X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=40ab6bbe5693623afdc133f60a2d07c2c6463a8e;hb=06ce849ffedc7ab10a3c54cda96b9a7dec58c136;hp=370e6491df63be1711ae4abedc4a299c2acac424;hpb=95ebbef7b78bf266a8252bd479510be3c80cd234;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 370e649..40ab6bb 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -59,6 +59,7 @@ import jalview.datamodel.SeqCigar; 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; @@ -78,24 +79,11 @@ import jalview.io.JnetAnnotationMaker; 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; @@ -126,7 +114,6 @@ import java.awt.event.ItemEvent; 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; @@ -149,7 +136,6 @@ 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; @@ -160,7 +146,7 @@ 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; @@ -349,7 +335,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel); if (viewport.getAlignmentConservationAnnotation() == null) { - BLOSUM62Colour.setEnabled(false); + // BLOSUM62Colour.setEnabled(false); conservationMenuItem.setEnabled(false); modifyConservation.setEnabled(false); // PIDColour.setEnabled(false); @@ -369,19 +355,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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()) { @@ -848,27 +835,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * 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")); } /** @@ -894,7 +877,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, padGapsMenuitem.setSelected(av.isPadGaps()); colourTextMenuItem.setSelected(av.isShowColourText()); abovePIDThreshold.setSelected(av.getAbovePIDThreshold()); + modifyPID.setEnabled(abovePIDThreshold.isSelected()); conservationMenuItem.setSelected(av.getConservationSelected()); + modifyConservation.setEnabled(conservationMenuItem.isSelected()); seqLimits.setSelected(av.getShowJVSuffix()); idRightAlign.setSelected(av.isRightAlignIds()); centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels()); @@ -920,8 +905,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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()); @@ -931,9 +916,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); @@ -3290,146 +3272,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @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); } @@ -3440,37 +3295,57 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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()) { @@ -3484,11 +3359,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs, "Background")); } - if (cs instanceof TCoffeeColourScheme) - { - tcoffeeColour.setEnabled(true); - tcoffeeColour.setSelected(true); - } } viewport.setGlobalColourScheme(cs); @@ -3503,7 +3373,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - protected void modifyPID_actionPerformed(ActionEvent e) + protected void modifyPID_actionPerformed() { if (viewport.getAbovePIDThreshold() && viewport.getGlobalColourScheme() != null) @@ -3521,7 +3391,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - protected void modifyConservation_actionPerformed(ActionEvent e) + protected void modifyConservation_actionPerformed() { if (viewport.getConservationSelected() && viewport.getGlobalColourScheme() != null) @@ -3533,154 +3403,44 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Action on selecting or deselecting (Colour) By Conservation */ @Override - protected void conservationMenuItem_actionPerformed(ActionEvent e) + protected void conservationMenuItem_actionPerformed() { - viewport.setConservationSelected(conservationMenuItem.isSelected()); - - viewport.setAbovePIDThreshold(false); - abovePIDThreshold.setSelected(false); + boolean selected = conservationMenuItem.isSelected(); + modifyConservation.setEnabled(selected); + viewport.setConservationSelected(selected); changeColour(viewport.getGlobalColourScheme()); - - modifyConservation_actionPerformed(null); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void abovePIDThreshold_actionPerformed(ActionEvent e) - { - viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected()); - - conservationMenuItem.setSelected(false); - viewport.setConservationSelected(false); - - changeColour(viewport.getGlobalColourScheme()); - - modifyPID_actionPerformed(null); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - @Override - public void userDefinedColour_actionPerformed(ActionEvent e) - { - if (e.getActionCommand().equals( - MessageManager.getString("action.user_defined"))) + if (selected) { - new UserDefinedColours(alignPanel, null); + modifyConservation_actionPerformed(); } else { - UserColourScheme udc = (UserColourScheme) UserDefinedColours - .getUserColourSchemes().get(e.getActionCommand()); - - changeColour(udc); + SliderPanel.hideConservationSlider(); } } - public void updateUserColourMenu() + /** + * Action on selecting or deselecting (Colour) Above PID Threshold + */ + @Override + public void abovePIDThreshold_actionPerformed() { + boolean selected = abovePIDThreshold.isSelected(); + modifyPID.setEnabled(selected); + viewport.setAbovePIDThreshold(selected); - Component[] menuItems = colourMenu.getMenuComponents(); - int iSize = menuItems.length; - for (int i = 0; i < iSize; i++) + changeColour(viewport.getGlobalColourScheme()); + if (selected) { - if (menuItems[i].getName() != null - && menuItems[i].getName().equals("USER_DEFINED")) - { - colourMenu.remove(menuItems[i]); - iSize--; - } + modifyPID_actionPerformed(); } - if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) + else { - 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); - } + SliderPanel.hidePIDSlider(); } } @@ -3691,30 +3451,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * 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(); @@ -4342,12 +4078,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - @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); @@ -5013,8 +4743,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (tcf.annotateAlignment(viewport.getAlignment(), true)) { - tcoffeeColour.setEnabled(true); - tcoffeeColour.setSelected(true); + buildColourMenu(); changeColour(new TCoffeeColourScheme(viewport.getAlignment())); isAnnotation = true; statusBar @@ -5828,7 +5557,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } 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") + " " @@ -5944,6 +5673,41 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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