/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
package jalview.jbgui;
import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.gui.AlignmentPanel;
+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.ArrayList;
-import java.util.Vector;
+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.JMenuBar;
import javax.swing.JMenuItem;
+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 JMenu savemenu = new JMenu();
+ protected JMenu savemenu;
- protected JMenu viewMenu = new JMenu();
+ protected JMenu viewMenu;
- protected JMenu chainMenu = new JMenu();
+ protected JMenu colourMenu;
- protected JMenu viewerActionMenu = new JMenu();
+ protected JMenu chainMenu;
- protected JMenuItem alignStructs = new JMenuItem();
+ protected JMenu viewerActionMenu;
- protected JRadioButtonMenuItem seqColour = new JRadioButtonMenuItem();
+ protected JMenuItem alignStructs;
- protected JRadioButtonMenuItem chainColour = new JRadioButtonMenuItem();
+ protected JCheckBoxMenuItem showAlignmentOnly;
- protected JRadioButtonMenuItem chargeColour = new JRadioButtonMenuItem();
+ protected JMenuItem fitToWindow;
- protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem seqColour;
- protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem chainColour;
- protected JRadioButtonMenuItem hydroColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem chargeColour;
- protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem viewerColour;
- protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+ protected JMenuItem helpItem;
- protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+ protected JLabel statusBar;
- protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem userColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem viewerColour = new JRadioButtonMenuItem();
-
- protected JMenuItem helpItem = new JMenuItem();
-
- /**
- * list of sequenceSet ids associated with the view
- */
- protected ArrayList<String> _aps = new ArrayList<String>();
-
- /**
- * list of alignment panels to use for superposition
- */
- protected Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
-
- /**
- * list of alignment panels that are used for colouring structures by aligned
- * sequences
- */
- protected Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
-
- private String viewId = null;
+ protected JPanel statusPanel;
/**
* Constructor
JMenu fileMenu = new JMenu();
fileMenu.setText(MessageManager.getString("action.file"));
- savemenu.setActionCommand(MessageManager.getString("action.save_image"));
+ savemenu = new JMenu();
+ savemenu.setActionCommand(
+ MessageManager.getString("action.save_image"));
savemenu.setText(MessageManager.getString("action.save_as"));
JMenuItem pdbFile = new JMenuItem();
pdbFile.setText(MessageManager.getString("label.pdb_file"));
pdbFile.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
pdbFile_actionPerformed(actionEvent);
png.setText("PNG");
png.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
png_actionPerformed(actionEvent);
eps.setText("EPS");
eps.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
eps_actionPerformed(actionEvent);
viewMapping.setText(MessageManager.getString("label.view_mapping"));
viewMapping.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
viewMapping_actionPerformed(actionEvent);
}
});
- viewMenu.setText(MessageManager.getString("action.view"));
- chainMenu.setText(MessageManager.getString("action.show_chain"));
- JMenu colourMenu = new JMenu();
- colourMenu.setText(MessageManager.getString("label.colours"));
+ viewMenu = new JMenu();
+ viewMenu.setText(MessageManager.getString("action.view"));
- JMenuItem backGround = new JMenuItem();
- backGround.setText(MessageManager.getString("label.background_colour")
- + "...");
- backGround.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent actionEvent)
- {
- backGround_actionPerformed(actionEvent);
- }
- });
- seqColour.setSelected(false);
- seqColour.setText(MessageManager.getString("action.by_sequence"));
- seqColour.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent actionEvent)
- {
- seqColour_actionPerformed(actionEvent);
- }
- });
- chainColour.setText(MessageManager.getString("action.by_chain"));
- chainColour.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent actionEvent)
- {
- chainColour_actionPerformed(actionEvent);
- }
- });
- chargeColour.setText(MessageManager.getString("label.charge_cysteine"));
- chargeColour.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent actionEvent)
- {
- chargeColour_actionPerformed(actionEvent);
- }
- });
- zappoColour.setText(MessageManager.getString("label.zappo"));
- zappoColour.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent actionEvent)
- {
- zappoColour_actionPerformed(actionEvent);
- }
- });
- taylorColour.setText(MessageManager.getString("label.taylor"));
- taylorColour.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent actionEvent)
- {
- taylorColour_actionPerformed(actionEvent);
- }
- });
- hydroColour.setText(MessageManager.getString("label.hydrophobicity"));
- hydroColour.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent actionEvent)
- {
- hydroColour_actionPerformed(actionEvent);
- }
- });
- strandColour.setText(MessageManager
- .getString("label.strand_propensity"));
- strandColour.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent actionEvent)
- {
- strandColour_actionPerformed(actionEvent);
- }
- });
- helixColour.setText(MessageManager.getString("label.helix_propensity"));
- helixColour.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent actionEvent)
- {
- helixColour_actionPerformed(actionEvent);
- }
- });
- turnColour.setText(MessageManager.getString("label.turn_propensity"));
- turnColour.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent actionEvent)
- {
- turnColour_actionPerformed(actionEvent);
- }
- });
- buriedColour.setText(MessageManager.getString("label.buried_index"));
- buriedColour.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent actionEvent)
- {
- buriedColour_actionPerformed(actionEvent);
- }
- });
- purinePyrimidineColour.setText(MessageManager
- .getString("label.purine_pyrimidine"));
- purinePyrimidineColour.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent actionEvent)
- {
- purinePyrimidineColour_actionPerformed(actionEvent);
- }
- });
+ chainMenu = new JMenu();
+ chainMenu.setText(MessageManager.getString("action.show_chain"));
- userColour.setText(MessageManager.getString("action.user_defined"));
- userColour.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent actionEvent)
- {
- userColour_actionPerformed(actionEvent);
- }
- });
- 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()
+ fitToWindow = new JMenuItem();
+ fitToWindow.setText(MessageManager.getString("label.fit_to_window"));
+ fitToWindow.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
- viewerColour_actionPerformed(actionEvent);
+ fitToWindow_actionPerformed();
}
});
JMenu helpMenu = new JMenu();
helpMenu.setText(MessageManager.getString("action.help"));
+ helpItem = new JMenuItem();
helpItem.setText(MessageManager.getString("label.jmol_help"));
helpItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
showHelp_actionPerformed(actionEvent);
}
});
- alignStructs
- .setText(MessageManager.getString("label.align_structures"));
+ alignStructs = new JMenuItem();
+ alignStructs.setText(
+ MessageManager.getString("label.superpose_structures"));
alignStructs.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
alignStructs_actionPerformed(actionEvent);
}
});
- viewerActionMenu.setText(MessageManager.getString("label.jmol"));
- menuBar.add(fileMenu);
- menuBar.add(viewMenu);
- menuBar.add(colourMenu);
- menuBar.add(viewerActionMenu);
+
+ viewerActionMenu = new JMenu(); // text set in sub-classes
viewerActionMenu.setVisible(false);
- menuBar.add(helpMenu);
+ viewerActionMenu.add(alignStructs);
+ colourMenu = new JMenu();
+ colourMenu.setText(MessageManager.getString("label.colours"));
fileMenu.add(savemenu);
fileMenu.add(viewMapping);
savemenu.add(pdbFile);
savemenu.add(png);
savemenu.add(eps);
viewMenu.add(chainMenu);
+ helpMenu.add(helpItem);
- 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);
- colourMenu.add(userColour);
- colourMenu.add(viewerColour);
- colourMenu.add(backGround);
-
- ButtonGroup colourButtons = new ButtonGroup();
-
- 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(userColour);
- colourButtons.add(viewerColour);
+ menuBar.add(fileMenu);
+ menuBar.add(viewMenu);
+ menuBar.add(colourMenu);
+ menuBar.add(viewerActionMenu);
+ menuBar.add(helpMenu);
- helpMenu.add(helpItem);
- viewerActionMenu.add(alignStructs);
+ statusPanel = new JPanel();
+ statusPanel.setLayout(new GridLayout());
+ this.getContentPane().add(statusPanel, BorderLayout.SOUTH);
+ statusBar = new JLabel();
+ statusPanel.add(statusBar, null);
}
- protected void viewerColour_actionPerformed(ActionEvent actionEvent)
+ protected void fitToWindow_actionPerformed()
+ {
+ }
+
+ protected void highlightSelection_actionPerformed()
{
}
- protected void alignStructs_actionPerformed(ActionEvent actionEvent)
+ protected void viewerColour_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 helixColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void strandColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void turnColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void buriedColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void userColour_actionPerformed(ActionEvent actionEvent)
- {
-
- }
-
- public void backGround_actionPerformed(ActionEvent actionEvent)
+ public void background_actionPerformed(ActionEvent actionEvent)
{
}
}
- // {
- // return bindingModel;
- // }
-
- // public void setBindingModel(AAStructureBindingModel bindingModel)
- // {
- // this.bindingModel = bindingModel;
- // }
-
/**
- *
- * @param ap2
- * @return true if this Jmol instance is linked with the given alignPanel
+ * 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.
*/
- public boolean isLinkedWith(AlignmentPanel ap2)
+ protected void setSelectedChains()
{
- return _aps.contains(ap2.av.getSequenceSetId());
- }
-
- public boolean isUsedforaligment(AlignmentPanel ap2)
- {
-
- return (_alignwith != null) && _alignwith.contains(ap2);
- }
-
- public boolean isUsedforcolourby(AlignmentPanel ap2)
- {
- return (_colourwith != null) && _colourwith.contains(ap2);
- }
-
- /**
- *
- * @return TRUE if the view is NOT being coloured by the alignment colours.
- */
- public boolean isColouredByViewer()
- {
- return !getBinding().isColourBySequence();
- }
-
- public String getViewId()
- {
- if (viewId == null)
+ List<String> chains = new ArrayList<>();
+ for (int i = 0; i < chainMenu.getItemCount(); i++)
{
- viewId = System.currentTimeMillis() + "." + this.hashCode();
+ JMenuItem menuItem = chainMenu.getItem(i);
+ if (menuItem instanceof JCheckBoxMenuItem)
+ {
+ JCheckBoxMenuItem item = (JCheckBoxMenuItem) menuItem;
+ if (item.isSelected())
+ {
+ chains.add(item.getText());
+ }
+ }
}
- return viewId;
- }
-
- protected void setViewId(String viewId)
- {
- this.viewId = viewId;
- }
-
- public String getStateInfo()
- {
- return null;
+ getBinding().setChainsToShow(chains);
}
}
git://source.jalview.org / jalview.git / blobdiff