X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=3c4041413282c840e9631e2262e086c21321cbd1;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=b844b5213ec9113cb7ed9195b28037e318a9fdbf;hpb=619cc880371f3228e6a1fb33c6bfb6e7a7e2622c;p=jalview.git

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index b844b52..3c40414 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -1,9 +1,5 @@
 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 +11,10 @@ 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 +202,9 @@ 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 +212,7 @@ 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 +221,8 @@ 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 +268,7 @@ 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 +338,8 @@ 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 +352,7 @@ 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