X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=dc423158a27a1776209443cd9c9478c074694364;hb=0da0ed92182d198fd260866ee804eba9035de6b0;hp=b844b5213ec9113cb7ed9195b28037e318a9fdbf;hpb=2373f90e6077de127c55ec6cb7671d8ba2436684;p=jalview.git

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index b844b52..dc42315 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -1,9 +1,25 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.structures.models;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
 import jalview.api.StructureSelectionManagerProvider;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
@@ -15,6 +31,10 @@ import jalview.structure.StructureSelectionManager;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
 /**
  * 
  * A base class to hold common function for protein structure model binding.
@@ -202,7 +222,9 @@ public abstract class AAStructureBindingModel extends
   /**
    * Construct a title string for the viewer window based on the data Jalview
    * knows about
-   * @param viewerName TODO
+   * 
+   * @param viewerName
+   *          TODO
    * @param verbose
    * 
    * @return
@@ -210,8 +232,7 @@ public abstract class AAStructureBindingModel extends
   public String getViewerTitle(String viewerName, boolean verbose)
   {
     if (getSequence() == null || getSequence().length < 1
-            || getPdbCount() < 1
-            || getSequence()[0].length < 1)
+            || getPdbCount() < 1 || getSequence()[0].length < 1)
     {
       return ("Jalview " + viewerName + " Window");
     }
@@ -220,9 +241,8 @@ public abstract class AAStructureBindingModel extends
     StringBuilder title = new StringBuilder(64);
     final PDBEntry pdbEntry = getPdbEntry(0);
     title.append(viewerName + " view for " + getSequence()[0][0].getName()
-            + ":"
-            + pdbEntry.getId());
-  
+            + ":" + pdbEntry.getId());
+
     if (verbose)
     {
       if (pdbEntry.getProperty() != null)
@@ -268,8 +288,7 @@ public abstract class AAStructureBindingModel extends
     {
       throw new Error(MessageManager.formatMessage(
               "error.implementation_error_no_pdbentry_from_index",
-              new Object[]
-              { Integer.valueOf(pe).toString() }));
+              new Object[] { Integer.valueOf(pe).toString() }));
     }
     final String nullChain = "TheNullChain";
     List<SequenceI> s = new ArrayList<SequenceI>();
@@ -339,8 +358,8 @@ public abstract class AAStructureBindingModel extends
    * 
    * @returns the pdb entries added to the current set.
    */
-  public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe, SequenceI[][] seq,
-          String[][] chns)
+  public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
+          SequenceI[][] seq, String[][] chns)
   {
     List<PDBEntry> v = new ArrayList<PDBEntry>();
     List<int[]> rtn = new ArrayList<int[]>();
@@ -353,8 +372,7 @@ public abstract class AAStructureBindingModel extends
       int r = v.indexOf(pdbe[i]);
       if (r == -1 || r >= getPdbCount())
       {
-        rtn.add(new int[]
-        { v.size(), i });
+        rtn.add(new int[] { v.size(), i });
         v.add(pdbe[i]);
       }
       else
@@ -580,6 +598,10 @@ public abstract class AAStructureBindingModel extends
       for (String file : files)
       {
         notLoaded = file;
+        if (file == null)
+        {
+          continue;
+        }
         try
         {
           StructureMapping[] sm = getSsm().getMapping(file);
@@ -615,7 +637,10 @@ public abstract class AAStructureBindingModel extends
         {
           for (SequenceI s : seqs)
           {
-            if (s == seq)
+            if (s == seq
+                    || (s.getDatasetSequence() != null && s
+                            .getDatasetSequence() == seq
+                            .getDatasetSequence()))
             {
               return true;
             }
@@ -635,4 +660,4 @@ public abstract class AAStructureBindingModel extends
   {
     this.finishedInit = fi;
   }
-}
\ No newline at end of file
+}