JAL-3390 unit tests and command and menu refinements

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

diff --git a/src/jalview/gui/PymolViewer.java b/src/jalview/gui/PymolViewer.java
index d0c9ea2..8a4ce08 100644 (file)
--- a/src/jalview/gui/PymolViewer.java
+++ b/src/jalview/gui/PymolViewer.java
@@ -1,10 +1,14 @@
 package jalview.gui;
 
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Map;
 
 import javax.swing.JInternalFrame;
+import javax.swing.JMenuItem;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
 
@@ -13,6 +17,8 @@ import jalview.api.FeatureRenderer;
 import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.StructureViewerModel;
+import jalview.datamodel.StructureViewerModel.StructureData;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
@@ -68,22 +74,36 @@ public class PymolViewer extends StructureViewerBase
    * @param colourBySequence
    * @param newViewId
    */
-  public PymolViewer(String sessionFile, AlignmentPanel alignPanel,
-          PDBEntry[] pdbArray, SequenceI[][] seqsArray,
-          boolean colourByPymol, boolean colourBySequence, String newViewId)
+  public PymolViewer(StructureViewerModel viewerModel,
+          AlignmentPanel alignPanel, String sessionFile, String vid)
   {
     // TODO convert to base/factory class method
     this();
-    setViewId(newViewId);
+    setViewId(vid);
     this.pymolSessionFile = sessionFile;
+    Map<File, StructureData> pdbData = viewerModel.getFileData();
+    PDBEntry[] pdbArray = new PDBEntry[pdbData.size()];
+    SequenceI[][] seqsArray = new SequenceI[pdbData.size()][];
+    int i = 0;
+    for (StructureData data : pdbData.values())
+    {
+      PDBEntry pdbentry = new PDBEntry(data.getPdbId(), null,
+              PDBEntry.Type.PDB, data.getFilePath());
+      pdbArray[i] = pdbentry;
+      List<SequenceI> sequencesForPdb = data.getSeqList();
+      seqsArray[i] = sequencesForPdb
+              .toArray(new SequenceI[sequencesForPdb.size()]);
+      i++;
+    }
+
     openNewPymol(alignPanel, pdbArray, seqsArray);
-    if (colourByPymol)
+    if (viewerModel.isColourByViewer())
     {
       binding.setColourBySequence(false);
       seqColour.setSelected(false);
       viewerColour.setSelected(true);
     }
-    else if (colourBySequence)
+    else if (viewerModel.isColourWithAlignPanel())
     {
       binding.setColourBySequence(true);
       seqColour.setSelected(true);
@@ -230,7 +250,7 @@ public class PymolViewer extends StructureViewerBase
           } catch (Exception ex)
           {
             Cache.log.error(
-                    "Couldn't open " + pe.getFile() + " in Chimera viewer!",
+                    "Couldn't open " + pe.getFile() + " in Pymol viewer!",
                     ex);
           } finally
           {
@@ -290,7 +310,8 @@ public class PymolViewer extends StructureViewerBase
     if (!binding.launchPymol())
     {
       JvOptionPane.showMessageDialog(Desktop.desktop,
-              MessageManager.getString("label.pymol_failed"),
+              MessageManager.formatMessage("label.open_viewer_failed",
+                      getViewerName()),
               MessageManager.getString("label.error_loading_file"),
               JvOptionPane.ERROR_MESSAGE);
       this.dispose();
@@ -302,7 +323,8 @@ public class PymolViewer extends StructureViewerBase
       boolean opened = binding.openSession(pymolSessionFile);
       if (!opened)
       {
-        System.err.println("An error occurred opening PyMOL session file "
+        Cache.log.error(
+                "An error occurred opening PyMOL session file "
                 + pymolSessionFile);
       }
     }
@@ -316,44 +338,6 @@ public class PymolViewer extends StructureViewerBase
   }
 
   @Override
-  public void closeViewer(boolean closePymol)
-  {
-    if (binding != null && binding.isPymolRunning())
-    {
-      if (!closePymol)
-      {
-        // TODO i18n (and pull up)
-        String prompt = MessageManager
-                .formatMessage("label.confirm_close_pymol", new Object[]
-                { binding.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;
-        }
-        closePymol = confirm == JvOptionPane.YES_OPTION;
-      }
-      binding.closeViewer(closePymol);
-    }
-    setAlignmentPanel(null);
-    _aps.clear();
-    _alignwith.clear();
-    _colourwith.clear();
-    // TODO: check for memory leaks where instance isn't finalised because
-    // binding
-    // holds a reference to the window
-    binding = null;
-    dispose();
-  }
-
-  @Override
   public ViewerType getViewerType()
   {
     return ViewerType.PYMOL;
@@ -365,4 +349,34 @@ public class PymolViewer extends StructureViewerBase
     return "PyMOL";
   }
 
+  @Override
+  protected void initMenus()
+  {
+    super.initMenus();
+
+    savemenu.setVisible(false); // not yet implemented
+    viewMenu.add(fitToWindow);
+
+    JMenuItem writeFeatures = new JMenuItem(
+            MessageManager.getString("label.create_viewer_attributes"));
+    writeFeatures.setToolTipText(MessageManager
+            .getString("label.create_viewer_attributes_tip"));
+    writeFeatures.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        sendFeaturesToPymol();
+      }
+    });
+    viewerActionMenu.add(writeFeatures);
+  }
+
+  protected void sendFeaturesToPymol()
+  {
+    int count = binding.sendFeaturesToViewer(getAlignmentPanel());
+    statusBar.setText(
+            MessageManager.formatMessage("label.attributes_set", count));
+  }
+
 }