JAL-2422 pull up refactoring in preparation for ChimeraX subclasses

[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 2528286..b4e9dd2 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -21,6 +21,7 @@
 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;
@@ -57,6 +58,11 @@ public abstract class AAStructureBindingModel
         extends SequenceStructureBindingModel
         implements StructureListener, StructureSelectionManagerProvider
 {
+  /*
+   * the Jalview panel through which the user interacts
+   * with the structure viewer
+   */
+  private JalviewStructureDisplayI viewer;
 
   private StructureSelectionManager ssm;
 
@@ -355,8 +361,8 @@ public abstract class AAStructureBindingModel
               { Integer.valueOf(pe).toString() }));
     }
     final String nullChain = "TheNullChain";
-    List<SequenceI> s = new ArrayList<SequenceI>();
-    List<String> c = new ArrayList<String>();
+    List<SequenceI> s = new ArrayList<>();
+    List<String> c = new ArrayList<>();
     if (getChains() == null)
     {
       setChains(new String[getPdbCount()][]);
@@ -425,8 +431,8 @@ public abstract class AAStructureBindingModel
   public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
           SequenceI[][] seq, String[][] chns)
   {
-    List<PDBEntry> v = new ArrayList<PDBEntry>();
-    List<int[]> rtn = new ArrayList<int[]>();
+    List<PDBEntry> v = new ArrayList<>();
+    List<int[]> rtn = new ArrayList<>();
     for (int i = 0; i < getPdbCount(); i++)
     {
       v.add(getPdbEntry(i));
@@ -745,7 +751,12 @@ public abstract class AAStructureBindingModel
    */
   public JalviewStructureDisplayI getViewer()
   {
-    return null;
+    return viewer;
+  }
+
+  public void setViewer(JalviewStructureDisplayI v)
+  {
+    viewer = v;
   }
 
   public abstract void setJalviewColourScheme(ColourSchemeI cs);
@@ -821,6 +832,19 @@ public abstract class AAStructureBindingModel
     return fileLoadingError != null && fileLoadingError.length() > 0;
   }
 
-  public abstract jalview.api.FeatureRenderer getFeatureRenderer(
-          AlignmentViewPanel alignment);
+  /**
+   * Returns the FeatureRenderer for the given alignment view, or null if
+   * feature display is turned off in the view.
+   * 
+   * @param avp
+   * @return
+   */
+  public FeatureRenderer getFeatureRenderer(AlignmentViewPanel avp)
+  {
+    AlignmentViewPanel ap = (avp == null) ? getViewer().getAlignmentPanel()
+            : avp;
+    return ap.getAlignViewport().isShowSequenceFeatures()
+            ? ap.getFeatureRenderer()
+            : null;
+  }
 }