Bio::Graphics::FeatureFile 1.4

Bio::Graphics::FeatureFile is a set of Bio::Graphics features, stored in a file.

SYNOPSIS

use Bio::Graphics::FeatureFile;
my $data = Bio::Graphics::FeatureFile->new(-file => features.txt);


# create a new panel and render contents of the file onto it
my $panel = $data->new_panel;
my $tracks_rendered = $data->render($panel);

# or do it all in one step
my ($tracks_rendered,$panel) = $data->render;

# for more control, render tracks individually
my @feature_types = $data->types;
for my $type (@feature_types) {
my $features = $data->features($type);
my %options = $data->style($type);
$panel->add_track($features,%options); # assuming we have a Bio::Graphics::Panel
}

# get individual settings
my $est_fg_color = $data->setting(EST => fgcolor);

# or create the FeatureFile by hand

# add a type
$data->add_type(EST => {fgcolor=>blue,height=>12});

# add a feature
my $feature = Bio::Graphics::Feature->new(
# params
); # or some other SeqI
$data->add_feature($feature=>EST);

The Bio::Graphics::FeatureFile module reads and parses files that describe sequence features and their renderings. It accepts both GFF format and a more human-friendly file format described below. Once a FeatureFile object has been initialized, you can interrogate it for its consistuent features and their settings, or render the entire file onto a Bio::Graphics::Panel.

This moduel is a precursor of Jason Stajichs Bio::Annotation::Collection class, and fulfills a similar function of storing a collection of sequence features. However, it also stores rendering information about the features, and does not currently follow the CollectionI interface.