lib/SGN/Feature/GBrowse/DataSource.pm

   1 package SGN::Feature::GBrowse::DataSource;
   2 use Moose;
   3 use namespace::autoclean;
   4 use Carp;
   5 use MooseX::Types::Path::Class;
   6 use URI;
   7 use URI::Escape;
   8 use URI::QueryParam;
   9
  10 use Bio::Graphics::FeatureFile;
  11
  12 has 'name' => ( documentation => <<'',
  13 name of the data source
  14
  15     is  => 'ro',
  16     isa => 'Str',
  17     required => 1,
  18   );
  19
  20 has 'description' => ( documentation => <<'',
  21 short description of this data source - one line
  22
  23     is => 'ro',
  24     isa => 'Str',
  25     required => 1,
  26   );
  27
  28 has 'extended_description' => ( documentation => <<'',
  29 fuller description of this data source, 1-2 sentences
  30
  31     is => 'ro',
  32     isa => 'Maybe[Str]',
  33   );
  34
  35 has 'organism' => ( documentation => <<'',
  36 string name of the organism(s) the *reference sequences* for this set
  37 are from.  Usually species name.
  38
  39     is => 'ro',
  40     isa => 'Maybe[Str]',
  41   );
  42
  43 has 'gbrowse' => ( documentation => <<'',
  44 GBrowse Feature object this data source belongs to
  45
  46     is => 'ro',
  47     required => 1,
  48     weak_ref => 1,
  49   );
  50
  51 has 'path' => ( documentation => <<'',
  52 absolute path to the data source's config file
  53
  54     is  => 'ro',
  55     isa => 'Path::Class::File',
  56     required => 1,
  57    );
  58
  59 has 'config' => ( documentation => <<'',
  60 the parsed config of this data source, a Bio::Graphics::FeatureFile
  61
  62     is  => 'ro',
  63     isa => 'Bio::Graphics::FeatureFile',
  64     lazy_build => 1,
  65    ); sub _build_config {
  66        Bio::Graphics::FeatureFile->new(
  67 #           -file => shift->path->stringify,
  68 #           -safe => 1,
  69           );
  70    }
  71
  72 has '_databases' => (
  73     is => 'ro',
  74     isa => 'HashRef',
  75     traits => ['Hash'],
  76     lazy_build => 1,
  77     handles => {
  78         databases => 'values',
  79         database  => 'get',
  80     },
  81    ); sub _build__databases {
  82        die 'database parsing not implemented for gbrowse 1.x';
  83    }
  84
  85
  86 sub view_url {
  87     shift->_url( 'gbrowse', @_ );
  88 }
  89
  90 sub image_url {
  91     my ( $self, $q ) = @_;
  92     $q ||= {};
  93     $q->{width}    ||= 600;
  94     $q->{keystyle} ||= 'between',
  95     $q->{grid}     ||= 'on',
  96     return $self->_url( 'gbrowse_img', $q );
  97 }
  98
  99 sub _url {
 100     my ( $self, $script, $query ) = @_;
 101     my $url = $self->gbrowse->cgi_url->clone;
 102     $url->path( join '', map "$_/", $url->path, $script, $self->name );
 103     $url->query_form_hash( $query ) if $query;
 104     return $url;
 105 }
 106
 107
 108
 109 __PACKAGE__->meta->make_immutable;
 110 1;