X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=4b014d1868ff644863e1ce70116d8099b9ad6514;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=55df1940a468bb6061010968b2f44b671c701aa4;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 55df194..4b014d1 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
@@ -26,53 +29,65 @@ import jalview.datamodel.*;
 import jalview.structure.*;
 import jalview.io.*;
 
-import org.jmol.api.*;
-
-import org.jmol.popup.*;
-import org.jmol.viewer.JmolConstants;
-
 import jalview.schemes.*;
+import jalview.util.MessageManager;
 
 public class AppletJmol extends EmbmenuFrame implements
 // StructureListener,
-        KeyListener, ActionListener, ItemListener, SequenceStructureBinding
+        KeyListener, ActionListener, ItemListener
 
 {
-  Menu fileMenu = new Menu("File");
+  Menu fileMenu = new Menu(MessageManager.getString("action.file"));
+
+  Menu viewMenu = new Menu(MessageManager.getString("action.view"));
+
+  Menu coloursMenu = new Menu(MessageManager.getString("action.colour"));
 
-  Menu viewMenu = new Menu("View");
+  Menu chainMenu = new Menu(MessageManager.getString("action.show_chain"));
 
-  Menu coloursMenu = new Menu("Colours");
+  Menu helpMenu = new Menu(MessageManager.getString("action.help"));
 
-  Menu chainMenu = new Menu("Show Chain");
+  MenuItem mappingMenuItem = new MenuItem(
+          MessageManager.getString("label.view_mapping"));
 
-  Menu helpMenu = new Menu("Help");
+  CheckboxMenuItem seqColour = new CheckboxMenuItem(
+          MessageManager.getString("action.by_sequence"), true);
 
-  MenuItem mappingMenuItem = new MenuItem("View Mapping");
+  CheckboxMenuItem jmolColour = new CheckboxMenuItem(
+          MessageManager.getString("action.using_jmol"), false);
 
-  CheckboxMenuItem seqColour = new CheckboxMenuItem("By Sequence", true);
+  MenuItem chain = new MenuItem(MessageManager.getString("action.by_chain"));
 
-  MenuItem chain = new MenuItem("By Chain");
+  MenuItem charge = new MenuItem(
+          MessageManager.getString("label.charge_cysteine"));
 
-  MenuItem charge = new MenuItem("Charge & Cysteine");
+  MenuItem zappo = new MenuItem(MessageManager.getString("label.zappo"));
 
-  MenuItem zappo = new MenuItem("Zappo");
+  MenuItem taylor = new MenuItem(MessageManager.getString("label.taylor"));
 
-  MenuItem taylor = new MenuItem("Taylor");
+  MenuItem hydro = new MenuItem(
+          MessageManager.getString("label.hydrophobicity"));
 
-  MenuItem hydro = new MenuItem("Hydrophobicity");
+  MenuItem helix = new MenuItem(
+          MessageManager.getString("label.helix_propensity"));
 
-  MenuItem helix = new MenuItem("Helix Propensity");
+  MenuItem strand = new MenuItem(
+          MessageManager.getString("label.strand_propensity"));
 
-  MenuItem strand = new MenuItem("Strand Propensity");
+  MenuItem turn = new MenuItem(
+          MessageManager.getString("label.turn_propensity"));
 
-  MenuItem turn = new MenuItem("Turn Propensity");
+  MenuItem buried = new MenuItem(
+          MessageManager.getString("label.buried_index"));
 
-  MenuItem buried = new MenuItem("Buried Index");
+  MenuItem purinepyrimidine = new MenuItem(
+          MessageManager.getString("label.purine_pyrimidine"));
 
-  MenuItem user = new MenuItem("User Defined Colours");
+  MenuItem user = new MenuItem(
+          MessageManager.getString("label.user_defined_colours"));
 
-  MenuItem jmolHelp = new MenuItem("Jmol Help");
+  MenuItem jmolHelp = new MenuItem(
+          MessageManager.getString("label.jmol_help"));
 
   Panel scriptWindow;
 
@@ -84,6 +99,8 @@ public class AppletJmol extends EmbmenuFrame implements
 
   AlignmentPanel ap;
 
+  ArrayList _aps = new ArrayList();
+
   String fileLoadingError;
 
   boolean loadedInline;
@@ -98,25 +115,42 @@ public class AppletJmol extends EmbmenuFrame implements
    * datasource protocol for access to PDBEntry
    */
   String protocol = null;
+
   /**
-   * Load a bunch of pdb entries associated with sequences in the alignment and display them - aligning them if necessary.
-   * @param pdbentries each pdb file (at least one needed)
-   * @param boundseqs each set of sequences for each pdb file (must match number of pdb files)
-   * @param boundchains the target pdb chain corresponding with each sequence associated with each pdb file (may be null at any level)
-   * @param align true/false
-   * @param ap associated alignment
-   * @param protocol how to get pdb data
+   * Load a bunch of pdb entries associated with sequences in the alignment and
+   * display them - aligning them if necessary.
+   * 
+   * @param pdbentries
+   *          each pdb file (at least one needed)
+   * @param boundseqs
+   *          each set of sequences for each pdb file (must match number of pdb
+   *          files)
+   * @param boundchains
+   *          the target pdb chain corresponding with each sequence associated
+   *          with each pdb file (may be null at any level)
+   * @param align
+   *          true/false
+   * @param ap
+   *          associated alignment
+   * @param protocol
+   *          how to get pdb data
    */
-  public AppletJmol(PDBEntry[] pdbentries, SequenceI[][] boundseqs, String[][] boundchains, boolean align, AlignmentPanel ap, String protocol)
+  public AppletJmol(PDBEntry[] pdbentries, SequenceI[][] boundseqs,
+          String[][] boundchains, boolean align, AlignmentPanel ap,
+          String protocol)
   {
-    throw new Error("Not yet implemented.");
+    throw new Error(MessageManager.getString("error.not_yet_implemented"));
   }
+
   public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
           AlignmentPanel ap, String protocol)
   {
     this.ap = ap;
-    jmb = new AppletJmolBinding(this, new PDBEntry[]
-    { pdbentry }, new SequenceI[][]{seq}, new String[][]{ chains }, protocol);
+    jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
+            new PDBEntry[]
+            { pdbentry }, new SequenceI[][]
+            { seq }, new String[][]
+            { chains }, protocol);
     jmb.setColourBySequence(true);
     if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
     {
@@ -138,13 +172,14 @@ public class AppletJmol extends EmbmenuFrame implements
     }
 
     String alreadyMapped = StructureSelectionManager
-            .getStructureSelectionManager().alreadyMappedToFile(
-                    pdbentry.getId());
+            .getStructureSelectionManager(ap.av.applet)
+            .alreadyMappedToFile(pdbentry.getId());
     MCview.PDBfile reader = null;
     if (alreadyMapped != null)
     {
-      reader = StructureSelectionManager.getStructureSelectionManager()
-              .setMapping(seq, chains, pdbentry.getFile(), protocol);
+      reader = StructureSelectionManager.getStructureSelectionManager(
+              ap.av.applet).setMapping(seq, chains, pdbentry.getFile(),
+              protocol);
       // PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
       // FOR NOW, LETS JUST OPEN A NEW WINDOW
     }
@@ -161,12 +196,14 @@ public class AppletJmol extends EmbmenuFrame implements
     hydro.addActionListener(this);
     chain.addActionListener(this);
     seqColour.addItemListener(this);
+    jmolColour.addItemListener(this);
     zappo.addActionListener(this);
     taylor.addActionListener(this);
     helix.addActionListener(this);
     strand.addActionListener(this);
     turn.addActionListener(this);
     buried.addActionListener(this);
+    purinepyrimidine.addActionListener(this);
     user.addActionListener(this);
 
     jmolHelp.addActionListener(this);
@@ -181,8 +218,9 @@ public class AppletJmol extends EmbmenuFrame implements
     coloursMenu.add(strand);
     coloursMenu.add(turn);
     coloursMenu.add(buried);
+    coloursMenu.add(purinepyrimidine);
     coloursMenu.add(user);
-
+    coloursMenu.add(jmolColour);
     helpMenu.add(jmolHelp);
     this.setLayout(new BorderLayout());
 
@@ -194,12 +232,12 @@ public class AppletJmol extends EmbmenuFrame implements
     scriptWindow = new Panel();
     scriptWindow.setVisible(false);
     // this.add(scriptWindow, BorderLayout.SOUTH);
-    
+
     try
     {
-      jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()+"_jmol_",
-              ap.av.applet.getDocumentBase(), ap.av.applet.getCodeBase(),
-              "-applet", scriptWindow, null);
+      jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()
+              + "_jmol_", ap.av.applet.getDocumentBase(),
+              ap.av.applet.getCodeBase(), "-applet", scriptWindow, null);
     } catch (Exception e)
     {
       System.err
@@ -220,7 +258,7 @@ public class AppletJmol extends EmbmenuFrame implements
         closeViewer();
       }
     });
-    if (pdbentry.getProperty()==null)
+    if (pdbentry.getProperty() == null)
     {
       pdbentry.setProperty(new Hashtable());
       pdbentry.getProperty().put("protocol", protocol);
@@ -277,8 +315,7 @@ public class AppletJmol extends EmbmenuFrame implements
           }
           if (freader == null)
           {
-            throw new Exception(
-                    "Invalid datasource. Could not obtain Reader.");
+            throw new Exception(MessageManager.getString("exception.invalid_datasource_couldnt_obtain_reader"));
           }
           jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
                   freader);
@@ -306,7 +343,7 @@ public class AppletJmol extends EmbmenuFrame implements
   {
     chainMenu.removeAll();
 
-    MenuItem menuItem = new MenuItem("All");
+    MenuItem menuItem = new MenuItem(MessageManager.getString("label.all"));
     menuItem.addActionListener(this);
 
     chainMenu.add(menuItem);
@@ -359,23 +396,24 @@ public class AppletJmol extends EmbmenuFrame implements
       frame.add(cap);
 
       StringBuffer sb = new StringBuffer();
-      try {
-      for (int s = 0; s < jmb.pdbentry.length; s++)
+      try
       {
-        sb.append(StructureSelectionManager.getStructureSelectionManager()
-                .printMapping(jmb.pdbentry[s].getFile()));
-        sb.append("\n");
-      }
-      cap.setText(sb.toString());
-      }
-      catch (OutOfMemoryError ex)
+        for (int s = 0; s < jmb.pdbentry.length; s++)
+        {
+          sb.append(jmb.printMapping(jmb.pdbentry[s].getFile()));
+          sb.append("\n");
+        }
+        cap.setText(sb.toString());
+      } catch (OutOfMemoryError ex)
       {
         frame.dispose();
-        System.err.println("Out of memory when trying to create dialog box with sequence-structure mapping.");
+        System.err
+                .println("Out of memory when trying to create dialog box with sequence-structure mapping.");
         return;
       }
-      jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping",
-              550, 600);
+      jalview.bin.JalviewLite.addFrame(frame,
+              MessageManager.getString("label.pdb_sequence_mapping"), 550,
+              600);
     }
     else if (evt.getSource() == charge)
     {
@@ -423,6 +461,10 @@ public class AppletJmol extends EmbmenuFrame implements
       setEnabled(buried);
       jmb.setJalviewColourScheme(new BuriedColourScheme());
     }
+    else if (evt.getSource() == purinepyrimidine)
+    {
+      jmb.setJalviewColourScheme(new PurinePyrimidineColourScheme());
+    }
     else if (evt.getSource() == user)
     {
       setEnabled(user);
@@ -455,23 +497,29 @@ public class AppletJmol extends EmbmenuFrame implements
   }
 
   /**
-   * tick or untick the seqColour menu entry depending upon if it was selected
-   * or not.
+   * tick or untick the seqColour menu entry or jmoColour entry depending upon
+   * if it was selected or not.
    * 
    * @param itm
    */
   private void setEnabled(MenuItem itm)
   {
+    jmolColour.setState(itm == jmolColour);
     seqColour.setState(itm == seqColour);
     jmb.setColourBySequence(itm == seqColour);
   }
 
   public void itemStateChanged(ItemEvent evt)
   {
-    if (evt.getSource() == seqColour)
+    if (evt.getSource() == jmolColour)
+    {
+      setEnabled(jmolColour);
+      jmb.setColourBySequence(false);
+    }
+    else if (evt.getSource() == seqColour)
     {
       setEnabled(seqColour);
-      jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+      jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
     }
     else if (!allChainsSelected)
       centerViewer();
@@ -499,7 +547,7 @@ public class AppletJmol extends EmbmenuFrame implements
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
-    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
   }
 
   public void updateTitleAndMenus()
@@ -510,7 +558,7 @@ public class AppletJmol extends EmbmenuFrame implements
       return;
     }
     setChainMenuItems(jmb.chainNames);
-    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
 
     setTitle(jmb.getViewerTitle());
   }
@@ -525,26 +573,30 @@ public class AppletJmol extends EmbmenuFrame implements
     {
     }
   }
-  Panel splitPane=null;
+
+  Panel splitPane = null;
+
   public void showConsole(boolean showConsole)
   {
     if (showConsole)
     {
       remove(renderPanel);
       splitPane = new Panel();
-      
-      splitPane.setLayout(new java.awt.GridLayout(2,1));
+
+      splitPane.setLayout(new java.awt.GridLayout(2, 1));
       splitPane.add(renderPanel);
       splitPane.add(scriptWindow);
       scriptWindow.setVisible(true);
       this.add(splitPane, BorderLayout.CENTER);
       splitPane.setVisible(true);
       splitPane.validate();
-    } else {
+    }
+    else
+    {
       scriptWindow.setVisible(false);
       remove(splitPane);
       add(renderPanel, BorderLayout.CENTER);
-      splitPane=null;
+      splitPane = null;
     }
     validate();
   }
@@ -579,7 +631,8 @@ public class AppletJmol extends EmbmenuFrame implements
         g.fillRect(0, 0, currentSize.width, currentSize.height);
         g.setColor(Color.white);
         g.setFont(new Font("Verdana", Font.BOLD, 14));
-        g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
+        g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
+                20, currentSize.height / 2);
       }
       else
       {
@@ -610,4 +663,16 @@ public class AppletJmol extends EmbmenuFrame implements
   {
     jmb.setJalviewColourScheme(ucs);
   }
+
+  public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
+  {
+    for (int i = 0; i < _aps.size(); i++)
+    {
+      if (((AlignmentPanel) _aps.get(i)).av.getAlignment() == alignment)
+      {
+        return ((AlignmentPanel) _aps.get(i));
+      }
+    }
+    return ap;
+  }
 }