lib/CXGN/Cview/Map/SGN/Genetic.pm

   1 package CXGN::Cview::Map::SGN::Genetic;
   2
   3 =head1 NAME
   4
   5 CXGN::Cview::Map::SGN::Genetic - a class implementing a genetic map
   6
   7 =head1 DESCRIPTION
   8
   9 This class implements a genetic map populated from the SGN database. This class inherits from L<CXGN::Cview::Map>.
  10
  11 Note: the common name (available through get_common_name()) for the map organism is now taken through the following join: sgn.accession -> public.organism -> sgn.organismgroup_member ->sgn.organism_group (July 2010).
  12
  13 =head1 AUTHOR(S)
  14
  15 Lukas Mueller <lam87@cornell.edu>
  16
  17 =head1 FUNCTIONS
  18
  19 This class implements the following functions (for more information, see L<CXGN::Cview::Map>):
  20
  21 =cut
  22
  23 use strict;
  24 use warnings;
  25
  26 use CXGN::Cview::Legend::Genetic;
  27 use CXGN::Cview::Map;
  28 use CXGN::Cview::Map::Tools;
  29
  30 use base qw | CXGN::Cview::Map |;
  31
  32 =head2 function new
  33
  34   Synopsis:     my $genetic = CXGN::Cview::Map::SGN::Genetic->
  35                   new( $dbh, $map_version_id);
  36   Arguments:    (1) a database handle, preferably generated with
  37                     CXGN::DB::Connection
  38                 (2) the map version id for the desired map.
  39   Returns:      a Genetic map object
  40   Side effects: accesses the database
  41   Description:
  42
  43 =cut
  44
  45 sub new {
  46     my $class = shift;
  47     my $dbh = shift;
  48     my $map_version_id = shift;
  49
  50     my $self = $class->SUPER::new($dbh);
  51     $self->set_id($map_version_id);
  52     $self->fetch();
  53
  54     # set some defaults
  55     $self->set_preferred_chromosome_width(20);
  56
  57     # fetch the chromosome lengths
  58     #
  59     my $query = "SELECT lg_name, max(position) FROM sgn.linkage_group JOIN sgn.marker_location USING(lg_id) WHERE linkage_group.map_version_id=? GROUP BY lg_name, lg_order ORDER BY lg_order";
  60     my $sth = $self->get_dbh()->prepare($query);
  61     $sth->execute($self->get_id());
  62     my @chromosome_lengths = ();
  63     while (my ($lg_name, $length) = $sth->fetchrow_array()) {
  64         push @chromosome_lengths, $length;
  65     }
  66     $self->set_chromosome_lengths(@chromosome_lengths);
  67
  68     if ($self->get_chromosome_count() == 0) { return undef; }
  69
  70     my $legend = CXGN::Cview::Legend::Genetic->new($self);
  71 #    $legend->set_mode("marker_types");
  72     $self->set_legend($legend);
  73
  74     return $self;
  75 }
  76
  77 sub fetch {
  78     my $self = shift;
  79
  80     # get the map metadata
  81     #
  82     my $query = "
  83          SELECT map_version_id, map_type, short_name, long_name,
  84                 parent1_stock_id, parent2_stock_id,
  85                 abstract, public.organism.species, organismgroup.name
  86          FROM sgn.map JOIN sgn.map_version using(map_id)
  87               LEFT JOIN public.stock on(parent1_stock_id=stock.stock_id)
  88               LEFT JOIN public.organism on (stock.organism_id=public.organism.organism_id)
  89               LEFT JOIN sgn.organismgroup_member on (stock.organism_id=organismgroup_member.organism_id)
  90               LEFT JOIN sgn.organismgroup using(organismgroup_id)
  91          WHERE map_version_id=?";
  92
  93     my $sth = $self->get_dbh()->prepare($query);
  94     $sth->execute($self->get_id());
  95     my ($map_version_id, $map_type, $short_name, $long_name, $parent1_stock_id, $parent2_stock_id, $abstract, $organism_name, $common_name) = $sth->fetchrow_array();
  96     $self->set_id($map_version_id);
  97     $self->set_type($map_type);
  98     $self->set_short_name($short_name);
  99     $self->set_long_name($long_name);
 100     $self->set_parent1_stock_id($parent1_stock_id);
 101     $self->set_parent2_stock_id($parent2_stock_id);
 102     $self->set_abstract($abstract);
 103     $self->set_organism($organism_name);
 104     $self->set_common_name($common_name);
 105     $self->set_units("cM");
 106
 107     # get information about associated linkage_groups
 108     #
 109     my $chr_name_q = "SELECT distinct(linkage_group.lg_name), lg_order FROM sgn.linkage_group WHERE map_version_id=? ORDER BY lg_order";
 110     my $chr_name_h = $self->get_dbh()->prepare($chr_name_q);
 111     $chr_name_h->execute($self->get_id());
 112     my @names = ();
 113     while (my ($lg_name) = $chr_name_h->fetchrow_array()) {
 114         push @names, $lg_name;
 115     }
 116     $self->set_chromosome_names(@names);
 117     $self->set_chromosome_count(scalar(@names));
 118     $self->set_preferred_chromosome_width(20);
 119
 120     # get the location of  the centromeres
 121     #
 122     my $centromere_q = "SELECT lg_name, min(position) as north_centromere, max(position) as south_centromere FROM linkage_group left join marker_location on (north_location_id=location_id or south_location_id=location_id) where linkage_group.map_version_id=? group by linkage_group.lg_id, linkage_group.map_version_id, lg_order, lg_name order by lg_order";
 123     my $centromere_h = $self->get_dbh()->prepare($centromere_q);
 124     $centromere_h->execute($self->get_id());
 125     while (my ($lg_name, $north, $south) = $centromere_h->fetchrow_array()) {
 126         $self->set_centromere($lg_name, $north, $south);
 127     }
 128
 129
 130 }
 131
 132 =head2 function get_chromosome
 133   Synopsis:     see L<CXGN::Cview::Map>
 134   Arguments:
 135   Returns:
 136   Side effects:
 137   Description:
 138
 139 =cut
 140
 141 sub get_chromosome {
 142     my $self = shift;
 143     my $chr_nr = shift;
 144 #    my $marker_confidence_cutoff = shift; # the confidence cutoff. 3=frame 2=coseg 1=interval LOD=2 0=interval
 145
 146 #    if (!$marker_confidence_cutoff) { $marker_confidence_cutoff=-1; }
 147
 148     my $chromosome = CXGN::Cview::Chromosome->new();
 149     $chromosome->set_name($chr_nr);
 150     $chromosome->set_caption($chr_nr);
 151
 152     my %seq_bac = ();
 153
 154     my $physical = 'physical';
 155
 156     if ($self->get_id() == CXGN::Cview::Map::Tools::find_current_version($self->get_dbh(), CXGN::Cview::Map::Tools::current_tomato_map_id())) {
 157
 158         # get the sequenced BACs
 159         #
 160         my $Sequenced_BAC_query =
 161         "
 162             SELECT
 163                 distinct $physical.bac_marker_matches.bac_id,
 164                 $physical.bac_marker_matches.cornell_clone_name,
 165                 $physical.bac_marker_matches.marker_id,
 166                 $physical.bac_marker_matches.position
 167             FROM
 168                 $physical.bac_marker_matches
 169                 LEFT JOIN sgn.linkage_group USING (lg_id)
 170                 LEFT JOIN sgn_people.bac_status USING (bac_id)
 171             WHERE
 172                 sgn.linkage_group.lg_name=?
 173                 AND sgn_people.bac_status.status='complete'
 174         ";
 175         my $sth2 = $self->get_dbh->prepare($Sequenced_BAC_query);
 176         $sth2->execute($chr_nr);
 177         while (my ($bac_id, $name, $marker_id, $offset)=$sth2->fetchrow_array()) {
 178 # print STDERR "Sequenced BAC for: $bac_id, $name, $marker_id, $offset...\n";
 179             $name = CXGN::Genomic::Clone->retrieve($bac_id)->clone_name();
 180
 181             my $m = CXGN::Cview::Marker::SequencedBAC->new($chromosome, $bac_id, $name, "", "", "", "", $offset);
 182             $m->get_label()->set_text_color(200,200,80);
 183             $m->get_label()->set_line_color(200,200,80);
 184             $seq_bac{$marker_id}=$m;
 185         }
 186     }
 187
 188     # get the "normal" markers
 189     #
 190     my $query =     "
 191         SELECT
 192             marker_experiment.marker_id,
 193             alias,
 194             mc_name,
 195             confidence_id,
 196             0,
 197             subscript,
 198             position,
 199             0
 200         FROM
 201             sgn.map_version
 202             inner join sgn.linkage_group using (map_version_id)
 203             inner join sgn.marker_location using (lg_id)
 204             inner join sgn.marker_experiment using (location_id)
 205             inner join sgn.marker_alias using (marker_id)
 206             inner join sgn.marker_confidence using (confidence_id)
 207             left join sgn.marker_collectible using (marker_id)
 208             left join sgn.marker_collection using (mc_id)
 209         WHERE
 210             map_version.map_version_id=?
 211             and lg_name=?
 212             and preferred='t'
 213          ORDER BY
 214             position,
 215             confidence_id desc
 216     ";
 217
 218     #print STDERR "MY ID: ".$self->get_id()." MY CHR NR: ".$chr_nr."\n";
 219
 220     my $sth =  $self->get_dbh -> prepare($query);
 221     $sth -> execute($self->get_id(), $chr_nr);
 222
 223     while (my ($marker_id, $marker_name, $marker_type, $confidence, $order_in_loc, $location_subscript, $offset, $loc_type) = $sth->fetchrow_array()) {
 224         #print STDERR "Marker Read: $marker_id\t$marker_name\t$marker_type\t$offset\n";
 225         my $m = CXGN::Cview::Marker -> new($chromosome, $marker_id, $marker_name, $marker_type, $confidence, $order_in_loc, $location_subscript, $offset, undef , $loc_type, 0);
 226         #print STDERR "dataadapter baccount = $bac_count!\n";
 227         if ($loc_type == 100) { $m -> set_frame_marker(); }
 228         $m -> set_url( $self->get_marker_link($m->get_id()));
 229         $self->set_marker_color($m, $self->get_legend()->get_mode());
 230
 231         #print STDERR "CURRENT MODE IS: ".$self->get_legend()->get_mode()."\n";
 232         $chromosome->add_marker($m);
 233
 234         if (exists($seq_bac{$marker_id})) {
 235             #print STDERR "Adding Sequenced BAC [".($seq_bac{$marker_id}->get_name())."] to map...[$marker_id]\n";
 236             $chromosome->add_marker($seq_bac{$marker_id});
 237         }
 238     }
 239
 240
 241     foreach my $mi ($self->get_map_items()) {
 242
 243         my ($chr, $offset, $name) = split /\s+/, $mi;
 244
 245
 246         if (!$chr || !$offset || !$name) { next; }
 247
 248         if ($chr ne $chr_nr) { next; }
 249
 250         my $m = CXGN::Cview::Marker->new($chromosome);
 251
 252         $m->get_label()->set_label_text($name);
 253         $m->set_offset($offset);
 254         $m->get_label()->set_hilited(1);
 255         $m->show_label();
 256         $m->get_label()->set_url('');
 257         $m->set_marker_name($name); # needed for proper marker ordering in the chromosome
 258         $chromosome->add_marker($m);
 259
 260
 261     }
 262
 263     $chromosome->sort_markers();
 264
 265     $chromosome -> _calculate_chromosome_length();
 266
 267     return $chromosome;
 268 }
 269
 270
 271 =head2 function get_chromosome_section
 272
 273   Synopsis:     my $chr_section = $map->get_chromosome_section(5, 120, 180);
 274   Arguments:    linkage group number, start offset, end offset
 275   Returns:
 276   Side effects:
 277   Description:
 278
 279 =cut
 280
 281 sub get_chromosome_section {
 282     my $self = shift;
 283     my $chr_nr = shift;     # the chromosome number
 284     my $start = shift;      # the start of the section in cM
 285     my $end = shift;        # the end of the section in cM
 286
 287     my $chromosome = CXGN::Cview::Chromosome->new();
 288
 289     # main query to get the marker data, including the BACs that
 290     # are associated with this marker -- needs to be refactored to
 291     # work with the materialized views for speed improvements.
 292     #
 293     my $query =
 294     "
 295         SELECT
 296             marker_experiment.marker_id,
 297             alias,
 298             mc_name,
 299             confidence_id,
 300             0,
 301             subscript,
 302             position,
 303             0,
 304             min(physical.probe_markers.overgo_probe_id),
 305             count(distinct(physical.overgo_associations.bac_id)),
 306             max(physical.oa_plausibility.plausible)
 307         FROM
 308             map_version
 309             inner join linkage_group using (map_version_id)
 310             inner join marker_location using (lg_id)
 311             inner join marker_experiment using (location_id)
 312             inner join marker_alias using (marker_id)
 313             inner join marker_confidence using (confidence_id)
 314             left join marker_collectible using (marker_id)
 315             left join marker_collection using (mc_id)
 316             LEFT JOIN physical.probe_markers ON (marker_experiment.marker_id=physical.probe_markers.marker_id)
 317             LEFT JOIN physical.overgo_associations USING (overgo_probe_id)
 318             LEFT JOIN physical.oa_plausibility USING (overgo_assoc_id)
 319         WHERE
 320             map_version.map_version_id=?
 321             and lg_name=?
 322             and preferred='t'
 323             -- and current_version='t'
 324             AND position >= ?
 325             AND position <= ?
 326         GROUP BY
 327             marker_experiment.marker_id,
 328             alias,
 329             mc_name,
 330             confidence_id,
 331             subscript,
 332             position
 333         ORDER BY
 334             position,
 335             confidence_id desc,
 336             max(physical.oa_plausibility.plausible),
 337             max(physical.probe_markers.overgo_probe_id)
 338     ";
 339
 340
 341     my $sth =  $self->get_dbh()-> prepare($query);
 342 #    print STDERR "START/END: $start/$end\n";
 343     $sth -> execute($self->get_id(), $chr_nr, $start, $end);
 344
 345     # for each marker, look if there is a associated fully sequenced BAC, and add that
 346     # as a marker of type Sequenced_BAC to the map at the right location
 347     #
 348     my $bac_status_q =
 349     "
 350         SELECT
 351             cornell_clone_name,
 352             bac_id
 353         FROM
 354             physical.bac_marker_matches
 355             JOIN sgn_people.bac_status using (bac_id)
 356         WHERE
 357             physical.bac_marker_matches.marker_id=?
 358             AND sgn_people.bac_status.status='complete'
 359     ";
 360
 361     my $bac_status_h = $self->get_dbh()->prepare($bac_status_q);
 362     my $seq_bac;
 363
 364     while (my ($marker_id, $marker_name, $marker_type, $confidence, $order_in_loc, $location_subscript, $offset, $loc_type, $overgo, $bac_count, $plausible, $status, $bac_name, $bac_id) = $sth->fetchrow_array()) {
 365         #print STDERR "Marker Read: $marker_id\t$marker_name\t$marker_type\toffset: $offset\tovergo: $overgo\tbac_count: $bac_count\tplausible: $plausible\n";
 366         my $seq_bac=undef;
 367         my $seq_bac_name="";
 368         my $seq_bac_id="";
 369         if (!$plausible || $plausible == 0)  { $bac_count = 0; }
 370         my $m = CXGN::Cview::Marker -> new($chromosome, $marker_id, $marker_name, $marker_type, $confidence, $order_in_loc, $location_subscript, $offset, , $loc_type, 0, $overgo, $bac_count);
 371         $m->set_url($self->get_marker_link($m->get_id()));
 372         $self->set_marker_color($m, $self->get_legend()->get_mode());
 373         #print STDERR "dataadapter baccount = $bac_count!\n";
 374         if ($loc_type == 100) { $m -> set_frame_marker(); }
 375
 376         # only add the sequenced BAC information to the F2-2000.
 377         #
 378         if ($self->get_id() == CXGN::Cview::Map::Tools::find_current_version($self->get_dbh(), CXGN::Cview::Map::Tools::current_tomato_map_id())) {
 379
 380             $bac_status_h->execute($marker_id);
 381             ($seq_bac_name, $seq_bac_id) = $bac_status_h->fetchrow_array();
 382
 383             # change the name to look more standard
 384             #
 385             if ($seq_bac_name) {
 386                  if ($seq_bac_name =~ m/(\d+)([A-Z])(\d+)/i) {
 387                     $seq_bac_name = sprintf ("%3s%04d%1s%02d", "HBa",$1,$2,$3);
 388                 }
 389                 $seq_bac = CXGN::Cview::Marker::SequencedBAC->new($chromosome, $seq_bac_id, $seq_bac_name, "", "", "", "", $offset);
 390             }
 391         }
 392
 393         # add the marker $m to the chromosome
 394         #
 395         $chromosome->add_marker($m);
 396
 397         if ($m->has_overgo()) {
 398                 $m->set_mark_color(100, 100, 100); # draw a gray circle for overgos
 399                 $m->set_show_mark(1);
 400                 $m->set_mark_link( "/tools/seedbac/sbfinder.pl?marker=".$m->get_marker_name()  );
 401             }
 402         #print STDERR "# BACS: ".($m2[$i]->has_bacs())."\n";
 403         if ($m->has_bacs()) {
 404             $m->set_mark_color(180, 0, 0); # draw a red circle for associated bacs
 405             $m->set_show_mark(1);
 406             $m->set_mark_link("/tools/seedbac/sbfinder.pl?marker=".$m->get_marker_name());
 407         }
 408         if (!$m->is_visible()) {
 409             $m->set_show_mark(0);
 410         }
 411
 412         # add the sequenced BAC to the chromosome
 413         # -url link needs to be changed
 414         # -add a confidence level of 3 so that it is always displayed.
 415         #
 416         if ($seq_bac) {
 417             $seq_bac->set_confidence(3);
 418             $seq_bac->set_url("/maps/physical/clone_info.pl?id=$seq_bac_id");
 419             $chromosome->add_marker($seq_bac);
 420         }
 421     }
 422     $chromosome->set_section($start, $end);
 423     $chromosome -> _calculate_chromosome_length();
 424
 425
 426
 427     return $chromosome;
 428 }
 429
 430 =head2 function get_overview_chromosome
 431
 432   Synopsis:
 433   Arguments:
 434   Returns:
 435   Side effects:
 436   Description:
 437
 438 =cut
 439
 440 sub get_overview_chromosome {
 441     my $self = shift;
 442     my $chr_nr = shift;
 443     my $chr = $self->get_chromosome($chr_nr);
 444     $chr->set_width( $self->get_preferred_chromosome_width()/2 );
 445     foreach my $m ($chr->get_markers()) {
 446         $m->hide_label();
 447         $m->hide_mark();
 448     }
 449     return $chr;
 450 }
 451
 452 =head2 get_chromosome_connections()
 453
 454  Usage:        @list = $map->get_chromosome_connections($lg_name)
 455  Args:         a linkage group name from the current map
 456  Returns:      a list of hashrefs, containing 4 keys
 457                map_version_id, lg_name, marker_count, short_name
 458                and the corresponding values
 459  Side Effects: the information will be used to populate the
 460                drop down menu in the comparative viewer.
 461  Example:
 462
 463 =cut
 464
 465 sub get_chromosome_connections {
 466     my $self = shift;
 467     my $chr_nr = shift;
 468
 469     my $query =
 470         "
 471         SELECT
 472             c_map_version.map_version_id,
 473             c_map.short_name,
 474             c_linkage_group.lg_name,
 475             count(distinct(marker.marker_id)) as marker_count
 476         from
 477             marker
 478             join marker_experiment using(marker_id)
 479             join marker_location using (location_id)
 480             join linkage_group on (marker_location.lg_id=linkage_group.lg_id)
 481             join map_version on (linkage_group.map_version_id=map_version.map_version_id)
 482
 483             join marker_experiment as c_marker_experiment on
 484                  (marker.marker_id=c_marker_experiment.marker_id)
 485             join marker_location as c_marker_location on
 486                  (c_marker_experiment.location_id=c_marker_location.location_id)
 487             join linkage_group as c_linkage_group on (c_marker_location.lg_id=c_linkage_group.lg_id)
 488             join map_version as c_map_version on
 489                  (c_linkage_group.map_version_id=c_map_version.map_version_id)
 490             join map as c_map on (c_map.map_id=c_map_version.map_id)
 491         where
 492             map_version.map_version_id=?
 493             and linkage_group.lg_name=?
 494             and c_map_version.map_version_id !=map_version.map_version_id
 495             and c_map_version.current_version='t'
 496         group by
 497             c_map_version.map_version_id,
 498             c_linkage_group.lg_name,
 499             c_map.short_name
 500         order by
 501             marker_count desc
 502     ";
 503
 504     my $sth = $self->get_dbh() -> prepare($query);
 505     $sth -> execute($self->get_id(), $chr_nr);
 506     my @chr_list = ();
 507
 508     #print STDERR "***************** Done with query..\n";
 509     while (my $hashref = $sth->fetchrow_hashref()) {
 510         #print STDERR "READING----> $hashref->{map_version_id} $hashref->{lg_name} $hashref->{marker_count}\n";
 511         push @chr_list, $hashref;
 512
 513     }
 514
 515     # hard code some connections to agp and fish maps.
 516     #
 517     my $tomato_version_id = CXGN::Cview::Map::Tools::find_current_version($self->get_dbh(), CXGN::Cview::Map::Tools::current_tomato_map_id());
 518     ###print STDERR $self->get_id()." VERSUS $tomato_version_id\n\n";
 519
 520     if ($self->get_id() == $tomato_version_id) {
 521
 522         ##print STDERR "***** Map ".$self->get_id(). " pushing agp and fish map!\n\n";
 523         push @chr_list, { map_version_id => "agp",
 524                           short_name => "Tomato AGP map",
 525                           lg_name => $chr_nr,
 526                           marker_count => "?"
 527                           };
 528         push @chr_list, { map_version_id => 25,
 529                           short_name => "FISH map",
 530                           lg_name => $chr_nr,
 531                           marker_count => "?"
 532                           };
 533     }
 534     else {
 535         warn $self->get_id()." has no other associated maps...\n\n";
 536     }
 537
 538     return @chr_list;
 539 }
 540
 541 =head2 function has_linkage_group
 542
 543   Synopsis:
 544   Arguments:
 545   Returns:
 546   Side effects:
 547   Description:
 548
 549 =cut
 550
 551 sub has_linkage_group {
 552     my $self = shift;
 553     my $candidate = shift;
 554     foreach my $lg ($self->get_chromosome_names()) {
 555         if ($lg eq $candidate) {
 556             return 1;
 557         }
 558     }
 559     return 0;
 560 }
 561
 562 =head2 function get_marker_count
 563
 564 accesses the database to count the marker on the given map/chromosome.
 565
 566 =cut
 567
 568 sub get_marker_count {
 569     my $self =shift;
 570     my $chr_name = shift;
 571     my $query = "SELECT count(distinct(location_id)) FROM sgn.map_version JOIN marker_location using (map_version_id)
 572                             JOIN linkage_group using (lg_id)
 573                       WHERE linkage_group.lg_name=? and map_version.map_version_id=?";
 574     my $sth = $self->get_dbh()->prepare($query);
 575     $sth->execute($chr_name, $self->get_id());
 576     my ($count) = $sth->fetchrow_array();
 577     return $count;
 578
 579 }
 580
 581 sub get_map_stats {
 582     my $self = shift;
 583     my $query =
 584     "
 585         select
 586             mc_name,
 587             count(distinct(marker.marker_id))
 588         from
 589             marker join marker_collectible using (marker_id)
 590             join marker_collection using(mc_id)
 591             join marker_experiment on (marker.marker_id=marker_experiment.marker_id)
 592             join marker_location on (marker_experiment.location_id=marker_location.location_id)
 593         where
 594             marker_location.map_version_id=?
 595         group by
 596             mc_name
 597     ";
 598
 599     my $total_count = 0;
 600
 601     my $s = <<"";
 602 <table summary="">
 603 <tr><td colspan="2"><b>Marker collections</b></td></tr>
 604
 605     my $sth = $self->get_dbh() -> prepare($query);
 606     $sth -> execute($self->get_id());
 607
 608     my $map_name = $self->get_short_name();
 609     $map_name =~ s/ /\+/g;
 610
 611     while (my ($type, $count)= $sth->fetchrow_array()) {
 612         $s .= <<"";
 613 <tr>
 614   <td>$type</td>
 615   <td align="right">
 616      <a href="/search/markers/markersearch.pl?types=$type&amp;maps=$map_name">$count</a>
 617   </td>
 618 </tr>
 619
 620         $total_count += $count;
 621     }
 622     $s .= <<"";
 623 <tr><td>&nbsp;</td><td>&nbsp;</td></tr>
 624 <tr>
 625   <td><b>Total</b>:</td>
 626   <td align="right">
 627       <a style="font-weight: bold" href="/search/markers/markersearch.pl?maps=$map_name">$total_count</a>
 628   </td>
 629 </tr>
 630 </table>
 631
 632     my $protocol_q = "SELECT distinct(marker_experiment.protocol), count(distinct(marker_experiment.marker_experiment_id))
 633                         FROM marker
 634                         JOIN marker_experiment using (marker_id)
 635                         JOIN marker_location using (location_id)
 636                         JOIN linkage_group using (map_version_id)
 637                        WHERE map_version_id=?
 638                        GROUP BY marker_experiment.protocol";
 639     my $pqh = $self->get_dbh()->prepare($protocol_q);
 640     $pqh ->execute($self->get_id());
 641
 642     my $total_protocols = 0;
 643     $s .= <<"";
 644 <br /><br />
 645 <table>
 646   <tr>
 647      <td colspan="2"><b>Protocols</b></td>
 648   </tr>
 649
 650     while (my ($protocol, $count) = $pqh->fetchrow_array()) {
 651         $s.= qq { <tr><td>$protocol</td><td align="right">$count</td></tr> };
 652         $total_protocols += $count;
 653     }
 654
 655     $s .= <<"";
 656 <tr><td colspan="2">&nbsp;</td></tr>
 657 <tr>
 658    <td><b>Total:</b></td>
 659    <td align="right"><b>$total_protocols</b></td>
 660 </tr>
 661 </table>
 662
 663     return $s;
 664 }
 665
 666
 667
 668 =head2 function has_IL
 669
 670   Synopsis:
 671   Arguments:
 672   Returns:
 673   Side effects:
 674   Description:
 675
 676 =cut
 677
 678 sub has_IL {
 679     my $self =shift;
 680
 681     if ($self->get_short_name()=~/1992|2000/) {
 682         #print STDERR "Map ".$self->get_short_name()." has an associated IL map.\n";
 683         return 1;
 684     }
 685     #print STDERR "Map ".$self->get_short_name()." does not have an associated IL map.\n";
 686     return 0;
 687 }
 688
 689 =head2 function has_physical
 690
 691   Synopsis:
 692   Arguments:
 693   Returns:
 694   Side effects:
 695   Description:
 696
 697 =cut
 698
 699 sub has_physical {
 700     my $self = shift;
 701     if ($self->get_short_name()=~/2000/) {
 702         return 1;
 703     }
 704     return 0;
 705 }
 706
 707 =head2 function can_zoom
 708
 709 Whether this map support zooming in. These ones do.
 710
 711 =cut
 712
 713 sub can_zoom {
 714     return 1;
 715 }
 716
 717 =head2 function get_marker_link
 718
 719   Synopsis:
 720   Arguments:
 721   Returns:
 722   Side effects:
 723   Description:
 724
 725 =cut
 726
 727 sub get_marker_link {
 728     my $self =shift;
 729     my $id = shift;
 730     return "/search/markers/markerinfo.pl?marker_id=$id";
 731 }
 732
 733
 734 =head2 function set_marker_color()
 735
 736   Synopsis:
 737   Parameters:   marker object [CXGN::Cview::Marker], color model [string]
 738   Returns:      nothing
 739   Side effects: sets the marker color according to the supplied marker color model
 740                 the color model is a string from the list:
 741                 "marker_types", "confidence"
 742   Status:       implemented
 743   Example:
 744   Note:         this function was moved to Utils from ChromosomeViewer, such that
 745                 it is available for other scripts, such as view_maps.pl
 746
 747 =cut
 748
 749 sub set_marker_color {
 750     my $self = shift;
 751     my $m = shift;
 752     my $color_model = shift || '';
 753
 754     if ($color_model eq "marker_types") {
 755         if ($m->get_marker_type() =~ /RFLP/i) {
 756             $m->set_color(255, 0, 0);
 757             $m->set_label_line_color(255, 0,0);
 758             $m->set_text_color(255,0,0);
 759         }
 760         elsif ($m->get_marker_type() =~ /SSR/i) {
 761             $m->set_color(0, 255, 0);
 762             $m->set_label_line_color(0, 255,0);
 763             $m->set_text_color(0,255,0);
 764         }
 765         elsif ($m->get_marker_type() =~ /CAPS/i) {
 766             $m->set_color(0, 0, 255);
 767             $m->set_label_line_color(0, 0,255);
 768             $m->set_text_color(0,0,255);
 769         }
 770         elsif ($m->get_marker_type() =~ /COS/i) {
 771             $m->set_color(255,0 , 255);
 772             $m->set_label_line_color(255,0, 255);
 773             $m->set_text_color(255,0,255);
 774         }
 775         else {
 776             $m->set_color(0, 0, 0);
 777             $m->set_label_line_color(0, 0,0);
 778             $m->set_text_color(0,0,0);
 779         }
 780
 781     }
 782     else {
 783         my $c = $m -> get_confidence();
 784         if ($c==0) {
 785             $m->set_color(0,0,0);
 786             $m->set_label_line_color(0,0,0);
 787             $m->set_text_color(0,0,0);
 788         }
 789         if ($c==1) {
 790             $m->set_color(0,0,255);
 791             $m->set_label_line_color(0,0,255);
 792             $m->set_text_color(0,0,255);
 793
 794         }
 795         if ($c==2) {
 796             $m->set_color(0,255, 0);
 797             $m->set_label_line_color(0,255,0);
 798             $m->set_text_color(0,255,0);
 799         }
 800         if ($c==3) {
 801             $m->set_color(255, 0, 0);
 802             $m->set_label_line_color(255, 0,0);
 803             $m->set_text_color(255, 0,0);
 804         }
 805         if ($c==4) {
 806             $m->set_color(128, 128, 128);
 807             $m->set_label_line_color(128, 128, 128);
 808             $m->set_text_color(128, 128, 128);
 809         }
 810     }
 811 }
 812
 813 sub can_overlay {
 814     return 1;
 815 }
 816
 817 sub get_stock_name {
 818     my $self = shift;
 819     my $id = shift;
 820     my $q = "SELECT name FROM stock WHERE stock_id=?";
 821     my $h = $self->get_dbh()->prepare($q);
 822     $h->execute($id);
 823     my ($name) = $h->fetchrow_array();
 824     return $name;
 825 }
 826
 827 sub get_parent1_stock_name {
 828     my $self = shift;
 829     return $self->get_stock_name($self->get_parent1_stock_id);
 830 }
 831
 832 sub get_parent2_stock_name {
 833     my $self = shift;
 834     return $self->get_stock_name($self->get_parent2_stock_id);
 835 }
 836
 837
 838 1;