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diff --git a/Bio/Ext/Align/test.pl b/Bio/Ext/Align/test.pl
index 72411f3..1deb77b 100755
--- a/Bio/Ext/Align/test.pl
+++ b/Bio/Ext/Align/test.pl
@@ -8,13 +8,10 @@ my $DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
BEGIN {
eval { require Test; };
use Test;
- plan tests => 9;
+ plan tests => 4;
}
use Bio::Ext::Align;
-use Bio::Tools::dpAlign;
-use Bio::Seq;
-use Bio::AlignIO;
$loaded = 1;
ok(1); # modules loaded
@@ -34,64 +31,3 @@ $alb = &Bio::Ext::Align::Align_Sequences_ProteinSmithWaterman($seq1,$seq2,
$seq2->seq,15,50,STDERR) if $DEBUG;
-warn( "Testing Local Alignment case...\n") if $DEBUg;
-
-$alnout = new Bio::AlignIO(-format => 'pfam', -fh => \*STDERR);
-$aln = &Bio::Ext::Align::Align_DNA_Sequences("AATGCCATTGACGG",
- "CAGCCTCGCTTAG",3,-1,3,1,
- Bio::Tools::dpAlign::DPALIGN_LOCAL_MILLER_MYERS);
-
-$out = Bio::SimpleAlign->new();
-
-$out->add_seq(Bio::LocatableSeq->new(-seq => $aln->aln1,
- -start => $aln->start1,
- -end => $aln->end1,
- -id => "one"));
-
-$out->add_seq(Bio::LocatableSeq->new(-seq => $aln->aln2,
- -start => $aln->start2,
- -end => $aln->end2,
- -id => "two"));
-$alnout->write_aln($out) if $DEBUG;
-
-$aln = &Bio::Ext::Align::Align_Protein_Sequences("WLGQRNLVSSTGGNLLNVWLKDW","WMGNRNVVNLLNVWFRDW",0,
- Bio::Tools::dpAlign::DPALIGN_LOCAL_MILLER_MYERS);
-$out = Bio::SimpleAlign->new();
-ok($aln);
-
-$out->add_seq(Bio::LocatableSeq->new(-seq => $aln->aln1,
- -start => $aln->start1,
- -end => $aln->end1,
- -id => "one"));
-
-$out->add_seq(Bio::LocatableSeq->new(-seq => $aln->aln2,
- -start => $aln->start2,
- -end => $aln->end2,
- -id => "two"));
-$alnout->write_aln($out) if $DEBUG;
-ok(1);
-
-warn( "Testing Global Alignment case...\n") if $DEBUG;
-
-$factory = new Bio::Tools::dpAlign('-alg' => Bio::Tools::dpAlign::DPALIGN_GLOBAL_MILLER_MYERS);
-$s1 = new Bio::Seq(-id => "one", -seq => "AATGCCATTGACGG", -alphabet => 'dna');
-$s2 = new Bio::Seq(-id => "two", -seq => "CAGCCTCGCTTAG", -alphabet => 'dna');
-$aln = $factory->pairwise_alignment($s1, $s2);
-$alnout->write_aln($aln) if $DEBUG;
-$factory->align_and_show($s1, $s2) if $DEBUG;
-
-ok(1);
-
-$s1 = new Bio::Seq(-id => "one", -seq => "WLGQRNLVSSTGGNLLNVWLKDW",
- -alphabet => 'protein');
-$s2 = new Bio::Seq(-id => "two", -seq => "WMGNRNVVNLLNVWFRDW",
- -alphabet => 'protein');
-$aln = $factory->pairwise_alignment($s1, $s2);
-$alnout->write_aln($aln) if $DEBUG;
-$factory->align_and_show($s1, $s2) if $DEBUG;
-ok(1);
-
-$prof = $factory->sequence_profile($s1);
-warn( "Optimal Alignment Score = %d\n", $factory->pairwise_alignment_score($prof, $s2)) if $DEBUG;
-
-ok($factory->pairwise_alignment_score($prof,$s2),77);
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