lib/CXGN/Cview/LocusChr.pm

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