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.ColourSchemeProperty;
-import jalview.schemes.UserColourScheme;
+import jalview.io.FileFormats;
import jalview.util.MessageManager;
import jalview.util.Platform;
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;
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();
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();
JMenu pasteMenu = new JMenu();
- protected JCheckBoxMenuItem applyToAllGroups;
-
protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
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();
protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
- protected ButtonGroup colours = new ButtonGroup();
-
protected JMenuItem showTranslation = new JMenuItem();
protected JMenuItem showReverse = new JMenuItem();
protected JMenuItem runGroovy = new JMenuItem();
- protected JMenuItem rnahelicesColour;
-
protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
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);
pasteMenu.setMnemonic('P');
reload.setMnemonic('R');
}
-
- // Map<String, UserColourScheme> userColourSchemes = UserDefinedColours
- // .getUserColourSchemes();
- // if (userColourSchemes != null)
- // {
- // int insertionPoint = findUserDefinedColourPosition();
- // 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.insert(radioItem, insertionPoint);
- // insertionPoint++;
- // colours.add(radioItem);
- // }
- // }
- //
- // /*
- // * 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, "None"));
- }
-
- public void setColourSelected(String defaultColour)
- {
-
- if (defaultColour != null)
- {
- int index = ColourSchemeProperty
- .getColourIndexFromName(defaultColour);
-
- switch (index)
- {
- case ColourSchemeProperty.CLUSTAL:
- clustalColour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.BLOSUM:
- BLOSUM62Colour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.PID:
- PIDColour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.ZAPPO:
- zappoColour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.TAYLOR:
- taylorColour.setSelected(true);
- break;
-
- case ColourSchemeProperty.HYDROPHOBIC:
- hydrophobicityColour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.HELIX:
- helixColour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.STRAND:
- strandColour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.TURN:
- turnColour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.BURIED:
- buriedColour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.NUCLEOTIDE:
- nucleotideColour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.TCOFFEE:
- tcoffeeColour.setSelected(true);
- break;
-
- case ColourSchemeProperty.PURINEPYRIMIDINE:
- purinePyrimidineColour.setSelected(true);
-
- break;
-
- case ColourSchemeProperty.RNAINTERACTION:
- RNAInteractionColour.setSelected(true);
-
- break;
- /*
- * case ColourSchemeProperty.COVARIATION:
- * covariationColour.setSelected(true);
- *
- * break;
- */
- case ColourSchemeProperty.USER_DEFINED:
- userDefinedColour.setSelected(true);
-
- break;
- case ColourSchemeProperty.NONE:
- default:
- noColourmenuItem.setSelected(true);
- break;
-
- }
- }
-
}
private void jbInit() throws Exception
{
initColourMenu();
- buildColourMenu();
JMenuItem saveAs = new JMenuItem(
MessageManager.getString("action.save_as"));
JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
- MessageManager.getString("label.average_distance_bloslum62"));
+ MessageManager.getString("label.average_distance_blosum62"));
avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
{
@Override
};
addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
+ conservationMenuItem.setText(MessageManager
+ .getString("action.by_conservation"));
+ conservationMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed();
+ }
+ });
+
wrapMenuItem.setText(MessageManager.getString("label.wrap"));
wrapMenuItem.addActionListener(new ActionListener()
{
};
addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
+ abovePIDThreshold.setText(MessageManager
+ .getString("label.above_identity_threshold"));
+ abovePIDThreshold.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ abovePIDThreshold_actionPerformed();
+ }
+ });
+
showSeqFeatures.setText(MessageManager
.getString("label.show_sequence_features"));
showSeqFeatures.addActionListener(new ActionListener()
});
+ modifyPID = new JMenuItem(
+ MessageManager.getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyPID_actionPerformed();
+ }
+ });
+ modifyConservation.setText(MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyConservation_actionPerformed();
+ }
+ });
+
sortByTreeMenu
.setText(MessageManager.getString("action.by_tree_order"));
sort.setText(MessageManager.getString("action.sort"));
}
/**
- * 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<String, UserColourScheme> 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, "None"));
-
- }
-
- /**
* Constructs the entries on the Colour menu (but does not add them to the
- * menu)
+ * menu).
*/
protected void initColourMenu()
{
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"));
conservationMenuItem_actionPerformed();
}
});
- noColourmenuItem = new JRadioButtonMenuItem(
- MessageManager.getString("label.none"));
- noColourmenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- noColourmenuItem_actionPerformed();
- }
- });
abovePIDThreshold = new JCheckBoxMenuItem(
MessageManager.getString("label.above_identity_threshold"));
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(
{
}
- 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 nucleotideColour_actionPerformed()
- {
- }
-
protected void deleteGroups_actionPerformed(ActionEvent e)
{
}
}
- /**
- * Template method to handle the 'Color T-Coffee scores' menu event.
- * <p>
- * Subclasses override this method to provide a custom action.
- */
- protected void tcoffeeColorScheme_actionPerformed()
- {
-
- }
-
protected void jpred_actionPerformed(ActionEvent e)
{
}
{
}
- public void rnahelicesColour_actionPerformed()
- {
-
- }
-
public void associatedData_actionPerformed(ActionEvent e)
{
git://source.jalview.org / jalview.git / blobdiff