import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
import jalview.io.TCoffeeScoreFile;
import jalview.jbgui.GAlignFrame;
import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.ColourSchemes;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.ResidueProperties;
import jalview.schemes.TCoffeeColourScheme;
-import jalview.schemes.UserColourScheme;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.DBRefFetcher;
import java.awt.event.ItemListener;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
-import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.print.PageFormat;
import java.awt.print.PrinterJob;
import java.util.List;
import java.util.Vector;
-import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JEditorPane;
import javax.swing.JInternalFrame;
import javax.swing.JLayeredPane;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JRadioButtonMenuItem;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
* @version $Revision$
*/
public class AlignFrame extends GAlignFrame implements DropTargetListener,
- IProgressIndicator, AlignViewControllerGuiI
+ IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
{
public static final int DEFAULT_WIDTH = 700;
*/
public void setGUINucleotide()
{
- boolean nucleotide = viewport.getAlignment().isNucleotide();
+ AlignmentI al = getViewport().getAlignment();
+ boolean nucleotide = al.isNucleotide();
showTranslation.setVisible(nucleotide);
showReverse.setVisible(nucleotide);
modifyConservation.setEnabled(!nucleotide);
showGroupConservation.setEnabled(!nucleotide);
- AlignmentI al = getViewport().getAlignment();
-
- /*
- * enable / disable colour schemes by querying whether they
- * are applicable to the alignment data (for example, peptide or
- * nucleotide specific, or require certain annotation present)
- */
- for (Component menuItem : colourMenu.getMenuComponents())
- {
- if (menuItem instanceof JRadioButtonMenuItem)
- {
- String colourName = ((JRadioButtonMenuItem) menuItem).getName();
- ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(
- colourName, viewport);
- if (cs != null)
- {
- ((JRadioButtonMenuItem) menuItem).setEnabled(cs
- .isApplicableTo(al));
- }
- }
- }
-
showComplementMenuItem.setText(nucleotide ? MessageManager
.getString("label.protein") : MessageManager
.getString("label.nucleotide"));
-
- String selectedColourScheme = Cache.getDefault(
- nucleotide ? Preferences.DEFAULT_COLOUR_NUC
- : Preferences.DEFAULT_COLOUR_PROT,
- ResidueColourScheme.NONE);
- setColourSelected(selectedColourScheme);
}
/**
showSequenceLogo.setSelected(av.isShowSequenceLogo());
normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
- setColourSelected(ColourSchemeProperty.getColourName(av
- .getGlobalColourScheme()));
+ ColourMenuHelper.setColourSelected(colourMenu,
+ av.getGlobalColourScheme());
showSeqFeatures.setSelected(av.isShowSequenceFeatures());
hiddenMarkers.setState(av.getShowHiddenMarkers());
new TextColourChooser().chooseColour(alignPanel, null);
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void noColourmenuItem_actionPerformed()
- {
- changeColour(null);
- }
-
/*
* public void covariationColour_actionPerformed() {
* changeColour(new
* @param name
* the name (not the menu item label!) of the colour scheme
*/
+ @Override
public void changeColour_actionPerformed(String name)
{
+ /*
+ * 'User Defined' opens a panel to configure or load a
+ * user-defined colour scheme
+ */
+ if (ResidueColourScheme.USER_DEFINED.equals(name))
+ {
+ new UserDefinedColours(alignPanel, null);
+ return;
+ }
+
+ /*
+ * otherwise set the chosen colour scheme (or null for 'None')
+ */
ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
- viewport);
+ viewport.getAlignment(), viewport.getHiddenRepSequences());
changeColour(cs);
}
// TODO: pull up to controller method
if (cs != null)
{
- setColourSelected(cs.getSchemeName());
+ ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
// Make sure viewport is up to date w.r.t. any sliders
if (viewport.getAbovePIDThreshold())
{
}
/**
- * Action on the user selecting the option "User Defined" to create or load a
- * new colour scheme
- *
- * @param e
- */
- @Override
- public void userDefinedColour_actionPerformed(ActionEvent e)
- {
- new UserDefinedColours(alignPanel, null);
- }
-
- /**
* DOCUMENT ME!
*
* @param e
{
if (tcf.annotateAlignment(viewport.getAlignment(), true))
{
- // tcoffeeColour.setEnabled(true);
- // tcoffeeColour.setSelected(true);
- for (Component menuItem : colourMenu.getMenuComponents())
- {
- if (menuItem instanceof JRadioButtonMenuItem
- && ((JRadioButtonMenuItem) menuItem).getText()
- .equals("T-Coffee Scores"))
- {
- ((JRadioButtonMenuItem) menuItem).setSelected(true);
- }
- }
buildColourMenu();
changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
isAnnotation = true;
{
colourMenu.removeAll();
- /*
- * ButtonGroup groups those items whose
- * selection is mutually exclusive
- */
- ButtonGroup colours = new ButtonGroup();
-
colourMenu.add(applyToAllGroups);
colourMenu.add(textColour);
colourMenu.addSeparator();
- colourMenu.add(noColourmenuItem);
- colours.add(noColourmenuItem);
-
- /*
- * scan registered colour schemes (built-in or user-defined
- * and add them to the menu (in the order they were added)
- */
- Iterable<ColourSchemeI> colourSchemes = ColourSchemes.getInstance()
- .getColourSchemes();
- for (ColourSchemeI scheme : colourSchemes)
- {
- /*
- * button text is i18n'd but the name is the canonical name of
- * the colour scheme (inspected in changeColour_actionPerformed)
- */
- final String name = scheme.getSchemeName();
- String label = MessageManager.getStringOrReturn("label.colourScheme_"
- + name.toLowerCase().replace(" ", "_"), name);
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(label);
- radioItem.setName(name);
- if (scheme instanceof UserColourScheme)
- {
- /*
- * user-defined colour scheme loaded on startup or during the
- * Jalview session; right-click on this offers the option to
- * remove it as a colour choice
- */
- radioItem.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Mac
- {
- offerRemoval();
- }
- }
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Windows
- {
- offerRemoval();
- }
- }
-
- void offerRemoval()
- {
- ActionListener al = radioItem.getActionListeners()[0];
- radioItem.removeActionListener(al);
- int option = JvOptionPane.showInternalConfirmDialog(
- Desktop.desktop, MessageManager
- .getString("label.remove_from_default_list"),
- MessageManager
- .getString("label.remove_user_defined_colour"),
- JvOptionPane.YES_NO_OPTION);
- if (option == JvOptionPane.YES_OPTION)
- {
- UserDefinedColours.removeColourFromDefaults(radioItem
- .getName());
- ColourSchemes.getInstance().removeColourScheme(
- radioItem.getName());
- colourMenu.remove(radioItem);
- }
- else
- {
- radioItem.addActionListener(al);
- }
- }
- });
- }
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- changeColour_actionPerformed(name);
- }
- });
- colourMenu.add(radioItem);
- colours.add(radioItem);
- }
-
- colourMenu.add(userDefinedColour);
- colours.add(userDefinedColour);
+ ColourMenuHelper
+ .addMenuItems(colourMenu, this, viewport.getAlignment());
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
- setColourSelected(Cache.getDefault(Preferences.DEFAULT_COLOUR,
- ResidueColourScheme.NONE));
+ /*
+ * select the default colour for the alignment (this may be
+ * overridden later)
+ */
+ boolean nucleotide = viewport.getAlignment().isNucleotide();
+ String defaultColourScheme = Cache.getDefault(
+ nucleotide ? Preferences.DEFAULT_COLOUR_NUC
+ : Preferences.DEFAULT_COLOUR_PROT,
+ ResidueColourScheme.NONE);
- setGUINucleotide();
+ ColourMenuHelper.setColourSelected(colourMenu, defaultColourScheme);
}
}
--- /dev/null
+package jalview.gui;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.ResidueColourScheme;
+import jalview.schemes.UserColourScheme;
+import jalview.util.MessageManager;
+
+import java.awt.Component;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JMenu;
+import javax.swing.JRadioButtonMenuItem;
+
+public class ColourMenuHelper
+{
+ public interface ColourChangeListener
+ {
+ void changeColour_actionPerformed(String name);
+ }
+
+ /**
+ * Adds items to the colour menu, as mutually exclusive members of a button
+ * group. The callback handler is responsible for the action on selecting any
+ * of these options. It is returned the name of the selected colour, or "None"
+ * or "User Defined".
+ * <ul>
+ * <li>None</li>
+ * <li>Clustal</li>
+ * <li>...other 'built-in' colours</li>
+ * <li>...any user-defined colours</li>
+ * <li>User Defined..</li>
+ * </ul>
+ *
+ * @param colourMenu
+ * the menu to attach items to
+ * @param client
+ * a callback to handle menu selection
+ * @param coll
+ * the data the menu is being built for
+ */
+ public static void addMenuItems(final JMenu colourMenu,
+ final ColourChangeListener client, AnnotatedCollectionI coll)
+ {
+ /*
+ * ButtonGroup groups those items whose
+ * selection is mutually exclusive
+ */
+ ButtonGroup colours = new ButtonGroup();
+ JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(
+ MessageManager.getString("label.none"));
+ noColourmenuItem.setName(ResidueColourScheme.NONE);
+ noColourmenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ client.changeColour_actionPerformed(ResidueColourScheme.NONE);
+ }
+ });
+ colourMenu.add(noColourmenuItem);
+ colours.add(noColourmenuItem);
+
+ /*
+ * scan registered colour schemes (built-in or user-defined
+ * and add them to the menu (in the order they were added)
+ */
+ Iterable<ColourSchemeI> colourSchemes = ColourSchemes.getInstance()
+ .getColourSchemes();
+ for (ColourSchemeI scheme : colourSchemes)
+ {
+ /*
+ * button text is i18n'd but the name is the canonical name of
+ * the colour scheme (inspected in changeColour_actionPerformed)
+ */
+ final String name = scheme.getSchemeName();
+ String label = MessageManager.getStringOrReturn("label.colourScheme_"
+ + name.toLowerCase().replace(" ", "_"), name);
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(label);
+ radioItem.setName(name);
+ radioItem.setEnabled(scheme.isApplicableTo(coll));
+ if (scheme instanceof UserColourScheme)
+ {
+ /*
+ * user-defined colour scheme loaded on startup or during the
+ * Jalview session; right-click on this offers the option to
+ * remove it as a colour choice
+ */
+ radioItem.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger()) // Mac
+ {
+ offerRemoval();
+ }
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger()) // Windows
+ {
+ offerRemoval();
+ }
+ }
+
+ void offerRemoval()
+ {
+ ActionListener al = radioItem.getActionListeners()[0];
+ radioItem.removeActionListener(al);
+ int option = JvOptionPane.showInternalConfirmDialog(
+ Desktop.desktop, MessageManager
+ .getString("label.remove_from_default_list"),
+ MessageManager
+ .getString("label.remove_user_defined_colour"),
+ JvOptionPane.YES_NO_OPTION);
+ if (option == JvOptionPane.YES_OPTION)
+ {
+ UserDefinedColours.removeColourFromDefaults(radioItem
+ .getName());
+ ColourSchemes.getInstance().removeColourScheme(
+ radioItem.getName());
+ colourMenu.remove(radioItem);
+ }
+ else
+ {
+ radioItem.addActionListener(al);
+ }
+ }
+ });
+ }
+ radioItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent evt)
+ {
+ client.changeColour_actionPerformed(name);
+ }
+ });
+ colourMenu.add(radioItem);
+ colours.add(radioItem);
+ }
+
+ final String label = MessageManager.getString("action.user_defined");
+ JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem(label);
+ userDefinedColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ client.changeColour_actionPerformed(ResidueColourScheme.USER_DEFINED);
+ }
+ });
+ colourMenu.add(userDefinedColour);
+ colours.add(userDefinedColour);
+ }
+
+ /**
+ * Marks as selected the colour menu item matching the given name, or the
+ * first item ('None') if no match is found
+ *
+ * @param colourMenu
+ * @param colourName
+ */
+ public static void setColourSelected(JMenu colourMenu, String colourName)
+ {
+ if (colourName == null)
+ {
+ return;
+ }
+
+ JRadioButtonMenuItem none = null;
+
+ /*
+ * select the radio button whose name matches the colour name
+ * (not the button text, as it may be internationalised)
+ */
+ for (Component menuItem : colourMenu.getMenuComponents())
+ {
+ if (menuItem instanceof JRadioButtonMenuItem)
+ {
+ String buttonName = ((JRadioButtonMenuItem) menuItem).getName();
+ if (colourName.equals(buttonName))
+ {
+ ((JRadioButtonMenuItem) menuItem).setSelected(true);
+ return;
+ }
+ if (ResidueColourScheme.NONE.equals(buttonName))
+ {
+ none = (JRadioButtonMenuItem) menuItem;
+ }
+ }
+ }
+ if (none != null)
+ {
+ none.setSelected(true);
+ }
+ }
+
+ /**
+ * Marks as selected the colour menu item matching the given colour scheme, or
+ * the first item ('None') if no match is found
+ *
+ * @param colourMenu
+ * @param cs
+ */
+ public static void setColourSelected(JMenu colourMenu, ColourSchemeI cs)
+ {
+ setColourSelected(colourMenu, cs == null ? ResidueColourScheme.NONE
+ : cs.getSchemeName());
+ }
+}
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();
- }
- });
+ }
+ });
}
/**
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);
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();
}
}
import java.awt.BorderLayout;
import java.awt.Color;
-import java.awt.Component;
import java.awt.GridLayout;
import java.awt.Toolkit;
import java.awt.event.ActionEvent;
protected JRadioButtonMenuItem textColour;
- protected JRadioButtonMenuItem userDefinedColour;
-
protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem conservationMenuItem;
- protected JRadioButtonMenuItem noColourmenuItem;
-
protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
}
}
- /**
- * Marks as selected the colour menu item matching the given name, or the
- * first item ('None') if no match is found
- *
- * @param colourName
- */
- protected void setColourSelected(String colourName)
- {
- noColourmenuItem.setSelected(true);
- if (colourName == null)
- {
- return;
- }
-
- /*
- * 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())
- {
- if (menuItem instanceof JRadioButtonMenuItem)
- {
- if (colourName.equals(((JRadioButtonMenuItem) menuItem).getName()))
- {
- ((JRadioButtonMenuItem) menuItem).setSelected(true);
- return;
- }
- }
- }
- }
-
private void jbInit() throws Exception
{
initColourMenu();
/**
* Constructs the entries on the Colour menu (but does not add them to the
- * menu). The 'name' property of each item is set to the canonical name of the
- * corresponding colour scheme (may not match the display name), to allow
- * selection of items by colour scheme name.
+ * menu).
*/
protected void initColourMenu()
{
}
});
- userDefinedColour = new JRadioButtonMenuItem(
- MessageManager
- .getString("action.user_defined"));
- userDefinedColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- userDefinedColour_actionPerformed(e);
- }
- });
-
conservationMenuItem = new JCheckBoxMenuItem(
MessageManager.getString("action.by_conservation"));
conservationMenuItem.addActionListener(new ActionListener()
conservationMenuItem_actionPerformed();
}
});
- noColourmenuItem = new JRadioButtonMenuItem(
- MessageManager.getString("label.none"));
- noColourmenuItem.setName("None");
- noColourmenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- noColourmenuItem_actionPerformed();
- }
- });
abovePIDThreshold = new JCheckBoxMenuItem(
MessageManager.getString("label.above_identity_threshold"));
{
}
- protected void userDefinedColour_actionPerformed(ActionEvent e)
- {
- }
-
-
-
- /*
- * protected void covariationColour_actionPerformed() { }
- */
-
- protected void noColourmenuItem_actionPerformed()
- {
- }
-
protected void conservationMenuItem_actionPerformed()
{
}
* create a new instance of it
*/
ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(
- name, forData);
+ name, forData, null);
if (scheme != null)
{
return scheme;
package jalview.schemes;
-import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
import java.util.LinkedHashMap;
import java.util.Map;
*
* @param name
* name of the colour scheme
- * @param viewport
+ * @param forData
+ * the data to be coloured
+ * @param optional
+ * map from hidden representative sequences to the sequences they
+ * represent
* @return
*/
- public ColourSchemeI getColourScheme(String name, AlignViewportI viewport)
+ public ColourSchemeI getColourScheme(String name,
+ AnnotatedCollectionI forData,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
if (name == null)
{
return null;
}
ColourSchemeI cs = schemes.get(name.toLowerCase());
- return cs == null ? null : cs.getInstance(viewport.getAlignment(),
- viewport.getHiddenRepSequences());
+ return cs == null ? null : cs.getInstance(forData, hiddenRepSequences);
}
/**
- * Returns an instance of the colour scheme with which the given data may be
+ * Returns an instance of the colour scheme with which the given view may be
* coloured
*
* @param name
+ * name of the colour scheme
* @param forData
+ * the data to be coloured
* @return
*/
public ColourSchemeI getColourScheme(String name,
AnnotatedCollectionI forData)
{
- ColourSchemeI cs = schemes.get(name.toLowerCase());
- return cs == null ? null : cs.getInstance(forData, null);
+ return getColourScheme(name, forData, null);
}
/**
{
public static final String NONE = "None";
+ public static final String USER_DEFINED = "User Defined";
+
/*
* lookup up by character value e.g. 'G' to the colors array index
* e.g. if symbolIndex['K'] = 11 then colors[11] is the colour for K
}
/*
- * inspect the data context (alignment dataset) for residue type
+ * inspect the data context (alignment) for residue type
*/
boolean nucleotide = false;
- AnnotatedCollectionI context = ac.getContext();
- if (context != null)
+ if (ac instanceof AlignmentI)
+ {
+ nucleotide = ((AlignmentI) ac).isNucleotide();
+ }
+ else
{
+ AnnotatedCollectionI context = ac.getContext();
if (context instanceof AlignmentI)
{
nucleotide = ((AlignmentI) context).isNucleotide();
return true;
}
}
- else if (ac instanceof AlignmentI)
- {
- nucleotide = ((AlignmentI) ac).isNucleotide();
- }
- else
- {
- return true;
- }
/*
* does data type match colour scheme type?
import jalview.bin.Cache;
import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
}
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ public ColourSchemeI getInstance(AnnotatedCollectionI ac,
+ Map<SequenceI, SequenceCollectionI> hrs)
{
return null;
}
ColourSchemes cs = ColourSchemes.getInstance();
AlignViewport viewport = af.getViewport();
+ AlignmentI alignment = viewport.getAlignment();
assertTrue(cs.getColourScheme(JalviewColourScheme.Blosum62.toString(),
- viewport) instanceof Blosum62ColourScheme);
+ alignment) instanceof Blosum62ColourScheme);
assertTrue(cs.getColourScheme(JalviewColourScheme.Buried.toString(),
- viewport) instanceof BuriedColourScheme);
+ alignment) instanceof BuriedColourScheme);
assertTrue(cs.getColourScheme(JalviewColourScheme.Clustal.toString(),
- viewport) instanceof ClustalxColourScheme);
+ alignment) instanceof ClustalxColourScheme);
assertTrue(cs.getColourScheme(JalviewColourScheme.Helix.toString(),
- viewport) instanceof HelixColourScheme);
+ alignment) instanceof HelixColourScheme);
assertTrue(cs.getColourScheme(
- JalviewColourScheme.Hydrophobic.toString(), viewport) instanceof HydrophobicColourScheme);
+ JalviewColourScheme.Hydrophobic.toString(), alignment) instanceof HydrophobicColourScheme);
assertTrue(cs.getColourScheme(
- JalviewColourScheme.Nucleotide.toString(), viewport) instanceof NucleotideColourScheme);
+ JalviewColourScheme.Nucleotide.toString(), alignment) instanceof NucleotideColourScheme);
assertTrue(cs.getColourScheme(JalviewColourScheme.PID.toString(),
- viewport) instanceof PIDColourScheme);
+ alignment) instanceof PIDColourScheme);
assertTrue(cs.getColourScheme(
- JalviewColourScheme.PurinePyrimidine.toString(), viewport) instanceof PurinePyrimidineColourScheme);
+ JalviewColourScheme.PurinePyrimidine.toString(), alignment) instanceof PurinePyrimidineColourScheme);
assertTrue(cs.getColourScheme(
- JalviewColourScheme.RNAHelices.toString(), viewport) instanceof RNAHelicesColour);
+ JalviewColourScheme.RNAHelices.toString(), alignment) instanceof RNAHelicesColour);
assertTrue(cs.getColourScheme(JalviewColourScheme.Strand.toString(),
- viewport) instanceof StrandColourScheme);
+ alignment) instanceof StrandColourScheme);
assertTrue(cs.getColourScheme(JalviewColourScheme.Taylor.toString(),
- viewport) instanceof TaylorColourScheme);
+ alignment) instanceof TaylorColourScheme);
assertTrue(cs.getColourScheme(JalviewColourScheme.TCoffee.toString(),
- viewport) instanceof TCoffeeColourScheme);
+ alignment) instanceof TCoffeeColourScheme);
assertTrue(cs.getColourScheme(JalviewColourScheme.Turn.toString(),
- viewport) instanceof TurnColourScheme);
+ alignment) instanceof TurnColourScheme);
assertTrue(cs.getColourScheme(JalviewColourScheme.Zappo.toString(),
- viewport) instanceof ZappoColourScheme);
+ alignment) instanceof ZappoColourScheme);
af.closeMenuItem_actionPerformed(true);
}
.isApplicableTo(peptide));
assertFalse(new ClustalxColourScheme(nucleotide, null)
.isApplicableTo(nucleotide));
- // Blosum requires presence of Conservation annotation
- assertFalse(new Blosum62ColourScheme().isApplicableTo(peptide));
+ assertTrue(new Blosum62ColourScheme().isApplicableTo(peptide));
assertFalse(new Blosum62ColourScheme().isApplicableTo(nucleotide));
assertTrue(new BuriedColourScheme().isApplicableTo(peptide));
assertFalse(new BuriedColourScheme().isApplicableTo(nucleotide));
assertTrue(new ZappoColourScheme().isApplicableTo(peptide));
assertFalse(new ZappoColourScheme().isApplicableTo(nucleotide));
- peptide.addAnnotation(new AlignmentAnnotation("Conservation",
- "Conservation", new Annotation[1], 0f, 11f,
- AlignmentAnnotation.BAR_GRAPH));
- assertTrue(new Blosum62ColourScheme().isApplicableTo(peptide));
-
/*
* nucleotide-specific colour schemes
*/
git://source.jalview.org / jalview.git / commitdiff