JAL-2177 Jmol update from: Jmol-14.2.14_2015.06.11 to Jmol-14.6.4_2016.10.26

[jalview.git] / src / jalview / ext / jmol / JmolParser.java

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index ca45d7b..180da8f 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -38,8 +38,6 @@ import java.util.List;
 import java.util.Map;
 import java.util.Vector;
 
-import javajs.awt.Dimension;
-
 import org.jmol.api.JmolStatusListener;
 import org.jmol.api.JmolViewer;
 import org.jmol.c.CBK;
@@ -150,7 +148,17 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       List<SequenceI> prot = new ArrayList<SequenceI>();
       PDBChain tmpchain;
       String pdbId = (String) ms.getInfo(0, "title");
-      setId(pdbId);
+
+      if (pdbId == null)
+      {
+        setId(safeName(getDataName()));
+        setPDBIdAvailable(false);
+      }
+      else
+      {
+        setId(pdbId);
+        setPDBIdAvailable(true);
+      }
       List<Atom> significantAtoms = convertSignificantAtoms(ms);
       for (Atom tmpatom : significantAtoms)
       {
@@ -165,7 +173,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           tmpchain.atoms.addElement(tmpatom);
         } catch (Exception e)
         {
-          tmpchain = new PDBChain(pdbId, tmpatom.chain);
+          tmpchain = new PDBChain(getId(), tmpatom.chain);
           getChains().add(tmpchain);
           tmpchain.atoms.addElement(tmpatom);
         }
@@ -176,10 +184,6 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       makeResidueList();
       makeCaBondList();
 
-      if (getId() == null)
-      {
-        setId(safeName(getDataName()));
-      }
       for (PDBChain chain : getChains())
       {
         SequenceI chainseq = postProcessChain(chain);
@@ -620,7 +624,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
    * Not implemented - returns null
    */
   @Override
-  public Dimension resizeInnerPanel(String data)
+  public int[] resizeInnerPanel(String data)
   {
     return null;
   }