/ 
Bio-DOOP-DOOP-0.26
River stage zero No dependents
/ Bio::DOOP::Graphics::Feature

NAME

Bio::DOOP::Graphics::Feature - graphical representation of the features.

SYNOPSIS

VERSION

Version 0.15

DESCRIPTION

This object represents a picture that contains all the sequence features of a subset.
The module is quick enough to use it in your CGI scripts. You can also use it to visualize
the subset.

AUTHOR

Tibor Nagy, Godollo, Hungary

METHODS

create

$pic = Bio::DOOP::Graphics::Feature->create($db,"1234");

Create new picture. Later you can add your own graphics elements to it.
Arguments: 
1. Bio::DOOP::DBSQL object
2. Subset primary id.
Return type: Bio::DOOP::Graphics::Feature object

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, frame, fuzzres.

set_colors

Set all the 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, results will be strange.

add_scale

Draws 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, so do not use it directly.

add_all_seq

Draws all sequences from the subset. The first one is the reference species.

get_png

open IMAGE,">picture.png";
binmode IMAGE;
print IMAGE $image->get_png;
close IMAGE;

Returns the png image. Use this when you finish the work and would like to see the result.

get_image

Returns the drawn image pointer. Useful for adding your own GD methods for uniq picture manipulation.

get_map

Returns a hash of arrays of hash of arrays reference that contains 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}}){
  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 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

$motifi = $image->get_motif_id_by_coord(100,200);

Maybe this is the most useful method. You can get a motif id, if you specify a coordinate of a point.
Return type: string

draw_motif_frame

$image->draw_motif_frame($motifid);

This method draw a frame around the given motif.
Return type: 0 in success, -1 if the given motif id is not in the picture
Arguments: motifid: the motif primary id.

draw_fuzz_result

You can draw a fuzznuc result with this method. The arguments are the following:
Sequence DB id, the start position, end posiion.
To set the drawing color, you can use the setcolor("fuzzres",$r,$g,$b) method.
Return value: 0 if successful or -1 if the given seq id can not found.
$image->draw_fuzz_result(357,20,70);