JAL-2388 Preliminary refactor check-in, does not compile

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 7bebfa9..f1bb8de 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -150,10 +150,11 @@ public class AlignViewport extends AlignmentViewport implements
   public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
   {
     setAlignment(al);
-    if (hiddenColumns != null)
+    posProps.setHiddenColumns(hiddenColumns);
+    /*if (hiddenColumns != null)
     {
       colSel = hiddenColumns;
-    }
+    }*/
     init();
   }
 
@@ -197,10 +198,11 @@ public class AlignViewport extends AlignmentViewport implements
       Cache.log.debug("Setting viewport's view id : " + viewId);
     }
     setAlignment(al);
-    if (hiddenColumns != null)
+    posProps.setHiddenColumns(hiddenColumns);
+    /*if (hiddenColumns != null)
     {
       colSel = hiddenColumns;
-    }
+    }*/
     init();
   }
 
@@ -533,7 +535,9 @@ public class AlignViewport extends AlignmentViewport implements
     {
       end = alignment.getWidth();
     }
-    viscontigs = colSel.getVisibleContigs(start, end);
+    viscontigs = posProps.getColumnSelection()
+            .getVisibleContigs(start, end);
+    // viscontigs = colSel.getVisibleContigs(start, end);
     return viscontigs;
   }