JAL-2609 process only up to end of alignment when shifting sequences

[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 82ba2d7..1637631 100644 (file)
--- 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;
@@ -532,7 +532,7 @@ public abstract class AAStructureBindingModel extends
           BitSet matched, SuperposeData[] structures)
   {
     int refStructure = -1;
-    String[] files = getPdbFile();
+    String[] files = getStructureFiles();
     if (files == null)
     {
       return -1;
@@ -716,8 +716,8 @@ 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);
 
@@ -756,7 +756,7 @@ public abstract class AAStructureBindingModel extends
     {
       return;
     }
-    String[] files = getPdbFile();
+    String[] files = getStructureFiles();
   
     SequenceRenderer sr = getSequenceRenderer(alignmentv);
   
@@ -770,6 +770,6 @@ public abstract class AAStructureBindingModel extends
     return fileLoadingError != null && fileLoadingError.length() > 0;
   }
 
-  protected abstract jalview.api.FeatureRenderer getFeatureRenderer(
+  public abstract jalview.api.FeatureRenderer getFeatureRenderer(
           AlignmentViewPanel alignment);
 }