From 121674f0d3eed26524584cf4b50b36a67de8a556 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 8 Dec 2008 13:02:53 +0000
Subject: [PATCH] output average score to stdout

---
 src/jalview/analysis/AlignmentSorter.java |    4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index d801ad8..cf5a57a 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -668,6 +668,7 @@ public class AlignmentSorter
     boolean ignoreScore=method!=FEATURE_SCORE;
     StringBuffer scoreLabel = new StringBuffer();
     scoreLabel.append(start+stop+method);
+    // This doesn't work yet - we'd like to have a canonical ordering that can be preserved from call to call
     for (int i=0;featureLabels!=null && i<featureLabels.length; i++)
     {
       scoreLabel.append(featureLabels[i]==null ? "null" : featureLabels[i]);
@@ -799,6 +800,9 @@ public class AlignmentSorter
         if (!hasScore[i])
         {
           scores[i] = (max + i);
+        } else {
+          int nf=(feats[i]==null) ? 0 :((SequenceFeature[]) feats[i]).length;
+          System.err.println("Sorting on Score: seq "+seqs[i].getName()+ " Feats: "+nf+" Score : "+scores[i]);
         }
       }
     }
-- 
1.7.10.2