JAL-2351 first refactoring and outline of read/write Jmol properties

[jalview.git] / src / jalview / gui / AppJmol.java

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 1c0dfe6..29c388c 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -53,6 +53,8 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -68,7 +70,6 @@ import javax.swing.JColorChooser;
 import javax.swing.JInternalFrame;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JSplitPane;
 import javax.swing.SwingUtilities;
@@ -131,7 +132,7 @@ public class AppJmol extends StructureViewerBase
     // / TODO: check if protocol is needed to be set, and if chains are
     // autodiscovered.
     jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
-            pdbentrys, seqs, null, null);
+            pdbentrys, seqs, null);
 
     jmb.setLoadingFromArchive(true);
     addAlignmentPanel(ap);
@@ -172,6 +173,8 @@ public class AppJmol extends StructureViewerBase
 
   private void initMenus()
   {
+    String jmol = MessageManager.getString("label.jmol");
+    viewerActionMenu.setText(jmol);
     seqColour.setSelected(jmb.isColourBySequence());
     viewerColour.setSelected(!jmb.isColourBySequence());
     if (_colourwith == null)
@@ -245,6 +248,35 @@ public class AppJmol extends StructureViewerBase
 
       }
     });
+
+    JMenuItem writeFeatures = new JMenuItem(
+            MessageManager.getString("label.create_viewer_attributes"));
+    writeFeatures.setToolTipText(MessageManager.formatMessage(
+            "label.create_viewer_attributes_tip", jmol));
+    writeFeatures.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        sendFeaturesToViewer();
+      }
+    });
+    viewerActionMenu.add(writeFeatures);
+
+    final JMenu fetchAttributes = new JMenu(MessageManager.formatMessage(
+            "label.fetch_viewer_attributes", jmol));
+    fetchAttributes.setToolTipText(MessageManager.formatMessage(
+            "label.fetch_viewer_attributes_tip", jmol));
+    fetchAttributes.addMouseListener(new MouseAdapter()
+    {
+
+      @Override
+      public void mouseEntered(MouseEvent e)
+      {
+        buildAttributesMenu(fetchAttributes);
+      }
+    });
+    viewerActionMenu.add(fetchAttributes);
   }
 
   IProgressIndicator progressBar = null;
@@ -301,7 +333,7 @@ public class AppJmol extends StructureViewerBase
   {
     progressBar = ap.alignFrame;
     jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
-            pdbentrys, seqs, null, null);
+            pdbentrys, seqs, null);
     addAlignmentPanel(ap);
     useAlignmentPanelForColourbyseq(ap);
     if (pdbentrys.length > 1)
@@ -394,57 +426,12 @@ public class AppJmol extends StructureViewerBase
     jmb.setFinishedInit(true);
   }
 
-  void setChainMenuItems(Vector<String> chains)
-  {
-    chainMenu.removeAll();
-    if (chains == null)
-    {
-      return;
-    }
-    JMenuItem menuItem = new JMenuItem(
-            MessageManager.getString("label.all"));
-    menuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent evt)
-      {
-        allChainsSelected = true;
-        for (int i = 0; i < chainMenu.getItemCount(); i++)
-        {
-          if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
-          {
-            ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
-          }
-        }
-        centerViewer();
-        allChainsSelected = false;
-      }
-    });
 
-    chainMenu.add(menuItem);
-
-    for (String chain : chains)
-    {
-      menuItem = new JCheckBoxMenuItem(chain, true);
-      menuItem.addItemListener(new ItemListener()
-      {
-        @Override
-        public void itemStateChanged(ItemEvent evt)
-        {
-          if (!allChainsSelected)
-          {
-            centerViewer();
-          }
-        }
-      });
-
-      chainMenu.add(menuItem);
-    }
-  }
 
   boolean allChainsSelected = false;
 
-  void centerViewer()
+  @Override
+  void showSelectedChains()
   {
     Vector<String> toshow = new Vector<String>();
     for (int i = 0; i < chainMenu.getItemCount(); i++)
@@ -722,11 +709,11 @@ public class AppJmol extends StructureViewerBase
     }
     if (errormsgs.length() > 0)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
               .formatMessage("label.pdb_entries_couldnt_be_retrieved",
                       new String[] { errormsgs.toString() }),
               MessageManager.getString("label.couldnt_load_file"),
-              JOptionPane.ERROR_MESSAGE);
+              JvOptionPane.ERROR_MESSAGE);
     }
     return files;
   }
@@ -1075,13 +1062,13 @@ public class AppJmol extends StructureViewerBase
       repaint();
       return;
     }
-    setChainMenuItems(jmb.chainNames);
+    setChainMenuItems(jmb.getChainNames());
 
     this.setTitle(jmb.getViewerTitle());
-    if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
-    {
+    // if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
+    // {
       viewerActionMenu.setVisible(true);
-    }
+    // }
     if (!jmb.isLoadingFromArchive())
     {
       seqColour_actionPerformed(null);
@@ -1190,4 +1177,36 @@ public class AppJmol extends StructureViewerBase
     return jmb;
   }
 
+  @Override
+  protected void sendFeaturesToViewer()
+  {
+    /*
+     * Atom properties may also be set directly using {atom expression}.xxxx = y.
+     */
+  }
+
+  @Override
+  protected void getResidueAttributes(String attName)
+  {
+    /*
+     * getproperty atominfo returns properties for all atoms
+     * - could parse this for unique/specific property names?
+     *
+     * _ipt atomID atomIndex atomno bondCount chain clickabilityFlags colix color coord 
+     * element elemno formalCharge groupID info model name occupancy partialCharge 
+     * polymerLength radius resname resno shape spacefill structure sym temp 
+     * visibilityFlags visible x y z
+     *
+     * getproperty chaininfo is residue level info
+     * no sign of average bfactor for a residue :-(
+     */
+  }
+
+  @Override
+  protected List<String> getResidueAttributeNames()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
 }