From: jprocter <Jim Procter>
Date: Mon, 8 Dec 2008 13:02:53 +0000 (+0000)
Subject: output average score to stdout
X-Git-Tag: Release_2_5~380
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=121674f0d3eed26524584cf4b50b36a67de8a556;hp=12b42b6a5712870227d73b2285c338f9f5438b3a;p=jalview.git

output average score to stdout
---

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]);
         }
       }
     }