NAME
Bio::DOOP::Graphics::Feature - graphical representation of the features
SYNOPSIS
VERSION
Version 0.03
DESCRIPTION
This object is represent a picture that is contain all the sequence features in the subset.
This module is enough quick to use it in your CGI scripts.
AUTHOR
Tibor Nagy, Godollo, Hungary
METHODS
create
Create new picture. Later you can add your own graphics element to this.
add_color
Add an RGB color to the specified drawing element.
$image->add_color("background",200,200,200);
$image->set_colors;
The available drawing elements are the following: background, label, strip, utr, motif, tss
set_colors
Set all the usage colors. Preveously allocate colors with add_color. Use this method only ONCE after you set
all the colors.
If you use it more than one, the results will be strange.
add_scale
Add scale to the picture
add_bck_lines
Add scale lines through the whole image background
add_seq
Add a specified seq to the picture. This is an internal code, so do not use it directly
get_png
Return the png image. Use this when you finish the work and would like to see the results.
get_image
Return the drawed image pointer. Useful for add your own GD methods for uniq picture manipulating.
get_map
Return a hash of arrays of hash of arrays reference that is contain the map information.
Here is a real world example of how to handle this method:
use Bio::DOOP::DOOP;
$db = Bio::DOOP::DBSQL->connect($user,$passwd,"doop-plant-1_5","localhost");
$cluster = Bio::DOOP::Cluster->new($db,'81001110','500');
$image = Bio::DOOP::Graphics::Feature->create($db,$cluster);
for $motif (@{$image->get_map->{motif}}){ # You can use
for $motif_id (keys %{$motif}){
@coords = @{$$motif{$motif_id}};
# Print out the motif primary id and the four coordinates in the picture
# id x1 y1 x2 y2
print "$motif_id $coords[0] $coords[1] $coords[2] $coords[3]\n";
}
}
It is a little bit difficult, but if you familiar with references and hash of array, you
will be understand.
get_motif_map
Return only the arrayref of motif hashes
get_motif_id_by_coord
Maybe this is the most useful method. You can get a motif id, if you specify a coordinate of a point