Init switch point line module for #26. Recording Taxid, AssmGrp, Assm…

…Unit, TPFType in SP.pm for now.

lib/Bio/GenomeUpdate/SP/SPLine.pm

@@ -0,0 +1,77 @@
+package  Bio::GenomeUpdate::SP::SPLine;
+use strict;
+use warnings;
+
+use Moose;
+use MooseX::FollowPBP;
+use Moose::Util::TypeConstraints;
+
+use Data::Dumper;#for debugging
+
+=head1 NAME
+
+    SP - Switch point lines for NCBI GRC pipeline with instructions used to generate a Accessioned Golden Path (AGP) file
+
+=head1 SYNOPSIS
+
+    my $variable = SPLine->new();
+
+=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. 
+
+=head2 Methods
+
+=over 
+
+=cut
+
+=item C<set_chromosome ( $chromosome )>
+
+Sets the chromosome. Valid values for Solanum lycopersicum are 1-12 and Un (required).
+
+=item C<get_chromosome >
+
+Gets the chromosome.
+
+=cut
+
+has 'chromosome' => ( isa => 'Str', 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' );
+
+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 'SPComment',
+  as 'Str',
+  where { scalar $_ >= 25 },
+  message { "The string, $_, was shorter than the minimum length of 25 characters." };
+has 'comment' => ( isa => 'SPComment', is => 'rw', required => 1, clearer => 'clear_comment' );
+
+###
+1;    #do not remove
+###
+
+=pod
+
+=back
+
+=head1 LICENSE
+
+Same as Perl.
+
+=head1 AUTHORS
+
+  Surya Saha        <[email protected]>
+
+=cut