X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=670d830b22329967ece65ae40223b4a1330ab997;hb=d4c27a996e22436dd4c4d8f64f6341d5315ff621;hp=7bebfa9aeb9c30939a37e1d1aeea647fa3a1b8d6;hpb=fed9c76e8cb081649dc3c7594c9f3ae1f251d32a;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 7bebfa9..670d830 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -35,6 +35,7 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
@@ -51,7 +52,6 @@ import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
-import jalview.viewmodel.ViewportPositionProps;
 import jalview.ws.params.AutoCalcSetting;
 
 import java.awt.Container;
@@ -105,7 +105,7 @@ public class AlignViewport extends AlignmentViewport implements
    */
   public AlignViewport(AlignmentI al)
   {
-    setAlignment(al);
+    super(al);
     init();
   }
 
@@ -123,6 +123,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   public AlignViewport(AlignmentI al, String seqsetid, String viewid)
   {
+    super(al);
     sequenceSetID = seqsetid;
     viewId = viewid;
     // TODO remove these once 2.4.VAMSAS release finished
@@ -135,8 +136,8 @@ public class AlignViewport extends AlignmentViewport implements
     {
       Cache.log.debug("Setting viewport's view id : " + viewId);
     }
-    setAlignment(al);
     init();
+
   }
 
   /**
@@ -147,12 +148,12 @@ public class AlignViewport extends AlignmentViewport implements
    * @param hiddenColumns
    *          ColumnSelection
    */
-  public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
+  public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns)
   {
-    setAlignment(al);
+    super(al);
     if (hiddenColumns != null)
     {
-      colSel = hiddenColumns;
+      al.setHiddenColumns(hiddenColumns);
     }
     init();
   }
@@ -165,7 +166,7 @@ public class AlignViewport extends AlignmentViewport implements
    * @param seqsetid
    *          (may be null)
    */
-  public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+  public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
           String seqsetid)
   {
     this(al, hiddenColumns, seqsetid, null);
@@ -181,9 +182,10 @@ public class AlignViewport extends AlignmentViewport implements
    * @param viewid
    *          (may be null)
    */
-  public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+  public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
           String seqsetid, String viewid)
   {
+    super(al);
     sequenceSetID = seqsetid;
     viewId = viewid;
     // TODO remove these once 2.4.VAMSAS release finished
@@ -196,10 +198,10 @@ public class AlignViewport extends AlignmentViewport implements
     {
       Cache.log.debug("Setting viewport's view id : " + viewId);
     }
-    setAlignment(al);
+
     if (hiddenColumns != null)
     {
-      colSel = hiddenColumns;
+      al.setHiddenColumns(hiddenColumns);
     }
     init();
   }
@@ -238,11 +240,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   void init()
   {
-
-    /*setStartRes(0);
-    setEndRes(alignment.getWidth() - 1);
-    setStartSeq(0);
-    setEndSeq(alignment.getHeight() - 1);*/
     applyViewProperties();
 
     String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
@@ -309,8 +306,6 @@ public class AlignViewport extends AlignmentViewport implements
     {
       residueShading.setConsensus(hconsensus);
     }
-
-    posProps = new ViewportPositionProps(this.alignment, this.viewStyle);
   }
 
   /**
@@ -533,7 +528,7 @@ public class AlignViewport extends AlignmentViewport implements
     {
       end = alignment.getWidth();
     }
-    viscontigs = colSel.getVisibleContigs(start, end);
+    viscontigs = alignment.getHiddenColumns().getVisibleContigs(start, end);
     return viscontigs;
   }
 
@@ -603,7 +598,9 @@ public class AlignViewport extends AlignmentViewport implements
     jalview.structure.StructureSelectionManager
             .getStructureSelectionManager(Desktop.instance).sendSelection(
                     new SequenceGroup(getSelectionGroup()),
-                    new ColumnSelection(getColumnSelection()), this);
+                    new ColumnSelection(getColumnSelection()),
+                    new HiddenColumns(getAlignment().getHiddenColumns()),
+                    this);
   }
 
   /**
@@ -858,7 +855,7 @@ public class AlignViewport extends AlignmentViewport implements
       }
     }
 
-    setEndSeq(getAlignment().getHeight());
+    ranges.setEndSeq(getAlignment().getHeight());
     firePropertyChange("alignment", null, getAlignment().getSequences());
   }