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);

cpanm Bio::DOOP::DOOP

perl -MCPAN -e shell
install Bio::DOOP::DOOP