Merge remote-tracking branch 'origin/develop' into

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

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index f927e63..61621ae 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -27,6 +27,7 @@ import jalview.bin.JalviewLite;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
@@ -39,6 +40,7 @@ import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.Font;
 
@@ -74,12 +76,10 @@ public class AlignViewport extends AlignmentViewport implements
     calculator = new jalview.workers.AlignCalcManager();
     this.applet = applet;
     alignment = al;
+    ranges = new ViewportRanges(this.alignment);
     // we always pad gaps
     this.setPadGaps(true);
-    this.setStartRes(0);
-    this.setEndRes(al.getWidth() - 1);
-    this.setStartSeq(0);
-    this.setEndSeq(al.getHeight() - 1);
+
     if (applet != null)
     {
       // get the width and height scaling factors if they were specified
@@ -150,6 +150,9 @@ public class AlignViewport extends AlignmentViewport implements
       showConsensus = applet.getDefaultParameter("showConsensus",
               showConsensus);
 
+      showOccupancy = applet.getDefaultParameter("showOccupancy",
+              showOccupancy);
+
       setShowUnconserved(applet.getDefaultParameter("showUnconserved",
               getShowUnconserved()));
 
@@ -298,7 +301,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   public void resetSeqLimits(int height)
   {
-    setEndSeq(height / getCharHeight());
+    ranges.setEndSeq(height / getCharHeight());
   }
 
   public void setCurrentTree(NJTree tree)
@@ -334,7 +337,8 @@ public class AlignViewport extends AlignmentViewport implements
   {
     getStructureSelectionManager().sendSelection(
             new SequenceGroup(getSelectionGroup()),
-            new ColumnSelection(getColumnSelection()), this);
+            new ColumnSelection(getColumnSelection()),
+            new HiddenColumns(getAlignment().getHiddenColumns()), this);
   }
 
   /**