check for exe

svn path=/bioperl-run/trunk/; revision=13161
bioperl · Jul 29, 2002 · 09c9f3d · 09c9f3d
1 parent 7164629
commit 09c9f3d
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Showing 4 changed files with 22 additions and 22 deletions.
diff --git a/t/DBA.t b/t/DBA.t
@@ -29,6 +29,11 @@ ok(1);
 my $verbose = -1;
 my @params = ('matchA' => 0.75, 'matchB' => '0.55','dymem'=>'linear');
 my  $factory = Bio::Tools::Run::Alignment::DBA->new(@params);
+unless (defined $factory->executable) {
+    warn("DBA program not found. Skipping tests $Test::ntest to $NTESTS.\n");
+    exit 0;
+}
+
 ok $factory->isa('Bio::Tools::Run::Alignment::DBA');
 my $bequiet = 1;
 $factory->quiet($bequiet);  # Suppress clustal messages to terminal
@@ -39,11 +44,6 @@ my $inputfilename_1a = Bio::Root::IO->catfile("t","data","dba1a.fa");
 my $inputfilename_1b = Bio::Root::IO->catfile("t","data","dba1b.fa");
 my $inputfilename2 = Bio::Root::IO->catfile("t","data","dba2.fa");
 my $aln;
-my $dba_present = $factory->executable();
-unless (defined $dba_present) {
-    warn("DBA program not found. Skipping tests $Test::ntest to $NTESTS.\n");
-    exit 0;
-}
 my @hsps = $factory->align($inputfilename2);
 ok($hsps[0]->isa("Bio::Search::HSP::GenericHSP"));
 ok($hsps[0]->query->start,4);

diff --git a/t/Neighbor.t b/t/Neighbor.t
@@ -28,6 +28,10 @@ ok(1);
 my $verbose = -1;
 my @params = ('type'=>'UPGMA','outgroup'=>2,'lowtri'=>1,'upptri'=>1,'subrep'=>1,'jumble'=>13);
 my $tree_factory = Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params);
+unless ($tree_factory->executable) {
+    warn("neighbor program not found. Skipping tests $Test::ntest to $NTESTS.\n") if( $DEBUG);    
+    exit 0;
+}
 
 ok $tree_factory->isa('Bio::Tools::Run::Phylo::Phylip::Neighbor');
 
@@ -66,11 +70,6 @@ $tree_factory->quiet($bequiet);  # Suppress protpars messages to terminal
 
 my $inputfilename = Bio::Root::IO->catfile("t","data","neighbor.dist");
 my $tree;
-my $neighbor_present = $tree_factory->exists_neighbor();
-unless ($neighbor_present) {
-    warn("neighbor program not found. Skipping tests $Test::ntest to $NTESTS.\n") if( $DEBUG);    
-    exit 0;
-}
 
 $tree = $tree_factory->create_tree($inputfilename);
 my @nodes = sort { defined $a->id && defined $b->id &&

diff --git a/t/ProtDist.t b/t/ProtDist.t
@@ -13,7 +13,7 @@ BEGIN {
     }
     use Test;
     use vars qw($NTESTS);
-    $NTESTS = 9;
+    $NTESTS = 10;
     plan tests => $NTESTS;
 }
 
@@ -29,6 +29,11 @@ ok(1);
 my $verbose = -1;
 my @params = ('idlength'=>30,'model'=>'cat','gencode'=>'U','category'=>'H','probchange'=>'0.4','trans'=>'5','freq'=>'0.25,0.5,0.125,0.125');
 my $dist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
+unless($dist_factory->executable){
+        warn("Protdist program not found. Skipping tests $Test::ntest to $NTESTS.\n");
+            exit 0;
+}
+
 
 ok $dist_factory->isa('Bio::Tools::Run::Phylo::Phylip::ProtDist');
 
@@ -98,4 +103,4 @@ unless ($clustal_present) {
 my $aln = $align_factory->align($inputfilename);
 $matrix = $dist_factory->create_distance_matrix($aln);
 
-ok ($matrix->{'ALEU_HORVU'}{'CATL_HUMAN'},3.34186,"failed creating distance matrix");
+ok ($matrix->{'ALEU_HORVU'}{'CATL_HUMAN'},3.07376,"failed creating distance matrix");
diff --git a/t/ProtPars.t b/t/ProtPars.t
@@ -29,8 +29,12 @@ ok(1);
 my $verbose = -1;
 my @params = ('threshold'=>10,'jumble'=>'17,10',outgroup=>2,'idlength'=>10);
 my $tree_factory = Bio::Tools::Run::Phylo::Phylip::ProtPars->new(@params);
-
 ok $tree_factory->isa('Bio::Tools::Run::Phylo::Phylip::ProtPars');
+unless($tree_factory->executable){
+    warn("Protpars program not found. Skipping tests $Test::ntest to $NTESTS.\n");
+    exit 0;
+}
+
 
 my $threshold = 5;
 $tree_factory->threshold($threshold);
@@ -56,14 +60,6 @@ $tree_factory->quiet($bequiet);  # Suppress protpars messages to terminal
 
 my $inputfilename = Bio::Root::IO->catfile("t","data","protpars.phy");
 my $tree;
-my $protpars_present = $tree_factory->exists_protpars();
-unless ($protpars_present) {
-    if($DEBUG ){ 
-	warn("protpars program not found. Skipping tests $Test::ntest to $NTESTS.\n");    
-    }
-    exit 0;
-}
-
 
 $tree = $tree_factory->create_tree($inputfilename);
 
@@ -88,5 +84,5 @@ my $aln = $align_factory->align($inputfilename);
 $tree = $tree_factory->create_tree($aln);
 
 @nodes = sort { defined $a->id && defined $b->id && $a->id cmp $b->id } $tree->get_nodes();
-ok ($nodes[6]->id, 'CYS1_DICDI', 
+ok ($nodes[5]->id, 'CYS1_DICDI', 
     "failed creating tree by protpars");