package jalview.jbgui;
import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.gui.UserDefinedColours;
-import jalview.schemes.UserColourScheme;
+import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
import java.awt.GridLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.util.Map;
+import java.util.ArrayList;
+import java.util.List;
-import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JMenu;
import javax.swing.JPanel;
import javax.swing.JRadioButtonMenuItem;
-public abstract class GStructureViewer extends JInternalFrame implements
- JalviewStructureDisplayI
+public abstract class GStructureViewer extends JInternalFrame
+ implements JalviewStructureDisplayI, ColourChangeListener
{
// private AAStructureBindingModel bindingModel;
protected JMenuItem alignStructs;
+ protected JCheckBoxMenuItem showAlignmentOnly;
+
protected JMenuItem fitToWindow;
protected JRadioButtonMenuItem seqColour;
protected JRadioButtonMenuItem chargeColour;
- protected JRadioButtonMenuItem zappoColour;
-
- protected JRadioButtonMenuItem taylorColour;
-
- protected JRadioButtonMenuItem hydroColour;
-
- protected JRadioButtonMenuItem strandColour;
-
- protected JRadioButtonMenuItem helixColour;
-
- protected JRadioButtonMenuItem turnColour;
-
- protected JRadioButtonMenuItem buriedColour;
-
- protected JRadioButtonMenuItem nucleotideColour;
-
- protected JRadioButtonMenuItem purinePyrimidineColour;
-
- protected JRadioButtonMenuItem userColour;
-
protected JRadioButtonMenuItem viewerColour;
protected JMenuItem helpItem;
fileMenu.setText(MessageManager.getString("action.file"));
savemenu = new JMenu();
- savemenu.setActionCommand(MessageManager.getString("action.save_image"));
+ savemenu.setActionCommand(
+ MessageManager.getString("action.save_image"));
savemenu.setText(MessageManager.getString("action.save_as"));
JMenuItem pdbFile = new JMenuItem();
}
});
alignStructs = new JMenuItem();
- alignStructs
- .setText(MessageManager.getString("label.align_structures"));
+ alignStructs.setText(
+ MessageManager.getString("label.superpose_structures"));
alignStructs.addActionListener(new ActionListener()
{
@Override
}
});
- viewerActionMenu = new JMenu(MessageManager.getString("label.jmol"));
+ viewerActionMenu = new JMenu(); // text set in sub-classes
viewerActionMenu.setVisible(false);
viewerActionMenu.add(alignStructs);
colourMenu = new JMenu();
- buildColourMenu();
+ colourMenu.setText(MessageManager.getString("label.colours"));
fileMenu.add(savemenu);
fileMenu.add(viewMapping);
savemenu.add(pdbFile);
statusPanel.add(statusBar, null);
}
- /**
- * Builds the colour menu
- */
- protected void buildColourMenu()
- {
- colourMenu.removeAll();
- colourMenu.setText(MessageManager.getString("label.colours"));
-
- JMenuItem backGround = new JMenuItem();
- backGround
- .setText(MessageManager.getString("action.background_colour"));
- backGround.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- backGround_actionPerformed(actionEvent);
- }
- });
- seqColour = new JRadioButtonMenuItem();
- seqColour.setSelected(false);
- seqColour.setText(MessageManager.getString("action.by_sequence"));
- seqColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- seqColour_actionPerformed(actionEvent);
- }
- });
- chainColour = new JRadioButtonMenuItem();
- chainColour.setText(MessageManager.getString("action.by_chain"));
- chainColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- chainColour_actionPerformed(actionEvent);
- }
- });
- chargeColour = new JRadioButtonMenuItem();
- chargeColour.setText(MessageManager.getString("label.charge_cysteine"));
- chargeColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- chargeColour_actionPerformed(actionEvent);
- }
- });
- zappoColour = new JRadioButtonMenuItem();
- zappoColour.setText(MessageManager.getString("label.zappo"));
- zappoColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- zappoColour_actionPerformed(actionEvent);
- }
- });
- taylorColour = new JRadioButtonMenuItem();
- taylorColour.setText(MessageManager.getString("label.taylor"));
- taylorColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- taylorColour_actionPerformed(actionEvent);
- }
- });
- hydroColour = new JRadioButtonMenuItem();
- hydroColour.setText(MessageManager.getString("label.hydrophobicity"));
- hydroColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- hydroColour_actionPerformed(actionEvent);
- }
- });
- strandColour = new JRadioButtonMenuItem();
- strandColour.setText(MessageManager
- .getString("label.strand_propensity"));
- strandColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- strandColour_actionPerformed(actionEvent);
- }
- });
- helixColour = new JRadioButtonMenuItem();
- helixColour.setText(MessageManager.getString("label.helix_propensity"));
- helixColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- helixColour_actionPerformed(actionEvent);
- }
- });
- turnColour = new JRadioButtonMenuItem();
- turnColour.setText(MessageManager.getString("label.turn_propensity"));
- turnColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- turnColour_actionPerformed(actionEvent);
- }
- });
- buriedColour = new JRadioButtonMenuItem();
- buriedColour.setText(MessageManager.getString("label.buried_index"));
- buriedColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- buriedColour_actionPerformed(actionEvent);
- }
- });
- nucleotideColour = new JRadioButtonMenuItem();
- nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
- nucleotideColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- nucleotideColour_actionPerformed(actionEvent);
- }
- });
- purinePyrimidineColour = new JRadioButtonMenuItem();
- purinePyrimidineColour.setText(MessageManager
- .getString("label.purine_pyrimidine"));
- purinePyrimidineColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- purinePyrimidineColour_actionPerformed(actionEvent);
- }
- });
- userColour = new JRadioButtonMenuItem();
- userColour.setText(MessageManager.getString("action.user_defined"));
- userColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- userColour_actionPerformed(actionEvent);
- }
- });
- viewerColour = new JRadioButtonMenuItem();
- viewerColour.setSelected(false);
- viewerColour
- .setText(MessageManager.getString("label.colour_with_jmol"));
- viewerColour.setToolTipText(MessageManager
- .getString("label.let_jmol_manage_structure_colours"));
- viewerColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- viewerColour_actionPerformed(actionEvent);
- }
- });
-
- /*
- * add colour buttons to a group so their selection
- * is mutually exclusive
- */
- ButtonGroup colourButtons = new ButtonGroup();
-
- colourMenu.add(seqColour);
- colourMenu.add(chainColour);
- colourMenu.add(chargeColour);
- colourMenu.add(zappoColour);
- colourMenu.add(taylorColour);
- colourMenu.add(hydroColour);
- colourMenu.add(helixColour);
- colourMenu.add(strandColour);
- colourMenu.add(turnColour);
- colourMenu.add(buriedColour);
- colourMenu.add(purinePyrimidineColour);
-
- /*
- * add any user-defined colours that are loaded
- */
- Map<String, UserColourScheme> userColourSchemes = UserDefinedColours
- .getUserColourSchemes();
- if (userColourSchemes != null)
- {
- for (String schemeName : userColourSchemes.keySet())
- {
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
- schemeName);
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userColour_actionPerformed(evt);
- }
- });
- colourMenu.add(radioItem);
- colourButtons.add(radioItem);
- }
- }
- colourMenu.add(userColour);
- colourMenu.add(viewerColour);
- colourMenu.add(backGround);
-
- colourButtons.add(seqColour);
- colourButtons.add(chainColour);
- colourButtons.add(chargeColour);
- colourButtons.add(zappoColour);
- colourButtons.add(taylorColour);
- colourButtons.add(hydroColour);
- colourButtons.add(helixColour);
- colourButtons.add(strandColour);
- colourButtons.add(turnColour);
- colourButtons.add(buriedColour);
- colourButtons.add(purinePyrimidineColour);
- colourButtons.add(userColour);
- colourButtons.add(viewerColour);
- }
-
protected void fitToWindow_actionPerformed()
{
}
{
}
- protected void alignStructs_actionPerformed(ActionEvent actionEvent)
- {
- }
+ protected abstract String alignStructs_actionPerformed(
+ ActionEvent actionEvent);
public void pdbFile_actionPerformed(ActionEvent actionEvent)
{
}
- public void zappoColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void taylorColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void hydroColour_actionPerformed(ActionEvent actionEvent)
+ public void background_actionPerformed(ActionEvent actionEvent)
{
}
- public void helixColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void strandColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void turnColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void buriedColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void nucleotideColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void userColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void backGround_actionPerformed(ActionEvent actionEvent)
+ public void showHelp_actionPerformed(ActionEvent actionEvent)
{
}
- public void showHelp_actionPerformed(ActionEvent actionEvent)
+ /**
+ * Saves the selected entries in the 'View Chain' menu into a list. Entries are
+ * formatted as "pdbid:chainid". Only the selected chains should be drawn in the
+ * structure display.
+ */
+ protected void setSelectedChains()
{
-
+ List<String> chains = new ArrayList<>();
+ for (int i = 0; i < chainMenu.getItemCount(); i++)
+ {
+ JMenuItem menuItem = chainMenu.getItem(i);
+ if (menuItem instanceof JCheckBoxMenuItem)
+ {
+ JCheckBoxMenuItem item = (JCheckBoxMenuItem) menuItem;
+ if (item.isSelected())
+ {
+ chains.add(item.getText());
+ }
+ }
+ }
+ getBinding().setChainsToShow(chains);
}
-
- // {
- // return bindingModel;
- // }
-
- // public void setBindingModel(AAStructureBindingModel bindingModel)
- // {
- // this.bindingModel = bindingModel;
- // }
-
}
git://source.jalview.org / jalview.git / blobdiff