NAME
Bio::DOOP::Graphics::Feature - Graphical representation of the features
VERSION
Version 0.18
SYNOPSIS
DESCRIPTION
This object represents a picture that contains all the sequences and sequence features of a subset. The module is fast enough to use it in your CGI scripts. You can also use it to visualize the subset.
AUTHOR
Tibor Nagy, Godollo, Hungary
METHODS
create
Creates a new picture. Later you can add your own graphical elements to it.
Arguments: Bio::DOOP::DBSQL object and subset primary id.
Return type: Bio::DOOP::Graphics::Feature object
$picture = Bio::DOOP::Graphics::Feature->create($db,"1234");add_color
Add an RGB color to the specified element.
The available elements are the following : background, label, strip, utr, motif, tss, frame, fuzzres.
$image->add_color("background",200,200,200);
$image->set_colors;set_colors
Sets all colors. Allocate colors previously with add_color. Use this method only ONCE after you set all the colors. If you use it more than once, the results will be strange.
add_scale
Draws the scale on the picture.
add_bck_lines
Draws scale lines through the whole image background.
add_seq
Draws a specified sequence on the picture. This is internal code, do not use it directly.
add_all_seq
Draws all sequences of the subset. The first one is the reference species.
get_png
Returns the png image. Use this when you finish the work and would like to see the result.
open IMAGE,">picture.png";
binmode IMAGE;
print IMAGE $image->get_png;
close IMAGE;get_image
Returns the drawn image pointer. Useful for adding your own GD methods for unique picture manipulation.
get_map
Returns a hash of arrays of hash of arrays reference that contains the image 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}}){
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 somewhat difficult, but if you are familiar with references and nested data structures, you will understand it.
get_motif_map
Returns only the arrayref of motif hashes.
get_motif_id_by_coord
With this, you can get a motif id, if you specify the coordinates of a pixel.
$motif_id = $image->get_motif_id_by_coord(100,200);draw_motif_frame
This method draws a frame around a given motif.
Arguments: motif primary id
Return type: 0 if success, -1 if the given motif id is not in the picture.
$image->draw_motif_frame($motifid);draw_fuzz_result
You can draw the fuzznuc result on the picture with this method.
Arguments : sequence primary id, start position, end position
To set drawing color, you can use the setcolor("fuzzres",$r,$g,$b) method. The method shows the orientation. The arrow always points to the start position.
Return value : 0 if success, -1 if the given sequence id can't be found.
$image->draw_fuzz_result(357,20,70);