Tibor Nagy > Bio-DOOP-DOOP-1.02 > Bio::DOOP::Graphics::Feature

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Module Version: 0.17   Source   Latest Release: Bio-DOOP-DOOP-1.04

NAME ^

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

SYNOPSIS ^

VERSION ^

Version 0.17

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 a new picture. Later you can add your own graphical 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 element.

  $image->add_color("background",200,200,200);
  $image->set_colors;

  The available 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 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, so do not use it directly.

add_all_seq

  Draws all sequences of 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 unique 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

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

  Maybe this is the most useful method. You can get a motif id, if you specify the coordinates of a pixel.

  Return type :

  string

draw_motif_frame

  $image->draw_motif_frame($motifid);

  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.

draw_fuzz_result

  $image->draw_fuzz_result(357,20,70);

  You can draw a fuzznuc result 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.
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