Comment out all PID and frequency calcs for the moment

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index c697d1e..1339988 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -287,28 +287,28 @@ public class SeqCanvas extends JPanel
     g.setFont(av.getFont());\r
     double            charWidth  = av.getCharWidth();\r
     int               charHeight = av.getCharHeight();\r
+    RendererI sr = av.getRenderer();\r
 \r
- //   Vector    pid    = av.calcNewConsensus();\r
 \r
-    RendererI sr = av.getRenderer();\r
+    /*Vector    pid    = av.getConsensus(false);\r
 \r
-/*    Vector tmpseq = new Vector();\r
+    Vector tmpseq = new Vector();\r
 \r
-    for (int i = 0; i < av.getAlignment().getHeight(); i++) {\r
-       if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {\r
+    for (int i = 0; i < av.getAlignment().getHeight(); i++)\r
+       if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i)))\r
            tmpseq.addElement(av.getAlignment().getSequenceAt(i));\r
-       }\r
-    }\r
 \r
-    if (sr instanceof SequenceRenderer) {\r
+\r
+\r
+    if (sr instanceof SequenceRenderer)\r
        pid    = AAFrequency.calculate(tmpseq,x1,x2);\r
 \r
-    } else if (sr instanceof GraphRenderer) {\r
+    else if (sr instanceof GraphRenderer)\r
        pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0),\r
                                       av.getAlignment().getSequences(),\r
                                       av.getPIDWindow(),x1,x2);\r
 \r
-    }*/\r
+*/\r
 \r
     if (y2 > starty && y1 < av.getEndSeq()) {\r
 \r
@@ -323,16 +323,17 @@ public class SeqCanvas extends JPanel
     for (int i = y1 ; i < y2 ;i++) {\r
 \r
       RendererI r = sr;\r
-\r
-    /*  if (av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {\r
+/*\r
+      if (av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {\r
           r = fr;\r
           System.out.println("use feature renderer");\r
-    //  } else if ( i == 0) {\r
-       //   r = br;\r
+      } else if ( i == 0) {\r
+        //  r = br;\r
       } else if (av.getAlignment().getSequenceAt(i).getName().equals("CpG")) {\r
           r = cgr;\r
           System.out.println("cg renderer");\r
-      }*/\r
+      }\r
+*/\r
 \r
       r.drawSequence(g,cs,av.getAlignment().getSequenceAt(i),\r
                       x1,\r