From f87a66b36ba4c060658158a1c7180297e32fd396 Mon Sep 17 00:00:00 2001
From: cjfields <cjfields@bioperl.org>
Date: Thu, 8 Mar 2007 14:40:47 +0000
Subject: [PATCH] removed tests from old bracket_string method (will add to
 Simplealign tests)

svn path=/bioperl-live/trunk/; revision=11266
---
 t/alignUtilities.t | 63 ++++++++----------------------------------------------
 1 file changed, 9 insertions(+), 54 deletions(-)

diff --git a/t/alignUtilities.t b/t/alignUtilities.t
index 785018c82..f57d9ae33 100644
--- a/t/alignUtilities.t
+++ b/t/alignUtilities.t
@@ -2,7 +2,7 @@
 ## Bioperl Test Harness Script for Modules
 ## $Id$
 use strict;
-use constant NUMTESTS => 35;
+use constant NUMTESTS => 14;
 use vars qw($DEBUG);
 $DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
 
@@ -55,56 +55,11 @@ is scalar @$replicates, 3;
 my $repl_aln = pop @$replicates;
 is $repl_aln->no_sequences, 3;
 
-my %testdata = (
-	'allele1' => 'GGATCCATT[G/C]CTACT',
-	'allele2' => 'GGAT[C/-][C/-]ATT[G/C]CT[A/C]CT',
-	'allele3' => 'G[G/C]ATCCATTGCTACT',
-	'allele4' => 'GGATCCATTGCTACT',
-	'allele5' => 'GGATCCATTGCTAC[T/A]',
-	'allele6' => 'GGATCCATTGCTA[C/G][T/A]',
-	'testseq' => 'GGATCCATTGCTACT'
-	);
-
-my $alnin = Bio::AlignIO->new(-format => 'fasta',
-							 -file   => Bio::Root::IO->catfile(
-                        "t","data","alleles.fas"));
-
-$dna_aln = $alnin->next_aln;
-
-# compare all to test seq
-my %bic = bracket_strings($dna_aln, 'allele2');
-
-is (scalar(keys %bic), 7);
-
-for my $key (sort keys %bic) {
-	ok(exists $testdata{$key});
-}
-
-# fall back to first seq as ref seq
-%bic = bracket_strings($dna_aln);
-
-is (scalar(keys %bic), 7);
-
-for my $key (sort keys %bic) {
-	ok(exists $testdata{$key});
-}
-
-# only compare these seqids to ref seq
-my @seqids = qw(allele1 allele2 allele4 allele6);
-
-%bic = bracket_strings($dna_aln, undef, \@seqids);
-
-is (scalar(keys %bic), 4);
-
-for my $key (sort keys %bic) {
-	ok(exists $testdata{$key});
-}
-
-#use IO::String;
-#use Bio::AlignIO;
-#my $string;
-#my $out = IO::String->new($string);
-#
-#my $strout = Bio::AlignIO->new(-fh   => $out,'-format' => 'pfam');
-#$strout->write_aln($repl_aln);
-#is $string, "";
+##use IO::String;
+##use Bio::AlignIO;
+##my $string;
+##my $out = IO::String->new($string);
+##
+##my $strout = Bio::AlignIO->new(-fh   => $out,'-format' => 'pfam');
+##$strout->write_aln($repl_aln);
+##is $string, "";
-- 
2.11.4.GIT