Updated dox, fixed checks for SPChromosome, added PositiveInt subtype…

…, fixed SPComment length check. For #25

lib/Bio/GenomeUpdate/SP/SPLine.pm

@@ -18,7 +18,7 @@ use Data::Dumper;#for debugging
 
 =head1 DESCRIPTION
 
-This class stores information for transitions between TPF components including chromosome, accessions and coordinates for generating a switch point (SP) file. The switch point file specifies the exact point of transition between two consecutive components in the TPF file. 
+This class stores information for transitions between TPF components including chromosome, accessions and coordinates for generating a switch point (SP) file. The switch point file specifies the exact point of transition between two consecutive components in the AGP file. 
 
 =head2 Methods
 
@@ -36,7 +36,11 @@ Gets the chromosome.
 
 =cut
 
-has 'chromosome' => ( isa => 'Str', is => 'rw', required => 1, clearer => 'clear_chromosome' );
+subtype 'SPChromosome', #only works for genomes with 12 chrs or less.
+  as 'Str',
+  where { $_ eq '1' || $_ eq '2' || $_ eq '3' || $_ eq '4' || $_ eq '5' || $_ eq '6' || $_ eq '7' || $_ eq '8' || $_ eq '9' || $_ eq '10' || $_ eq '11' || $_ eq '12' || $_ eq "Un" },#does NOT work. need to do -> if int check 1-12, if str check Un
+  message { "The string, $_, was not a valid chromosome number.  Valid values for Solanum lycopersicum are 1-12 and Un." };
+has 'chromosome' => ( isa => 'SPChromosome', is => 'rw', required => 1, clearer => 'clear_chromosome' );
 
 has 'accession_prefix' => ( isa => 'Str', is => 'rw', required => 1, clearer => 'clear_accession_prefix' );
 has 'accession_suffix' => ( isa => 'Str', is => 'rw', required => 1, clearer => 'clear_accession_suffix' );
@@ -45,16 +49,19 @@ subtype 'SPOrientationType',
   as 'Str',
   where { $_ eq "+" || $_ eq "-" || $_ eq "?" || $_ eq "0" || $_ eq "na"},
   message { "The string, $_, was not a valid orientation type.  Valid types are: + - ? 0 na" };
-
 has 'accession_prefix_orientation' => ( isa => 'SPOrientationType', is => 'rw', required => 1, clearer => 'clear_accession_prefix_orientation' );
 has 'accession_suffix_orientation' => ( isa => 'SPOrientationType', is => 'rw', required => 1, clearer => 'clear_accession_suffix_orientation' );
 
-has 'accession_prefix_last_base' => ( isa => 'Int', is => 'rw', required => 1, clearer => 'clear_accession_prefix_last_base' );
-has 'accession_suffix_first_base' => ( isa => 'Int', is => 'rw', required => 1, clearer => 'clear_accession_suffix_first_base' );
+subtype 'PositiveInt',
+	as 'Int',
+	where { $_ > 0 },
+	message { "The string, $_, was not a positive coordinate" };
+has 'accession_prefix_last_base' => ( isa => 'PositiveInt', is => 'rw', required => 1, clearer => 'clear_accession_prefix_last_base' );
+has 'accession_suffix_first_base' => ( isa => 'PositiveInt', is => 'rw', required => 1, clearer => 'clear_accession_suffix_first_base' );
 
 subtype 'SPComment',
   as 'Str',
-  where { scalar $_ >= 25 },
+  where { (length $_) >= 25 },
   message { "The string, $_, was shorter than the minimum length of 25 characters." };
 has 'comment' => ( isa => 'SPComment', is => 'rw', required => 1, clearer => 'clear_comment' );