X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=b39f4a82b6fb287648918a2bbe9336dbc8ff1e2e;hb=c00cfcb9f2223f1225fba57e5de85141cfa4570c;hp=b38fab4d1fba9bbc140939b2a1383025292dd97f;hpb=b0cee3aaf7d8873910939f97b6acb217d518968d;p=jalview.git diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index b38fab4..b39f4a8 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -23,15 +23,9 @@ package jalview.jbgui; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.api.SplitContainerI; import jalview.bin.Cache; -import jalview.gui.Desktop; -import jalview.gui.JvOptionPane; import jalview.gui.JvSwingUtils; import jalview.gui.Preferences; -import jalview.gui.UserDefinedColours; -import jalview.io.FileFormat; -import jalview.schemes.JalviewColourScheme; -import jalview.schemes.ResidueColourScheme; -import jalview.schemes.UserColourScheme; +import jalview.io.FileFormats; import jalview.util.MessageManager; import jalview.util.Platform; @@ -67,14 +61,10 @@ import javax.swing.event.MenuListener; public class GAlignFrame extends JInternalFrame { - protected static final String USER_DEFINED_COLOUR_SCHEME = "USER_DEFINED"; - protected JMenuBar alignFrameMenuBar = new JMenuBar(); protected JMenuItem closeMenuItem = new JMenuItem(); - protected JMenu colourMenu = new JMenu(); - protected JMenu webService = new JMenu(); protected JMenuItem webServiceNoServices; @@ -89,40 +79,6 @@ public class GAlignFrame extends JInternalFrame protected JMenu outputTextboxMenu = new JMenu(); - protected JRadioButtonMenuItem textColour; - - protected JRadioButtonMenuItem clustalColour; - - protected JRadioButtonMenuItem zappoColour; - - protected JRadioButtonMenuItem taylorColour; - - protected JRadioButtonMenuItem hydrophobicityColour; - - protected JRadioButtonMenuItem helixColour; - - protected JRadioButtonMenuItem strandColour; - - protected JRadioButtonMenuItem turnColour; - - protected JRadioButtonMenuItem buriedColour; - - protected JRadioButtonMenuItem userDefinedColour; - - protected JRadioButtonMenuItem PIDColour; - - protected JRadioButtonMenuItem BLOSUM62Colour; - - protected JRadioButtonMenuItem nucleotideColour; - - protected JRadioButtonMenuItem purinePyrimidineColour; - - protected JRadioButtonMenuItem RNAInteractionColour; - - // protected JRadioButtonMenuItem covariationColour; - - protected JRadioButtonMenuItem tcoffeeColour; - protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem(); @@ -133,16 +89,10 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem redoMenuItem = new JMenuItem(); - protected JCheckBoxMenuItem conservationMenuItem; - - JRadioButtonMenuItem noColourmenuItem; - protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem abovePIDThreshold; - public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem(); JMenuItem copy = new JMenuItem(); @@ -151,8 +101,6 @@ public class GAlignFrame extends JInternalFrame JMenu pasteMenu = new JMenu(); - protected JCheckBoxMenuItem applyToAllGroups; - protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem(); @@ -161,10 +109,20 @@ public class GAlignFrame extends JInternalFrame protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem(); - protected JMenuItem modifyPID; + protected JCheckBoxMenuItem applyToAllGroups; + + protected JMenu colourMenu = new JMenu(); + + protected JRadioButtonMenuItem textColour; + + protected JCheckBoxMenuItem conservationMenuItem; protected JMenuItem modifyConservation; + protected JCheckBoxMenuItem abovePIDThreshold; + + protected JMenuItem modifyPID; + protected JMenuItem annotationColour; protected JMenu sortByTreeMenu = new JMenu(); @@ -179,8 +137,6 @@ public class GAlignFrame extends JInternalFrame protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem(); - protected ButtonGroup colours = new ButtonGroup(); - protected JMenuItem showTranslation = new JMenuItem(); protected JMenuItem showReverse = new JMenuItem(); @@ -191,8 +147,6 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem runGroovy = new JMenuItem(); - protected JMenuItem rnahelicesColour; - protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem(); @@ -257,7 +211,7 @@ public class GAlignFrame extends JInternalFrame setJMenuBar(alignFrameMenuBar); // dynamically fill save as menu with available formats - for (String ff : FileFormat.getWritableFormats(true)) + for (String ff : FileFormats.getInstance().getWritableFormats(true)) { JMenuItem item = new JMenuItem(ff); @@ -290,75 +244,9 @@ public class GAlignFrame extends JInternalFrame } } - public void setColourSelected(String defaultColour) - { - JalviewColourScheme scheme = JalviewColourScheme.forName(defaultColour); - if (scheme == null) - { - noColourmenuItem.setSelected(true); - return; - } - switch (scheme) - { - - case Clustal: - clustalColour.setSelected(true); - break; - case Blosum62: - BLOSUM62Colour.setSelected(true); - break; - case PID: - PIDColour.setSelected(true); - break; - case Zappo: - zappoColour.setSelected(true); - break; - case Taylor: - taylorColour.setSelected(true); - break; - case Hydrophobic: - hydrophobicityColour.setSelected(true); - break; - case Helix: - helixColour.setSelected(true); - break; - case Strand: - strandColour.setSelected(true); - break; - case Turn: - turnColour.setSelected(true); - break; - case Buried: - buriedColour.setSelected(true); - break; - case Nucleotide: - nucleotideColour.setSelected(true); - break; - case TCoffee: - tcoffeeColour.setSelected(true); - break; - case PurinePyrimidine: - purinePyrimidineColour.setSelected(true); - break; - // case RNAInteraction: - // RNAInteractionColour.setSelected(true); - // break; - case RNAHelices: - rnahelicesColour.setSelected(true); - break; - case UserDefined: - userDefinedColour.setSelected(true); - break; - default: - noColourmenuItem.setSelected(true); - break; - } - } - private void jbInit() throws Exception { initColourMenu(); - buildColourMenu(); JMenuItem saveAs = new JMenuItem( MessageManager.getString("action.save_as")); @@ -677,7 +565,7 @@ public class GAlignFrame extends JInternalFrame JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem( - MessageManager.getString("label.average_distance_bloslum62")); + MessageManager.getString("label.average_distance_blosum62")); avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener() { @Override @@ -2017,146 +1905,8 @@ public class GAlignFrame extends JInternalFrame } /** - * 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(); - colours = new ButtonGroup(); - - colourMenu.add(applyToAllGroups); - colourMenu.add(textColour); - colourMenu.addSeparator(); - colourMenu.add(noColourmenuItem); - colourMenu.add(clustalColour); - colourMenu.add(BLOSUM62Colour); - colourMenu.add(PIDColour); - colourMenu.add(zappoColour); - colourMenu.add(taylorColour); - colourMenu.add(hydrophobicityColour); - colourMenu.add(helixColour); - colourMenu.add(strandColour); - colourMenu.add(turnColour); - colourMenu.add(buriedColour); - colourMenu.add(nucleotideColour); - colourMenu.add(purinePyrimidineColour); - // colourMenu.add(RNAInteractionColour); - // colourMenu.add(covariationColour); - colourMenu.add(tcoffeeColour); - - /* - * add any user-defined colours - */ - Map userColourSchemes = UserDefinedColours - .getUserColourSchemes(); - if (userColourSchemes != null) - { - for (String userColour : userColourSchemes.keySet()) - { - final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem( - userColour); - radioItem.setName(USER_DEFINED_COLOUR_SCHEME); - 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() - { - radioItem.removeActionListener(radioItem.getActionListeners()[0]); - - 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 - .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.add(radioItem); - colours.add(radioItem); - } - } - - colourMenu.add(userDefinedColour); - colourMenu.addSeparator(); - colourMenu.add(conservationMenuItem); - colourMenu.add(modifyConservation); - colourMenu.add(abovePIDThreshold); - colourMenu.add(modifyPID); - colourMenu.add(annotationColour); - colourMenu.add(rnahelicesColour); - - /* - * add colours to a ButtonGroup to make their - * selection mutually exclusive - */ - colours.add(noColourmenuItem); - colours.add(clustalColour); - colours.add(zappoColour); - colours.add(taylorColour); - colours.add(hydrophobicityColour); - colours.add(helixColour); - colours.add(strandColour); - colours.add(turnColour); - colours.add(buriedColour); - colours.add(userDefinedColour); - colours.add(PIDColour); - colours.add(BLOSUM62Colour); - colours.add(nucleotideColour); - colours.add(purinePyrimidineColour); - // colours.add(covariationColour); - colours.add(tcoffeeColour); - colours.add(RNAInteractionColour); - setColourSelected(Cache.getDefault(Preferences.DEFAULT_COLOUR, - ResidueColourScheme.NONE)); - - } - - /** * Constructs the entries on the Colour menu (but does not add them to the - * menu) + * menu). */ protected void initColourMenu() { @@ -2167,7 +1917,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - applyToAllGroups_actionPerformed(); + applyToAllGroups_actionPerformed(applyToAllGroups.isSelected()); } }); @@ -2181,168 +1931,6 @@ public class GAlignFrame extends JInternalFrame textColour_actionPerformed(); } }); - clustalColour = new JRadioButtonMenuItem( - MessageManager.getString("label.clustalx")); - clustalColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - clustalColour_actionPerformed(); - } - }); - zappoColour = new JRadioButtonMenuItem( - MessageManager.getString("label.zappo")); - zappoColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - zappoColour_actionPerformed(); - } - }); - taylorColour = new JRadioButtonMenuItem( - MessageManager.getString("label.taylor")); - taylorColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - taylorColour_actionPerformed(); - } - }); - hydrophobicityColour = new JRadioButtonMenuItem( - MessageManager - .getString("label.hydrophobicity")); - hydrophobicityColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - hydrophobicityColour_actionPerformed(); - } - }); - helixColour = new JRadioButtonMenuItem( - MessageManager.getString("label.helix_propensity")); - helixColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - helixColour_actionPerformed(); - } - }); - strandColour = new JRadioButtonMenuItem( - MessageManager - .getString("label.strand_propensity")); - strandColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - strandColour_actionPerformed(); - } - }); - turnColour = new JRadioButtonMenuItem( - MessageManager.getString("label.turn_propensity")); - turnColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - turnColour_actionPerformed(); - } - }); - buriedColour = new JRadioButtonMenuItem( - MessageManager.getString("label.buried_index")); - buriedColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - buriedColour_actionPerformed(); - } - }); - userDefinedColour = new JRadioButtonMenuItem( - MessageManager - .getString("action.user_defined")); - userDefinedColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - userDefinedColour_actionPerformed(e); - } - }); - PIDColour = new JRadioButtonMenuItem( - MessageManager.getString("label.percentage_identity")); - PIDColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - PIDColour_actionPerformed(); - } - }); - BLOSUM62Colour = new JRadioButtonMenuItem( - MessageManager.getString("label.blosum62_score")); - BLOSUM62Colour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - BLOSUM62Colour_actionPerformed(); - } - }); - nucleotideColour = new JRadioButtonMenuItem( - MessageManager.getString("label.nucleotide")); - nucleotideColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - nucleotideColour_actionPerformed(); - } - }); - purinePyrimidineColour = new JRadioButtonMenuItem( - MessageManager.getString("label.purine_pyrimidine")); - purinePyrimidineColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - purinePyrimidineColour_actionPerformed(); - } - }); - - tcoffeeColour = new JRadioButtonMenuItem( - MessageManager.getString("label.tcoffee_scores")); - tcoffeeColour.setEnabled(false); - tcoffeeColour.addActionListener(new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent e) - { - tcoffeeColorScheme_actionPerformed(); - } - }); - - RNAInteractionColour = new JRadioButtonMenuItem("RNA Interaction type"); - RNAInteractionColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - RNAInteractionColour_actionPerformed(); - } - }); - /* - * covariationColour = new JRadioButtonMenuItem("Covariation"); - * covariationColour.addActionListener(new ActionListener() { public void - * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(); } - * }); - */ conservationMenuItem = new JCheckBoxMenuItem( MessageManager.getString("action.by_conservation")); @@ -2351,17 +1939,8 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - conservationMenuItem_actionPerformed(); - } - }); - noColourmenuItem = new JRadioButtonMenuItem( - MessageManager.getString("label.none")); - noColourmenuItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - noColourmenuItem_actionPerformed(); + conservationMenuItem_actionPerformed(conservationMenuItem + .isSelected()); } }); @@ -2372,7 +1951,7 @@ public class GAlignFrame extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - abovePIDThreshold_actionPerformed(); + abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected()); } }); modifyPID = new JMenuItem( @@ -2407,17 +1986,6 @@ public class GAlignFrame extends JInternalFrame annotationColour_actionPerformed(); } }); - - rnahelicesColour = new JMenuItem( - MessageManager.getString("action.by_rna_helixes")); - rnahelicesColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - rnahelicesColour_actionPerformed(); - } - }); } protected void selectHighlightedColumns_actionPerformed( @@ -2775,67 +2343,7 @@ public class GAlignFrame extends JInternalFrame { } - protected void clustalColour_actionPerformed() - { - } - - protected void zappoColour_actionPerformed() - { - } - - protected void taylorColour_actionPerformed() - { - } - - protected void hydrophobicityColour_actionPerformed() - { - } - - protected void helixColour_actionPerformed() - { - } - - protected void strandColour_actionPerformed() - { - } - - protected void turnColour_actionPerformed() - { - } - - protected void buriedColour_actionPerformed() - { - } - - protected void userDefinedColour_actionPerformed(ActionEvent e) - { - } - - protected void PIDColour_actionPerformed() - { - } - - protected void BLOSUM62Colour_actionPerformed() - { - } - - protected void purinePyrimidineColour_actionPerformed() - { - } - - protected void RNAInteractionColour_actionPerformed() - { - } - - /* - * protected void covariationColour_actionPerformed() { } - */ - - protected void noColourmenuItem_actionPerformed() - { - } - - protected void conservationMenuItem_actionPerformed() + protected void conservationMenuItem_actionPerformed(boolean selected) { } @@ -2851,7 +2359,7 @@ public class GAlignFrame extends JInternalFrame { } - protected void abovePIDThreshold_actionPerformed() + protected void abovePIDThreshold_actionPerformed(boolean selected) { } @@ -2859,10 +2367,6 @@ public class GAlignFrame extends JInternalFrame { } - protected void nucleotideColour_actionPerformed() - { - } - protected void deleteGroups_actionPerformed(ActionEvent e) { } @@ -2895,7 +2399,7 @@ public class GAlignFrame extends JInternalFrame { } - protected void applyToAllGroups_actionPerformed() + protected void applyToAllGroups_actionPerformed(boolean selected) { } @@ -2943,16 +2447,6 @@ public class GAlignFrame extends JInternalFrame } - /** - * Template method to handle the 'Color T-Coffee scores' menu event. - *

- * Subclasses override this method to provide a custom action. - */ - protected void tcoffeeColorScheme_actionPerformed() - { - - } - protected void jpred_actionPerformed(ActionEvent e) { } @@ -3023,11 +2517,6 @@ public class GAlignFrame extends JInternalFrame { } - public void rnahelicesColour_actionPerformed() - { - - } - public void associatedData_actionPerformed(ActionEvent e) {