X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=9f4cea03736531ce3371e702969eaaea58ae5d8f;hb=bd4ab013e64863bbbffa93c58953051e11cfb236;hp=84475feb836006fd6a3ba07a5cbbf16e87057c86;hpb=6ce5fc3e89e229a20027189745a80ef6df953c27;p=jalview.git

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index 84475fe..9f4cea0 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -25,7 +25,7 @@ import jalview.api.SequenceRenderer;
 import jalview.api.StructureSelectionManagerProvider;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
@@ -53,9 +53,9 @@ import java.util.List;
  * @author gmcarstairs
  *
  */
-public abstract class AAStructureBindingModel extends
-        SequenceStructureBindingModel implements StructureListener,
-        StructureSelectionManagerProvider
+public abstract class AAStructureBindingModel
+        extends SequenceStructureBindingModel
+        implements StructureListener, StructureSelectionManagerProvider
 {
 
   private StructureSelectionManager ssm;
@@ -300,7 +300,8 @@ 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>();
@@ -532,7 +533,7 @@ public abstract class AAStructureBindingModel extends
           BitSet matched, SuperposeData[] structures)
   {
     int refStructure = -1;
-    String[] files = getPdbFile();
+    String[] files = getStructureFiles();
     if (files == null)
     {
       return -1;
@@ -638,8 +639,8 @@ public abstract class AAStructureBindingModel extends
 
     if (waiting)
     {
-      System.err
-              .println("Timed out waiting for structure viewer to load file "
+      System.err.println(
+              "Timed out waiting for structure viewer to load file "
                       + notLoaded);
       return false;
     }
@@ -657,10 +658,8 @@ public abstract class AAStructureBindingModel extends
         {
           for (SequenceI s : seqs)
           {
-            if (s == seq
-                    || (s.getDatasetSequence() != null && s
-                            .getDatasetSequence() == seq
-                            .getDatasetSequence()))
+            if (s == seq || (s.getDatasetSequence() != null
+                    && s.getDatasetSequence() == seq.getDatasetSequence()))
             {
               return true;
             }
@@ -716,8 +715,8 @@ public abstract class AAStructureBindingModel extends
    *          an array of corresponding hidden columns for each alignment
    * @return
    */
-  public abstract String superposeStructures(AlignmentI[] alignments, int[] structureIndices,
-          ColumnSelection[] hiddenCols);
+  public abstract String superposeStructures(AlignmentI[] alignments,
+          int[] structureIndices, HiddenColumns[] hiddenCols);
 
   public abstract void setBackgroundColour(Color col);
 
@@ -732,7 +731,8 @@ public abstract class AAStructureBindingModel extends
    * 
    * @return
    */
-  public abstract SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment);
+  public abstract SequenceRenderer getSequenceRenderer(
+          AlignmentViewPanel alignment);
 
   protected abstract void colourBySequence(
           StructureMappingcommandSet[] colourBySequenceCommands);
@@ -756,10 +756,10 @@ public abstract class AAStructureBindingModel extends
     {
       return;
     }
-    String[] files = getPdbFile();
-  
+    String[] files = getStructureFiles();
+
     SequenceRenderer sr = getSequenceRenderer(alignmentv);
-  
+
     StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
             files, sr, alignmentv);
     colourBySequence(colourBySequenceCommands);