lib/CXGN/Cview/Utils.pm

   1
   2 =head1 NAME
   3
   4 CXGN::Cview::Utils - library for cview-related helper code
   5
   6 =head1 DESCRIPTION
   7
   8 =head1 AUTHOR(S)
   9
  10 Lukas Mueller (lam87@cornell.edu)
  11
  12 =cut
  13
  14 use strict;
  15
  16 package CXGN::Cview::Utils;
  17
  18 use CXGN::Cview::ChrLinkList;
  19
  20 require Exporter;
  21 our (@ISA) = qw(Exporter);
  22 our (@EXPORT_OK) = qw | get_maps_select set_marker_color get_chromosome_links |;  # symbols to export on request
  23
  24 =head2 get_chromosome_links
  25
  26  Usage:        my @chromosome_links = CXGN::Cview::Utils::get_chromosome_links($chr1_object, $chr2_object)
  27  Desc:         get_chromosome_links gets all the links between two
  28                chromosomes (CXGN::Cview::Chromosome and subclasses).
  29  Ret:          returns a list of CXGN::Cview::ChrLink objects
  30  Args:         two CXGN::Cview::Chromosome objects (or subclasses)
  31  Side Effects: none
  32  Example:
  33
  34 =cut
  35
  36 sub get_chromosome_links {
  37     my $chr1 = shift;
  38     my $chr2 = shift;
  39
  40     my %find_by_id=();
  41     my %find_by_name=();
  42
  43     my $link_list = CXGN::Cview::ChrLinkList->new();
  44
  45     #print STDERR "Finding links between chr ".$chr1->get_caption()." and ".$chr2->get_caption()."\n";
  46
  47     foreach my $m1 ($chr1->get_markers()) {
  48         my $name1 = uc($m1->get_marker_name());
  49         $find_by_name{$name1}=$m1->get_offset();
  50         $find_by_id{$m1->get_id()}=$m1->get_offset();
  51     }
  52     foreach my $m2 ($chr2->get_markers()) {
  53         # we want to connect if either the marker names are identical (but not undef),
  54         # or the ids are identical (but not undef).
  55         my $name2 = uc($m2->get_marker_name());
  56         my $id2 = $m2->get_id();
  57         my $offset1 = 0;
  58         if (exists($find_by_name{$name2}) && defined($find_by_name{$name2})) {
  59             $offset1=$find_by_name{$name2};
  60         }
  61
  62         if (exists($find_by_id{$id2}) && defined($find_by_id{$id2})) {
  63             $offset1=$find_by_id{$id2};
  64         }
  65         if ($offset1) {
  66             my $clink = CXGN::Cview::ChrLink -> new($chr1, $offset1, $chr2, $m2->get_offset(), $name2) ;
  67             $clink -> set_color(100,100,100);
  68             $link_list->add_link($name2, $clink);
  69         }
  70
  71     }
  72     return $link_list;
  73 }
  74
  75
  76
  77 =head2 function get_maps_select()
  78
  79   Synopsis:
  80   Parameters:   none
  81   Returns:      a string with html code for the maps select pull down menu
  82   Side effects: none
  83   Status:       implemented
  84   Example:
  85   Notes:
  86   Version:
  87
  88 =cut
  89
  90 sub get_maps_select {
  91     my $dbh = shift;
  92     my $selected_map_version = shift;
  93     my $field_name = shift;
  94     my $db_backend = shift;
  95     my $add_empty_selection =1;
  96
  97
  98     #print STDERR "DB BACKEND IS $db_backend\n";
  99
 100     if (!$field_name) { $field_name = "map_version_id"; }
 101
 102     #    my $query = "select map.map_id, short_name from map join "
 103     #   . "map_version using (map_id) where current_version = 't' order by short_name";
 104     #     my $sth = $self -> prepare($query);
 105     #     $sth -> execute();
 106
 107     my $select = qq { <select name="$field_name" > };
 108     my $selected="";
 109     my $map_factory = CXGN::Cview::MapFactory->new($dbh, { cview_db_backend=>$db_backend });
 110     my @maps = $map_factory->get_all_maps();
 111
 112     if ($add_empty_selection) {
 113         $select .= qq { <option value=""></option> };
 114     }
 115
 116     foreach my $m (@maps) {
 117         my ($map_version_id, $short_name) = ($m->get_id(), $m->get_short_name());
 118         if ($map_version_id =~ /^$selected_map_version$/) { $selected="selected=\"selected\""; }
 119         else {$selected=""; }
 120         $select .= "<option value=\"$map_version_id\" $selected>$short_name</option>";
 121     }
 122     $select .= "</select>";
 123     return $select;
 124 }
 125
 126 =head2 function set_marker_color()
 127
 128   Synopsis:
 129   Parameters:   marker object [CXGN::Cview::Marker], color model [string]
 130   Returns:      nothing
 131   Side effects: sets the marker color according to the supplied marker color model
 132                 the color model is a string from the list:
 133                 "marker_types", "confidence"
 134   Status:       implemented
 135   Example:
 136   Note:         this function was moved to Utils from ChromosomeViewer, such that
 137                 it is available for other scripts, such as view_maps.pl
 138
 139 =cut
 140
 141 sub set_marker_color {
 142     my $m = shift;
 143     my $color_model = shift;
 144     if ($color_model eq "marker_types") {
 145         if ($m->get_marker_type() =~ /RFLP/i) {
 146             $m->set_color(255, 0, 0);
 147             $m->set_label_line_color(255, 0,0);
 148             $m->set_text_color(255,0,0);
 149         }
 150         elsif ($m->get_marker_type() =~ /SSR/i) {
 151             $m->set_color(0, 255, 0);
 152             $m->set_label_line_color(0, 255,0);
 153             $m->set_text_color(0,255,0);
 154         }
 155         elsif ($m->get_marker_type() =~ /CAPS/i) {
 156             $m->set_color(0, 0, 255);
 157             $m->set_label_line_color(0, 0,255);
 158             $m->set_text_color(0,0,255);
 159         }
 160         elsif ($m->get_marker_type() =~ /COS/i) {
 161             $m->set_color(255,0 , 255);
 162             $m->set_label_line_color(255,0, 255);
 163             $m->set_text_color(255,0,255);
 164         }
 165         else {
 166             $m->set_color(0, 0, 0);
 167             $m->set_label_line_color(0, 0,0);
 168             $m->set_text_color(0,0,0);
 169         }
 170
 171     }
 172     else {
 173         my $c = $m -> get_confidence();
 174         if ($c==0) {
 175             $m->set_color(0,0,0);
 176             $m->set_label_line_color(0,0,0);
 177             $m->set_text_color(0,0,0);
 178         }
 179         if ($c==1) {
 180             $m->set_color(0,0,255);
 181             $m->set_label_line_color(0,0,255);
 182             $m->set_text_color(0,0,255);
 183
 184         }
 185         if ($c==2) {
 186             $m->set_color(0,255, 0);
 187             $m->set_label_line_color(0,255,0);
 188             $m->set_text_color(0,255,0);
 189         }
 190         if ($c==3) {
 191             $m->set_color(255, 0, 0);
 192             $m->set_label_line_color(255, 0,0);
 193             $m->set_text_color(255, 0,0);
 194         }
 195         if ($c==4) {
 196             $m->set_color(128, 128, 128);
 197             $m->set_label_line_color(128, 128, 128);
 198             $m->set_text_color(128, 128, 128);
 199         }
 200     }
 201 }
 202
 203
 204
 205 return 1;