Merge branch 'develop' into features/JAL-2446NCList

[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 bb9ee85..1637631 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -21,12 +21,11 @@
 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;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
@@ -533,7 +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;
@@ -717,24 +716,13 @@ 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);
 
   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;
@@ -770,19 +756,12 @@ public abstract class AAStructureBindingModel extends
     {
       return;
     }
-    String[] files = getPdbFile();
+    String[] files = getStructureFiles();
   
     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);
 }