From d4371f070dd23ca62ba43d1b281891ac1565cb96 Mon Sep 17 00:00:00 2001
From: jason <jason@bioperl.org>
Date: Mon, 18 Mar 2002 14:31:09 +0000
Subject: [PATCH] use average and overall percentage identity methods

svn path=/bioperl-run/branches/branch-1-0-0/; revision=13051
---
 t/EMBOSS.t  | 9 ++++++---
 t/TCoffee.t | 8 +++++---
 2 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/t/EMBOSS.t b/t/EMBOSS.t
index d13c30ec..660d86b3 100644
--- a/t/EMBOSS.t
+++ b/t/EMBOSS.t
@@ -17,7 +17,7 @@ BEGIN {
 	use lib 't';
     }
     use Test;
-    $NTESTS = 16;
+    $NTESTS = 18;
     plan tests => $NTESTS }
 
 use Bio::Factory::EMBOSS;
@@ -102,13 +102,16 @@ ok( $alnin);
 my $aln = $alnin->next_aln;
 ok($aln);
 ok($aln->length, 43);
-ok($aln->percentage_identity, 100);
+ok($aln->overall_percentage_identity, 100);
+ok($aln->average_percentage_identity, 100);
+
 my ($first) = $aln->each_seq();
 ok($first->seq(), 'SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE');
 $aln = $alnin->next_aln;
 ok($aln);
 ok($aln->length, 339);
-ok(sprintf("%.2f",$aln->percentage_identity), 33.04);
+ok(sprintf("%.2f",$aln->overall_percentage_identity), 33.04);
+ok(sprintf("%.2f",$aln->average_percentage_identity), 40.58);
 
 my $cons = $factory->program('cons');
 $cons->verbose(0);
diff --git a/t/TCoffee.t b/t/TCoffee.t
index bc32a2e2..9cfc8697 100644
--- a/t/TCoffee.t
+++ b/t/TCoffee.t
@@ -103,11 +103,13 @@ $str2 = Bio::SeqIO->new(-file=> Bio::Root::IO->catfile("t","data","cysprot1b.fa"
 my $seq = $str2->next_seq();
 
 ok $aln1->no_sequences, 3;
-ok( int($aln1->percentage_identity), 24) ;
+ok( int($aln1->average_percentage_identity), 39);
 $aln = $factory->profile_align($aln1,$seq);
 ok( $aln->no_sequences, 4);
 if( $version <= 1.22 ) {
-    ok( int($aln->percentage_identity), 18);    
+    ok( int($aln->overall_percentage_identity), 18);    
+    ok( int($aln->average_percentage_identity), 44);
 } else {
-    ok( int($aln->percentage_identity), 21);
+    ok( int($aln->overall_percentage_identity), 21);
+    ok( int($aln->average_percentage_identity), 39);    
 }