lib/CXGN/Cview/LocusChr.pm

   1 package CXGN::Cview::LocusChr;
   2 use strict;
   3 use warnings;
   4
   5 use CXGN::Cview;
   6 use CXGN::Cview::Chromosome;
   7 use CXGN::Cview::Cview_data_adapter;
   8 use CXGN::Configuration;
   9 use CXGN::Cview::MapImage;
  10
  11
  12 use base qw/ CXGN::Cview::MapImage /;
  13
  14 =head2 new
  15
  16  Usage:
  17  Desc:
  18  Ret:
  19  Args:
  20  Side Effects:
  21  Example:
  22
  23 =cut
  24
  25 sub new {
  26     my $class=shift;
  27     my $name = shift;
  28     my $width = shift;
  29     my $height = shift;
  30     my $self= $class->SUPER::new($name, $width, $height);
  31     my $dbh=shift;
  32     my $lg_name= shift;
  33     my $map = shift;
  34     my $marker_name= shift;
  35     $self->set_dbh($dbh);
  36     $self->set_lg_name($lg_name);
  37     $self->set_map($map);
  38     $self->set_marker_name($marker_name);
  39     return $self;
  40 }
  41
  42
  43 =head2 get_image_filename
  44
  45  Usage:
  46  Desc:
  47  Ret:
  48  Args:
  49  Side Effects:
  50  Example:
  51
  52 =cut
  53
  54 sub get_image_filename {
  55     my $self=shift;
  56
  57     my $filename = time().".$$.png";
  58     my $vhost_conf=CXGN::CView::Config->new();
  59     my $image_path = $vhost_conf->get_conf('basepath').$vhost_conf->get_conf('tempfiles_subdir')."/cview/$filename";
  60     my $image_url = $vhost_conf->get_conf('tempfiles_subdir')."/cview/$filename";
  61
  62     my $chromosome= CXGN::Cview::Chromosome->new($self->get_lg_name(), 100,50, 25 );
  63     CXGN::Cview::Cview_data_adapter::fetch_chromosome($self->get_dbh(), $chromosome, $self->get_map(), $self->get_lg_name());
  64     $chromosome->set_caption($self->get_lg_name);
  65     $chromosome->set_width(12);
  66     my $map_id= $self->get_map()->map_id();
  67     my $marker_name= $self->get_marker_name();
  68     my $lg_name=$self->get_lg_name();
  69     $chromosome->set_url("/cview/view_chromosome.pl?map_id=$map_id&amp;chr_nr=$lg_name&amp;hilite=$marker_name");
  70
  71     my @markers= $chromosome->get_markers();
  72
  73     foreach my $m(@markers) {
  74         if ($m->get_name() eq $self->get_marker_name()) {
  75             $m->hilite();
  76             $m->set_label_spacer(20);
  77         }
  78         else { $m->hide_label(); }
  79         $m->set_color(150, 80, 50);
  80     }
  81
  82     $self->add_chromosome($chromosome);
  83
  84     $self -> render_png_file($image_path);
  85     return ($image_path, $image_url);
  86
  87 }
  88
  89 =head2 get_dbh
  90
  91  Usage:
  92  Desc:
  93  Ret:
  94  Args:
  95  Side Effects:
  96  Example:
  97
  98 =cut
  99
 100 sub get_dbh {
 101   my $self=shift;
 102   return $self->{dbh};
 103
 104 }
 105
 106 =head2 set_dbh
 107
 108  Usage:
 109  Desc:
 110  Ret:
 111  Args:
 112  Side Effects:
 113  Example:
 114
 115 =cut
 116
 117 sub set_dbh {
 118   my $self=shift;
 119   $self->{dbh}=shift;
 120 }
 121
 122
 123
 124 =head2 get_lg_name
 125
 126  Usage:
 127  Desc:
 128  Ret:
 129  Args:
 130  Side Effects:
 131  Example:
 132
 133 =cut
 134
 135 sub get_lg_name {
 136   my $self=shift;
 137   return $self->{lg_name};
 138
 139 }
 140
 141 =head2 set_lg_name
 142
 143  Usage:
 144  Desc:
 145  Ret:
 146  Args:
 147  Side Effects:
 148  Example:
 149
 150 =cut
 151
 152 sub set_lg_name {
 153   my $self=shift;
 154   $self->{lg_name}=shift;
 155 }
 156
 157 =head2 get_map
 158
 159  Usage:
 160  Desc:
 161  Ret:
 162  Args:
 163  Side Effects:
 164  Example:
 165
 166 =cut
 167
 168 sub get_map {
 169   my $self=shift;
 170   return $self->{map};
 171
 172 }
 173
 174 =head2 set_map
 175
 176  Usage:
 177  Desc:
 178  Ret:
 179  Args:
 180  Side Effects:
 181  Example:
 182
 183 =cut
 184
 185 sub set_map {
 186   my $self=shift;
 187   $self->{map}=shift;
 188 }
 189
 190
 191 =head2 get_marker_name
 192
 193  Usage:
 194  Desc:
 195  Ret:
 196  Args:
 197  Side Effects:
 198  Example:
 199
 200 =cut
 201
 202 sub get_marker_name {
 203   my $self=shift;
 204   return $self->{marker_name};
 205
 206 }
 207
 208 =head2 set_marker_name
 209
 210  Usage:
 211  Desc:
 212  Ret:
 213  Args:
 214  Side Effects:
 215  Example:
 216
 217 =cut
 218
 219 sub set_marker_name {
 220   my $self=shift;
 221   $self->{marker_name}=shift;
 222 }
 223
 224
 225
 226 return 1;
 227
 228