ensure enfin service is started in background when desktop is displayed

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

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 32fc85f..c18015a 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview.
  * 
- * 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.
+ * 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.
  * 
- * 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
+ * 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.gui;
 
@@ -76,8 +75,10 @@ public class AppJmol extends GStructureViewer implements StructureListener,
   {
     this(file, id, seq, ap, loadStatus, bounds, null);
   }
+
   public AppJmol(String file, String id, SequenceI[] seq,
-            AlignmentPanel ap, String loadStatus, Rectangle bounds, String viewid)
+          AlignmentPanel ap, String loadStatus, Rectangle bounds,
+          String viewid)
   {
     loadingFromArchive = true;
     pdbentry = new PDBEntry();
@@ -315,11 +316,27 @@ public class AppJmol extends GStructureViewer implements StructureListener,
   {
     try
     {
-      EBIFetchClient ebi = new EBIFetchClient();
-      String query = "pdb:" + pdbentry.getId();
-      pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
-              .getAbsolutePath());
-      initJmol("load " + pdbentry.getFile());
+      // TODO: replace with reference fetching/transfer code (validate PDBentry
+      // as a DBRef?)
+      jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
+      AlignmentI pdbseq;
+      if ((pdbseq = pdbclient.getSequenceRecords(pdbentry.getId())) != null)
+      {
+        // just transfer the file name from the first seuqence's first PDBEntry
+        pdbentry.setFile(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
+                .elementAt(0)).getFile());
+        initJmol("load " + pdbentry.getFile());
+      }
+      else
+      {
+        JOptionPane
+                .showInternalMessageDialog(
+                        Desktop.desktop,
+                        pdbentry.getId()
+                                + " could not be retrieved. Please try downloading the file manually.",
+                        "Couldn't load file", JOptionPane.ERROR_MESSAGE);
+
+      }
     } catch (OutOfMemoryError oomerror)
     {
       new OOMWarning("Retrieving PDB id " + pdbentry.getId() + " from MSD",
@@ -379,7 +396,7 @@ public class AppJmol extends GStructureViewer implements StructureListener,
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void eps_actionPerformed(ActionEvent e)
   {
@@ -390,7 +407,7 @@ public class AppJmol extends GStructureViewer implements StructureListener,
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void png_actionPerformed(ActionEvent e)
   {
@@ -580,6 +597,7 @@ public class AppJmol extends GStructureViewer implements StructureListener,
   public void highlightAtom(int atomIndex, int pdbResNum, String chain,
           String pdbfile)
   {
+    // TODO: rna: remove CA dependency in select string
     if (!pdbfile.equals(pdbentry.getFile()))
       return;
 
@@ -594,19 +612,22 @@ public class AppJmol extends GStructureViewer implements StructureListener,
     resetLastRes.setLength(0);
     resetLastRes.append("select " + pdbResNum);
 
+    eval.append(":");
+    resetLastRes.append(":");
     if (!chain.equals(" "))
     {
-      eval.append(":" + chain);
-      resetLastRes.append(":" + chain);
+      eval.append(chain);
+      resetLastRes.append(chain);
     }
 
-    eval.append(";wireframe 100;" + eval.toString() + ".CA;");
+    eval.append(";wireframe 100;" + eval.toString() + " and not hetero;"); // ".*;");
 
     resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
-            + ".CA;spacefill 0;");
+    // + ".*;spacefill 0;");
+            + " and not hetero;spacefill 0;");
 
     eval.append("spacefill 200;select none");
-
+    // System.out.println("jmol:\n"+eval+"\n");
     viewer.evalStringQuiet(eval.toString());
   }
 
@@ -973,12 +994,14 @@ public class AppJmol extends GStructureViewer implements StructureListener,
       }
     }
   }
-  String viewId=null;
+
+  String viewId = null;
+
   public String getViewId()
   {
-    if (viewId==null)
+    if (viewId == null)
     {
-      viewId=System.currentTimeMillis()+"."+this.hashCode();
+      viewId = System.currentTimeMillis() + "." + this.hashCode();
     }
     return viewId;
   }