X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=f22a9111981856ca63ac24a83d57b173c5ec86bf;hb=2ef218faa692153c09a328d40b8f4724d69355f2;hp=f1bb8decb7924e04ba84ced59054a42cb8f351b3;hpb=79631ef84a124bfefa84c24b85dc77883366ad4a;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index f1bb8de..f22a911 100644
--- 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;
 
@@ -150,11 +150,10 @@ public class AlignViewport extends AlignmentViewport implements
   public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
   {
     setAlignment(al);
-    posProps.setHiddenColumns(hiddenColumns);
-    /*if (hiddenColumns != null)
+    if (hiddenColumns != null)
     {
       colSel = hiddenColumns;
-    }*/
+    }
     init();
   }
 
@@ -198,11 +197,10 @@ public class AlignViewport extends AlignmentViewport implements
       Cache.log.debug("Setting viewport's view id : " + viewId);
     }
     setAlignment(al);
-    posProps.setHiddenColumns(hiddenColumns);
-    /*if (hiddenColumns != null)
+    if (hiddenColumns != null)
     {
       colSel = hiddenColumns;
-    }*/
+    }
     init();
   }
 
@@ -240,11 +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");
@@ -285,6 +279,8 @@ public class AlignViewport extends AlignmentViewport implements
               false);
       showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
       showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
+
+      showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
     }
     initAutoAnnotation();
     String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
@@ -311,8 +307,6 @@ public class AlignViewport extends AlignmentViewport implements
     {
       residueShading.setConsensus(hconsensus);
     }
-
-    posProps = new ViewportPositionProps(this.alignment, this.viewStyle);
   }
 
   /**
@@ -499,7 +493,7 @@ public class AlignViewport extends AlignmentViewport implements
    * @param tree
    *          DOCUMENT ME!
    */
-  public void setCurrentTree(NJTree tree)
+  public void setCurrentTree(TreeModel tree)
   {
     currentTree = tree;
   }
@@ -509,7 +503,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @return DOCUMENT ME!
    */
-  public NJTree getCurrentTree()
+  public TreeModel getCurrentTree()
   {
     return currentTree;
   }
@@ -535,9 +529,7 @@ public class AlignViewport extends AlignmentViewport implements
     {
       end = alignment.getWidth();
     }
-    viscontigs = posProps.getColumnSelection()
-            .getVisibleContigs(start, end);
-    // viscontigs = colSel.getVisibleContigs(start, end);
+    viscontigs = colSel.getVisibleContigs(start, end);
     return viscontigs;
   }
 
@@ -862,7 +854,7 @@ public class AlignViewport extends AlignmentViewport implements
       }
     }
 
-    setEndSeq(getAlignment().getHeight());
+    ranges.setEndSeq(getAlignment().getHeight());
     firePropertyChange("alignment", null, getAlignment().getSequences());
   }