X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;h=d37975d59cc071bfa90a912c981edf3df468ed25;hb=f14ab8c56014768bb0f94df591e83511aa506bdd;hp=5866d51c03893e079f24277232a9f1ac78402a04;hpb=dbd2c7a3bee8879f3f5af8c3959af22cce0b4085;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index 5866d51..d37975d 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -24,6 +24,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 import jalview.io.StructureFile;
 import jalview.schemes.ResidueProperties;
@@ -38,8 +39,6 @@ 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;
@@ -61,9 +60,10 @@ public class JmolParser extends StructureFile implements JmolStatusListener
 {
   Viewer viewer = null;
 
-  public JmolParser(String inFile, String type) throws IOException
+  public JmolParser(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   public JmolParser(FileParse fp) throws IOException
@@ -154,10 +154,12 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       if (pdbId == null)
       {
         setId(safeName(getDataName()));
+        setPDBIdAvailable(false);
       }
       else
       {
         setId(pdbId);
+        setPDBIdAvailable(true);
       }
       List<Atom> significantAtoms = convertSignificantAtoms(ms);
       for (Atom tmpatom : significantAtoms)
@@ -184,6 +186,14 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       makeResidueList();
       makeCaBondList();
 
+      if (getId() == null)
+      {
+        // always use resource name, not the hardwired file
+        // Does the value of ID get used ? Behaviour needs to be
+        // documented and tested
+        setId(getDataName());
+      }
+
       for (PDBChain chain : getChains())
       {
         SequenceI chainseq = postProcessChain(chain);
@@ -470,7 +480,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
    * Not implemented - returns null
    */
   @Override
-  public String print()
+  public String print(SequenceI[] seqs, boolean jvSuffix)
   {
     return null;
   }
@@ -624,7 +634,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
    * Not implemented - returns null
    */
   @Override
-  public Dimension resizeInnerPanel(String data)
+  public int[] resizeInnerPanel(String data)
   {
     return null;
   }