lib/CXGN/Marker.pm

   1
   2 =head1 NAME
   3
   4 CXGN::Cview::Marker - a class for drawing markers
   5
   6 =head1 DESCRIPTION
   7
   8 Inherits from L<CXGN::Cview::ImageObject>. Defines a marker object on a Cview image. Markers can be rendered in different colors, and have labels associated with them, L<CXGN::Cview::Label>, that can be hilited, rendered in different colors, etc. See the L<CXGN::Cview::Label> class for more information. The two label objects that are associated with each marker are:
   9
  10 =over 5
  11
  12 =item o
  13
  14 a name label object. The label object can in theory be accessed using the accessors for this label are get_label() and set_label(), however it is best to use the standard accessors of the marker object and let it deal with the label object itself.
  15
  16 =item o
  17
  18 an offset label that gives the distance in cM (or in the current map units) and is drawn symmetrically on the other side of the chromosome to the name label. The accessors for this label are get_offset_label() and set_offset_label(). It is currently not drawn by default in the Cview programs. The accessor show_offset_label() will cause the offset label to be displayed.
  19
  20 =back
  21
  22 Labels also have a mark associated with them. That's a small round circle after the label that can be colored to provide some additional visual information about the marker. See the mark related functions below.
  23
  24 Markers can be hidden using the set_hidden(1) accessor. Only the small tick on the chromosome will be drawn, and the label will be omitted.
  25
  26 For a marker that can define a range on the chromosome instead of a specific location use the L<CXGN::Cview::Marker::RangeMarker> class. See that class for more information.
  27
  28 Other Marker properties are inherited from ImageObject, such as the enclosing_rect accessors, set_url and get_url, and others. See L<CXGN::Cview::ImageObject>.
  29
  30 =head1 SEE ALSO
  31
  32 See also the documentation in L<CXGN::Cview>.
  33
  34 =head1 AUTHOR(S)
  35
  36 Lukas Mueller (lam87@cornell.edu)
  37
  38 =head1 VERSION and CHANGE HISTORY
  39
  40 Original version July 2004
  41
  42 [2006-07-07] Replaced label functions with CXGN::Cview::Label class.
  43
  44 =head1 FUNCTIONS
  45
  46
  47 =cut
  48
  49 return 1;
  50
  51 use strict;
  52 use CXGN::Cview::ImageObject;
  53 use CXGN::Cview::Label;
  54
  55 package CXGN::Cview::Marker;
  56
  57 use base qw/ CXGN::Cview::ImageObject /;
  58
  59 =head2 function new()
  60
  61     my $m -> new ($chr, $marker_id, $marker_name, $marker_type, $confidence, $order_in_loc, $location_subscript, $cM_offset, $loc_type, $loc_order, $overgo, $bac_count);
  62
  63 Creates a new marker. The $chr is the chromosome object the marker belongs to. The marker_id has to be a unique id for the marker. The marker_name is any string, marker_type should be CAPS, COSII, RFLP, SNP etc, confidence is -1 for undefined, 0 = ? .. 4= LOD(3). order_in_loc is deprecated, location_subscript is the subscript of the marker on that chromosome, if any. cM_offset is the offset of the marker on the chr, in cM. overgo should be set to true if the marker has an overgo marker, has_bacs should be set to true if there are BACs associated to that overgo marker.
  64
  65 =cut
  66
  67 sub new {
  68     my $class = shift;
  69     my $self = $class -> SUPER::new(@_);
  70     my $chromosome = shift;
  71
  72     $self->set_chromosome($chromosome);
  73     my ($marker_id, $marker_name, $marker_type, $confidence, $order_in_loc, $location_subscript, $offset, $loc_type, $loc_order, $has_overgo, $has_bacs) = @_;
  74 #    print STDERR "\@_ = @_\n";
  75
  76     # initialize the marker object with what was supplied by
  77     # the call and some reasonable default parameters
  78     #
  79     $self->set_id($marker_id);
  80
  81     $self->set_marker_type($marker_type);
  82     $self->set_confidence($confidence);
  83     $self->set_order_in_loc($order_in_loc);
  84     $self->set_location_subscript($location_subscript);
  85     $self->set_offset($offset);
  86     $self->set_loc_type($loc_type);
  87     $self->set_loc_order($loc_order);
  88     $self->set_has_overgo($has_overgo);
  89     $self->set_has_bacs($has_bacs);
  90     $self->set_color(50, 50 , 50);
  91     $self->set_label(CXGN::Cview::Label->new());
  92     #$self->set_label_side("right");
  93     $self->set_show_tick(1);
  94     $self->set_north_range(0);
  95     $self->set_south_range(0);
  96
  97
  98     # initialize the label
  99     #
 100     $self->get_label()->set_hilite_color(255, 255, 0);
 101     $self->get_label()->set_line_color(150,150,150);
 102     if (!$location_subscript) { $location_subscript=""; }
 103     if (!$marker_name) { $marker_name = ""; }
 104     $self->get_label()->set_name($marker_name.$location_subscript);
 105     $self->set_marker_name($marker_name);
 106
 107     $self->unhilite();
 108     $self->unhide();
 109 #    $self->set_north_range(0);
 110 #    $self->set_south_range(0);
 111     $self->set_mark_color(255, 255, 255);
 112     $self->set_mark_size(8);
 113     $self->set_mark_link("");
 114     $self->hide_mark();
 115     # the default for this is set in the label object. $self->set_label_spacer(); # the distance between the label and the midline of the chromosome
 116     $self->set_font(GD::Font->Small());
 117
 118     # the offset label is shown on the opposite side of
 119     # the name label
 120     #
 121     my $offset_label = CXGN::Cview::Label->new();
 122     $offset_label->set_text_color(150, 150, 150);
 123     $offset_label->set_name( (sprintf "%5.2f", $offset)." ");
 124     $self->set_offset_label($offset_label);
 125
 126     # print STDERR "Marker new: $self->{has_bacs}\n";
 127     #
 128     return $self;
 129 }
 130
 131 =head2 function get_color()
 132
 133 Gets the color of the marker (more specifically, the line of the marker on the chromosome). Three numbers between 0 and 255 for red, green and blue channels are returned as a list.
 134
 135 =cut
 136
 137 sub get_color {
 138     my $self = shift;
 139     if (!exists($self->{marker_color})) { @{$self->{marker_color}}=(); }
 140     return @{$self->{marker_color}};
 141 }
 142
 143 =head2 function set_color()
 144
 145 Sets the color of the marker (more specifically, the line of the marker on the chromosome). Three numbers between 0 and 255 for red, green and blue channels are required. Default color is black.
 146
 147 =cut
 148
 149 sub set_color {
 150     my $self = shift;
 151     $self->{marker_color}[0]=shift;
 152     $self->{marker_color}[1]=shift;
 153     $self->{marker_color}[2]=shift;
 154 }
 155
 156
 157 =head2 function get_name()
 158
 159  Gets the complete name of the marker including the suffix.
 160
 161 =cut
 162
 163 sub get_name {
 164     my $self = shift;
 165     # test if there is anything in loation_subscript and set to empty string
 166     # otherwise a 0 may be appended.
 167     if (!$self->get_location_subscript()) { $self->set_location_subscript(""); }
 168     return $self->get_marker_name().$self->get_location_subscript();
 169 }
 170
 171 =head2 functions get_marker_name(), set_marker_name()
 172
 173  gets the marker name, excluding the suffix.
 174
 175 =cut
 176
 177 sub get_marker_name {
 178     my $self = shift;
 179     # this function returns the marker name without the subscript. This is useful for constructing links to the marker detail page
 180     # which requires a type/name tuple
 181     if (!exists($self->{marker_name}) || !defined($self->{marker_name})) { $self->{marker_name}=""; }
 182     return $self->{marker_name};
 183 }
 184
 185 sub set_marker_name {
 186     my $self = shift;
 187     my $name = shift;
 188     $self->{marker_name}=$name;
 189 }
 190
 191 =head2 functions get_id(), set_id()
 192
 193 gets the unique id associated with the marker.
 194
 195 =cut
 196
 197 sub get_id {
 198     my $self = shift;
 199     if (!exists($self->{marker_id}) || !defined($self->{marker_id})) {
 200         $self->{marker_id}="";
 201     }
 202     return $self->{marker_id};
 203 }
 204
 205 sub set_id {
 206     my $self = shift;
 207     $self->{marker_id}=shift;
 208 }
 209
 210 =head2 functions set_confidence() and get_confidence()
 211
 212   Synopsis:     my $confidence = $m->get_confidence()
 213   Arguments:    setter function: -1 ... 3.
 214                 -1 means uncalculated confidence
 215                 1 is ILOD<3
 216                 2 is CFLOD=3
 217                 3 is FLOD>3
 218   Returns:      getter returns values above
 219                 defaults to -1 if confidence property has not been set.
 220   Side effects: display in the chromosome viewer depends on confidence values.
 221   Description:
 222
 223 =cut
 224
 225 sub set_confidence {
 226     my $self = shift;
 227     $self->{confidence}=shift;
 228 }
 229
 230 sub get_confidence {
 231     my $self= shift;
 232     if (!exists($self->{confidence}) || !defined($self->{confidence}) || !$self->{confidence}) {
 233         $self->{confidence}=-1;
 234     }
 235     return $self->{confidence};
 236 }
 237
 238
 239
 240 =head2 accessors set_marker_type() and get_marker_type()
 241
 242   Synopsis:     accessors for the marker_type property.
 243   Arguments:
 244   Returns:
 245   Side effects: rendering in the chromosome viewer depends on
 246                 marker type.
 247   Description:  marker types are: RFLP, SSR, CAPS and COS.
 248
 249 =cut
 250
 251 sub set_marker_type {
 252     my $self = shift;
 253     $self->{marker_type} = shift;
 254 }
 255
 256 sub get_marker_type {
 257     my $self = shift;
 258     if (!exists($self->{marker_type}) || !defined($self->{marker_type})) {
 259         $self->{marker_type}="";
 260     }
 261     return $self->{marker_type};
 262 }
 263
 264 =head2 function get_mark_color()
 265
 266 the mark is a little circle displayed after the marker name.
 267 it can be used to add additional visual information for a marker.
 268 The mark is clickable. The link can be set using set_mark_link().
 269 The default color is white with no link.
 270
 271 =cut
 272
 273 sub get_mark_color {
 274     my $self = shift;
 275     return @{$self->{mark_color}};
 276 }
 277
 278 =head2 function set_mark_color()
 279
 280 the mark is a little circle displayed after the marker name.
 281 it can be used to add additional visual information for a marker.
 282 The mark is clickable. The link can be set using set_mark_link().
 283 The default color is white with no link.
 284
 285 =cut
 286
 287 sub set_mark_color {
 288     # the mark is a little circle displayed after the marker name.
 289     # it can be used to add additional visual information for a marker.
 290     # The mark is clickable. The link can be set using set_mark_link().
 291     # The default color is white with no link.
 292     my $self = shift;
 293     $self->{mark_color}[0] = shift;
 294     $self->{mark_color}[1] = shift;
 295     $self->{mark_color}[2] = shift;
 296 }
 297
 298 =head2 function set_show_mark()
 299
 300   Synopsis:     $m->set_show_mark()
 301   Arguments:    none
 302   Returns:      nothing
 303   Side effects: causes the mark to be displayed when the marker
 304                 is renderd.
 305   Description:
 306
 307 =cut
 308
 309 sub set_show_mark {
 310     my $self = shift;
 311     $self->{show_mark} = 1;
 312 }
 313
 314 =head2 function hide_mark()
 315
 316   Synopsis:     $m->hide_mark()
 317   Arguments:
 318   Returns:
 319   Side effects: hides the mark
 320   Description:
 321
 322 =cut
 323
 324 sub hide_mark {
 325     my $self = shift;
 326     $self->{show_mark}=0;
 327 }
 328
 329 =head2 function get_show_mark()
 330
 331   Synopsis:
 332   Arguments:
 333   Returns:
 334   Side effects:
 335   Description:
 336
 337 =cut
 338
 339 sub get_show_mark {
 340     my $self = shift;
 341     return $self->{show_mark};
 342 }
 343
 344 =head2 functions set_mark_link(), get_mark_link()
 345
 346   Synopsis:
 347   Arguments:
 348   Returns:
 349   Side effects:
 350   Description:
 351
 352 =cut
 353
 354 sub set_mark_link {
 355     my $self = shift;
 356     $self->{mark_link} = shift;
 357 }
 358
 359 sub get_mark_link {
 360     my $self = shift;
 361     if (!exists($self->{mark_link})) { $self->{mark_link}=""; }
 362     return $self ->{mark_link};
 363 }
 364
 365 =head2 functions has_overgo(), set_has_overgo()
 366
 367   Synopsis:     $m->has_overgo()
 368   Arguments:
 369   Returns:
 370   Side effects: used to derive the mark\'s color
 371   Description:
 372
 373 =cut
 374
 375 sub has_overgo {
 376     my $self = shift;
 377     return $self->{has_overgo};
 378 }
 379
 380 sub set_has_overgo {
 381     my $self = shift;
 382     $self->{has_overgo}=1;
 383 }
 384
 385 =head2 functions has_bacs(), set_has_bacs()
 386
 387   Synopsis:     $m->set_has_bacs(1)
 388   Arguments:
 389   Returns:      nothing
 390   Side effects: causes the mark to be displayed in red.
 391   Description:
 392
 393 =cut
 394
 395 sub set_has_bacs {
 396     my $self = shift;
 397     $self->{has_bacs} = shift; # the number of bacs associated with this marker
 398 }
 399
 400 sub has_bacs {
 401     my $self = shift;
 402     return $self->{has_bacs};
 403 }
 404
 405 =head2 functions get_mark_rect(), set_mark_rect()
 406
 407   Synopsis:
 408   Arguments:
 409   Returns:
 410   Side effects:
 411   Description:
 412
 413 =cut
 414
 415 sub get_mark_rect {
 416     my $self = shift;
 417     if (! exists($self->{mark_rect})) { @{$self->{mark_rect}} = (0,0,0,0); }
 418     return ($self ->{mark_rect}[0], $self->{mark_rect}[1], $self->{mark_rect}[2], $self->{mark_rect}[3]);
 419 }
 420
 421 sub set_mark_rect {
 422     my $self = shift;
 423     ($self ->{mark_rect}[0], $self->{mark_rect}[1], $self->{mark_rect}[2], $self->{mark_rect}[3]) = @_;
 424 }
 425
 426 =head2 functions set_mark_size(), get_mark_size()
 427
 428   Synopsis:
 429   Arguments:
 430   Returns:
 431   Side effects:
 432   Description:
 433
 434 =cut
 435
 436 sub set_mark_size {
 437     my $self = shift;
 438     $self->{mark_size} = shift;
 439 }
 440
 441 sub get_mark_size {
 442     my $self = shift;
 443     if (!exists($self->{mark_size})) { $self->{mark_size}=0; }
 444     return $self->{mark_size};
 445 }
 446
 447 =head2 functions is_frame_marker(), set_frame_marker()
 448
 449   Synopsis:
 450   Arguments:    none
 451   Returns:      returns true if the object represents
 452                 a frame marker.
 453   Side effects: the chromosome viewer may decide to render
 454                 these markers differently
 455   Description:  set_frame_marker just sets the property to 1.
 456                 It cannot be unset.
 457
 458 =cut
 459
 460 sub is_frame_marker {
 461     my $self = shift;
 462     if (!exists($self->{loc_type})) { $self->{loc_type}=""; }
 463     return ($self->{loc_type} eq "frame");
 464 }
 465
 466 sub set_frame_marker {
 467     my $self = shift;
 468     $self->{loc_type} = "frame";
 469 }
 470
 471
 472 =head2 functions set_chromosome(), get_chromosome()
 473
 474   Synopsis:     accessors for the chromosome property, representing
 475                 the chromosome this marker is associated with.
 476   Arguments:    setter: a CXGN::Cview::Chromosome object.
 477   Returns:      getter: a CXGN::Cview::Chromosome object.
 478   Side effects: the marker will be drawn on this chromosome. The
 479                 marker also needs to be added to the marker list of
 480                 the chromosome. Calling add_marker on the chromosome
 481                 object takes care of all that.
 482   Description:
 483
 484 =cut
 485
 486 sub get_chromosome {
 487     my $self=shift;
 488     return $self->{chromosome};
 489 }
 490
 491 sub set_chromosome {
 492     my $self =shift;
 493     $self->{chromosome}=shift;
 494 }
 495
 496 =head2 function hide()
 497
 498 Hides the marker completely from the chromosome.
 499
 500 =cut
 501
 502 sub hide {
 503     my $self = shift;
 504     #$self -> {hidden} = 1;
 505     $self->get_label()->set_hidden(1);
 506 }
 507
 508 =head2 function unhide()
 509
 510 Unhides the marker.
 511
 512 =cut
 513
 514 sub unhide {
 515     my $self = shift;
 516     #$self -> {hidden} = 0;
 517     $self->get_label()->set_hidden(0);
 518 }
 519
 520 =head2 function is_hidden()
 521
 522 Returns true if marker is hidden.
 523
 524 =cut
 525
 526 sub is_hidden {
 527     my $self = shift;
 528     #return $self -> {hidden};
 529     return $self->get_label()->is_hidden();
 530 }
 531
 532 =head2 function hide_label()
 533
 534 Hides the label of the marker only. The marker 'tick' is still being drawn.
 535
 536 =cut
 537
 538 sub hide_label {
 539     my $self= shift;
 540     #$self->{label_hidden} = 1;
 541     $self->get_label()->set_hidden(1);
 542 }
 543
 544 =head2 function show_label()
 545
 546 Unhides the label if it was previously hidden. Otherwise has no effect.
 547
 548 =cut
 549
 550 sub show_label {
 551     my $self=shift;
 552     #$self ->{label_hidden} = 0;
 553     $self->get_label()->set_hidden(0);
 554 }
 555
 556 =head2 function is_label_visible()
 557
 558 Returns true if the label is not hidden.
 559
 560 =cut
 561
 562 sub is_label_visible {
 563     my $self = shift;
 564     return !$self->is_hidden();
 565 }
 566
 567 =head2 function get_image_map()
 568
 569 Returns the image map for this label as a string. Usually the chromosome object calls this function.
 570
 571 =cut
 572
 573 sub get_image_map {
 574     my $self = shift;
 575     #print STDERR "get_image_mapo marker\n";
 576 #    my $coords = join ",", ($self -> get_label_rect());
 577     my $s = "";
 578     if ($self->get_url()) {
 579         $s = $self->get_label()->get_image_map();
 580 #       $s = "<area shape=\"rect\" coords=\"".$coords."\" href=\"".$self->get_url()."\" alt=\"\" />\n";
 581     }
 582     if ($self->get_show_mark()) {
 583         $s .= "<area shape=\"rect\" coords=\"".(join(",", $self->get_mark_rect()))."\" href=\"".$self->get_mark_link()."\" alt=\"\" title=\"".($self->get_tooltip())."\"  />\n";
 584
 585     }
 586     return $s;
 587
 588 }
 589
 590 =head2 function render()
 591
 592     $marker -> render($image);
 593
 594 Renders the marker on a GD image object. The chromosome object usually calls this function to render the entire chromosome.
 595
 596 =cut
 597
 598 sub render {
 599     my $self = shift;
 600     my $image = shift;
 601
 602     # calculate y position in pixels
 603     #
 604     my $y = $self->get_chromosome()->get_vertical_offset() + $self->get_chromosome()->mapunits2pixels($self->get_offset());
 605
 606     #warn "[Marker.pm] ".$self->get_offset()."cM is $y pixels...\n";
 607     # determine the side which this label should be drawn on. If it was not set manually,
 608     # retrieve the side from the chromosome as a default.
 609     #
 610     if (!$self->get_label_side()) {
 611         $self->set_label_side($self->get_chromosome()->get_label_side());
 612     }
 613
 614     # render marker only if it is visible (markers outside of sections or hidden markers are not visible)
 615     if ($self -> is_visible()) {
 616
 617         # draw the tick on the chromosome
 618         #
 619         my $color = $image -> colorResolve($self->get_color());
 620         my $chromosome_width = $self->get_chromosome()->get_width();
 621         my $halfwidth = int($chromosome_width/2);
 622         $self->draw_tick($image);
 623
 624         # deal with label stuff
 625         #
 626         # the $label object deals with displaying the marker's name
 627         # the $offset_label object deals with displaying the marker's offset
 628         # on the opposite side
 629         #
 630         my $label = $self->get_label();
 631         my $offset_label = $self->get_offset_label();
 632
 633         if ($self->get_hilited()) {
 634             $label->set_hilited(1);
 635         }
 636
 637         # draw the labels left of the chromosome if label_side eq left
 638         #
 639         if ($self->get_label_side() eq "left") {
 640
 641             # define the Label's reference point
 642             #
 643             $label->set_reference_point($self->get_chromosome()->get_horizontal_offset()-$halfwidth,$y);
 644             $label->set_horizontal_offset($self->get_chromosome()->get_horizontal_offset()- $label->get_label_spacer());
 645
 646             # draw the offset on the right if label_side eq left, if display_marker
 647             # offset is true in the chromosome object
 648             #
 649             if ($self->get_chromosome()->{display_marker_offset}) {
 650
 651                 # define the label's reference point
 652                 #
 653                 $offset_label->set_reference_point($self->get_chromosome()->get_horizontal_offset()+$halfwidth, $y);
 654                 $offset_label->set_horizontal_offset($self->get_chromosome()->get_horizontal_offset()+ $label->get_label_spacer()
 655                                                      );
 656                 $offset_label->set_vertical_offset($label->get_vertical_offset());
 657                 $offset_label->set_align_side("left");
 658
 659                 $offset_label->set_hidden($label->is_hidden());
 660                 $offset_label->render($image);
 661             }
 662         }
 663
 664         # draw the labels on the right side if label_side is right
 665         #
 666         elsif ($self->get_label_side() eq "right") {
 667
 668             # define the Label's reference point (the point where the label points to)
 669             # and the horizontal offset (the actual position of the text label)
 670             #
 671             $label->set_reference_point($self->get_chromosome()->get_horizontal_offset()+$halfwidth,$y);
 672             $label->set_horizontal_offset($self->get_chromosome()->get_horizontal_offset()+$label->get_label_spacer());
 673
 674             # if show offset is turned on, draw a label on the opposite side of the chromosome
 675             # showing the cM position
 676             #
 677             if ($self->get_chromosome()->{display_marker_offset}) {
 678
 679                 $offset_label->set_reference_point(
 680                                                    $self->get_chromosome()->get_horizontal_offset()-$halfwidth, $y
 681
 682                                                    );
 683                 $offset_label->set_horizontal_offset($self->get_chromosome()->get_horizontal_offset()-
 684                                                      $label->get_label_spacer()
 685                                                      );
 686                 $offset_label->set_vertical_offset($label->get_vertical_offset());
 687                 $offset_label->set_align_side("right");
 688                 $offset_label->set_hidden($label->is_hidden());
 689                 $offset_label->render($image);
 690
 691             }
 692         }
 693         $label->render($image);
 694
 695         # draw the offset on the left if label_side eq right, if display_marker
 696         # offset is true in the chromosome object
 697         #
 698         $self->draw_mark($image);
 699     }
 700
 701 }
 702
 703 =head2 function draw_tick
 704
 705   Synopsis:
 706   Arguments:
 707   Returns:
 708   Side effects:
 709   Description:
 710
 711 =cut
 712
 713 sub draw_tick {
 714     my $self  =shift;
 715     my $image = shift;
 716
 717     my $color = $image -> colorResolve($self->get_color());
 718     my $halfwidth = int($self->get_chromosome->get_width/2);
 719     my $y = $self->get_chromosome()->get_vertical_offset() + $self->get_chromosome()->mapunits2pixels($self->get_offset());
 720
 721     if ($self->get_show_tick()) {
 722         $image -> line($self->get_chromosome()->get_horizontal_offset() - $halfwidth +1, $y, $self->get_chromosome()->get_horizontal_offset()+$halfwidth-1, $y, $color);
 723     }
 724 }
 725
 726 =head2 functions get_label(), set_label()
 727
 728   Synopsis:     Accessors for the label property, which
 729                 is a CXGN::Cview::Label object. This attribute
 730                 is set automatically in the constructor and the
 731                 label name set to the marker name.
 732   Arguments:    the setter takes a CXGN::Cview::Label object as a
 733                 parameter.
 734   Returns:      the getter returns the marker\'s label object.
 735   Side effects: the label object attributes are used for rendering
 736                 the label.
 737   Description:
 738
 739 =cut
 740
 741 sub get_label {
 742     my $self=shift;
 743     return $self->{label};
 744 }
 745
 746 sub set_label {
 747     my $self=shift;
 748     $self->{label}=shift;
 749 }
 750
 751 =head2 function is_visible()
 752
 753 returns true if the marker is visible, meaning it is not hidden and it lies not outside the chromosome section, if defined.
 754
 755 =cut
 756
 757 sub is_visible {
 758     my $self = shift;
 759     #
 760     # if it is hidden, we know its not visible...
 761     #
 762     if ($self->{hidden}) { return 0; }
 763     #
 764     # if the chromosome is a section, we return true if the offset is in that inverval, not otherwise
 765     if ($self->get_chromosome()->is_section()) {
 766         if ($self->get_offset() >= $self->get_chromosome()->get_start_cM() && $self->get_offset() <= $self ->get_chromosome()->{end_cM}) {
 767             return 1;
 768         }
 769         else {return 0; }
 770     }
 771     #
 772     # it's not hidden, and it's not a section, so it has to be visible...
 773     #
 774     return 1;
 775 }
 776
 777 sub get_type{
 778     my $self = shift;
 779     return $self -> {type};
 780 }
 781
 782 =head2 function draw_mark()
 783
 784   Synopsis:     draws the mark as specified with the other mark functions.
 785   Arguments:
 786   Returns:
 787   Side effects:
 788   Description:  the mark is a little circle next to the marker name that
 789                 can be used to convey additional information about the marker.
 790                 The color can be set using set_mark_color() and the link can be
 791                 set using set_mark_url(). The mark should be its own object...
 792
 793 =cut
 794
 795 sub draw_mark {
 796     my $self = shift;
 797     my $image = shift;
 798
 799     my $halfwidth = $self -> get_chromosome()->get_width() / 2;
 800     my $label = $self->get_label();
 801     my $x = 0;
 802     my $y = $label->get_vertical_offset();
 803     my $circle_color = $image -> colorResolve($self->{mark_color}[0], $self->{mark_color}[1], $self->{mark_color}[2]);
 804
 805     if ($self->get_show_mark()) {
 806         if ($self->get_label_side() eq "left") {
 807
 808             # draw the mark for the left labels
 809             #
 810             my $circle_color = $image -> colorResolve($self->get_mark_color());
 811
 812             $x = $self->get_chromosome()->get_horizontal_offset()-$label->get_label_spacer()-$label->get_width()-$self->get_mark_size();
 813
 814             $self->set_mark_rect($x, $y, $x+$self->get_mark_size(), $y+$self->get_mark_size());
 815         }
 816         elsif ($self->get_label_side() eq "right") {
 817             $x = $self->get_chromosome()->get_horizontal_offset()+$label->get_label_spacer()+$self->get_label_width()+$self->get_mark_size();
 818
 819             $self->set_mark_rect($x, $y, $x+$self->get_mark_size(), $y+$self->get_mark_size());
 820         }
 821         for (my $i=1; $i<=$self->get_mark_size(); $i++) {
 822             $image -> arc($x,$y, $i, $i, 0, 360, $circle_color);
 823         }
 824     }
 825 }
 826
 827 =head2 accessors get_offset(), set_offset()
 828
 829 Returns the offset of the marker in map units (by default cM).
 830
 831 =cut
 832
 833 sub get_offset {
 834     my $self = shift;
 835     return $self->{offset};
 836 }
 837
 838 sub set_offset {
 839     my $self = shift;
 840     $self->{offset}=shift;
 841 }
 842
 843 =head2 functions get_north_range(), set_north_range
 844
 845   Synopsis:     $m->set_north_range(5)
 846   Args/returns: a range in cM that describes the uncertainty
 847                 of the marker\'s location
 848   Side effects: the label is drawn reflecting the uncertainty.
 849   Description:
 850
 851 =cut
 852
 853 sub get_north_range {
 854     my $self=shift;
 855     return $self->{north_range};
 856 }
 857
 858 sub set_north_range {
 859     my $self=shift;
 860     $self->{north_range}=shift;
 861 }
 862
 863 =head2 functions get_south_range(), set_south_range()
 864
 865   Synopsis:     $m->set_south_range(4)
 866   Description:  see set_north_range()
 867
 868 =cut
 869
 870 sub get_south_range {
 871     my $self=shift;
 872     return $self->{south_range};
 873 }
 874
 875 sub set_south_range {
 876     my $self=shift;
 877     $self->{south_range}=shift;
 878 }
 879
 880
 881 =head2 set_range_coords
 882
 883  Usage:        $m->set_range_coords($start, $end)
 884  Desc:         for markers that require a range, sets
 885                the feature start to $start and end to $end,
 886                calling set_offset(), set_north_range(), and
 887                set_south_range() with the appropriate values.
 888  Ret:          nothing
 889  Args:         start [int], end [int]
 890  Side Effects:
 891  Example:
 892
 893 =cut
 894
 895 sub set_range_coords {
 896     my $self = shift;
 897     my $start = shift;
 898     my $end = shift;
 899     $self->set_offset(($start + $end )/2);
 900     $self->set_north_range(($end - $start)/2);
 901     $self->set_south_range(($end-$start)/2);
 902
 903 }
 904
 905 =head2 get_start
 906
 907  Usage:        my $s = $m->get_start();
 908  Desc:         accessor for the start coord of the marker.
 909                no corresponding setter. Use set_range_coords().
 910  Ret:
 911  Args:
 912  Side Effects:
 913  Example:
 914
 915 =cut
 916
 917 sub get_start {
 918     my $self = shift;
 919     return $self->get_offset()-$self->get_north_range();
 920 }
 921
 922 =head2 get_end
 923
 924  Usage:        my $e = $m->get_end();
 925  Desc:         accessor for the end coord of the marker.
 926  Ret:          no corresponding setter. Use set_range_coords().
 927  Args:
 928  Side Effects:
 929  Example:
 930
 931 =cut
 932
 933 sub get_end {
 934     my $self = shift;
 935     return $self->get_offset()+$self->get_south_range();
 936 }
 937
 938 =head2 accessors get_orientation, set_orientation
 939
 940  Usage:        $m->set_orientation("F");
 941  Desc:
 942  Property      the orientation of the feature, either "F" or "R".
 943  Side Effects:
 944  Example:
 945
 946 =cut
 947
 948 sub get_orientation {
 949   my $self = shift;
 950
 951   # make F the default
 952   #
 953   if (!exists($self->{orientation})) {
 954       $self->{orientation} = "F";
 955   }
 956   return $self->{orientation};
 957 }
 958
 959 sub set_orientation {
 960   my $self = shift;
 961   my $orientation = shift;
 962   if ($orientation !~ /F|R/i) {
 963       die "Orientation has to be either F or R!";
 964   }
 965   $self->{orientation} = uc($orientation);
 966 }
 967
 968
 969 =head2 functions get_label_side(), set_label_side()
 970
 971   Synopsis:
 972   Args/Returns: either "right" or "left"
 973   Side effects: labels are drawn on the right of the
 974                 chromosome object if this equals "right", on
 975                 the left if equal to "left".
 976   Description:
 977
 978 =cut
 979
 980 sub get_label_side {
 981     my $self=shift;
 982     if (!exists($self->{label_side})) {
 983         return $self->get_chromosome()->get_label_side();
 984     }
 985     return $self->{label_side};
 986 }
 987
 988 sub set_label_side {
 989     my $self=shift;
 990     my $side = shift;
 991     $self->{label_side}=$side;
 992 }
 993
 994 =head2 function get_offset_label()
 995
 996   Synopsis:
 997   Arguments:
 998   Returns:
 999   Side effects:
1000   Description:
1001
1002 =cut
1003
1004 sub get_offset_label {
1005     my $self=shift;
1006     return $self->{offset_label};
1007 }
1008
1009 =head2 function set_offset_label()
1010
1011   Synopsis:
1012   Arguments:
1013   Returns:
1014   Side effects:
1015   Description:
1016
1017 =cut
1018
1019 sub set_offset_label {
1020     my $self=shift;
1021     $self->{offset_label}=shift;
1022 }
1023
1024 =head2 function show_offset_label()
1025
1026   Synopsis:
1027   Arguments:
1028   Returns:
1029   Side effects:
1030   Description:
1031
1032 =cut
1033
1034 sub show_offset_label {
1035     my $self = shift;
1036     my $show = shift;
1037     if ($show != undef) {
1038         my $self->{show_offset_label}=$show;
1039     }
1040     else {
1041         return $self->{show_offset_label};
1042     }
1043 }
1044
1045 =head2 function get_show_tick
1046
1047   Synopsis:
1048   Arguments:
1049   Returns:
1050   Side effects:
1051   Description:
1052
1053 =cut
1054
1055 sub get_show_tick {
1056 my $self=shift;
1057 return $self->{show_tick};
1058 }
1059
1060 =head2 function set_show_tick
1061
1062   Synopsis:
1063   Arguments:
1064   Returns:
1065   Side effects:
1066   Description:
1067
1068 =cut
1069
1070 sub set_show_tick {
1071 my $self=shift;
1072 $self->{show_tick}=shift;
1073 }
1074
1075 =head2 functions set_url(), get_url()
1076
1077  sets the url that this marker links to.
1078
1079 =cut
1080
1081 sub set_url {
1082     my $self = shift;
1083     $self->get_label()->set_url(shift);
1084 }
1085
1086 sub get_url {
1087     my $self = shift;
1088     return $self->get_label()->get_url();
1089 }
1090
1091 =head2 accessors set_tooltip, get_tooltip
1092
1093   Property:
1094   Setter Args:
1095   Getter Args:
1096   Getter Ret:
1097   Side Effects:
1098   Description:
1099
1100 =cut
1101
1102 sub get_tooltip {
1103     my $self=shift;
1104     return $self->{tooltip};
1105 }
1106
1107 sub set_tooltip {
1108     my $self=shift;
1109     $self->{tooltip}=shift;
1110 }
1111
1112
1113
1114 =head2 function hilite()
1115
1116  Hilites the marker in the hilite color (default is yellow).
1117
1118 =cut
1119
1120 sub hilite {
1121     my $self = shift;
1122     $self->get_label()->set_hilited(1);
1123 }
1124
1125 sub unhilite {
1126     my $self = shift;
1127     $self->get_label()->set_hilited(0);
1128 }
1129
1130 sub get_hilited {
1131     my $self = shift;
1132     return $self->get_label()->get_hilited();
1133 }
1134
1135
1136
1137 =head2 functions get_label_height()
1138
1139   Synopsis:     gets the height of the label.
1140                 note: the height can\'t be set because
1141                 it depends on the font size.
1142   Arguments:
1143   Returns:
1144   Side effects:
1145   Description:
1146
1147 =cut
1148
1149
1150 sub get_label_height {
1151     my $self = shift;
1152     return $self ->get_label()->get_font()->height();
1153 }
1154
1155 =head2 function get_label_width()
1156
1157   Synopsis:     gets the width of the label.
1158                 note - the width can\'t be set because
1159                 it depends on the text in the label
1160                 and the current font size.
1161   Arguments:
1162   Returns:
1163   Side effects:
1164   Description:
1165
1166 =cut
1167
1168
1169 sub get_label_width {
1170     my $self = shift;
1171     return $self->get_label()->get_width();
1172 }
1173
1174 =head2 functions set_label_pos(), get_label_pos()
1175
1176   Synopsis:
1177   Arguments:
1178   Returns:
1179   Side effects:
1180   Description:
1181
1182 =cut
1183
1184
1185 sub set_label_pos {
1186     #
1187     # sets the position of the label in pixels.
1188     #
1189     my $self = shift;
1190     my $vertical_position = shift;
1191 #    $self -> {label_position} = $vertical_position;
1192     $self->get_label()->set_vertical_offset($vertical_position);
1193 }
1194
1195 sub get_label_pos {
1196     my $self = shift;
1197     #return $self->{label_position};
1198     return $self->get_label()->get_vertical_offset();
1199 }
1200
1201 =head2 functions set_label_spacer(), get_label_spacer()
1202
1203   Synopsis:     Accessors for the label_spacer property, which
1204                 represents the number of pixels from the edge of the
1205                 label to the mid-line of the chromosome.
1206   Arguments:
1207   Returns:
1208   Side effects:
1209   Description:
1210
1211 =cut
1212
1213
1214 sub set_label_spacer {
1215     my $self = shift;
1216     my $label_spacer = shift;
1217     $self->get_label()->set_label_spacer($label_spacer);
1218 }
1219
1220 sub get_label_spacer {
1221     my $self = shift;
1222
1223     return $self->get_label()->get_label_spacer();
1224 }
1225
1226 =head2 function get_label_line_color()
1227
1228   Synopsis:
1229   Arguments:
1230   Returns:
1231   Side effects:
1232   Description:
1233
1234 =cut
1235
1236 sub get_label_line_color {
1237     my $self=shift;
1238     return $self->get_label()->get_line_color();
1239 }
1240
1241 =head2 function set_label_line_color()
1242
1243   Synopsis:
1244   Arguments:
1245   Returns:
1246   Side effects:
1247   Description:
1248
1249 =cut
1250
1251 sub set_label_line_color {
1252     my $self=shift;
1253     $self->get_label()->set_line_color(@_);
1254 }
1255
1256 =head2 function get_hilite_color()
1257
1258  Gets the hilite color. Returns the RGB components of the color
1259  as a list of three elements.
1260
1261 =cut
1262
1263 sub get_hilite_color {
1264     my $self = shift;
1265 #    if (!exists($self->{hilite_color})) { @{$self->{hilite_color}}=(); }
1266 #    return @{$self->{hilite_color}};
1267     return $self->get_label()->get_hilite_color();
1268 }
1269
1270 =head2 function set_hilite_color()
1271
1272 Sets the hilite color. Default is yellow. Three numbers between 0 and 255 for red, green and blue channels are required.
1273
1274 =cut
1275
1276 sub set_hilite_color {
1277     my $self = shift;
1278     $self->get_label()->set_hilite_color(@_);
1279 }
1280
1281 =head2 function get_offset_text_color()
1282
1283  Gets the current offset text color (the color of the line
1284  that connects the marker tick with the marker name).
1285
1286 =cut
1287
1288 sub get_offset_text_color {
1289     my $self = shift;
1290     #if (!exists($self->{offset_text_color})) { @{$self->{offset_text_color}}=(); }
1291     return $self->get_offset_label()->get_text_color();
1292     #return @{$self->{offset_text_color}};
1293 }
1294
1295 =head2 function set_offset_text_color()
1296
1297   Sets the color of the offset scale text, if enabled.
1298
1299 =cut
1300
1301 sub set_offset_text_color {
1302     my $self = shift;
1303     $self->get_offset_label()->set_text_color(@_);
1304 }
1305
1306 =head2 function get_text_color()
1307
1308  gets the color of the label text.
1309
1310 =cut
1311
1312
1313 sub get_text_color {
1314     my $self = shift;
1315     return $self->get_label()->get_text_color();
1316 }
1317
1318 =head2 function set_text_color()
1319
1320  sets the color of the label text.
1321
1322 =cut
1323
1324 sub set_text_color {
1325     my $self = shift;
1326     $self->get_label()->set_text_color(@_);
1327
1328 }
1329
1330 =head2 accessors get_order_in_loc(), set_order_in_loc()
1331
1332   Synopsis:     I think this is deprecated...
1333   Arguments:
1334   Returns:
1335   Side effects:
1336   Description:
1337
1338 =cut
1339
1340 sub get_order_in_loc {
1341     my $self=shift;
1342     return $self->{order_in_loc};
1343 }
1344
1345 sub set_order_in_loc {
1346     my $self=shift;
1347     $self->{order_in_loc}=shift;
1348 }
1349
1350
1351 =head2 functions get_location_subscript(), set_location_subscript()
1352
1353   Synopsis:     sets the location subscript of this marker position
1354   Arguments:    setter: a subscript, usually "a".."c" or similar
1355   Returns:      getter: the current subscript
1356   Side effects: the subscript will be rendered on the map,
1357                 added to the marker name. The CXGN::Cview::Marker function
1358                 get_name() will also include the subscript, whereas
1359                 get_marker_name() will not.
1360   Description:
1361
1362 =cut
1363
1364 sub get_location_subscript {
1365     my $self=shift;
1366     return $self->{location_subscript};
1367 }
1368
1369 sub set_location_subscript {
1370     my $self=shift;
1371     $self->{location_subscript}=shift;
1372 }
1373
1374 =head2 accessors get_loc_type(), set_loc_type()
1375
1376   Synopsis:
1377   Arguments:
1378   Returns:
1379   Side effects:
1380   Description:
1381
1382 =cut
1383
1384 sub get_loc_type {
1385     my $self=shift;
1386     return $self->{loc_type};
1387 }
1388
1389 sub set_loc_type {
1390     my $self=shift;
1391     $self->{loc_type}=shift;
1392 }
1393
1394 =head2 accessors get_loc_order(), set_loc_order()
1395
1396   Synopsis:     I think this is deprecated.
1397   Arguments:
1398   Returns:
1399   Side effects:
1400   Description:
1401
1402 =cut
1403
1404 sub get_loc_order {
1405     my $self=shift;
1406     return $self->{loc_order};
1407 }
1408
1409 sub set_loc_order {
1410     my $self=shift;
1411     $self->{loc_order}=shift;
1412 }
1413
1414 =head2 has_range
1415
1416  Usage:        my $flag = $m->has_range()
1417  Desc:         returns true if the marker has a range defined
1418                (usually using set_north_range() and set_south_range())
1419                false otherwise.
1420  Side Effects: none
1421  Example:
1422
1423 =cut
1424
1425 sub has_range {
1426     my $self = shift;
1427     if ( ($self->get_end() - $self->get_start()) >  12) { return 1;}
1428     return 0;
1429 }
1430