X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGStructureViewer.java;h=28d2c7aac117423cd6cd25238e8975518ece599e;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=3616a79183a3e747a10d686793b30305697ba898;hpb=70c13443ed352d9b3de815fdab2bd920c243c6eb;p=jalview.git

diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index 3616a79..28d2c7a 100644
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -1,322 +1,398 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.jbgui;
-
-import javax.swing.*;
-import java.awt.event.ActionListener;
-import java.awt.event.ActionEvent;
-
-public class GStructureViewer  extends JInternalFrame
-{
-  public GStructureViewer()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
-
-  private void jbInit()
-      throws Exception
-  {
-    this.setJMenuBar(menuBar);
-    fileMenu.setText("File");
-    savemenu.setActionCommand("Save Image");
-    savemenu.setText("Save As");
-    pdbFile.setText("PDB File");
-    pdbFile.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        pdbFile_actionPerformed(actionEvent);
-      }
-    });
-    png.setText("PNG");
-    png.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        png_actionPerformed(actionEvent);
-      }
-    });
-    eps.setText("EPS");
-    eps.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        eps_actionPerformed(actionEvent);
-      }
-    });
-    viewMapping.setText("View Mapping");
-    viewMapping.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        viewMapping_actionPerformed(actionEvent);
-      }
-    });
-    viewMenu.setText("View");
-    chainMenu.setText("Show Chain");
-    colourMenu.setText("Colours");
-    backGround.setText("Background Colour...");
-    backGround.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        backGround_actionPerformed(actionEvent);
-      }
-    });
-    seqColour.setSelected(true);
-    seqColour.setText("By Sequence");
-    seqColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        seqColour_actionPerformed(actionEvent);
-      }
-    });
-    chainColour.setText("By Chain");
-    chainColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        chainColour_actionPerformed(actionEvent);
-      }
-    });
-    chargeColour.setText("Charge & Cysteine");
-    chargeColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        chargeColour_actionPerformed(actionEvent);
-      }
-    });
-    zappoColour.setText("Zappo");
-    zappoColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        zappoColour_actionPerformed(actionEvent);
-      }
-    });
-    taylorColour.setText("Taylor");
-    taylorColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        taylorColour_actionPerformed(actionEvent);
-      }
-    });
-    hydroColour.setText("Hydro");
-    hydroColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        hydroColour_actionPerformed(actionEvent);
-      }
-    });
-    strandColour.setText("Strand");
-    strandColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        strandColour_actionPerformed(actionEvent);
-      }
-    });
-    helixColour.setText("Helix");
-    helixColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        helixColour_actionPerformed(actionEvent);
-      }
-    });
-    turnColour.setText("Turn");
-    turnColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        turnColour_actionPerformed(actionEvent);
-      }
-    });
-    buriedColour.setText("Buried");
-    buriedColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        buriedColour_actionPerformed(actionEvent);
-      }
-    });
-    userColour.setText("User Defined ...");
-    userColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        userColour_actionPerformed(actionEvent);
-      }
-    });
-    helpMenu.setText("Help");
-    jmolHelp.setText("Jmol Help");
-    jmolHelp.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        jmolHelp_actionPerformed(actionEvent);
-      }
-    });
-    menuBar.add(fileMenu);
-    menuBar.add(viewMenu);
-    menuBar.add(colourMenu);
-    menuBar.add(helpMenu);
-    fileMenu.add(savemenu);
-    fileMenu.add(viewMapping);
-    savemenu.add(pdbFile);
-    savemenu.add(png);
-    savemenu.add(eps);
-    viewMenu.add(chainMenu);
-    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(userColour);
-    colourMenu.add(backGround);
-    helpMenu.add(jmolHelp);
-  }
-
-  JMenuBar menuBar = new JMenuBar();
-  JMenu fileMenu = new JMenu();
-  JMenu savemenu = new JMenu();
-  JMenuItem pdbFile = new JMenuItem();
-  JMenuItem png = new JMenuItem();
-  JMenuItem eps = new JMenuItem();
-  JMenuItem viewMapping = new JMenuItem();
-  JMenu viewMenu = new JMenu();
-  protected JMenu chainMenu = new JMenu();
-  JMenu jMenu1 = new JMenu();
-  JMenu colourMenu = new JMenu();
-  JMenuItem backGround = new JMenuItem();
-  protected JCheckBoxMenuItem seqColour = new JCheckBoxMenuItem();
-  JMenuItem chainColour = new JMenuItem();
-  JMenuItem chargeColour = new JMenuItem();
-  JMenuItem zappoColour = new JMenuItem();
-  JMenuItem taylorColour = new JMenuItem();
-  JMenuItem hydroColour = new JMenuItem();
-  JMenuItem strandColour = new JMenuItem();
-  JMenuItem helixColour = new JMenuItem();
-  JMenuItem turnColour = new JMenuItem();
-  JMenuItem buriedColour = new JMenuItem();
-  JMenuItem userColour = new JMenuItem();
-  JMenu helpMenu = new JMenu();
-  JMenuItem jmolHelp = new JMenuItem();
-  public void pdbFile_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void png_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void eps_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void viewMapping_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void seqColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void chainColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void chargeColour_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 userColour_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void backGround_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-
-  public void jmolHelp_actionPerformed(ActionEvent actionEvent)
-  {
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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.
+ * 
+ * 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/>.
+ */
+package jalview.jbgui;
+
+import javax.swing.*;
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+
+public class GStructureViewer extends JInternalFrame
+{
+  public GStructureViewer()
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  private void jbInit() throws Exception
+  {
+    this.setJMenuBar(menuBar);
+    fileMenu.setText("File");
+    savemenu.setActionCommand("Save Image");
+    savemenu.setText("Save As");
+    pdbFile.setText("PDB File");
+    pdbFile.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        pdbFile_actionPerformed(actionEvent);
+      }
+    });
+    png.setText("PNG");
+    png.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        png_actionPerformed(actionEvent);
+      }
+    });
+    eps.setText("EPS");
+    eps.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        eps_actionPerformed(actionEvent);
+      }
+    });
+    viewMapping.setText("View Mapping");
+    viewMapping.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        viewMapping_actionPerformed(actionEvent);
+      }
+    });
+    viewMenu.setText("View");
+    chainMenu.setText("Show Chain");
+    colourMenu.setText("Colours");
+    backGround.setText("Background Colour...");
+    backGround.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        backGround_actionPerformed(actionEvent);
+      }
+    });
+    seqColour.setSelected(false);
+    seqColour.setText("By Sequence");
+    seqColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        seqColour_actionPerformed(actionEvent);
+      }
+    });
+    chainColour.setText("By Chain");
+    chainColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        chainColour_actionPerformed(actionEvent);
+      }
+    });
+    chargeColour.setText("Charge & Cysteine");
+    chargeColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        chargeColour_actionPerformed(actionEvent);
+      }
+    });
+    zappoColour.setText("Zappo");
+    zappoColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        zappoColour_actionPerformed(actionEvent);
+      }
+    });
+    taylorColour.setText("Taylor");
+    taylorColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        taylorColour_actionPerformed(actionEvent);
+      }
+    });
+    hydroColour.setText("Hydro");
+    hydroColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        hydroColour_actionPerformed(actionEvent);
+      }
+    });
+    strandColour.setText("Strand");
+    strandColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        strandColour_actionPerformed(actionEvent);
+      }
+    });
+    helixColour.setText("Helix Propensity");
+    helixColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        helixColour_actionPerformed(actionEvent);
+      }
+    });
+    turnColour.setText("Turn Propensity");
+    turnColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        turnColour_actionPerformed(actionEvent);
+      }
+    });
+    buriedColour.setText("Buried Index");
+    buriedColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        buriedColour_actionPerformed(actionEvent);
+      }
+    });
+    userColour.setText("User Defined ...");
+    userColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        userColour_actionPerformed(actionEvent);
+      }
+    });
+    jmolColour.setSelected(false);
+    jmolColour.setText("Colour with Jmol");
+    jmolColour.setToolTipText("Let Jmol manage structure colours.");
+    jmolColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        jmolColour_actionPerformed(actionEvent);
+      }
+    }
+    );
+    helpMenu.setText("Help");
+    jmolHelp.setText("Jmol Help");
+    jmolHelp.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        jmolHelp_actionPerformed(actionEvent);
+      }
+    });
+    alignStructs.setText("Align structures");
+    alignStructs.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        alignStructs_actionPerformed(actionEvent);
+      }
+    });
+    jmolActionMenu.setText("Jmol");
+    menuBar.add(fileMenu);
+    menuBar.add(viewMenu);
+    menuBar.add(colourMenu);
+    menuBar.add(jmolActionMenu);
+    jmolActionMenu.setVisible(false);
+    menuBar.add(helpMenu);
+    fileMenu.add(savemenu);
+    fileMenu.add(viewMapping);
+    savemenu.add(pdbFile);
+    savemenu.add(png);
+    savemenu.add(eps);
+    viewMenu.add(chainMenu);
+
+    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(userColour);
+    colourMenu.add(jmolColour);
+    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(userColour);
+    colourButtons.add(jmolColour);
+
+    helpMenu.add(jmolHelp);
+    jmolActionMenu.add(alignStructs);
+  }
+
+  protected void jmolColour_actionPerformed(ActionEvent actionEvent)
+  {
+  }
+
+  protected void alignStructs_actionPerformed(ActionEvent actionEvent)
+  {
+  }
+
+  JMenuBar menuBar = new JMenuBar();
+
+  JMenu fileMenu = new JMenu();
+
+  JMenu savemenu = new JMenu();
+
+  JMenuItem pdbFile = new JMenuItem();
+
+  JMenuItem png = new JMenuItem();
+
+  JMenuItem eps = new JMenuItem();
+
+  JMenuItem viewMapping = new JMenuItem();
+
+  protected JMenu viewMenu = new JMenu();
+
+  protected JMenu chainMenu = new JMenu();
+
+  JMenu jMenu1 = new JMenu();
+
+  protected JMenu colourMenu = new JMenu();
+
+  protected JMenu jmolActionMenu = new JMenu();
+
+  protected JMenuItem alignStructs = new JMenuItem();
+
+  JMenuItem backGround = new JMenuItem();
+
+  protected JRadioButtonMenuItem seqColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem chainColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem chargeColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem hydroColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem userColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem jmolColour = new JRadioButtonMenuItem();
+
+  protected ButtonGroup colourButtons = new ButtonGroup();
+
+  JMenu helpMenu = new JMenu();
+
+  JMenuItem jmolHelp = new JMenuItem();
+
+  public void pdbFile_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void png_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void eps_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void viewMapping_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void seqColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void chainColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void chargeColour_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 userColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void backGround_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
+  public void jmolHelp_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+}