lib/CXGN/Cview/Map_overviews/ProjectStats.pm

   1
   2
   3 =head1 NAME
   4
   5 CXGN::Cview::Map_overviews::ProjectStats - a class to display the tomato genome sequence project status.
   6
   7 =head1 SYNOPSYS
   8
   9 see L<CXGN::Cview::Map_overviews>.
  10
  11 =head1 DESCRIPTION
  12
  13 This class implements the project status overview graph found on the SGN homepage and the /about/tomato_sequencing.pl page, where each chromosome is represented by a glyph that is filled to the fraction of the estimated number of BACs needed to complete the chromosome sequence.
  14
  15 =head1 AUTHOR(S)
  16
  17 Lukas Mueller (lam87@cornell.edu)
  18
  19 =head1 FUNCTIONS
  20
  21 This class implements the following functions:
  22
  23 =cut
  24
  25 use strict;
  26
  27 package CXGN::Cview::Map_overviews::ProjectStats;
  28
  29 use CXGN::Cview::Map_overviews;
  30 use CXGN::Cview::Map::SGN::ProjectStats;
  31 use CXGN::People::BACStatusLog;
  32 use List::Util;
  33
  34
  35 use base qw( CXGN::Cview::Map_overviews );
  36
  37 =head2 constructor new()
  38
  39   Synopsis:
  40   Arguments:
  41   Returns:
  42   Side effects:
  43   Description:
  44
  45 =cut
  46
  47 sub new {
  48     my $class = shift;
  49     my $force = shift;
  50
  51     my $self = $class->SUPER::new($force);
  52
  53     $self->set_horizontal_spacing(50);
  54     $self->set_image_width(586);
  55     $self->set_image_height(160);
  56     $self->set_chr_height(80);
  57
  58 #    print STDERR "Generating new map object...\n";
  59     $self->set_map(CXGN::Cview::Map::SGN::ProjectStats->new($self));
  60     return $self;
  61 }
  62
  63 =head2 function generate_image()
  64
  65   Synopsis:
  66   Arguments:
  67   Returns:
  68   Side effects:
  69   Description:
  70
  71 =cut
  72
  73 sub generate_image {
  74     my $self = shift;
  75     $self->render_map();
  76 }
  77
  78 =head2 function send_image()
  79
  80   Synopsis:
  81   Arguments:
  82   Returns:
  83   Side effects:
  84   Description:
  85
  86 =cut
  87
  88 sub send_image {
  89     my $self = shift;
  90     print "Content-Type: image/png\n\n";
  91     return $self->{map_image}->render_png();
  92 }
  93
  94 =head2 function render_map()
  95
  96   Synopsis:
  97   Arguments:
  98   Returns:
  99   Side effects:
 100   Description:
 101
 102 =cut
 103
 104 sub render_map {
 105     my $self = shift;
 106
 107     $self->get_cache()->set_key("project stats overview graph");
 108     $self->get_cache()->set_force(1);
 109     $self->get_cache()->set_expiration_time(40000);  # set expiration time of cache to half a day.
 110     $self->get_cache()->set_map_name("overview_map");
 111
 112     if ($self->get_cache()->is_valid()) {  return; }
 113
 114     my $bac_status_log=CXGN::People::BACStatusLog->new($self);
 115
 116 #    print STDERR "WIDTH=".$self->get_image_width()." HEIGHT ".$self->get_image_height()."\n";
 117     $self->{map_image}=CXGN::Cview::MapImage->new("", $self->get_image_width(), $self->get_image_height());
 118     my @c = ();
 119     my @c_len = $bac_status_log->get_chromosome_graph_lengths();
 120     my @bacs_to_complete = $bac_status_log->get_number_bacs_to_complete();
 121     my @c_percent_finished = $bac_status_log->get_chromosomes_percent_finished();
 122
 123     my @bacs_in_progress = $bac_status_log->get_number_bacs_in_progress();
 124     my @bacs_submitted = $bac_status_log->get_number_bacs_uploaded();
 125
 126     my @bacs_phase = $bac_status_log->get_number_bacs_in_phase(3);
 127
 128
 129     for my $i (1..12) {
 130         $c[$i]= CXGN::Cview::Chromosome::Glyph -> new(1, 100, $self->get_horizontal_spacing()*($i-1)+17, 25);
 131         my $m = CXGN::Cview::Marker->new($c[$i],0,0,0,0,0,0,$c_len[$i]);
 132         $m -> hide();
 133         $c[$i]->add_marker($m);
 134         $c[$i]->set_caption($i);
 135         $c[$i]->set_height($self->get_chr_height());
 136         $c[$i]->set_url("/cview/view_chromosome.pl?map_version_id=agp&show_offsets=1&show_ruler=1&chr_nr=$i");
 137
 138         my $percent_in_progress = $bacs_in_progress[$i]/$bacs_to_complete[$i]*100;
 139
 140         my $percent_finished = $c_percent_finished[$i];
 141
 142         my $percent_htgs3 = $bacs_phase[$i]/$bacs_to_complete[$i]*100;
 143
 144         my $percent_available = $bacs_submitted[$i]/$bacs_to_complete[$i]*100;
 145
 146         #$percent_submitted = $percent_submitted - $percent_htgs3;
 147
 148         my $percent_in_progress_base_level = List::Util::max($percent_finished, $percent_htgs3, $percent_available);
 149
 150         $percent_in_progress += $percent_in_progress_base_level;
 151
 152         #print STDERR "Chromosome $i $percent_htgs3, $percent_available, $percent_finished, $percent_in_progress\n";
 153
 154
 155         $c[$i]->set_fill_level(0, $percent_htgs3);
 156         $c[$i]->set_fill_level(1, $percent_available);
 157         $c[$i]->set_fill_level(2, $percent_finished);
 158         $c[$i]->set_fill_level(3, $percent_in_progress);
 159         $c[$i]->set_bac_count(0);
 160         $self->{map_image}->add_chromosome($c[$i]);
 161     }
 162     my $white = $self->{map_image}->get_image()->colorResolve(255,255,255);
 163     $self->{map_image}->get_image()->transparent($white);
 164
 165
 166
 167     $self->get_cache()->set_image_data( $self->{map_image}->render_png_string());
 168     $self->get_cache()->set_image_map_data ($self->{map_image}->get_image_map("overview_map") );
 169
 170 }
 171
 172 =head2 function create_mini_overview()
 173
 174   Synopsis:
 175   Arguments:    none
 176   Returns:      nothing
 177   Side effects: creates the mini overview png image that goes on the
 178                 homepage
 179   Description:
 180
 181 =cut
 182
 183 sub create_mini_overview {
 184     my $self = shift;
 185     $self->set_image_width(400);
 186     $self->set_image_height(100);
 187     $self->set_chr_height(50);
 188     $self->set_horizontal_spacing(30);
 189
 190     my $url = "/documents/tempfiles/frontpage/project_stats_overview.png";
 191     my $path = File::Spec->catfile($self->get_vhost()->get_conf("basepath"), $url);
 192
 193     $self->render_map();
 194     $self->get_file_png($path);
 195
 196 }
 197
 198
 199 =head2 DEPRECATED CLASS CXGN::Cview::Map_overviews::project_stats
 200
 201   Synopsis:
 202   Arguments:
 203   Returns:
 204   Side effects:
 205   Description:  This class is deprecated. It now inherits from
 206                 CXGN::Cview::Map_overviews::ProjectStats
 207                 Use CXGN::Cview::Map_overview::ProjectStats
 208                 directly.
 209
 210 =cut
 211
 212
 213
 214
 215 package CXGN::Cview::Map_overviews::project_stats;
 216
 217 use base qw | CXGN::Cview::Map_overviews::ProjectStats |;
 218
 219 sub new {
 220     my $class = shift;
 221     my $self = $class->SUPER::new(@_);
 222     return $self;
 223 }
 224
 225 return 1;