move test file to proper namespace

bioperl · May 27, 2010 · 6444b22 · 6444b22
1 parent 09aa1b5
commit 6444b22
Showing 1 changed file with 97 additions and 0 deletions.
diff --git a/t/Align/Graphics.t b/t/Align/Graphics.t
@@ -0,0 +1,97 @@
+#!usr/bin/perl -w
+use strict;
+
+BEGIN
+{     
+  use lib 't/lib';
+
+#  use BioperlTest;
+  use Test::More tests=>41;
+
+#Check if module and all its methods can be loaded
+use_ok('Bio::Align::Graphics');
+require_ok('Bio::Align::Graphics');
+can_ok('Bio::Align::Graphics', qw(new draw height width aln_length aln_format no_sequences));
+}      
+
+#Get an alignment file
+my $file = Bio::Root::IO->catfile("t","data","pep-266.aln");
+ok($file, 'input is defined');
+
+#Create an AlignI object using AlignIO
+my $in=new Bio::AlignIO(-file=>$file, -format=>'clustalw');
+ok(defined $in, 'AlignIO object is defined');
+isa_ok($in, 'Bio::AlignIO');
+
+#Read the alignment
+my $aln=$in->next_aln();
+ok(defined $aln, 'alignment is there and defined');
+
+#Create some domains for highlighting
+my @domain_start = ( 25, 50, 80 );
+my @domain_end = ( 40 , 65 , 100 );
+my @domain_color = ( 'red' , 'cyan' , 'green' );
+ok(exists $domain_start[2], 'all starts are present');
+ok(exists $domain_end[2],'all ends are present');
+ok(exists $domain_color[2], 'all colors are present');
+ok($domain_start[0]<=$domain_end[0],'first end is further than first start');   #Some  
+ok($domain_start[1]<=$domain_end[1],'second end is further than second start');	#logical
+ok($domain_start[2]<=$domain_end[2],'third end is further than third start');   #tests 
+
+#Create Labels for the domains
+my @dml = ("CARD", "Proline Rich", "Transmembrane");
+my @dml_start = (25, 50, 80);
+my @dml_end = (40, 65, 100);
+my @dml_color = ("lightpink", "lightblue", "lightgreen");
+ok(exists $dml[2], 'domain labels are present');
+ok(exists $dml_start[2], 'domain starts are present');
+ok(exists $dml_end[2], 'domain ends are present');
+ok(exists $dml_color[2], 'domain colors are present');
+
+#Some logical tests 
+ok($dml_start[0]<=$dml_end[0],'label - first end is further than first start');         
+ok($dml_start[1]<=$dml_end[1],'label - second end is further than second start');	
+ok($dml_start[2]<=$dml_end[2],'label - third end is further than third start');          
+is($domain_start[0]=>$dml_start[0],'first label start is within domain range');        
+is($domain_start[1]=>$dml_start[1],'second label start is within domain range');        
+is($domain_start[2]=>$dml_start[2],'third label start is within domain range');        
+is($domain_end[0]=>$dml_end[0],'first label end is within domain range');        
+is($domain_end[1]=>$dml_end[1],'second label end is within domain range');        
+is($domain_end[2]=>$dml_end[2],'third label end is within domain range');        
+
+#Create individual labels
+my %labels = ( 145 => "Hep-c target");
+ok(exists $labels{145}, 'individual labels work');
+
+#my $output_file = test_output_file();
+
+my $print_align = Bio::Align::Graphics->new( align => $aln,
+					pad_bottom => 5,
+					dm_start => \@domain_start,
+					dm_end => \@domain_end,
+					dm_color => \@domain_color,
+					dm_labels => \@dml,
+					dml_start => \@dml_start,
+					dml_end => \@dml_end,
+					dml_color => \@dml_color,
+				 	labels => \%labels,
+					out_format => "png",
+#					output=>$output_file,
+					wrap=>80);
+
+isa_ok($print_align, 'Bio::Align::Graphics');
+ok( defined $print_align, 'new object is defined');
+is($print_align->{pad_bottom}, 5, '  pad_bottom is right');
+is($print_align->{pad_top}, 5, '  default pad_top is right');
+is($print_align->{domain_start}, \@domain_start,'  start point loaded');
+is($print_align->{domain_end}, \@domain_end,'  end point loaded');
+is($print_align->{domain_color}, \@domain_color,'  color of domain loaded');
+is($print_align->{dm_labels}, \@dml, '  domain labels loaded');
+is($print_align->{dm_label_start}, \@dml_start, '  label starts loaded');
+is($print_align->{dm_label_end}, \@dml_end, '  label ends loaded');
+is($print_align->{dm_label_color}, \@dml_color, '  label colors loaded');
+is($print_align->{labels}, \%labels, '  labels loaded');
+is($print_align->{out_format}, 'png', '  output file is png');
+isnt($print_align->{wrapping}, 0, '  wrapping length is not zero');
+
+exit;