trimmed down

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 7352495..3620bc0 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -41,8 +41,6 @@ public class AlignViewport
   Selection       sel    = new Selection(this);\r
   ColumnSelection colSel = new ColumnSelection();\r
 \r
-  OutputGenerator og;\r
-\r
   String visibleConsensus;\r
 \r
   int threshold;\r
@@ -50,10 +48,6 @@ public class AlignViewport
 \r
   NJTree currentTree = null;\r
 \r
-  int window   = 50;\r
-  int baseline = 30;\r
-\r
-  Vector kmers;\r
 \r
   public AlignViewport(AlignmentI da,\r
                        boolean showScores,\r
@@ -325,9 +319,7 @@ public class AlignViewport
   public ColumnSelection getColumnSelection() {\r
     return colSel;\r
   }\r
-  public OutputGenerator getOutputGenerator() {\r
-    return og;\r
-  }\r
+\r
   public void resetSeqLimits(int height) {\r
     setStartSeq(0);\r
     setEndSeq(height/getCharHeight());\r
@@ -346,27 +338,5 @@ public class AlignViewport
     public RendererI getRenderer() {\r
        return renderer;\r
     }\r
-    public int getPIDWindow() {\r
-       return window;\r
-    }\r
-    public void setPIDWindow(int window) {\r
-       this.window = window;\r
-    }\r
-\r
-    public int getPIDBaseline() {\r
-       return baseline;\r
-    }\r
-    public void setPIDBaseline(int baseline) {\r
-       this.baseline = baseline;\r
-    }\r
-\r
-    public void setKmers(Vector kmers) {\r
-        this.kmers = kmers;\r
-    }\r
-\r
-    public Vector getKmers() {\r
-        return this.kmers;\r
-    }\r
-\r
 \r
 }\r