<commit_before>
use strict;

package CXGN::Cview::Map::SGN::ITAG;

use File::Spec;
use CXGN::ITAG::Release;
use CXGN::Cview::Chromosome::ITAG;
use CXGN::Cview::Map::Tools;
use CXGN::Genomic::Clone;
use CXGN::Genomic::BACMarkerAssoc;

use base qw | CXGN::Cview::Map | ;

sub new { 
    my $class = shift;
    my $dbh = shift;
    my $id = shift;
    my $args = shift;

    my $self = $class->SUPER::new($dbh);

    $self->set_abstract($args->{abstract} || "");
    $self->set_short_name($args->{short_name} || "ITAG map");
    $self->set_long_name($args->{long_name});
    

    $self->set_id($id);

    $self->set_chromosome_names( "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12");
    #print STDERR "ITAG map constructor...\n";

    #print STDERR "FILENAMES = ". (join " ", (map  {$_.":".$self->get_files()->{$_} } keys %{$self->get_files()}) ) ."\n";
    #print STDERR "Constructor: generating AGP chr ".$self->get_name()."\n";

    $self->set_chromosome_count(12);
    $self->set_units("MB");

    #print STDERR "Caching chromosome lengths...\n";
    my @ITAG_releases = CXGN::ITAG::Release->find();

    # if we can't find any ITAG releases, just return
    # otherwise the comparative viewer may crash...
    #
    if (! @ITAG_releases) { return $self; }
	
    $self->set_release_gff($ITAG_releases[0]->get_file_info('contig_gff3')->{file});
    print STDERR  "Working with the file ".($self->get_release_gff())."\n";

    # we need to cache the chromosome length information on the filesystem...
    $self->cache_chromosome_lengths();
    return $self;
}

our $SCALE=1_000_000;
our $INTER_CONTIG_DISTANCE=100_000;
<commit_msg>setting the temp_dir correctly M    ITAG.pm<commit_after>
use strict;

package CXGN::Cview::Map::SGN::ITAG;

use File::Spec;
use CXGN::ITAG::Release;
use CXGN::Cview::Chromosome::ITAG;
use CXGN::Cview::Map::Tools;
use CXGN::Genomic::Clone;
use CXGN::Genomic::BACMarkerAssoc;

use base qw | CXGN::Cview::Map | ;

sub new { 
    my $class = shift;
    my $dbh = shift;
    my $id = shift;
    my $args = shift;

    my $self = $class->SUPER::new($dbh);

    $self->set_abstract($args->{abstract} || "");
    $self->set_short_name($args->{short_name} || "ITAG map");
    $self->set_long_name($args->{long_name});
    $self->set_temp_dir($args->{temp_dir});

    $self->set_id($id);

    $self->set_chromosome_names( "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12");
    #print STDERR "ITAG map constructor...\n";

    #print STDERR "FILENAMES = ". (join " ", (map  {$_.":".$self->get_files()->{$_} } keys %{$self->get_files()}) ) ."\n";
    #print STDERR "Constructor: generating AGP chr ".$self->get_name()."\n";

    $self->set_chromosome_count(12);
    $self->set_units("MB");

    #print STDERR "Caching chromosome lengths...\n";
    my @ITAG_releases = CXGN::ITAG::Release->find();

    # if we can't find any ITAG releases, just return
    # otherwise the comparative viewer may crash...
    #
    if (! @ITAG_releases) { return $self; }
	
    $self->set_release_gff($ITAG_releases[0]->get_file_info('contig_gff3')->{file});
    print STDERR  "Working with the file ".($self->get_release_gff())."\n";

    # we need to cache the chromosome length information on the filesystem...
    $self->cache_chromosome_lengths();
    return $self;
}

our $SCALE=1_000_000;
our $INTER_CONTIG_DISTANCE=100_000;

{'fraction_non_alphanumeric': 0.2017256768818804, 'fraction_numerical': 0.019041951800059506, 'mean_word_length': 3.9441176470588237, 'pattern_counts': {'":': 2, '<': 3, '<?xml version=': 0, '>': 47, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2110654', 'n_tokens_mistral': 1360, 'n_tokens_neox': 1249, 'n_words': 272}