From 12e8a2c705f610cea939036cd14178daa7ec8f01 Mon Sep 17 00:00:00 2001
From: Surya Saha <ss2489@cornell.edu>
Date: Wed, 13 May 2015 14:29:59 -0400
Subject: [PATCH] Cleaned up class variable names, fixed type checks and
 function to get formatted trim point file. Re #45

---
 lib/Bio/GenomeUpdate/TP.pm        | 19 ++++++++-----------
 lib/Bio/GenomeUpdate/TP/TPLine.pm | 12 ++++++++----
 2 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/lib/Bio/GenomeUpdate/TP.pm b/lib/Bio/GenomeUpdate/TP.pm
index afed7ba..9a89d64 100644
--- a/lib/Bio/GenomeUpdate/TP.pm
+++ b/lib/Bio/GenomeUpdate/TP.pm
@@ -33,12 +33,12 @@ Gets the taxonomy identifier for the SP file.
 
 =cut
 
-has 'tp_taxid' => (
+has 'taxid' => (
 	isa     => 'Str',
 	is      => 'rw',
 	default => '4081',
 	required => 1,
-	clearer => 'clear_tp_taxid'
+	clearer => 'clear_taxid'
 );
 
 =item C<set_assembly_group ( $organism_string )>
@@ -80,7 +80,7 @@ Gets the TPF type.
 subtype 'TPTPFType', as 'Str', where { $_ eq "chromosome" || $_ eq "contig" },
   message { "The string, $_, was not a valid TPF type. See http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/overlap/ specification link" };
 
-has 'tp_tpf_type' => ( isa => 'TPTPFType', is => 'rw', default => 'chromosome', required => 1, clearer => 'clear_chromosome' );
+has 'tpf_type' => ( isa => 'TPTPFType', is => 'rw', default => 'chromosome', required => 1, clearer => 'clear_tpf_type' );
 
 subtype 'TPLine',
   as 'Bio::GenomeUpdate::TP::TPLine',
@@ -145,17 +145,14 @@ sub get_formatted_tp {
 		%lines = %{ $self->get_tp_lines() };
 		my @sorted_line_numbers = sort { $a <=> $b } keys %lines;
 		foreach my $line_key (@sorted_line_numbers) {
-			$out_str .= $self->get_tp_taxid() . "\t";
+			$out_str .= $self->get_taxid() . "\t";
 			$out_str .= $self->get_assembly_group() . "\t";
 			$out_str .= $self->get_assembly_unit() . "\t";
 			$out_str .= $lines{$line_key}->get_chromosome() . "\t";
-			$out_str .= $self->get_tp_tpf_type() . "\t";
-			$out_str .= $lines{$line_key}->get_accession_prefix() . "\t";
-			$out_str .= $lines{$line_key}->get_accession_suffix() . "\t";
-			$out_str .= $lines{$line_key}->get_accession_prefix_orientation() . "\t";
-			$out_str .= $lines{$line_key}->get_accession_suffix_orientation() . "\t";
-			$out_str .= $lines{$line_key}->get_accession_prefix_last_base() . "\t";
-			$out_str .= $lines{$line_key}->get_accession_suffix_first_base() . "\t";
+			$out_str .= $self->get_tpf_type() . "\t";
+			$out_str .= $lines{$line_key}->get_accession() . "\t";
+			$out_str .= $lines{$line_key}->get_accession_prefix_first_or_last_base() . "\t";
+			$out_str .= $lines{$line_key}->get_trim_from_end() . "\t";
 			$out_str .= $lines{$line_key}->get_comment() . "\n";
 		}
 	}
diff --git a/lib/Bio/GenomeUpdate/TP/TPLine.pm b/lib/Bio/GenomeUpdate/TP/TPLine.pm
index 61f7781..4dad481 100644
--- a/lib/Bio/GenomeUpdate/TP/TPLine.pm
+++ b/lib/Bio/GenomeUpdate/TP/TPLine.pm
@@ -6,8 +6,6 @@ use Moose;
 use MooseX::FollowPBP;
 use Moose::Util::TypeConstraints;
 
-use Data::Dumper;#for debugging
-
 =head1 NAME
 
     TP - Trim point lines for NCBI GRC pipeline with instructions used to generate a Accessioned Golden Path (AGP) file
@@ -38,7 +36,7 @@ Gets the chromosome.
 
 subtype 'TPChromosome',
   as 'Str',
-  where { ( $_ >= 1 && $_ <=12 ) || ( $_ eq "Un" )},#does NOT work. need to do -> if int check 1-12, if str check Un
+  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" },
   message { "The string, $_, was not a valid chromosome number.  Valid values for Solanum lycopersicum are 1-12 and Un." };
 has 'chromosome' => ( isa => 'TPChromosome', is => 'rw', required => 1, clearer => 'clear_chromosome' );
 
@@ -50,9 +48,15 @@ subtype 'PositiveInt',
 	message { "The string, $_, was not a positive coordinate" };
 has 'accession_prefix_first_or_last_base' => ( isa => 'PositiveInt', is => 'rw', required => 1, clearer => 'clear_accession_prefix_first_or_last_base' );
 
+subtype 'TPTrimDirection',
+  as 'Str',
+  where { ( $_ eq 'L' ) || ( $_ eq "H" )},
+  message { "The string, $_, was not a valid trim direction.  Valid values values are L and H where L: trim bases with values lt accession_prefix_first_or_last_base; H: trim bases with values gt accession_prefix_first_or_last_base." };
+has 'trim_from_end' => ( isa => 'TPTrimDirection', is => 'rw', required => 1, clearer => 'clear_trim_from_end' );
+
 subtype 'TPComment',
   as 'Str',
-  where { (scalar $_) >= 25 },#does not work!!
+  where { (length $_) >= 25 },
   message { "The string, $_, was shorter than the minimum length of 25 characters." };
 has 'comment' => ( isa => 'TPComment', is => 'rw', required => 1, clearer => 'clear_comment' );