X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;h=183b475c7391350d3e56f2393d769486d43b6f3d;hb=e739c2824d4d6a93c3e0f255780259c7daf2dc21;hp=b4520c4ccbf8ee00c383de6aac459b862a69416c;hpb=e06ef51ba3dd8cdae7632d71db162ff416b88256;p=jalview.git

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index b4520c4..183b475 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -25,7 +25,6 @@ import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
-import jalview.ext.rbvi.chimera.ChimeraCommands;
 import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
@@ -100,41 +99,34 @@ public class ChimeraViewFrame extends StructureViewerBase
     savemenu.setVisible(false); // not yet implemented
     viewMenu.add(fitToWindow);
 
-    /*
-     * exchange of Jalview features and Chimera attributes is for now
-     * an optionally enabled experimental feature
-     */
-    if (Desktop.instance.showExperimental())
+    JMenuItem writeFeatures = new JMenuItem(
+            MessageManager.getString("label.create_chimera_attributes"));
+    writeFeatures.setToolTipText(MessageManager
+            .getString("label.create_chimera_attributes_tip"));
+    writeFeatures.addActionListener(new ActionListener()
     {
-      JMenuItem writeFeatures = new JMenuItem(
-              MessageManager.getString("label.create_chimera_attributes"));
-      writeFeatures.setToolTipText(MessageManager
-              .getString("label.create_chimera_attributes_tip"));
-      writeFeatures.addActionListener(new ActionListener()
+      @Override
+      public void actionPerformed(ActionEvent e)
       {
-        @Override
-        public void actionPerformed(ActionEvent e)
-        {
-          sendFeaturesToChimera();
-        }
-      });
-      viewerActionMenu.add(writeFeatures);
+        sendFeaturesToChimera();
+      }
+    });
+    viewerActionMenu.add(writeFeatures);
 
-      final JMenu fetchAttributes = new JMenu(
-              MessageManager.getString("label.fetch_chimera_attributes"));
-      fetchAttributes.setToolTipText(MessageManager
-              .getString("label.fetch_chimera_attributes_tip"));
-      fetchAttributes.addMouseListener(new MouseAdapter()
-      {
+    final JMenu fetchAttributes = new JMenu(
+            MessageManager.getString("label.fetch_chimera_attributes"));
+    fetchAttributes.setToolTipText(
+            MessageManager.getString("label.fetch_chimera_attributes_tip"));
+    fetchAttributes.addMouseListener(new MouseAdapter()
+    {
 
-        @Override
-        public void mouseEntered(MouseEvent e)
-        {
-          buildAttributesMenu(fetchAttributes);
-        }
-      });
-      viewerActionMenu.add(fetchAttributes);
-    }
+      @Override
+      public void mouseEntered(MouseEvent e)
+      {
+        buildAttributesMenu(fetchAttributes);
+      }
+    });
+    viewerActionMenu.add(fetchAttributes);
   }
 
   /**
@@ -145,34 +137,21 @@ public class ChimeraViewFrame extends StructureViewerBase
    */
   protected void buildAttributesMenu(JMenu attributesMenu)
   {
-    List<String> atts = jmb.sendChimeraCommand("list resattr", true);
-    if (atts == null)
-    {
-      return;
-    }
+    List<String> atts = jmb.getChimeraAttributes();
     attributesMenu.removeAll();
     Collections.sort(atts);
-    for (String att : atts)
+    for (String attName : atts)
     {
-      final String attName = att.split(" ")[1];
-
-      /*
-       * ignore 'jv_*' attributes, as these are Jalview features that have
-       * been transferred to residue attributes in Chimera!
-       */
-      if (!attName.startsWith(ChimeraCommands.NAMESPACE_PREFIX))
+      JMenuItem menuItem = new JMenuItem(attName);
+      menuItem.addActionListener(new ActionListener()
       {
-        JMenuItem menuItem = new JMenuItem(attName);
-        menuItem.addActionListener(new ActionListener()
+        @Override
+        public void actionPerformed(ActionEvent e)
         {
-          @Override
-          public void actionPerformed(ActionEvent e)
-          {
-            getChimeraAttributes(attName);
-          }
-        });
-        attributesMenu.add(menuItem);
-      }
+          getChimeraAttributes(attName);
+        }
+      });
+      attributesMenu.add(menuItem);
     }
   }
 
@@ -487,7 +466,7 @@ public class ChimeraViewFrame extends StructureViewerBase
         {
           filePDB.add(thePdbEntry);
           filePDBpos.add(Integer.valueOf(pi));
-          files.append(" \"" + Platform.escapeString(file) + "\"");
+          files.append(" \"" + Platform.escapeBackslashes(file) + "\"");
         }
       }
     } catch (OutOfMemoryError oomerror)
@@ -635,7 +614,6 @@ public class ChimeraViewFrame extends StructureViewerBase
 
   private String fetchPdbFile(PDBEntry processingEntry) throws Exception
   {
-    // FIXME: this is duplicated code with Jmol frame ?
     String filePath = null;
     Pdb pdbclient = new Pdb();
     AlignmentI pdbseq = null;
@@ -732,10 +710,14 @@ public class ChimeraViewFrame extends StructureViewerBase
   {
     try
     {
-      BrowserLauncher
-              .openURL("https://www.cgl.ucsf.edu/chimera/docs/UsersGuide");
+      String url = jmb.isChimeraX()
+              ? "http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html"
+              : "https://www.cgl.ucsf.edu/chimera/docs/UsersGuide";
+      BrowserLauncher.openURL(url);
     } catch (IOException ex)
     {
+      System.err
+              .println("Show Chimera help failed with: " + ex.getMessage());
     }
   }
 
@@ -760,7 +742,8 @@ public class ChimeraViewFrame extends StructureViewerBase
     {
       if (pathUsed == null)
       {
-        File tempFile = File.createTempFile("chimera", ".py");
+        String suffix = jmb.isChimeraX() ? ".cxs" : ".py";
+        File tempFile = File.createTempFile("chimera", suffix);
         tempFile.deleteOnExit();
         pathUsed = tempFile.getPath();
       }