Merge branch 'bug/JAL-2317_jmol_chimera-chain-factorisation' into develop

[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 fbac400..56287a9 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -74,7 +74,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   Vector<String> atomsPicked = new Vector<String>();
 
-  public Vector<String> chainNames;
+  private List<String> chainNames;
 
   Hashtable<String, String> chainFile;
 
@@ -99,10 +99,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   public Viewer viewer;
 
   public JalviewJmolBinding(StructureSelectionManager ssm,
-          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
+          PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
           String protocol)
   {
-    super(ssm, pdbentry, sequenceIs, chains, protocol);
+    super(ssm, pdbentry, sequenceIs, protocol);
     /*
      * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
      * "jalviewJmol", ap.av.applet .getDocumentBase(),
@@ -1083,7 +1083,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     fileLoadingError = null;
     String[] oldmodels = modelFileNames;
     modelFileNames = null;
-    chainNames = new Vector<String>();
+    chainNames = new ArrayList<String>();
     chainFile = new Hashtable<String, String>();
     boolean notifyLoaded = false;
     String[] modelfilenames = getPdbFile();
@@ -1143,6 +1143,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       for (int pe = 0; pe < getPdbCount(); pe++)
       {
         boolean matches = false;
+        addSequence(pe, getSequence()[pe]);
         if (fileName == null)
         {
           if (false)
@@ -1194,7 +1195,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
             String chid = new String(pdb.getId() + ":"
                     + pdb.getChains().elementAt(i).id);
             chainFile.put(chid, fileName);
-            chainNames.addElement(chid);
+            chainNames.add(chid);
           }
           notifyLoaded = true;
         }
@@ -1242,6 +1243,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     setLoadingFromArchive(false);
   }
 
+  @Override
+  public List<String> getChainNames()
+  {
+    return chainNames;
+  }
+
   public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
   {
     notifyAtomPicked(iatom, strMeasure, null);