ActionListener()
sequenceMenu.add(sequenceDetails);
sequenceMenu.add(makeReferenceSeq);
+ initColourMenu();
buildColourMenu();
editMenu.add(copy);
jMenu1.add(showColourText);
jMenu1.add(outline);
jMenu1.add(displayNonconserved);
-
- initColourMenu();
}
/**
textColour_actionPerformed();
}
});
- noColourmenuItem.setText(MessageManager.getString("label.none"));
- noColourmenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- noColourmenuItem_actionPerformed();
- }
- });
-
- clustalColour.setText(MessageManager
- .getString("label.colourScheme_clustal"));
- clustalColour.setName(JalviewColourScheme.Clustal.toString());
- clustalColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- clustalColour_actionPerformed();
- }
- });
- zappoColour.setText(MessageManager
- .getString("label.colourScheme_zappo"));
- zappoColour.setName(JalviewColourScheme.Zappo.toString());
- zappoColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- zappoColour_actionPerformed();
- }
- });
- taylorColour.setText(MessageManager
- .getString("label.colourScheme_taylor"));
- taylorColour.setName(JalviewColourScheme.Taylor.toString());
- taylorColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- taylorColour_actionPerformed();
- }
- });
- hydrophobicityColour.setText(MessageManager
- .getString("label.colourScheme_hydrophobic"));
- hydrophobicityColour
- .setName(JalviewColourScheme.Hydrophobic.toString());
- hydrophobicityColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hydrophobicityColour_actionPerformed();
- }
- });
- helixColour.setText(MessageManager
- .getString("label.colourScheme_helix_propensity"));
- helixColour.setName(JalviewColourScheme.Helix.toString());
- helixColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- helixColour_actionPerformed();
- }
- });
- strandColour.setText(MessageManager
- .getString("label.colourScheme_strand_propensity"));
- strandColour.setName(JalviewColourScheme.Strand.toString());
- strandColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- strandColour_actionPerformed();
- }
- });
- turnColour.setText(MessageManager
- .getString("label.colourScheme_turn_propensity"));
- turnColour.setName(JalviewColourScheme.Turn.toString());
- turnColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- turnColour_actionPerformed();
- }
- });
- buriedColour.setText(MessageManager
- .getString("label.colourScheme_buried_index"));
- buriedColour.setName(JalviewColourScheme.Buried.toString());
- buriedColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- buriedColour_actionPerformed();
- }
- });
abovePIDColour.setText(MessageManager
.getString("label.above_identity_threshold"));
abovePIDColour.addActionListener(new ActionListener()
abovePIDColour_actionPerformed();
}
});
- userDefinedColour.setText(MessageManager
- .getString("action.user_defined"));
- userDefinedColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- userDefinedColour_actionPerformed(e);
- }
- });
- PIDColour
-.setText(MessageManager
- .getString("label.colourScheme_%_identity"));
- PIDColour.setName(JalviewColourScheme.PID.toString());
- PIDColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- PIDColour_actionPerformed();
- }
- });
- BLOSUM62Colour
-.setText(MessageManager
- .getString("label.colourScheme_blosum62"));
- BLOSUM62Colour.setName(JalviewColourScheme.Blosum62.toString());
- BLOSUM62Colour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- BLOSUM62Colour_actionPerformed();
- }
- });
- nucleotideColour.setText(MessageManager
- .getString("label.colourScheme_nucleotide"));
- nucleotideColour.setName(JalviewColourScheme.Nucleotide.toString());
- nucleotideColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- nucleotideMenuItem_actionPerformed();
- }
- });
- purinePyrimidineColour.setText(MessageManager
- .getString("label.colourScheme_purine/pyrimidine"));
- purinePyrimidineColour.setName(JalviewColourScheme.PurinePyrimidine
- .toString());
- purinePyrimidineColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- purinePyrimidineColour_actionPerformed();
- }
- });
-
- tcoffeeColour.setText(MessageManager
- .getString("label.colourScheme_t-coffee_scores"));
- tcoffeeColour.setName(JalviewColourScheme.TCoffee.toString());
- tcoffeeColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- tcoffeeColorScheme_actionPerformed();
- }
- });
-
- /*
- * covariationColour.addActionListener(new ActionListener() {
- * public void actionPerformed(ActionEvent e) {
- * covariationColour_actionPerformed(); } });
- */
conservationMenuItem.setText(MessageManager
.getString("action.by_conservation"));
public void actionPerformed(ActionEvent e)
{
conservationMenuItem_actionPerformed();
- }
- });
+ }
+ });
}
/**
protected void buildColourMenu()
{
SequenceGroup sg = getGroup();
+ if (sg == null)
+ {
+ /*
+ * popup menu with no sequence group scope
+ */
+ return;
+ }
colourMenu.removeAll();
colourMenu.add(textColour);
colourMenu.addSeparator();
- colourMenu.add(noColourmenuItem);
- colourMenu.add(clustalColour);
- // in Java 8, isApplicableTo can be a static method on the interface
- clustalColour.setEnabled(new ClustalxColourScheme(sg, null)
- .isApplicableTo(sg));
- colourMenu.add(BLOSUM62Colour);
- BLOSUM62Colour
- .setEnabled(new Blosum62ColourScheme().isApplicableTo(sg));
- colourMenu.add(PIDColour);
- PIDColour.setEnabled(new PIDColourScheme().isApplicableTo(sg));
- colourMenu.add(zappoColour);
- zappoColour.setEnabled(new ZappoColourScheme().isApplicableTo(sg));
- colourMenu.add(taylorColour);
- taylorColour.setEnabled(new TaylorColourScheme().isApplicableTo(sg));
- colourMenu.add(hydrophobicityColour);
- hydrophobicityColour.setEnabled(new HydrophobicColourScheme()
- .isApplicableTo(sg));
- colourMenu.add(helixColour);
- helixColour.setEnabled(new HelixColourScheme().isApplicableTo(sg));
- colourMenu.add(strandColour);
- strandColour.setEnabled(new StrandColourScheme().isApplicableTo(sg));
- colourMenu.add(turnColour);
- turnColour.setEnabled(new TurnColourScheme().isApplicableTo(sg));
- colourMenu.add(buriedColour);
- buriedColour.setEnabled(new BuriedColourScheme().isApplicableTo(sg));
- colourMenu.add(nucleotideColour);
- nucleotideColour.setEnabled(new NucleotideColourScheme()
- .isApplicableTo(sg));
- colourMenu.add(purinePyrimidineColour);
- purinePyrimidineColour.setEnabled(new PurinePyrimidineColourScheme()
- .isApplicableTo(sg));
- colourMenu.add(tcoffeeColour);
- tcoffeeColour
- .setEnabled(new TCoffeeColourScheme(sg).isApplicableTo(sg));
- /*
- * add some of these items to a ButtonGroup so their
- * selection is mutually exclusive
- */
- ButtonGroup colours = new ButtonGroup();
-
- /*
- * add any user-defined colours loaded on startup or
- * during the application session
- */
- SortedMap<String, UserColourScheme> userColourSchemes = UserDefinedColours
- .getUserColourSchemes();
- if (userColourSchemes != null)
- {
- for (String userColour : userColourSchemes.keySet())
- {
- JRadioButtonMenuItem item = new JRadioButtonMenuItem(userColour);
- item.setName(userColour); // button name identifies selected colour
- item.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- colourMenu.add(item);
- colours.add(item);
- }
- }
- colourMenu.add(userDefinedColour);
+ ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
colourMenu.add(abovePIDColour);
-
- colours.add(noColourmenuItem);
- colours.add(clustalColour);
- colours.add(BLOSUM62Colour);
- colours.add(PIDColour);
- colours.add(zappoColour);
- colours.add(taylorColour);
- colours.add(hydrophobicityColour);
- colours.add(helixColour);
- colours.add(strandColour);
- colours.add(turnColour);
- colours.add(buriedColour);
- colours.add(purinePyrimidineColour);
- colours.add(tcoffeeColour);
- colours.add(nucleotideColour);
- colours.add(userDefinedColour);
- colours.add(abovePIDColour);
- // colours.add(RNAInteractionColour);
-
}
/**
PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void clustalColour_actionPerformed()
- {
- SequenceGroup sg = getGroup();
- sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void zappoColour_actionPerformed()
- {
- getGroup().cs = new ZappoColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void taylorColour_actionPerformed()
- {
- getGroup().cs = new TaylorColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void hydrophobicityColour_actionPerformed()
- {
- getGroup().cs = new HydrophobicColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void helixColour_actionPerformed()
- {
- getGroup().cs = new HelixColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void strandColour_actionPerformed()
- {
- getGroup().cs = new StrandColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void turnColour_actionPerformed()
- {
- getGroup().cs = new TurnColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void buriedColour_actionPerformed()
- {
- getGroup().cs = new BuriedColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void nucleotideMenuItem_actionPerformed()
- {
- getGroup().cs = new NucleotideColourScheme();
- refresh();
- }
-
- protected void purinePyrimidineColour_actionPerformed()
- {
- getGroup().cs = new PurinePyrimidineColourScheme();
- refresh();
- }
-
- protected void tcoffeeColorScheme_actionPerformed()
- {
- getGroup().cs = new TCoffeeColourScheme(getGroup());
- refresh();
- }
-
/*
* protected void covariationColour_actionPerformed() { getGroup().cs = new
* CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void userDefinedColour_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = getGroup();
-
- if (e.getSource().equals(userDefinedColour))
- {
- new UserDefinedColours(ap, sg);
- }
- else
- {
- UserColourScheme udc = UserDefinedColours
- .getUserColourSchemes().get(e.getActionCommand());
-
- sg.cs = udc;
- }
- refresh();
- }
-
- /**
* Open a panel where the user can choose which types of sequence annotation
* to show or hide.
*
* @param e
* DOCUMENT ME!
*/
- protected void PIDColour_actionPerformed()
- {
- SequenceGroup sg = getGroup();
- sg.cs = new PIDColourScheme();
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(ap.av.getHiddenRepSequences()),
- sg.getStartRes(), sg.getEndRes() + 1));
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void BLOSUM62Colour_actionPerformed()
- {
- SequenceGroup sg = getGroup();
-
- sg.cs = new Blosum62ColourScheme();
-
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(ap.av.getHiddenRepSequences()),
- sg.getStartRes(), sg.getEndRes() + 1));
-
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void noColourmenuItem_actionPerformed()
- {
- getGroup().cs = null;
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
protected void conservationMenuItem_actionPerformed()
{
SequenceGroup sg = getGroup();
}
/**
- * Marks as selected the colour menu item matching the given name, or the
- * first item ('None') if no match is found
- *
- * @param cs
+ * Action on user selecting an item from the colour menu (that does not have
+ * its bespoke action handler)
*/
- protected void setColourSelected(ColourSchemeI cs)
+ @Override
+ public void changeColour_actionPerformed(String colourSchemeName)
{
- noColourmenuItem.setSelected(true);
- if (cs == null)
+ SequenceGroup sg = getGroup();
+ if (ResidueColourScheme.USER_DEFINED.equals(colourSchemeName))
{
- return;
+ /*
+ * open a panel to load or configure a user-defined colour scheme
+ */
+ new UserDefinedColours(ap, sg);
}
-
- String schemeName = cs.getSchemeName();
- /*
- * look for a radio button with a name that matches the colour name
- * (note the button text may not as it may be internationalised)
- */
- for (Component menuItem : colourMenu.getMenuComponents())
+ else
{
- if (menuItem instanceof JRadioButtonMenuItem)
+ /*
+ * 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)
{
- if (schemeName.equals(((JRadioButtonMenuItem) menuItem).getName()))
- {
- ((JRadioButtonMenuItem) menuItem).setSelected(true);
- return;
- }
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
}
}
+
+ refresh();
}
}
git://source.jalview.org / jalview.git / blobdiff