refactored old jalview service code to its own package.

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

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 3b94bf4..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 (Development Version 2.4.1)
- * Copyright (C) 2009 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;
 
@@ -317,13 +316,15 @@ public class AppJmol extends GStructureViewer implements StructureListener,
   {
     try
     {
-      // TODO: replace with reference fetching/transfer code (validate PDBentry as a DBRef?)
+      // 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)
+      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());
+        pdbentry.setFile(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
+                .elementAt(0)).getFile());
         initJmol("load " + pdbentry.getFile());
       }
       else
@@ -596,6 +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;
 
@@ -610,19 +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());
   }