lib/CXGN/ChrMarkerImage.pm

   1 =head1 NAME
   2
   3 CXGN::Cview::ChrMarkerImage - a class for drawing small  chromosome image wit a specific marker hilited.
   4
   5 =head1 DESCRIPTION
   6
   7 Inherits from L<CXGN::Cview::MapImage>.
   8
   9 =head1 AUTHOR(S)
  10
  11 Lukas Mueller (lam87@cornell.edu)
  12 Naama Menda (nm249@cornell.edu)
  13
  14 =head1 FUNCTIONS
  15
  16
  17 =cut
  18
  19 1;
  20
  21 use strict;
  22
  23 use CXGN::Cview;
  24 use CXGN::Cview::Chromosome;
  25 #use CXGN::Cview::Cview_data_adapter;
  26 use CXGN::Cview::MapImage;
  27 use File::Temp qw / tempfile /;
  28 use File::Basename qw / basename /;
  29
  30 package CXGN::Cview::ChrMarkerImage;
  31
  32 use base qw/ CXGN::Cview::MapImage /;
  33
  34 =head2 new
  35
  36  Usage: my $chromosome= CXGN::Cview::ChrmarkerImage->new("map name", width,height,$dbh, $lg_name, $map, $marker_name);
  37  Desc:
  38  Ret:
  39  Args: name of a map, width and height of the image in pixles, linkage group name, map object (my $map=CXGN::Map->new($dbh,$map_version_id);), $marker_name.
  40  Side Effects:
  41  Example:
  42
  43 =cut
  44
  45 sub new {
  46     my $class=shift;
  47     my $name = shift;
  48     my $width = shift;
  49     my $height = shift;
  50     my $self= $class->SUPER::new($name, $width, $height);
  51     my $dbh=shift;
  52     my $lg_name= shift;
  53     my $map = shift;
  54     my $marker_name= shift;
  55     $self->set_dbh($dbh);
  56     $self->set_lg_name($lg_name);
  57     $self->set_map($map);
  58     $self->set_marker_name($marker_name);
  59
  60     my $chromosome = $map->get_chromosome($lg_name);
  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_horizontal_offset(50);
  64     $chromosome->set_vertical_offset(25);
  65     $chromosome->set_height(100);
  66     $chromosome->set_caption($self->get_lg_name);
  67     $chromosome->set_width(12);
  68     my $map_version_id= $self->get_map()->get_id();
  69     my $marker_name= $self->get_marker_name();
  70     my $lg_name=$self->get_lg_name();
  71     $chromosome->set_url("/cview/view_chromosome.pl?map_version_id=$map_version_id&amp;chr_nr=$lg_name&amp;hilite=$marker_name");
  72
  73     my @markers= $chromosome->get_markers();
  74
  75     foreach my $m(@markers) {
  76         if ($m->get_name() eq $self->get_marker_name()) {
  77             $m->hilite();
  78             $m->set_label_spacer(20);
  79         }
  80         else { $m->hide_label(); }
  81         $m->set_color(150, 80, 50);
  82     }
  83
  84     $self->add_chromosome($chromosome);
  85
  86     return $self;
  87 }
  88
  89
  90 =head2 get_image_filename
  91
  92  Usage: my ($image_path, $image_url)=$chromosome->get_image_filename();
  93  Desc: returns a tmp .png file of the chromosome image object
  94  Ret: $image_path, $image_url
  95  Args:
  96  Side Effects:
  97  Example:
  98
  99 =cut
 100
 101 sub get_image_filename {
 102     my $self=shift;
 103     my $vhost_conf=CXGN::VHost->new();
 104     my $dir = $vhost_conf->get_conf('basepath').$vhost_conf->get_conf('tempfiles_subdir')."/cview/";
 105
 106     my $template = 'tempXXXX'; #not needed. The function tempfile seems to generate a default TEMPLATE 'XXXXXXXXXX$suffix'
 107     my $suffix = '.png';
 108     my ($fh, $image_path) = File::Temp::tempfile( DIR => $dir,
 109                                                   SUFFIX => $suffix
 110                                                   );
 111
 112     #my $filename = time().".$$.png";
 113
 114     my $filename = File::Basename::basename($image_path);
 115
 116     print STDERR "IMAGE PATH: $image_path\n";
 117    my $image_url = $vhost_conf->get_conf('tempfiles_subdir')."/cview/$filename";
 118
 119     $self -> render_png_file($image_path);
 120     return ($image_path, $image_url);
 121
 122 }
 123
 124 =head2 get_dbh
 125
 126  Usage:
 127  Desc:
 128  Ret:
 129  Args:
 130  Side Effects:
 131  Example:
 132
 133 =cut
 134
 135 sub get_dbh {
 136   my $self=shift;
 137   return $self->{dbh};
 138
 139 }
 140
 141 =head2 set_dbh
 142
 143  Usage:
 144  Desc:
 145  Ret:
 146  Args:
 147  Side Effects:
 148  Example:
 149
 150 =cut
 151
 152 sub set_dbh {
 153   my $self=shift;
 154   $self->{dbh}=shift;
 155 }
 156
 157
 158
 159 =head2 get_lg_name
 160
 161  Usage:
 162  Desc:
 163  Ret:
 164  Args:
 165  Side Effects:
 166  Example:
 167
 168 =cut
 169
 170 sub get_lg_name {
 171   my $self=shift;
 172   return $self->{lg_name};
 173
 174 }
 175
 176 =head2 set_lg_name
 177
 178  Usage:
 179  Desc:
 180  Ret:
 181  Args:
 182  Side Effects:
 183  Example:
 184
 185 =cut
 186
 187 sub set_lg_name {
 188   my $self=shift;
 189   $self->{lg_name}=shift;
 190 }
 191
 192 =head2 get_map
 193
 194  Usage:
 195  Desc:
 196  Ret:
 197  Args:
 198  Side Effects:
 199  Example:
 200
 201 =cut
 202
 203 sub get_map {
 204   my $self=shift;
 205   return $self->{map};
 206
 207 }
 208
 209 =head2 set_map
 210
 211  Usage:
 212  Desc:
 213  Ret:
 214  Args:
 215  Side Effects:
 216  Example:
 217
 218 =cut
 219
 220 sub set_map {
 221   my $self=shift;
 222   $self->{map}=shift;
 223 }
 224
 225
 226 =head2 get_marker_name
 227
 228  Usage:
 229  Desc:
 230  Ret:
 231  Args:
 232  Side Effects:
 233  Example:
 234
 235 =cut
 236
 237 sub get_marker_name {
 238   my $self=shift;
 239   return $self->{marker_name};
 240
 241 }
 242
 243 =head2 set_marker_name
 244
 245  Usage:
 246  Desc:
 247  Ret:
 248  Args:
 249  Side Effects:
 250  Example:
 251
 252 =cut
 253
 254 sub set_marker_name {
 255   my $self=shift;
 256   $self->{marker_name}=shift;
 257 }
 258
 259
 260
 261 return 1;
 262
 263