JAL-553 JAL-1557 always send selections after triggering the PaintRefreser for a...

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

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index a1b6917..3f0847b 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -28,6 +28,7 @@ import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.StructureFile;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.AtomSpec;
@@ -1121,7 +1122,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     {
       String fileName = modelfilenames[modelnum];
       boolean foundEntry = false;
-      MCview.PDBfile pdb = null;
+      StructureFile pdb = null;
       String pdbfile = null;
       // model was probably loaded inline - so check the pdb file hashcode
       if (loadedInline)
@@ -1144,7 +1145,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
           {
             pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
                     pdbfile, AppletFormatAdapter.PASTE);
-            getPdbEntry(modelnum).setFile("INLINE" + pdb.id);
+            getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
             matches = true;
             foundEntry = true;
           }
@@ -1183,10 +1184,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
         if (matches)
         {
           // add an entry for every chain in the model
-          for (int i = 0; i < pdb.chains.size(); i++)
+          for (int i = 0; i < pdb.getChains().size(); i++)
           {
-            String chid = new String(pdb.id + ":"
-                    + pdb.chains.elementAt(i).id);
+            String chid = new String(pdb.getId() + ":"
+                    + pdb.getChains().elementAt(i).id);
             chainFile.put(chid, fileName);
             chainNames.addElement(chid);
           }