X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=03e4534ce5c287987fd5ca5276c4d0e08e6448d8;hb=36c0eac11fb0d0ac6df2d971fabf524325db5e97;hp=9c4ff81cd14d0a3c4b7c9d8c912981fb40da99d3;hpb=18a91cf8bf71500b0bfa020c8348227cce2fc279;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 9c4ff81..03e4534 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -125,7 +125,6 @@ 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; @@ -146,7 +145,6 @@ 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; @@ -856,14 +854,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, conservationMenuItem.setEnabled(!nucleotide); modifyConservation.setEnabled(!nucleotide); showGroupConservation.setEnabled(!nucleotide); + clustalColour.setEnabled(!nucleotide); + zappoColour.setEnabled(!nucleotide); + taylorColour.setEnabled(!nucleotide); + hydrophobicityColour.setEnabled(!nucleotide); + helixColour.setEnabled(!nucleotide); + strandColour.setEnabled(!nucleotide); + turnColour.setEnabled(!nucleotide); + buriedColour.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( + String selectedColourScheme = Cache.getDefault( nucleotide ? Preferences.DEFAULT_COLOUR_NUC - : Preferences.DEFAULT_COLOUR_PROT, "None")); + : Preferences.DEFAULT_COLOUR_PROT, "None"); + setColourSelected(selectedColourScheme); } /** @@ -3298,7 +3307,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override - public void textColour_actionPerformed(ActionEvent e) + public void textColour_actionPerformed() { new TextColourChooser().chooseColour(alignPanel, null); } @@ -3310,7 +3319,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - protected void noColourmenuItem_actionPerformed(ActionEvent e) + protected void noColourmenuItem_actionPerformed() { changeColour(null); } @@ -3322,7 +3331,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void clustalColour_actionPerformed(ActionEvent e) + public void clustalColour_actionPerformed() { changeColour(new ClustalxColourScheme(viewport.getAlignment(), viewport.getHiddenRepSequences())); @@ -3335,7 +3344,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void zappoColour_actionPerformed(ActionEvent e) + public void zappoColour_actionPerformed() { changeColour(new ZappoColourScheme()); } @@ -3347,7 +3356,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void taylorColour_actionPerformed(ActionEvent e) + public void taylorColour_actionPerformed() { changeColour(new TaylorColourScheme()); } @@ -3359,7 +3368,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void hydrophobicityColour_actionPerformed(ActionEvent e) + public void hydrophobicityColour_actionPerformed() { changeColour(new HydrophobicColourScheme()); } @@ -3371,7 +3380,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void helixColour_actionPerformed(ActionEvent e) + public void helixColour_actionPerformed() { changeColour(new HelixColourScheme()); } @@ -3383,7 +3392,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void strandColour_actionPerformed(ActionEvent e) + public void strandColour_actionPerformed() { changeColour(new StrandColourScheme()); } @@ -3395,7 +3404,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void turnColour_actionPerformed(ActionEvent e) + public void turnColour_actionPerformed() { changeColour(new TurnColourScheme()); } @@ -3407,7 +3416,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void buriedColour_actionPerformed(ActionEvent e) + public void buriedColour_actionPerformed() { changeColour(new BuriedColourScheme()); } @@ -3419,25 +3428,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void nucleotideColour_actionPerformed(ActionEvent e) + public void nucleotideColour_actionPerformed() { changeColour(new NucleotideColourScheme()); } @Override - public void purinePyrimidineColour_actionPerformed(ActionEvent e) + public void purinePyrimidineColour_actionPerformed() { 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); } @@ -3449,7 +3458,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override - public void rnahelicesColour_actionPerformed(ActionEvent e) + public void rnahelicesColour_actionPerformed() { new RNAHelicesColourChooser(viewport, alignPanel); } @@ -3457,11 +3466,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! * - * @param e - * DOCUMENT ME! */ @Override - protected void applyToAllGroups_actionPerformed(ActionEvent e) + protected void applyToAllGroups_actionPerformed() { viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected()); } @@ -3511,7 +3518,7 @@ 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) @@ -3529,7 +3536,7 @@ 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) @@ -3547,7 +3554,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - protected void conservationMenuItem_actionPerformed(ActionEvent e) + protected void conservationMenuItem_actionPerformed() { viewport.setConservationSelected(conservationMenuItem.isSelected()); @@ -3556,7 +3563,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, changeColour(viewport.getGlobalColourScheme()); - modifyConservation_actionPerformed(null); + modifyConservation_actionPerformed(); } /** @@ -3566,7 +3573,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void abovePIDThreshold_actionPerformed(ActionEvent e) + public void abovePIDThreshold_actionPerformed() { viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected()); @@ -3575,7 +3582,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, changeColour(viewport.getGlobalColourScheme()); - modifyPID_actionPerformed(null); + modifyPID_actionPerformed(); } /** @@ -3594,104 +3601,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - UserColourScheme udc = (UserColourScheme) UserDefinedColours + UserColourScheme udc = 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! * @@ -3699,7 +3615,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void PIDColour_actionPerformed(ActionEvent e) + public void PIDColour_actionPerformed() { changeColour(new PIDColourScheme()); } @@ -3711,7 +3627,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void BLOSUM62Colour_actionPerformed(ActionEvent e) + public void BLOSUM62Colour_actionPerformed() { changeColour(new Blosum62ColourScheme()); } @@ -4351,7 +4267,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override - protected void tcoffeeColorScheme_actionPerformed(ActionEvent e) + protected void tcoffeeColorScheme_actionPerformed() { changeColour(new TCoffeeColourScheme(alignPanel.getAlignment())); } @@ -5836,7 +5752,7 @@ 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") + " "