X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=84475feb836006fd6a3ba07a5cbbf16e87057c86;hb=03beb4f2f8719088cc8c92a7ebc1ad9f2c257426;hp=bb9ee8541fe758f334391c08084b025fe696703f;hpb=bdf1428136ce701e58a90f346973dbdf9d42b316;p=jalview.git

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index bb9ee85..84475fe 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -21,7 +21,6 @@
 package jalview.structures.models;
 
 import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.api.StructureSelectionManagerProvider;
 import jalview.api.structures.JalviewStructureDisplayI;
@@ -723,18 +722,7 @@ public abstract class AAStructureBindingModel extends
   public abstract void setBackgroundColour(Color col);
 
   protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
-          String[] files, SequenceRenderer sr, FeatureRenderer fr,
-          AlignmentI alignment);
-
-  /**
-   * returns the current featureRenderer that should be used to colour the
-   * structures
-   * 
-   * @param alignment
-   * 
-   * @return
-   */
-  public abstract FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment);
+          String[] files, SequenceRenderer sr, AlignmentViewPanel avp);
 
   /**
    * returns the current sequenceRenderer that should be used to colour the
@@ -760,8 +748,6 @@ public abstract class AAStructureBindingModel extends
    */
   public void colourBySequence(AlignmentViewPanel alignmentv)
   {
-    boolean showFeatures = alignmentv.getAlignViewport()
-            .isShowSequenceFeatures();
     if (!colourBySequence || !isLoadingFinished())
     {
       return;
@@ -774,15 +760,8 @@ public abstract class AAStructureBindingModel extends
   
     SequenceRenderer sr = getSequenceRenderer(alignmentv);
   
-    FeatureRenderer fr = null;
-    if (showFeatures)
-    {
-      fr = getFeatureRenderer(alignmentv);
-    }
-    AlignmentI alignment = alignmentv.getAlignment();
-  
     StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
-            files, sr, fr, alignment);
+            files, sr, alignmentv);
     colourBySequence(colourBySequenceCommands);
   }
 
@@ -790,4 +769,7 @@ public abstract class AAStructureBindingModel extends
   {
     return fileLoadingError != null && fileLoadingError.length() > 0;
   }
+
+  public abstract jalview.api.FeatureRenderer getFeatureRenderer(
+          AlignmentViewPanel alignment);
 }