added tests for creating objects and lines, adding lines, testing for…

…matted switch point files. Re #26

t/GenomeUpdate/sp.t

@@ -2,8 +2,7 @@
 
 =head1 NAME
 
-tpf.t
-A test for Bio::GenomeUpdate::SP class
+sp.t - A test for Bio::GenomeUpdate::SP class
 
 =cut
 
@@ -27,6 +26,8 @@ use warnings;
 use autodie;
 
 use Test::More tests => 1;
+use Test::Exception;
+
 BEGIN {use_ok( 'Bio::GenomeUpdate::SP' ); }
 require_ok( 'Bio::GenomeUpdate::SP::SPLine' );
 
@@ -39,8 +40,8 @@ ok(my $sp_line1 = Bio::GenomeUpdate::SP::SPLine->new(
 	accession_suffix_orientation => '-',
 	accession_prefix_last_base => 100,
 	accession_suffix_first_base => 200,
-	comment => 'test line 1 comment'
-));
+	comment => 'test line 1 comment some nonsense here and here too'
+), 'created $sp_line1');
 #create another sp line
 ok(my $sp_line2 = Bio::GenomeUpdate::SP::SPLine->new( 
 	chromosome => 1,
@@ -50,19 +51,53 @@ ok(my $sp_line2 = Bio::GenomeUpdate::SP::SPLine->new(
 	accession_suffix_orientation => '-',
 	accession_prefix_last_base => 300,
 	accession_suffix_first_base => 100,
-	comment => 'test line 1 comment'
-));
-
-#get various values and test
-
+	comment => 'test line 2 comment some nonsense here and here too'
+),'created $sp_line2');
+
+#get various values 
+is($sp_line1->get_chromosome(), 'Un', 'Got correct chr from $sp_line1');
+is($sp_line1->get_accession_prefix(), 'accession1', 'Got correct accession_prefix from $sp_line1');
+is($sp_line1->get_accession_suffix(), 'accession2', 'Got correct accession_suffix from $sp_line1');
+is($sp_line1->get_accession_prefix_orientation(), '+', 'Got correct accession_prefix_orientation from $sp_line1');
+is($sp_line1->get_accession_suffix_orientation(), '-', 'Got correct accession_suffix_orientation from $sp_line1');
+is($sp_line1->get_accession_prefix_last_base(), 100, 'Got correct accession_prefix_last_base from $sp_line1');
+is($sp_line1->get_accession_suffix_first_base(), 200, 'Got correct accession_suffix_first_base from $sp_line1');
+is($sp_line1->get_comment(), 'test line 1 comment some nonsense here and here too', 'Got correct comment from $sp_line1');
+
+#test for type checks
+throws_ok{$sp_line1->set_chromosome(13)} qr/not a valid chromosome number/, "invalid chr exception caught"; 
+throws_ok{$sp_line1->set_accession_prefix_orientation('3')} qr/not a valid orientation type/, "invalid orientation exception caught";
+throws_ok{$sp_line1->set_accession_prefix_last_base(-1)} qr/not a positive coordinate/, "negative coordinate exception caught";
+throws_ok{$sp_line1->set_accession_suffix_first_base('A')} qr/not a positive coordinate/, "character coordinate exception caught";
+throws_ok{$sp_line1->set_comment('short comment')} qr/shorter than the minimum length/, "short comment exception caught";
 
 #add to SP object
-
+ok(my $sp = Bio::GenomeUpdate::SP->new(
+	taxid => '001',
+	assembly_group => 'TGP',
+	assembly_unit => 'Primary',
+	tpf_type => 'chromosome',
+), 'Created sp object');
+ok ($sp->add_line_to_end($sp_line1), 'added $sp_line1');
+ok ($sp->add_line_to_end($sp_line2), 'added $sp_line2');
 
 #print out SP object and compare to string
-
+ok(my $sp_file_string = $sp->get_formatted_sp(), 'got switch point file content' );
+print $sp_file_string;
+my $expected_sp_file_string = q(001	TGP	Primary	Un	chromosome	accession1	accession2	+	-	100	200	test line 1 comment some nonsense here and here too
+001	TGP	Primary	1	chromosome	accession3	accession4	-	-	300	100	test line 2 comment some nonsense here and here too
+);
+ok( $sp_file_string eq $expected_sp_file_string, 'switch point file content looks good ' );
 
 #modify values for #sp_line1 and add to SP object
-
+ok($sp_line1->set_accession_prefix_last_base(110), 'Set accession_prefix_last_base in $sp_line1');
+ok($sp_line1->set_accession_suffix_first_base(210), 'Set accession_suffix_first_base in $sp_line1');
+ok ($sp->add_line_to_end($sp_line1), 'added modified $sp_line1');
 
 #print out SP object and compare to string
+ok($sp_file_string = $sp->get_formatted_sp(), 'got switch point file content again' );
+$expected_sp_file_string = q(001	TGP	Primary	Un	chromosome	accession1	accession2	+	-	110	210	test line 1 comment some nonsense here and here too
+001	TGP	Primary	1	chromosome	accession3	accession4	-	-	300	100	test line 2 comment some nonsense here and here too
+001	TGP	Primary	Un	chromosome	accession1	accession2	+	-	110	210	test line 1 comment some nonsense here and here too
+); #$sp_line1 also changes as its a hashref
+ok( $sp_file_string eq $expected_sp_file_string, 'modified switch point file content looks good' );