From f59219438e94c6c782995d472b654fb2526cb293 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 4 Nov 2004 18:03:44 +0000
Subject: [PATCH] Comment out all PID and frequency calcs for the moment

---
 src/jalview/gui/SeqCanvas.java |   31 ++++++++++++++++---------------
 1 file changed, 16 insertions(+), 15 deletions(-)

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index c697d1e..1339988 100755
--- 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());
     double            charWidth  = av.getCharWidth();
     int               charHeight = av.getCharHeight();
+    RendererI sr = av.getRenderer();
 
- //   Vector    pid    = av.calcNewConsensus();
 
-    RendererI sr = av.getRenderer();
+    /*Vector    pid    = av.getConsensus(false);
 
-/*    Vector tmpseq = new Vector();
+    Vector tmpseq = new Vector();
 
-    for (int i = 0; i < av.getAlignment().getHeight(); i++) {
-	if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {
+    for (int i = 0; i < av.getAlignment().getHeight(); i++)
+	if (!av.getSelection().contains(av.getAlignment().getSequenceAt(i)))
 	    tmpseq.addElement(av.getAlignment().getSequenceAt(i));
-	}
-    }
 
-    if (sr instanceof SequenceRenderer) {
+
+
+    if (sr instanceof SequenceRenderer)
 	pid    = AAFrequency.calculate(tmpseq,x1,x2);
 
-    } else if (sr instanceof GraphRenderer) {
+    else if (sr instanceof GraphRenderer)
 	pid = AAFrequency.calculatePID(av.getAlignment().getSequenceAt(0),
 				       av.getAlignment().getSequences(),
 				       av.getPIDWindow(),x1,x2);
 
-    }*/
+*/
 
     if (y2 > starty && y1 < av.getEndSeq()) {
 
@@ -323,16 +323,17 @@ public class SeqCanvas extends JPanel
     for (int i = y1 ; i < y2 ;i++) {
 
       RendererI r = sr;
-
-    /*  if (av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {
+/*
+      if (av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {
           r = fr;
           System.out.println("use feature renderer");
-    //  } else if ( i == 0) {
-       //   r = br;
+      } else if ( i == 0) {
+        //  r = br;
       } else if (av.getAlignment().getSequenceAt(i).getName().equals("CpG")) {
           r = cgr;
           System.out.println("cg renderer");
-      }*/
+      }
+*/
 
       r.drawSequence(g,cs,av.getAlignment().getSequenceAt(i),
                       x1,
-- 
1.7.10.2