From: jprocter <Jim Procter>
Date: Thu, 26 May 2005 17:21:48 +0000 (+0000)
Subject: fixed use of PID rather than 'Comparison' Alignment percentage id
X-Git-Tag: Release_2_0~169
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a877f7df0b7d796154087e77a424888e66f36e88;p=jalview.git

fixed use of PID rather than 'Comparison' Alignment percentage id
calculation.
---

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index d953598..9deb7e2 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -223,8 +223,8 @@ public class Alignment implements AlignmentI
         if (!del.contains( (SequenceI) sel.elementAt(i)) ||
             !del.contains( (SequenceI) sel.elementAt(j)))
         {
-
-          float pid = Comparison.compare( (SequenceI) sel.elementAt(j),
+          // use PID instead of Comparison (which is really not pleasant)
+          float pid = Comparison.PID( (SequenceI) sel.elementAt(j),
                                          (SequenceI) sel.elementAt(i));
 
           if (pid >= threshold)