Vista.t: The 'java Vista 2>&1' command to determine if Vista

is installed gives me a different error message than the one expected in the match (/NoClassDefFoundError/), so adding another option (/^Error\:/). Also removed tabs.
bioperl · Dec 11, 2013 · 1714031 · 1714031
1 parent 61b8f85
commit 1714031
Showing 1 changed file with 69 additions and 64 deletions.
diff --git a/t/Vista.t b/t/Vista.t
@@ -6,71 +6,76 @@ BEGIN {
     use Bio::Root::Test;
     test_begin(-tests => 7);
 
-	use_ok('Bio::Tools::Run::Vista');
-	use_ok('Bio::AlignIO');
+    use_ok('Bio::Tools::Run::Vista');
+    use_ok('Bio::AlignIO');
 }
 
 SKIP: {
-	#Java and java version check
-	my $v;
-	if (-d "java") {
-		skip("Skipping because no java present to run vista",5);
-	}
-	my $output = `java -version 2>&1`;
-	open(PIPE,"java -version 2>&1 |");
-
-	while (<PIPE>) { 
-		if (/Java\sVersion\:\s(\d+\.\d+)/) {
-		$v = $1;
-		last;
-		}
-		elsif (/java version\s.(\d+\.\d+)/) {
-		$v = $1;
-		last;
-		}
-		elsif (/java version\s\"(\d\.\d)"/) {
-		 $v = $1;
-			last;
-		}
-	}
-	if ($v < 1.2) {
-		skip("Skipping due to old java version",5);
-	}   
-	open (PIPE ,'java Vista 2>&1 |');
-	while(<PIPE>){
-	  if(/NoClassDefFoundError/){
-		diag('Vista.jar is not in your class path:'.$_);
-		skip("Vista.jar is not in your class path",5);
-	  }
-	}
-	my $inputfilename= test_input_file("vista.cls");
-	my $gff_file = test_input_file("vista.gff");
-	my $aio = Bio::AlignIO->new(-file=>$inputfilename,-format=>'clustalw');
-	my $aln = $aio->next_aln;
-
-	my $out= test_output_file();
-	my $vis = Bio::Tools::Run::Vista->new('outfile'=>$out,
-										  'title' => "My Vista Plot",
-											'annotation'=>$gff_file,
-											'annotation_format'=>'GFF',
-											'min_perc_id'=>75,
-											'min_length'=>100,
-											'plotmin'   => 50,
-											'tickdist' => 2000,
-											'window'=>40,
-											'numwindows'=>4,
-											'start'=>50,
-											'end'=>1500,
-											'tickdist'=>100,
-											'bases'=>1000,
-											'color'=> {'EXON'=>'45 25 54','CNS'=>'0 0 100'},
-											'quiet'=>1);
-	isa_ok $vis,'Bio::Tools::Run::Vista';
-	is $vis->plotmin, 50;
-	is $vis->annotation, $gff_file;
-
-	$vis->run($aln,1);
-	ok -e $out;
-	$vis->run($aln,'mouse');
-	ok -e $out;
+    #Java and java version check
+    my $v;
+    if (-d "java") {
+        skip("Skipping because no java present to run vista", 5);
+    }
+
+    open(PIPE,"java -version 2>&1 |");
+    while (<PIPE>) {
+        if (/Java\sVersion\:\s(\d+\.\d+)/) {
+            $v = $1;
+            last;
+        }
+        elsif (/java version\s.(\d+\.\d+)/) {
+            $v = $1;
+            last;
+        }
+        elsif (/java version\s\"(\d\.\d)"/) {
+            $v = $1;
+            last;
+        }
+    }
+    if ($v < 1.2) {
+        skip("Skipping due to old java version", 5);
+    }
+
+    open (PIPE ,'java Vista 2>&1 |');
+    while(<PIPE>){
+        if (   /NoClassDefFoundError/
+            # For JRE 1.7.0_25 - Win7 - Spanish, the message is:
+            # "Error: no se ha encontrado o cargado la clase principal Vista"
+            or /^Error\:/
+            ){
+            diag('Vista.jar is not in your class path: '.$_);
+            skip("Vista.jar is not in your class path",5);
+        }
+    }
+    my $inputfilename= test_input_file("vista.cls");
+    my $gff_file = test_input_file("vista.gff");
+    my $aio = Bio::AlignIO->new(-file   => $inputfilename,
+                                -format => 'clustalw');
+    my $aln = $aio->next_aln;
+
+    my $out= test_output_file();
+    my $vis = Bio::Tools::Run::Vista->new('outfile'           => $out,
+                                          'title'             => "My Vista Plot",
+                                          'annotation'        => $gff_file,
+                                          'annotation_format' => 'GFF',
+                                          'min_perc_id'       => 75,
+                                          'min_length'        => 100,
+                                          'plotmin'           => 50,
+                                          'tickdist'          => 2000,
+                                          'window'            => 40,
+                                          'numwindows'        => 4,
+                                          'start'             => 50,
+                                          'end'               => 1500,
+                                          'tickdist'          => 100,
+                                          'bases'             => 1000,
+                                          'color'             => {'EXON'=>'45 25 54','CNS'=>'0 0 100'},
+                                          'quiet'             =>1);
+    isa_ok $vis,'Bio::Tools::Run::Vista';
+    is $vis->plotmin, 50;
+    is $vis->annotation, $gff_file;
+
+    $vis->run($aln,1);
+    ok -e $out;
+    $vis->run($aln,'mouse');
+    ok -e $out;
 }