JAL-3551 copy Jalview features to Pymol 'p' (with pull refactoring)

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

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 24ac87a..65b002b 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -25,7 +25,6 @@ import java.awt.event.ActionListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.io.File;
-import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
@@ -46,7 +45,7 @@ import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.BrowserLauncher;
+import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 
@@ -79,16 +78,13 @@ public class ChimeraViewFrame extends StructureViewerBase
   {
     super.initMenus();
 
-    viewerActionMenu.setText(MessageManager.getString("label.chimera"));
-
-    helpItem.setText(MessageManager.getString("label.chimera_help"));
     savemenu.setVisible(false); // not yet implemented
     viewMenu.add(fitToWindow);
 
     JMenuItem writeFeatures = new JMenuItem(
-            MessageManager.getString("label.create_chimera_attributes"));
+            MessageManager.getString("label.create_viewer_attributes"));
     writeFeatures.setToolTipText(MessageManager
-            .getString("label.create_chimera_attributes_tip"));
+            .getString("label.create_viewer_attributes_tip"));
     writeFeatures.addActionListener(new ActionListener()
     {
       @Override
@@ -153,14 +149,12 @@ public class ChimeraViewFrame extends StructureViewerBase
   }
 
   /**
-   * Send a command to Chimera to create residue attributes for Jalview features
-   * <p>
-   * The syntax is: setattr r &lt;attName&gt; &lt;attValue&gt; &lt;atomSpec&gt;
-   * <p>
-   * For example: setattr r jv_chain "Ferredoxin-1, Chloroplastic" #0:94.A
+   * Sends command(s) to the structure viewer to create residue attributes for
+   * visible Jalview features
    */
   protected void sendFeaturesToChimera()
   {
+    // todo pull up?
     int count = jmb.sendFeaturesToViewer(getAlignmentPanel());
     statusBar.setText(
             MessageManager.formatMessage("label.attributes_set", count));
@@ -314,7 +308,8 @@ public class ChimeraViewFrame extends StructureViewerBase
     if (!jmb.launchChimera())
     {
       JvOptionPane.showMessageDialog(Desktop.desktop,
-              MessageManager.getString("label.chimera_failed"),
+              MessageManager.formatMessage("label.open_viewer_failed",
+                      getViewerName()),
               MessageManager.getString("label.error_loading_file"),
               JvOptionPane.ERROR_MESSAGE);
       this.dispose();
@@ -335,50 +330,6 @@ public class ChimeraViewFrame extends StructureViewerBase
   }
 
   /**
-   * Close down this instance of Jalview's Chimera viewer, giving the user the
-   * option to close the associated Chimera window (process). They may wish to
-   * keep it open until they have had an opportunity to save any work.
-   * 
-   * @param closeChimera
-   *          if true, close any linked Chimera process; if false, prompt first
-   */
-  @Override
-  public void closeViewer(boolean closeChimera)
-  {
-    if (jmb != null && jmb.isChimeraRunning())
-    {
-      if (!closeChimera)
-      {
-        String prompt = MessageManager
-                .formatMessage("label.confirm_close_chimera", new Object[]
-                { jmb.getViewerTitle(getViewerName(), false) });
-        prompt = JvSwingUtils.wrapTooltip(true, prompt);
-        int confirm = JvOptionPane.showConfirmDialog(this, prompt,
-                MessageManager.getString("label.close_viewer"),
-                JvOptionPane.YES_NO_CANCEL_OPTION);
-        /*
-         * abort closure if user hits escape or Cancel
-         */
-        if (confirm == JvOptionPane.CANCEL_OPTION
-                || confirm == JvOptionPane.CLOSED_OPTION)
-        {
-          return;
-        }
-        closeChimera = confirm == JvOptionPane.YES_OPTION;
-      }
-      jmb.closeViewer(closeChimera);
-    }
-    setAlignmentPanel(null);
-    _aps.clear();
-    _alignwith.clear();
-    _colourwith.clear();
-    // TODO: check for memory leaks where instance isn't finalised because jmb
-    // holds a reference to the window
-    jmb = null;
-    dispose();
-  }
-
-  /**
    * Open any newly added PDB structures in Chimera, having first fetched data
    * from PDB (if not already saved).
    */
@@ -564,31 +515,10 @@ public class ChimeraViewFrame extends StructureViewerBase
   }
 
   @Override
-  public void eps_actionPerformed()
+  public void makePDBImage(TYPE imageType)
   {
-    throw new Error(MessageManager
-            .getString("error.eps_generation_not_implemented"));
-  }
-
-  @Override
-  public void png_actionPerformed()
-  {
-    throw new Error(MessageManager
-            .getString("error.png_generation_not_implemented"));
-  }
-
-  @Override
-  public void showHelp_actionPerformed()
-  {
-    try
-    {
-      String url = jmb.getHelpURL();
-      BrowserLauncher.openURL(url);
-    } catch (IOException ex)
-    {
-      System.err
-              .println("Show Chimera help failed with: " + ex.getMessage());
-    }
+    throw new UnsupportedOperationException(
+            "Image export for Chimera is not implemented");
   }
 
   @Override