lib/CXGN/Cview/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 use strict;
  20
  21 use CXGN::Cview;
  22 use CXGN::Cview::Chromosome;
  23 #use CXGN::Cview::Cview_data_adapter;
  24 use CXGN::Cview::MapImage;
  25 #use CXGN::VHost;
  26 use File::Temp qw / tempfile /;
  27 use File::Basename qw / basename /;
  28 use File::Spec;
  29
  30 package CXGN::Cview::ChrMarkerImage;
  31
  32 use base "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
  51     my $self= $class->SUPER::new($name, $width, $height);
  52
  53     my $dbh=shift;
  54     my $lg_name= shift;
  55     my $map = shift;
  56     my $marker_name= shift;
  57     my $basedir = shift;
  58     my $tempdir = shift;
  59
  60     $self->set_dbh($dbh);
  61     $self->set_lg_name($lg_name);
  62     $self->set_map($map);
  63     $self->set_marker_name($marker_name);
  64     $self->{basedir} = $basedir;
  65     $self->{tempdir} = $tempdir;
  66
  67     my $chromosome = $map->get_chromosome($lg_name);
  68
  69     $chromosome->set_horizontal_offset(50);
  70     $chromosome->set_vertical_offset(25);
  71     $chromosome->set_height(100);
  72     $chromosome->set_caption($self->get_lg_name);
  73     $chromosome->set_width(12);
  74     my $map_version_id= $self->get_map()->get_id();
  75     my $marker_name= $self->get_marker_name();
  76     my $lg_name=$self->get_lg_name();
  77     $chromosome->set_url("/cview/view_chromosome.pl?map_version_id=$map_version_id&amp;chr_nr=$lg_name&amp;hilite=$marker_name");
  78
  79     my @markers= $chromosome->get_markers();
  80
  81     foreach my $m(@markers) {
  82         if ($m->get_name() eq $self->get_marker_name()) {
  83             $m->hilite();
  84             $m->set_label_spacer(20);
  85         }
  86         else { $m->hide_label(); }
  87         $m->set_color(150, 80, 50);
  88     }
  89
  90     $self->add_chromosome($chromosome);
  91
  92     return $self;
  93 }
  94
  95
  96 =head2 get_image_filename
  97
  98  Usage: my ($image_path, $image_url)=$chromosome->get_image_filename();
  99  Desc: returns a tmp .png file of the chromosome image object
 100  Ret: $image_path, $image_url
 101  Args:
 102  Side Effects:
 103  Example:
 104
 105 =cut
 106
 107 sub get_image_filename {
 108     my $self=shift;
 109
 110     my $dir = File::Spec->catfile($self->{basedir}, $self->{tempdir});
 111     my $template = 'tempXXXX'; #not needed. The function tempfile seems to generate a default TEMPLATE 'XXXXXXXXXX$suffix'
 112     my $suffix = '.png';
 113     my ($fh, $image_path) = File::Temp::tempfile( DIR => $dir,
 114                                                   SUFFIX => $suffix
 115                                                   );
 116
 117     #my $filename = time().".$$.png";
 118
 119     my $filename = File::Basename::basename($image_path);
 120
 121     #print STDERR "IMAGE PATH: $image_path\n";
 122     my $image_url = File::Spec->catfile($self->{tempdir}, $filename);
 123
 124     $self -> render_png_file($image_path);
 125     return ($image_path, $image_url);
 126
 127 }
 128
 129 =head2 get_dbh
 130
 131  Usage:
 132  Desc:
 133  Ret:
 134  Args:
 135  Side Effects:
 136  Example:
 137
 138 =cut
 139
 140 sub get_dbh {
 141   my $self=shift;
 142   return $self->{dbh};
 143
 144 }
 145
 146 =head2 set_dbh
 147
 148  Usage:
 149  Desc:
 150  Ret:
 151  Args:
 152  Side Effects:
 153  Example:
 154
 155 =cut
 156
 157 sub set_dbh {
 158   my $self=shift;
 159   $self->{dbh}=shift;
 160 }
 161
 162
 163
 164 =head2 get_lg_name
 165
 166  Usage:
 167  Desc:
 168  Ret:
 169  Args:
 170  Side Effects:
 171  Example:
 172
 173 =cut
 174
 175 sub get_lg_name {
 176   my $self=shift;
 177   return $self->{lg_name};
 178
 179 }
 180
 181 =head2 set_lg_name
 182
 183  Usage:
 184  Desc:
 185  Ret:
 186  Args:
 187  Side Effects:
 188  Example:
 189
 190 =cut
 191
 192 sub set_lg_name {
 193   my $self=shift;
 194   $self->{lg_name}=shift;
 195 }
 196
 197 =head2 get_map
 198
 199  Usage:
 200  Desc:
 201  Ret:
 202  Args:
 203  Side Effects:
 204  Example:
 205
 206 =cut
 207
 208 sub get_map {
 209   my $self=shift;
 210   return $self->{map};
 211
 212 }
 213
 214 =head2 set_map
 215
 216  Usage:
 217  Desc:
 218  Ret:
 219  Args:
 220  Side Effects:
 221  Example:
 222
 223 =cut
 224
 225 sub set_map {
 226   my $self=shift;
 227   $self->{map}=shift;
 228 }
 229
 230
 231 =head2 get_marker_name
 232
 233  Usage:
 234  Desc:
 235  Ret:
 236  Args:
 237  Side Effects:
 238  Example:
 239
 240 =cut
 241
 242 sub get_marker_name {
 243   my $self=shift;
 244   return $self->{marker_name};
 245
 246 }
 247
 248 =head2 set_marker_name
 249
 250  Usage:
 251  Desc:
 252  Ret:
 253  Args:
 254  Side Effects:
 255  Example:
 256
 257 =cut
 258
 259 sub set_marker_name {
 260   my $self=shift;
 261   $self->{marker_name}=shift;
 262 }
 263
 264 1;
 265
 266