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 b64d98e..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;
@@ -51,7 +51,7 @@ import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
-import jalview.viewmodel.ViewportPositionProps;
+import jalview.viewmodel.ViewportRanges;
 import jalview.ws.params.AutoCalcSetting;
 
 import java.awt.Container;
@@ -76,7 +76,7 @@ public class AlignViewport extends AlignmentViewport implements
 {
   Font font;
 
-  NJTree currentTree = null;
+  TreeModel currentTree = null;
 
   boolean cursorMode = false;
 
@@ -238,11 +238,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   void init()
   {
-
-    /*setStartRes(0);
-    setEndRes(alignment.getWidth() - 1);
-    setStartSeq(0);
-    setEndSeq(alignment.getHeight() - 1);*/
+    ranges = new ViewportRanges(this.alignment);
     applyViewProperties();
 
     String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
@@ -309,8 +305,6 @@ public class AlignViewport extends AlignmentViewport implements
     {
       residueShading.setConsensus(hconsensus);
     }
-
-    posProps = new ViewportPositionProps(this.alignment);
   }
 
   /**
@@ -497,7 +491,7 @@ public class AlignViewport extends AlignmentViewport implements
    * @param tree
    *          DOCUMENT ME!
    */
-  public void setCurrentTree(NJTree tree)
+  public void setCurrentTree(TreeModel tree)
   {
     currentTree = tree;
   }
@@ -507,7 +501,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @return DOCUMENT ME!
    */
-  public NJTree getCurrentTree()
+  public TreeModel getCurrentTree()
   {
     return currentTree;
   }
@@ -858,7 +852,7 @@ public class AlignViewport extends AlignmentViewport implements
       }
     }
 
-    setEndSeq(getAlignment().getHeight());
+    ranges.setEndSeq(getAlignment().getHeight());
     firePropertyChange("alignment", null, getAlignment().getSequences());
   }