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.NewickFile;
import jalview.io.TCoffeeScoreFile;
import jalview.jbgui.GAlignFrame;
-import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ClustalxColourScheme;
import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.NucleotideColourScheme;
-import jalview.schemes.PIDColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.RNAHelicesColourChooser;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.ResidueColourScheme;
import jalview.schemes.ResidueProperties;
-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.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 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;
alignPanel);
if (viewport.getAlignmentConservationAnnotation() == null)
{
- BLOSUM62Colour.setEnabled(false);
+ // BLOSUM62Colour.setEnabled(false);
conservationMenuItem.setEnabled(false);
modifyConservation.setEnabled(false);
// PIDColour.setEnabled(false);
sortPairwiseMenuItem_actionPerformed(null);
}
- if (Desktop.desktop != null)
- {
- this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
- addServiceListeners();
- setGUINucleotide(viewport.getAlignment().isNucleotide());
- }
-
this.alignPanel.av
.setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
buildTreeMenu();
+ buildColourMenu();
+
+ if (Desktop.desktop != null)
+ {
+ this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
+ addServiceListeners();
+ setGUINucleotide();
+ }
if (viewport.getWrapAlignment())
{
/**
* Configure menu items that vary according to whether the alignment is
* nucleotide or protein
- *
- * @param nucleotide
*/
- public void setGUINucleotide(boolean nucleotide)
+ public void setGUINucleotide()
{
+ AlignmentI al = getViewport().getAlignment();
+ boolean nucleotide = al.isNucleotide();
+
showTranslation.setVisible(nucleotide);
showReverse.setVisible(nucleotide);
showReverseComplement.setVisible(nucleotide);
conservationMenuItem.setEnabled(!nucleotide);
- modifyConservation.setEnabled(!nucleotide);
+ modifyConservation.setEnabled(!nucleotide
+ && conservationMenuItem.isSelected());
showGroupConservation.setEnabled(!nucleotide);
- rnahelicesColour.setEnabled(nucleotide);
- nucleotideColour.setEnabled(nucleotide);
- purinePyrimidineColour.setEnabled(nucleotide);
- RNAInteractionColour.setEnabled(nucleotide);
+
showComplementMenuItem.setText(nucleotide ? MessageManager
.getString("label.protein") : MessageManager
.getString("label.nucleotide"));
- setColourSelected(jalview.bin.Cache.getDefault(
- nucleotide ? Preferences.DEFAULT_COLOUR_NUC
- : Preferences.DEFAULT_COLOUR_PROT, "None"));
}
/**
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());
autoCalculate.setSelected(av.autoCalculateConsensus);
sortByTree.setSelected(av.sortByTree);
listenToViewSelections.setSelected(av.followSelection);
- rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
- rnahelicesColour
- .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
showProducts.setEnabled(canShowProducts());
setGroovyEnabled(Desktop.getGroovyConsole() != null);
}
@Override
- public void textColour_actionPerformed(ActionEvent e)
+ public void textColour_actionPerformed()
{
new TextColourChooser().chooseColour(alignPanel, null);
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
- {
- changeColour(null);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void clustalColour_actionPerformed(ActionEvent e)
- {
- changeColour(new ClustalxColourScheme(viewport.getAlignment(),
- viewport.getHiddenRepSequences()));
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void zappoColour_actionPerformed(ActionEvent e)
- {
- changeColour(new ZappoColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void taylorColour_actionPerformed(ActionEvent e)
- {
- changeColour(new TaylorColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void hydrophobicityColour_actionPerformed(ActionEvent e)
- {
- changeColour(new HydrophobicColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void helixColour_actionPerformed(ActionEvent e)
- {
- changeColour(new HelixColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void strandColour_actionPerformed(ActionEvent e)
- {
- changeColour(new StrandColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void turnColour_actionPerformed(ActionEvent e)
- {
- changeColour(new TurnColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void buriedColour_actionPerformed(ActionEvent e)
- {
- changeColour(new BuriedColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void nucleotideColour_actionPerformed(ActionEvent e)
- {
- changeColour(new NucleotideColourScheme());
- }
-
- @Override
- public void purinePyrimidineColour_actionPerformed(ActionEvent e)
- {
- changeColour(new PurinePyrimidineColourScheme());
- }
-
/*
- * public void covariationColour_actionPerformed(ActionEvent e) {
+ * public void covariationColour_actionPerformed() {
* changeColour(new
* CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
* ()[0])); }
*/
@Override
- public void annotationColour_actionPerformed(ActionEvent e)
+ public void annotationColour_actionPerformed()
{
new AnnotationColourChooser(viewport, alignPanel);
}
new AnnotationColumnChooser(viewport, alignPanel);
}
+ /**
+ * Action on the user checking or unchecking the option to apply the selected
+ * colour scheme to all groups. If unchecked, groups may have their own
+ * independent colour schemes.
+ *
+ */
@Override
- public void rnahelicesColour_actionPerformed(ActionEvent e)
+ protected void applyToAllGroups_actionPerformed()
{
- new RNAHelicesColourChooser(viewport, alignPanel);
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
}
/**
- * DOCUMENT ME!
+ * Action on user selecting a colour from the colour menu
*
- * @param e
- * DOCUMENT ME!
+ * @param name
+ * the name (not the menu item label!) of the colour scheme
*/
@Override
- protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ public void changeColour_actionPerformed(String name)
{
- viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
+ /*
+ * '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.getAlignment(), viewport.getHiddenRepSequences());
+ changeColour(cs);
}
/**
- * DOCUMENT ME!
+ * Actions on setting or changing the alignment colour scheme
*
* @param cs
- * DOCUMENT ME!
*/
@Override
public void changeColour(ColourSchemeI cs)
{
// TODO: pull up to controller method
-
if (cs != null)
{
+ ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
// Make sure viewport is up to date w.r.t. any sliders
if (viewport.getAbovePIDThreshold())
{
cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
cs, "Background"));
}
- if (cs instanceof TCoffeeColourScheme)
- {
- tcoffeeColour.setEnabled(true);
- tcoffeeColour.setSelected(true);
- }
}
viewport.setGlobalColourScheme(cs);
/**
* DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
@Override
protected void modifyPID_actionPerformed()
/**
* DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
@Override
protected void modifyConservation_actionPerformed()
* DOCUMENT ME!
*/
@Override
- public void userDefinedColour_actionPerformed(ActionEvent e)
- {
- if (e.getActionCommand().equals(
- MessageManager.getString("action.user_defined")))
- {
- new UserDefinedColours(alignPanel, null);
- }
- else
- {
- UserColourScheme udc = (UserColourScheme) UserDefinedColours
- .getUserColourSchemes().get(e.getActionCommand());
-
- changeColour(udc);
- }
- }
-
- public void updateUserColourMenu()
- {
-
- Component[] menuItems = colourMenu.getMenuComponents();
- int iSize = menuItems.length;
- for (int i = 0; i < iSize; i++)
- {
- if (menuItems[i].getName() != null
- && menuItems[i].getName().equals("USER_DEFINED"))
- {
- colourMenu.remove(menuItems[i]);
- iSize--;
- }
- }
- if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
- {
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours
- .getUserColourSchemes().keys();
-
- while (userColours.hasMoreElements())
- {
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
- userColours.nextElement().toString());
- radioItem.setName("USER_DEFINED");
- radioItem.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Mac
- {
- offerRemoval(radioItem);
- }
- }
-
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Windows
- {
- offerRemoval(radioItem);
- }
- }
-
- /**
- * @param radioItem
- */
- void offerRemoval(final JRadioButtonMenuItem radioItem)
- {
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
- int option = JvOptionPane.showInternalConfirmDialog(
- jalview.gui.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)
- {
- jalview.gui.UserDefinedColours
- .removeColourFromDefaults(radioItem.getText());
- colourMenu.remove(radioItem);
- }
- else
- {
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- }
- }
- });
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
-
- colourMenu.insert(radioItem, 15);
- colours.add(radioItem);
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void PIDColour_actionPerformed(ActionEvent e)
- {
- changeColour(new PIDColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)
- {
- changeColour(new Blosum62ColourScheme());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
}
}
- @Override
- protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
- {
- changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
- }
-
public TreePanel ShowNewickTree(NewickFile nf, String title)
{
return ShowNewickTree(nf, title, 600, 500, 4, 5);
{
if (tcf.annotateAlignment(viewport.getAlignment(), true))
{
- tcoffeeColour.setEnabled(true);
- tcoffeeColour.setSelected(true);
+ buildColourMenu();
changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
isAnnotation = true;
statusBar
}
AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
.size()]));
- AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
+ GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
cdna.alignAs(alignment);
String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
true,
(actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0);
}
+
+ /**
+ * Rebuilds the Colour menu, including any user-defined colours which have
+ * been loaded either on startup or during the session
+ */
+ public void buildColourMenu()
+ {
+ colourMenu.removeAll();
+
+ colourMenu.add(applyToAllGroups);
+ colourMenu.add(textColour);
+ colourMenu.addSeparator();
+
+ ColourMenuHelper.addMenuItems(colourMenu, this,
+ viewport.getAlignment(), false);
+
+ colourMenu.addSeparator();
+ colourMenu.add(conservationMenuItem);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDThreshold);
+ colourMenu.add(modifyPID);
+ colourMenu.add(annotationColour);
+
+ /*
+ * 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);
+
+ ColourMenuHelper.setColourSelected(colourMenu, defaultColourScheme);
+ }
}
class PrintThread extends Thread
git://source.jalview.org / jalview.git / blobdiff