Merge branch 'develop' into features/JAL-2393customMatrices

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 499faaf..a131910 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -22,7 +22,7 @@ package jalview.gui;
 
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureColourI;
@@ -46,12 +46,12 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.UserColourScheme;
-import jalview.structure.CommandListener;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
 import jalview.ws.params.AutoCalcSetting;
 
 import java.awt.Container;
@@ -72,11 +72,11 @@ import javax.swing.JInternalFrame;
  * @version $Revision: 1.141 $
  */
 public class AlignViewport extends AlignmentViewport implements
-        SelectionSource, CommandListener
+        SelectionSource
 {
   Font font;
 
-  NJTree currentTree = null;
+  TreeModel currentTree = null;
 
   boolean cursorMode = false;
 
@@ -238,10 +238,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   void init()
   {
-    this.startRes = 0;
-    this.endRes = alignment.getWidth() - 1;
-    this.startSeq = 0;
-    this.endSeq = alignment.getHeight() - 1;
+    ranges = new ViewportRanges(this.alignment);
     applyViewProperties();
 
     String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
@@ -384,11 +381,6 @@ public class AlignViewport extends AlignmentViewport implements
     super.setViewStyle(settingsForView);
     setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
             viewStyle.getFontSize()), false);
-    if (residueShading != null)
-    {
-      residueShading.setConservationApplied(settingsForView
-              .isConservationColourSelected());
-    }
   }
 
   /**
@@ -499,7 +491,7 @@ public class AlignViewport extends AlignmentViewport implements
    * @param tree
    *          DOCUMENT ME!
    */
-  public void setCurrentTree(NJTree tree)
+  public void setCurrentTree(TreeModel tree)
   {
     currentTree = tree;
   }
@@ -509,7 +501,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @return DOCUMENT ME!
    */
-  public NJTree getCurrentTree()
+  public TreeModel getCurrentTree()
   {
     return currentTree;
   }
@@ -860,7 +852,7 @@ public class AlignViewport extends AlignmentViewport implements
       }
     }
 
-    setEndSeq(getAlignment().getHeight());
+    ranges.setEndSeq(getAlignment().getHeight());
     firePropertyChange("alignment", null, getAlignment().getSequences());
   }