JAL-2089 patch broken merge to master for Release 2.10.0b1

[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 42fbfa9..b00f1bc 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -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
@@ -239,24 +248,21 @@ public abstract class AAStructureBindingModel extends
     // TODO: give a more informative title when multiple structures are
     // displayed.
     StringBuilder title = new StringBuilder(64);
-    final PDBEntry pdbEntry = getPdbEntry(0);
+    final PDBEntry pdbe = getPdbEntry(0);
     title.append(viewerName + " view for " + getSequence()[0][0].getName()
-            + ":" + pdbEntry.getId());
+            + ":" + pdbe.getId());
 
     if (verbose)
     {
-      if (pdbEntry.getProperty() != null)
+      String method = (String) pdbe.getProperty("method");
+      if (method != null)
       {
-        if (pdbEntry.getProperty().get("method") != null)
-        {
-          title.append(" Method: ");
-          title.append(pdbEntry.getProperty().get("method"));
-        }
-        if (pdbEntry.getProperty().get("chains") != null)
-        {
-          title.append(" Chain:");
-          title.append(pdbEntry.getProperty().get("chains"));
-        }
+        title.append(" Method: ").append(method);
+      }
+      String chain = (String) pdbe.getProperty("chains");
+      if (chain != null)
+      {
+        title.append(" Chain:").append(chain);
       }
     }
     return title.toString();
@@ -521,6 +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]);
@@ -565,7 +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;
           }
@@ -598,6 +612,10 @@ public abstract class AAStructureBindingModel extends
       for (String file : files)
       {
         notLoaded = file;
+        if (file == null)
+        {
+          continue;
+        }
         try
         {
           StructureMapping[] sm = getSsm().getMapping(file);