Merge branch 'releases/Release_2_10_0_Branch'

[jalview.git] / src / jalview / structures / models / AAStructureBindingModel.java

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index fc32fa3..4c1e9bb 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -51,6 +51,10 @@ public abstract class AAStructureBindingModel extends
 
   private StructureSelectionManager ssm;
 
+  /*
+   * distinct PDB entries (pdb files) associated
+   * with sequences
+   */
   private PDBEntry[] pdbEntry;
 
   /*
@@ -75,6 +79,11 @@ public abstract class AAStructureBindingModel extends
   private boolean finishedInit = false;
 
   /**
+   * current set of model filenames loaded in the Jmol instance
+   */
+  protected String[] modelFileNames = null;
+
+  /**
    * Data bean class to simplify parameterisation in superposeStructures
    */
   protected class SuperposeData
@@ -518,6 +527,10 @@ public abstract class AAStructureBindingModel extends
   {
     int refStructure = -1;
     String[] files = getPdbFile();
+    if (files == null)
+    {
+      return -1;
+    }
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
       StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]);
@@ -562,7 +575,11 @@ public abstract class AAStructureBindingModel extends
             }
             structures[pdbfnum].pdbId = mapping.getPdbId();
             structures[pdbfnum].isRna = theSequence.getRNA() != null;
-            // move on to next pdb file
+
+            /*
+             * move on to next pdb file (ignore sequences for other chains
+             * for the same structure)
+             */
             s = seqCountForPdbFile;
             break;
           }