Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e' into develop

[jalview.git] / src / jalview / gui / AlignmentPanel.java

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index e4a4c90..e8834bc 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -122,7 +122,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     setScrollValues(0, 0);
 
-    setAnnotationVisible(av.getShowAnnotation());
+    setAnnotationVisible(av.isShowAnnotation());
 
     hscroll.addAdjustmentListener(this);
     vscroll.addAdjustmentListener(this);
@@ -729,7 +729,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
         getSeqPanel().seqCanvas.fastPaint(scrollX, scrollY);
         getScalePanel().repaint();
 
-        if (av.getShowAnnotation() && scrollX != 0)
+        if (av.isShowAnnotation() && scrollX != 0)
         {
           getAnnotationPanel().fastPaint(scrollX);
         }
@@ -1249,7 +1249,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
 
     }
-    else if (av.getShowAnnotation())
+    else if (av.isShowAnnotation())
     {
       height += getAnnotationPanel().adjustPanelHeight() + 3;
     }
@@ -1513,11 +1513,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     return av.getAlignment();
   }
 
-  /**
-   * get the name for this view
-   * 
-   * @return
-   */
+
+  @Override
   public String getViewName()
   {
     return av.viewName;
@@ -1556,18 +1553,23 @@ public class AlignmentPanel extends GAlignmentPanel implements
     new OOMWarning(string, error, this);
   }
 
-  public FeatureRenderer cloneFeatureRenderer()
+  @Override
+  public jalview.api.FeatureRenderer cloneFeatureRenderer()
   {
 
     return new FeatureRenderer(this);
   }
-
-  public void updateFeatureRenderer(FeatureRenderer fr)
+  @Override 
+  public jalview.api.FeatureRenderer getFeatureRenderer()
+  {
+    return seqPanel.seqCanvas.getFeatureRenderer();
+  }
+  public void updateFeatureRenderer(jalview.renderer.seqfeatures.FeatureRenderer fr)
   {
     fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
   }
 
-  public void updateFeatureRendererFrom(FeatureRenderer fr)
+  public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
   {
     if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
     {