X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPymolViewer.java;h=3b6ea99087b972b43bffcb456c790b466299f26e;hb=57fd11364c284318be3cae3ded0df30a36ee0d98;hp=8f7f2c1209b1af14734510bf9615309f28fa89a9;hpb=28f21e26830c0df0529e74f8de1019476eaca7bf;p=jalview.git

diff --git a/src/jalview/gui/PymolViewer.java b/src/jalview/gui/PymolViewer.java
index 8f7f2c1..3b6ea99 100644
--- a/src/jalview/gui/PymolViewer.java
+++ b/src/jalview/gui/PymolViewer.java
@@ -1,24 +1,30 @@
 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;
+
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 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;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
 
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.swing.JInternalFrame;
-import javax.swing.event.InternalFrameAdapter;
-import javax.swing.event.InternalFrameEvent;
-
 public class PymolViewer extends StructureViewerBase
 {
   private static final int myWidth = 500;
@@ -57,6 +63,54 @@ public class PymolViewer extends StructureViewerBase
     openNewPymol(ap, pe, seqs);
   }
 
+  /**
+   * Constructor given a session file to be restored
+   * 
+   * @param sessionFile
+   * @param alignPanel
+   * @param pdbArray
+   * @param seqsArray
+   * @param colourByPymol
+   * @param colourBySequence
+   * @param newViewId
+   */
+  public PymolViewer(StructureViewerModel viewerModel,
+          AlignmentPanel alignPanel, String sessionFile, String vid)
+  {
+    // TODO convert to base/factory class method
+    this();
+    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 (viewerModel.isColourByViewer())
+    {
+      binding.setColourBySequence(false);
+      seqColour.setSelected(false);
+      viewerColour.setSelected(true);
+    }
+    else if (viewerModel.isColourWithAlignPanel())
+    {
+      binding.setColourBySequence(true);
+      seqColour.setSelected(true);
+      viewerColour.setSelected(false);
+    }
+  }
+
   private void openNewPymol(AlignmentPanel ap, PDBEntry[] pe,
           SequenceI[][] seqs)
   {
@@ -156,7 +210,9 @@ public class PymolViewer extends StructureViewerBase
           initPymol();
         } catch (Exception ex)
         {
-          Cache.log.error("Couldn't open PyMOL viewer!", ex);
+          Console.error("Couldn't open PyMOL viewer!", ex);
+          // if we couldn't open Pymol, no point continuing
+          return;
         }
       }
       int num = -1;
@@ -195,12 +251,12 @@ public class PymolViewer extends StructureViewerBase
             binding.stashFoundChains(pdb, pe.getFile());
           } catch (Exception ex)
           {
-            Cache.log.error(
+            Console.error(
                     "Couldn't open " + pe.getFile() + " in Chimera viewer!",
                     ex);
           } finally
           {
-            // Cache.log.debug("File locations are " + files);
+            // Cache.debug("File locations are " + files);
           }
         }
       }
@@ -256,9 +312,11 @@ 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);
+      binding.closeViewer(true);
       this.dispose();
       return;
     }
@@ -268,7 +326,8 @@ public class PymolViewer extends StructureViewerBase
       boolean opened = binding.openSession(pymolSessionFile);
       if (!opened)
       {
-        System.err.println("An error occurred opening PyMOL session file "
+        Console.error(
+                "An error occurred opening PyMOL session file "
                 + pymolSessionFile);
       }
     }
@@ -282,59 +341,52 @@ public class PymolViewer extends StructureViewerBase
   }
 
   @Override
-  public void closeViewer(boolean closePymol)
+  public ViewerType getViewerType()
   {
-    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();
+    return ViewerType.PYMOL;
   }
 
   @Override
-  public String getStateInfo()
+  protected String getViewerName()
   {
-    return null;
+    return "PyMOL";
   }
+  JMenuItem writeFeatures = null;
+  @Override
+  protected void initMenus()
+  {
+    super.initMenus();
+
+    savemenu.setVisible(false); // not yet implemented
+    viewMenu.add(fitToWindow);
 
+    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);
+  }
+  
   @Override
-  public ViewerType getViewerType()
+  protected void buildActionMenu()
   {
-    return ViewerType.PYMOL;
+    super.buildActionMenu();
+    viewerActionMenu.add(writeFeatures);
   }
 
-  @Override
-  protected String getViewerName()
+  protected void sendFeaturesToPymol()
   {
-    return "PyMOL";
+    int count = binding.sendFeaturesToViewer(getAlignmentPanel());
+    statusBar.setText(
+            MessageManager.formatMessage("label.attributes_set", count, getViewerName())); 
   }
 
 }