lib/CXGN/Cview/Marker.pm

   1 package CXGN::Cview::Marker;
   2
   3 =head1 NAME
   4
   5 CXGN::Cview::Marker - a class for drawing markers
   6
   7 =head1 DESCRIPTION
   8
   9 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:
  10
  11 =over 5
  12
  13 =item o
  14
  15 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.
  16
  17 =item o
  18
  19 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.
  20
  21 =back
  22
  23 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.
  24
  25 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.
  26
  27 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.
  28
  29 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>.
  30
  31 =head1 SEE ALSO
  32
  33 See also the documentation in L<CXGN::Cview>.
  34
  35 =head1 AUTHOR(S)
  36
  37 Lukas Mueller (lam87@cornell.edu)
  38
  39 =head1 VERSION and CHANGE HISTORY
  40
  41 Original version July 2004
  42
  43 [2006-07-07] Replaced label functions with CXGN::Cview::Label class.
  44
  45 =head1 FUNCTIONS
  46
  47
  48 =cut
  49
  50 return 1;
  51
  52 use strict;
  53 use warnings;
  54 use CXGN::Cview::ImageObject;
  55 use CXGN::Cview::Label;
  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 || 0) ) . " ");
 124     $self->set_offset_label($offset_label);
 125
 126     return $self;
 127 }
 128
 129 =head2 function get_color()
 130
 131 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.
 132
 133 =cut
 134
 135 sub get_color {
 136     my $self = shift;
 137     if (!exists($self->{marker_color})) { @{$self->{marker_color}}=(); }
 138     return @{$self->{marker_color}};
 139 }
 140
 141 =head2 function set_color()
 142
 143 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.
 144
 145 =cut
 146
 147 sub set_color {
 148     my $self = shift;
 149     $self->{marker_color}[0]=shift;
 150     $self->{marker_color}[1]=shift;
 151     $self->{marker_color}[2]=shift;
 152 }
 153
 154
 155 =head2 function get_name()
 156
 157  Gets the complete name of the marker including the suffix.
 158
 159 =cut
 160
 161 sub get_name {
 162     my $self = shift;
 163     # test if there is anything in loation_subscript and set to empty string
 164     # otherwise a 0 may be appended.
 165     if (!$self->get_location_subscript()) { $self->set_location_subscript(""); }
 166     return $self->get_marker_name().$self->get_location_subscript();
 167 }
 168
 169 =head2 functions get_marker_name(), set_marker_name()
 170
 171  gets the marker name, excluding the suffix.
 172
 173 =cut
 174
 175 sub get_marker_name {
 176     my $self = shift;
 177     # this function returns the marker name without the subscript. This is useful for constructing links to the marker detail page
 178     # which requires a type/name tuple
 179     if (!exists($self->{marker_name}) || !defined($self->{marker_name})) { $self->{marker_name}=""; }
 180     return $self->{marker_name};
 181 }
 182
 183 sub set_marker_name {
 184     my $self = shift;
 185     my $name = shift;
 186     $self->{marker_name}=$name;
 187 }
 188
 189 =head2 accessors get_synonyms, set_synonyms
 190
 191  Usage:
 192  Desc:
 193  Property
 194  Side Effects:
 195  Example:
 196
 197 =cut
 198
 199 sub get_synonyms {
 200   my $self = shift;
 201   if (!exists($self->{synonyms})) {
 202       $self->{synonyms} = [];
 203   }
 204   return @{$self->{synonyms}};
 205 }
 206
 207 sub set_synonyms {
 208   my $self = shift;
 209   $self->{synonyms} = shift;
 210 }
 211
 212
 213 =head2 functions get_id(), set_id()
 214
 215 gets the unique id associated with the marker.
 216
 217 =cut
 218
 219 sub get_id {
 220     my $self = shift;
 221     if (!exists($self->{marker_id}) || !defined($self->{marker_id})) {
 222         $self->{marker_id}="";
 223     }
 224     return $self->{marker_id};
 225 }
 226
 227 sub set_id {
 228     my $self = shift;
 229     $self->{marker_id}=shift;
 230 }
 231
 232 =head2 functions set_confidence() and get_confidence()
 233
 234   Synopsis:     my $confidence = $m->get_confidence()
 235   Arguments:    setter function: -1 ... 3.
 236                 -1 means uncalculated confidence
 237                 1 is ILOD<3
 238                 2 is CFLOD=3
 239                 3 is FLOD>3
 240   Returns:      getter returns values above
 241                 defaults to -1 if confidence property has not been set.
 242   Side effects: display in the chromosome viewer depends on confidence values.
 243   Description:
 244
 245 =cut
 246
 247 sub set_confidence {
 248     my $self = shift;
 249     $self->{confidence}=shift;
 250 }
 251
 252 sub get_confidence {
 253     my $self= shift;
 254     if (!exists($self->{confidence}) || !defined($self->{confidence}) || !$self->{confidence}) {
 255         $self->{confidence}=-1;
 256     }
 257     return $self->{confidence};
 258 }
 259
 260
 261
 262 =head2 accessors set_marker_type() and get_marker_type()
 263
 264   Synopsis:     accessors for the marker_type property.
 265   Arguments:
 266   Returns:
 267   Side effects: rendering in the chromosome viewer depends on
 268                 marker type.
 269   Description:  marker types are: RFLP, SSR, CAPS and COS.
 270
 271 =cut
 272
 273 sub set_marker_type {
 274     my $self = shift;
 275     $self->{marker_type} = shift;
 276 }
 277
 278 sub get_marker_type {
 279     my $self = shift;
 280     if (!exists($self->{marker_type}) || !defined($self->{marker_type})) {
 281         $self->{marker_type}="";
 282     }
 283     return $self->{marker_type};
 284 }
 285
 286 =head2 function get_mark_color()
 287
 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
 293 =cut
 294
 295 sub get_mark_color {
 296     my $self = shift;
 297     return @{$self->{mark_color}};
 298 }
 299
 300 =head2 function set_mark_color()
 301
 302 the mark is a little circle displayed after the marker name.
 303 it can be used to add additional visual information for a marker.
 304 The mark is clickable. The link can be set using set_mark_link().
 305 The default color is white with no link.
 306
 307 =cut
 308
 309 sub set_mark_color {
 310     # the mark is a little circle displayed after the marker name.
 311     # it can be used to add additional visual information for a marker.
 312     # The mark is clickable. The link can be set using set_mark_link().
 313     # The default color is white with no link.
 314     my $self = shift;
 315     $self->{mark_color}[0] = shift;
 316     $self->{mark_color}[1] = shift;
 317     $self->{mark_color}[2] = shift;
 318 }
 319
 320 =head2 function set_show_mark()
 321
 322   Synopsis:     $m->set_show_mark()
 323   Arguments:    none
 324   Returns:      nothing
 325   Side effects: causes the mark to be displayed when the marker
 326                 is renderd.
 327   Description:
 328
 329 =cut
 330
 331 sub set_show_mark {
 332     my $self = shift;
 333     $self->{show_mark} = 1;
 334 }
 335
 336 =head2 function hide_mark()
 337
 338   Synopsis:     $m->hide_mark()
 339   Arguments:
 340   Returns:
 341   Side effects: hides the mark
 342   Description:
 343
 344 =cut
 345
 346 sub hide_mark {
 347     my $self = shift;
 348     $self->{show_mark}=0;
 349 }
 350
 351 =head2 function get_show_mark()
 352
 353   Synopsis:
 354   Arguments:
 355   Returns:
 356   Side effects:
 357   Description:
 358
 359 =cut
 360
 361 sub get_show_mark {
 362     my $self = shift;
 363     return $self->{show_mark};
 364 }
 365
 366 =head2 functions set_mark_link(), get_mark_link()
 367
 368   Synopsis:
 369   Arguments:
 370   Returns:
 371   Side effects:
 372   Description:
 373
 374 =cut
 375
 376 sub set_mark_link {
 377     my $self = shift;
 378     $self->{mark_link} = shift;
 379 }
 380
 381 sub get_mark_link {
 382     my $self = shift;
 383     if (!exists($self->{mark_link})) { $self->{mark_link}=""; }
 384     return $self ->{mark_link};
 385 }
 386
 387 =head2 functions has_overgo(), set_has_overgo()
 388
 389   Synopsis:     $m->has_overgo()
 390   Arguments:
 391   Returns:
 392   Side effects: used to derive the mark\'s color
 393   Description:
 394
 395 =cut
 396
 397 sub has_overgo {
 398     my $self = shift;
 399     return $self->{has_overgo};
 400 }
 401
 402 sub set_has_overgo {
 403     my $self = shift;
 404     $self->{has_overgo}=1;
 405 }
 406
 407 =head2 functions has_bacs(), set_has_bacs()
 408
 409   Synopsis:     $m->set_has_bacs(1)
 410   Arguments:
 411   Returns:      nothing
 412   Side effects: causes the mark to be displayed in red.
 413   Description:
 414
 415 =cut
 416
 417 sub set_has_bacs {
 418     my $self = shift;
 419     $self->{has_bacs} = shift; # the number of bacs associated with this marker
 420 }
 421
 422 sub has_bacs {
 423     my $self = shift;
 424     return $self->{has_bacs};
 425 }
 426
 427 =head2 functions get_mark_rect(), set_mark_rect()
 428
 429   Synopsis:
 430   Arguments:
 431   Returns:
 432   Side effects:
 433   Description:
 434
 435 =cut
 436
 437 sub get_mark_rect {
 438     my $self = shift;
 439     if (! exists($self->{mark_rect}) || !defined($self->{mark_rect})) { @{$self->{mark_rect}} = (0,0,0,0); }
 440     return ($self ->{mark_rect}[0], $self->{mark_rect}[1], $self->{mark_rect}[2], $self->{mark_rect}[3]);
 441 }
 442
 443 sub set_mark_rect {
 444     my $self = shift;
 445     ($self ->{mark_rect}[0], $self->{mark_rect}[1], $self->{mark_rect}[2], $self->{mark_rect}[3]) = @_;
 446 }
 447
 448 =head2 functions set_mark_size(), get_mark_size()
 449
 450   Synopsis:
 451   Arguments:
 452   Returns:
 453   Side effects:
 454   Description:
 455
 456 =cut
 457
 458 sub set_mark_size {
 459     my $self = shift;
 460     $self->{mark_size} = shift;
 461 }
 462
 463 sub get_mark_size {
 464     my $self = shift;
 465     if (!exists($self->{mark_size}) || !defined($self->{mark_size})) { $self->{mark_size}=0; }
 466     return $self->{mark_size};
 467 }
 468
 469 =head2 functions is_frame_marker(), set_frame_marker()
 470
 471   Synopsis:
 472   Arguments:    none
 473   Returns:      returns true if the object represents
 474                 a frame marker.
 475   Side effects: the chromosome viewer may decide to render
 476                 these markers differently
 477   Description:  set_frame_marker just sets the property to 1.
 478                 It cannot be unset.
 479
 480 =cut
 481
 482 sub is_frame_marker {
 483     my $self = shift;
 484     if (!exists($self->{loc_type}) || !defined($self->{loc_type})) { $self->{loc_type}=""; }
 485     return ($self->{loc_type} eq "frame");
 486 }
 487
 488 sub set_frame_marker {
 489     my $self = shift;
 490     $self->{loc_type} = "frame";
 491 }
 492
 493
 494 =head2 functions set_chromosome(), get_chromosome()
 495
 496   Synopsis:     accessors for the chromosome property, representing
 497                 the chromosome this marker is associated with.
 498   Arguments:    setter: a CXGN::Cview::Chromosome object.
 499   Returns:      getter: a CXGN::Cview::Chromosome object.
 500   Side effects: the marker will be drawn on this chromosome. The
 501                 marker also needs to be added to the marker list of
 502                 the chromosome. Calling add_marker on the chromosome
 503                 object takes care of all that.
 504   Description:
 505
 506 =cut
 507
 508 sub get_chromosome {
 509     my $self=shift;
 510     return $self->{chromosome};
 511 }
 512
 513 sub set_chromosome {
 514     my $self =shift;
 515     $self->{chromosome}=shift;
 516 }
 517
 518 =head2 function hide()
 519
 520 Hides the marker completely from the chromosome.
 521
 522 =cut
 523
 524 sub hide {
 525     my $self = shift;
 526     #$self -> {hidden} = 1;
 527     $self->get_label()->set_hidden(1);
 528 }
 529
 530 =head2 function unhide()
 531
 532 Unhides the marker.
 533
 534 =cut
 535
 536 sub unhide {
 537     my $self = shift;
 538     #$self -> {hidden} = 0;
 539     $self->get_label()->set_hidden(0);
 540 }
 541
 542 =head2 function is_hidden()
 543
 544 Returns true if marker is hidden.
 545
 546 =cut
 547
 548 sub is_hidden {
 549     my $self = shift;
 550     #return $self -> {hidden};
 551     return $self->get_label()->is_hidden();
 552 }
 553
 554 =head2 function hide_label()
 555
 556 Hides the label of the marker only. The marker 'tick' is still being drawn.
 557
 558 =cut
 559
 560 sub hide_label {
 561     my $self= shift;
 562     #$self->{label_hidden} = 1;
 563     $self->get_label()->set_hidden(1);
 564 }
 565
 566 =head2 function show_label()
 567
 568 Unhides the label if it was previously hidden. Otherwise has no effect.
 569
 570 =cut
 571
 572 sub show_label {
 573     my $self=shift;
 574     #$self ->{label_hidden} = 0;
 575     $self->get_label()->set_hidden(0);
 576 }
 577
 578 =head2 function is_label_visible()
 579
 580 Returns true if the label is not hidden.
 581
 582 =cut
 583
 584 sub is_label_visible {
 585     my $self = shift;
 586     return !$self->is_hidden();
 587 }
 588
 589 =head2 function get_image_map()
 590
 591 Returns the image map for this label as a string. Usually the chromosome object calls this function.
 592
 593 =cut
 594
 595 sub get_image_map {
 596     my $self = shift;
 597     #print STDERR "get_image_mapo marker\n";
 598 #    my $coords = join ",", ($self -> get_label_rect());
 599     my $s = "";
 600     if ($self->get_url()) {
 601         $s = $self->get_label()->get_image_map();
 602 #       $s = "<area shape=\"rect\" coords=\"".$coords."\" href=\"".$self->get_url()."\" alt=\"\" />\n";
 603     }
 604     if ($self->get_show_mark()) {
 605         $s .= "<area shape=\"rect\" coords=\"".(join(",", $self->get_mark_rect()))."\" href=\"".$self->get_mark_link()."\" alt=\"\" title=\"".($self->get_tooltip())."\"  />\n";
 606
 607     }
 608     return $s;
 609
 610 }
 611
 612 =head2 function render()
 613
 614     $marker -> render($image);
 615
 616 Renders the marker on a GD image object. The chromosome object usually calls this function to render the entire chromosome.
 617
 618 =cut
 619
 620 sub render {
 621     my $self = shift;
 622     my $image = shift;
 623
 624     # calculate y position in pixels
 625     #
 626     my $y = $self->get_chromosome()->get_vertical_offset() + $self->get_chromosome()->mapunits2pixels($self->get_offset());
 627
 628     #warn "[Marker.pm] ".$self->get_offset()."cM is $y pixels...\n";
 629     # determine the side which this label should be drawn on. If it was not set manually,
 630     # retrieve the side from the chromosome as a default.
 631     #
 632     if (!$self->get_label_side()) {
 633         $self->set_label_side($self->get_chromosome()->get_label_side());
 634     }
 635
 636     # render marker only if it is visible (markers outside of sections or hidden markers are not visible)
 637     if ($self -> is_visible()) {
 638
 639         # draw the tick on the chromosome
 640         #
 641         my $color = $image -> colorResolve($self->get_color());
 642         my $chromosome_width = $self->get_chromosome()->get_width();
 643         my $halfwidth = int($chromosome_width/2);
 644         $self->draw_tick($image);
 645
 646         # deal with label stuff
 647         #
 648         # the $label object deals with displaying the marker's name
 649         # the $offset_label object deals with displaying the marker's offset
 650         # on the opposite side
 651         #
 652         my $label = $self->get_label();
 653         my $offset_label = $self->get_offset_label();
 654
 655         if ($self->get_hilited()) {
 656             $label->set_hilited(1);
 657         }
 658
 659         # draw the labels left of the chromosome if label_side eq left
 660         #
 661         if ($self->get_label_side() eq "left") {
 662
 663             # define the Label's reference point
 664             #
 665             $label->set_reference_point($self->get_chromosome()->get_horizontal_offset()-$halfwidth,$y);
 666             $label->set_horizontal_offset($self->get_chromosome()->get_horizontal_offset()- $label->get_label_spacer());
 667
 668             # draw the offset on the right if label_side eq left, if display_marker
 669             # offset is true in the chromosome object
 670             #
 671             if ($self->get_chromosome()->{display_marker_offset}) {
 672
 673                 # define the label's reference point
 674                 #
 675                 $offset_label->set_reference_point($self->get_chromosome()->get_horizontal_offset()+$halfwidth, $y);
 676                 $offset_label->set_horizontal_offset($self->get_chromosome()->get_horizontal_offset()+ $label->get_label_spacer()
 677                                                      );
 678                 $offset_label->set_vertical_offset($label->get_vertical_offset());
 679                 $offset_label->set_align_side("left");
 680
 681                 $offset_label->set_hidden($label->is_hidden());
 682                 $offset_label->render($image);
 683             }
 684         }
 685
 686         # draw the labels on the right side if label_side is right
 687         #
 688         elsif ($self->get_label_side() eq "right") {
 689
 690             # define the Label's reference point (the point where the label points to)
 691             # and the horizontal offset (the actual position of the text label)
 692             #
 693             $label->set_reference_point($self->get_chromosome()->get_horizontal_offset()+$halfwidth,$y);
 694             $label->set_horizontal_offset($self->get_chromosome()->get_horizontal_offset()+$label->get_label_spacer());
 695
 696             # if show offset is turned on, draw a label on the opposite side of the chromosome
 697             # showing the cM position
 698             #
 699             if ($self->get_chromosome()->{display_marker_offset}) {
 700
 701                 $offset_label->set_reference_point(
 702                                                    $self->get_chromosome()->get_horizontal_offset()-$halfwidth, $y
 703
 704                                                    );
 705                 $offset_label->set_horizontal_offset($self->get_chromosome()->get_horizontal_offset()-
 706                                                      $label->get_label_spacer()
 707                                                      );
 708                 $offset_label->set_vertical_offset($label->get_vertical_offset());
 709                 $offset_label->set_align_side("right");
 710                 $offset_label->set_hidden($label->is_hidden());
 711                 $offset_label->render($image);
 712
 713             }
 714         }
 715         $label->render($image);
 716
 717         # draw the offset on the left if label_side eq right, if display_marker
 718         # offset is true in the chromosome object
 719         #
 720         $self->draw_mark($image);
 721     }
 722
 723 }
 724
 725 =head2 function draw_tick
 726
 727   Synopsis:
 728   Arguments:
 729   Returns:
 730   Side effects:
 731   Description:
 732
 733 =cut
 734
 735 sub draw_tick {
 736     my $self  =shift;
 737     my $image = shift;
 738
 739     my $color = $image -> colorResolve($self->get_color());
 740     my $halfwidth = int($self->get_chromosome->get_width/2);
 741     my $y = $self->get_chromosome()->get_vertical_offset() + $self->get_chromosome()->mapunits2pixels($self->get_offset());
 742
 743     if ($self->get_show_tick()) {
 744         $image -> line($self->get_chromosome()->get_horizontal_offset() - $halfwidth +1, $y, $self->get_chromosome()->get_horizontal_offset()+$halfwidth-1, $y, $color);
 745     }
 746 }
 747
 748 =head2 functions get_label(), set_label()
 749
 750   Synopsis:     Accessors for the label property, which
 751                 is a CXGN::Cview::Label object. This attribute
 752                 is set automatically in the constructor and the
 753                 label name set to the marker name.
 754   Arguments:    the setter takes a CXGN::Cview::Label object as a
 755                 parameter.
 756   Returns:      the getter returns the marker\'s label object.
 757   Side effects: the label object attributes are used for rendering
 758                 the label.
 759   Description:
 760
 761 =cut
 762
 763 sub get_label {
 764     my $self=shift;
 765     return $self->{label};
 766 }
 767
 768 sub set_label {
 769     my $self=shift;
 770     $self->{label}=shift;
 771 }
 772
 773 =head2 function is_visible()
 774
 775 returns true if the marker is visible, meaning it is not hidden and it lies not outside the chromosome section, if defined.
 776
 777 =cut
 778
 779 sub is_visible {
 780     my $self = shift;
 781     #
 782     # if it is hidden, we know its not visible...
 783     #
 784     if ($self->{hidden}) { return 0; }
 785     #
 786     # if the chromosome is a section, we return true if the offset is in that inverval, not otherwise
 787     if ($self->get_chromosome()->is_section()) {
 788         if ($self->get_offset() >= $self->get_chromosome()->get_start_cM() && $self->get_offset() <= $self ->get_chromosome()->{end_cM}) {
 789             return 1;
 790         }
 791         else {return 0; }
 792     }
 793     #
 794     # it's not hidden, and it's not a section, so it has to be visible...
 795     #
 796     return 1;
 797 }
 798
 799 sub get_type{
 800     my $self = shift;
 801     return $self -> {type};
 802 }
 803
 804 =head2 function draw_mark()
 805
 806   Synopsis:     draws the mark as specified with the other mark functions.
 807   Arguments:
 808   Returns:
 809   Side effects:
 810   Description:  the mark is a little circle next to the marker name that
 811                 can be used to convey additional information about the marker.
 812                 The color can be set using set_mark_color() and the link can be
 813                 set using set_mark_url(). The mark should be its own object...
 814
 815 =cut
 816
 817 sub draw_mark {
 818     my $self = shift;
 819     my $image = shift;
 820
 821     my $halfwidth = $self -> get_chromosome()->get_width() / 2;
 822     my $label = $self->get_label();
 823     my $x = 0;
 824     my $y = $label->get_vertical_offset();
 825     my $circle_color = $image -> colorResolve($self->{mark_color}[0], $self->{mark_color}[1], $self->{mark_color}[2]);
 826
 827     if ($self->get_show_mark()) {
 828         if ($self->get_label_side() eq "left") {
 829
 830             # draw the mark for the left labels
 831             #
 832             my $circle_color = $image -> colorResolve($self->get_mark_color());
 833
 834             $x = $self->get_chromosome()->get_horizontal_offset()-$label->get_label_spacer()-$label->get_width()-$self->get_mark_size();
 835
 836             $self->set_mark_rect($x, $y, $x+$self->get_mark_size(), $y+$self->get_mark_size());
 837         }
 838         elsif ($self->get_label_side() eq "right") {
 839             $x = $self->get_chromosome()->get_horizontal_offset()+$label->get_label_spacer()+$self->get_label_width()+$self->get_mark_size();
 840
 841             $self->set_mark_rect($x, $y, $x+$self->get_mark_size(), $y+$self->get_mark_size());
 842         }
 843         for (my $i=1; $i<=$self->get_mark_size(); $i++) {
 844             $image -> arc($x,$y, $i, $i, 0, 360, $circle_color);
 845         }
 846     }
 847 }
 848
 849 =head2 accessors get_offset(), set_offset()
 850
 851 Returns the offset of the marker in map units (by default cM).
 852
 853 =cut
 854
 855 sub get_offset {
 856     my $self = shift;
 857     return $self->{offset};
 858 }
 859
 860 sub set_offset {
 861     my $self = shift;
 862     $self->{offset}=shift;
 863 }
 864
 865 =head2 functions get_north_range(), set_north_range
 866
 867   Synopsis:     $m->set_north_range(5)
 868   Args/returns: a range in cM that describes the uncertainty
 869                 of the marker\'s location
 870   Side effects: the label is drawn reflecting the uncertainty.
 871   Description:
 872
 873 =cut
 874
 875 sub get_north_range {
 876     my $self=shift;
 877     return $self->{north_range};
 878 }
 879
 880 sub set_north_range {
 881     my $self=shift;
 882     $self->{north_range}=shift;
 883 }
 884
 885 =head2 functions get_south_range(), set_south_range()
 886
 887   Synopsis:     $m->set_south_range(4)
 888   Description:  see set_north_range()
 889
 890 =cut
 891
 892 sub get_south_range {
 893     my $self=shift;
 894     return $self->{south_range};
 895 }
 896
 897 sub set_south_range {
 898     my $self=shift;
 899     $self->{south_range}=shift;
 900 }
 901
 902
 903 =head2 set_range_coords
 904
 905  Usage:        $m->set_range_coords($start, $end)
 906  Desc:         for markers that require a range, sets
 907                the feature start to $start and end to $end,
 908                calling set_offset(), set_north_range(), and
 909                set_south_range() with the appropriate values.
 910  Ret:          nothing
 911  Args:         start [int], end [int]
 912  Side Effects:
 913  Example:
 914
 915 =cut
 916
 917 sub set_range_coords {
 918     my $self = shift;
 919     my $start = shift;
 920     my $end = shift;
 921     $self->set_offset(($start + $end )/2);
 922     $self->set_north_range(($end - $start)/2);
 923     $self->set_south_range(($end-$start)/2);
 924
 925 }
 926
 927 =head2 get_start
 928
 929  Usage:        my $s = $m->get_start();
 930  Desc:         accessor for the start coord of the marker.
 931                no corresponding setter. Use set_range_coords().
 932  Ret:
 933  Args:
 934  Side Effects:
 935  Example:
 936
 937 =cut
 938
 939 sub get_start {
 940     my $self = shift;
 941     return $self->get_offset()-$self->get_north_range();
 942 }
 943
 944 =head2 get_end
 945
 946  Usage:        my $e = $m->get_end();
 947  Desc:         accessor for the end coord of the marker.
 948  Ret:          no corresponding setter. Use set_range_coords().
 949  Args:
 950  Side Effects:
 951  Example:
 952
 953 =cut
 954
 955 sub get_end {
 956     my $self = shift;
 957     return $self->get_offset()+$self->get_south_range();
 958 }
 959
 960 =head2 accessors get_orientation, set_orientation
 961
 962  Usage:        $m->set_orientation("F");
 963  Desc:
 964  Property      the orientation of the feature, either "F" or "R".
 965  Side Effects:
 966  Example:
 967
 968 =cut
 969
 970 sub get_orientation {
 971   my $self = shift;
 972
 973   # make F the default
 974   #
 975   if (!exists($self->{orientation})) {
 976       $self->{orientation} = "F";
 977   }
 978   return $self->{orientation};
 979 }
 980
 981 sub set_orientation {
 982   my $self = shift;
 983   my $orientation = shift;
 984   if ($orientation !~ /F|R/i) {
 985       die "Orientation has to be either F or R!";
 986   }
 987   $self->{orientation} = uc($orientation);
 988 }
 989
 990
 991 =head2 functions get_label_side(), set_label_side()
 992
 993   Synopsis:
 994   Args/Returns: either "right" or "left"
 995   Side effects: labels are drawn on the right of the
 996                 chromosome object if this equals "right", on
 997                 the left if equal to "left".
 998   Description:
 999
1000 =cut
1001
1002 sub get_label_side {
1003     my $self=shift;
1004     if (!exists($self->{label_side})) {
1005         return $self->get_chromosome()->get_label_side();
1006     }
1007     return $self->{label_side};
1008 }
1009
1010 sub set_label_side {
1011     my $self=shift;
1012     my $side = shift;
1013     $self->{label_side}=$side;
1014 }
1015
1016 =head2 function get_offset_label()
1017
1018   Synopsis:
1019   Arguments:
1020   Returns:
1021   Side effects:
1022   Description:
1023
1024 =cut
1025
1026 sub get_offset_label {
1027     my $self=shift;
1028     return $self->{offset_label};
1029 }
1030
1031 =head2 function set_offset_label()
1032
1033   Synopsis:
1034   Arguments:
1035   Returns:
1036   Side effects:
1037   Description:
1038
1039 =cut
1040
1041 sub set_offset_label {
1042     my $self=shift;
1043     $self->{offset_label}=shift;
1044 }
1045
1046 =head2 function show_offset_label()
1047
1048   Synopsis:
1049   Arguments:
1050   Returns:
1051   Side effects:
1052   Description:
1053
1054 =cut
1055
1056 sub show_offset_label {
1057     my $self = shift;
1058     my $show = shift;
1059     if ($show != undef) {
1060         my $self->{show_offset_label}=$show;
1061     }
1062     else {
1063         return $self->{show_offset_label};
1064     }
1065 }
1066
1067 =head2 function get_show_tick
1068
1069   Synopsis:
1070   Arguments:
1071   Returns:
1072   Side effects:
1073   Description:
1074
1075 =cut
1076
1077 sub get_show_tick {
1078 my $self=shift;
1079 return $self->{show_tick};
1080 }
1081
1082 =head2 function set_show_tick
1083
1084   Synopsis:
1085   Arguments:
1086   Returns:
1087   Side effects:
1088   Description:
1089
1090 =cut
1091
1092 sub set_show_tick {
1093 my $self=shift;
1094 $self->{show_tick}=shift;
1095 }
1096
1097 =head2 functions set_url(), get_url()
1098
1099  sets the url that this marker links to.
1100
1101 =cut
1102
1103 sub set_url {
1104     my $self = shift;
1105     $self->get_label()->set_url(shift);
1106 }
1107
1108 sub get_url {
1109     my $self = shift;
1110     return $self->get_label()->get_url();
1111 }
1112
1113 =head2 accessors set_tooltip, get_tooltip
1114
1115   Property:
1116   Setter Args:
1117   Getter Args:
1118   Getter Ret:
1119   Side Effects:
1120   Description:
1121
1122 =cut
1123
1124 sub get_tooltip {
1125     my $self=shift;
1126     if (!exists($self->{tooltip}) || !defined($self->{tooltip})) {
1127         $self->{tooltip} = '';
1128     }
1129     return $self->{tooltip};
1130 }
1131
1132 sub set_tooltip {
1133     my $self=shift;
1134     $self->{tooltip}=shift;
1135 }
1136
1137
1138
1139 =head2 function hilite()
1140
1141  Hilites the marker in the hilite color (default is yellow).
1142
1143 =cut
1144
1145 sub hilite {
1146     my $self = shift;
1147     $self->get_label()->set_hilited(1);
1148 }
1149
1150 sub unhilite {
1151     my $self = shift;
1152     $self->get_label()->set_hilited(0);
1153 }
1154
1155 sub get_hilited {
1156     my $self = shift;
1157     return $self->get_label()->get_hilited();
1158 }
1159
1160
1161
1162 =head2 functions get_label_height()
1163
1164   Synopsis:     gets the height of the label.
1165                 note: the height can\'t be set because
1166                 it depends on the font size.
1167   Arguments:
1168   Returns:
1169   Side effects:
1170   Description:
1171
1172 =cut
1173
1174
1175 sub get_label_height {
1176     my $self = shift;
1177     return $self ->get_label()->get_font()->height();
1178 }
1179
1180 =head2 function get_label_width()
1181
1182   Synopsis:     gets the width of the label.
1183                 note - the width can\'t be set because
1184                 it depends on the text in the label
1185                 and the current font size.
1186   Arguments:
1187   Returns:
1188   Side effects:
1189   Description:
1190
1191 =cut
1192
1193
1194 sub get_label_width {
1195     my $self = shift;
1196     return $self->get_label()->get_width();
1197 }
1198
1199 =head2 functions set_label_pos(), get_label_pos()
1200
1201   Synopsis:
1202   Arguments:
1203   Returns:
1204   Side effects:
1205   Description:
1206
1207 =cut
1208
1209
1210 sub set_label_pos {
1211     #
1212     # sets the position of the label in pixels.
1213     #
1214     my $self = shift;
1215     my $vertical_position = shift;
1216 #    $self -> {label_position} = $vertical_position;
1217     $self->get_label()->set_vertical_offset($vertical_position);
1218 }
1219
1220 sub get_label_pos {
1221     my $self = shift;
1222     #return $self->{label_position};
1223     return $self->get_label()->get_vertical_offset();
1224 }
1225
1226 =head2 functions set_label_spacer(), get_label_spacer()
1227
1228   Synopsis:     Accessors for the label_spacer property, which
1229                 represents the number of pixels from the edge of the
1230                 label to the mid-line of the chromosome.
1231   Arguments:
1232   Returns:
1233   Side effects:
1234   Description:
1235
1236 =cut
1237
1238
1239 sub set_label_spacer {
1240     my $self = shift;
1241     my $label_spacer = shift;
1242     $self->get_label()->set_label_spacer($label_spacer);
1243 }
1244
1245 sub get_label_spacer {
1246     my $self = shift;
1247
1248     return $self->get_label()->get_label_spacer();
1249 }
1250
1251 =head2 function get_label_line_color()
1252
1253   Synopsis:
1254   Arguments:
1255   Returns:
1256   Side effects:
1257   Description:
1258
1259 =cut
1260
1261 sub get_label_line_color {
1262     my $self=shift;
1263     return $self->get_label()->get_line_color();
1264 }
1265
1266 =head2 function set_label_line_color()
1267
1268   Synopsis:
1269   Arguments:
1270   Returns:
1271   Side effects:
1272   Description:
1273
1274 =cut
1275
1276 sub set_label_line_color {
1277     my $self=shift;
1278     $self->get_label()->set_line_color(@_);
1279 }
1280
1281 =head2 function get_hilite_color()
1282
1283  Gets the hilite color. Returns the RGB components of the color
1284  as a list of three elements.
1285
1286 =cut
1287
1288 sub get_hilite_color {
1289     my $self = shift;
1290 #    if (!exists($self->{hilite_color})) { @{$self->{hilite_color}}=(); }
1291 #    return @{$self->{hilite_color}};
1292     return $self->get_label()->get_hilite_color();
1293 }
1294
1295 =head2 function set_hilite_color()
1296
1297 Sets the hilite color. Default is yellow. Three numbers between 0 and 255 for red, green and blue channels are required.
1298
1299 =cut
1300
1301 sub set_hilite_color {
1302     my $self = shift;
1303     $self->get_label()->set_hilite_color(@_);
1304 }
1305
1306 =head2 function get_offset_text_color()
1307
1308  Gets the current offset text color (the color of the line
1309  that connects the marker tick with the marker name).
1310
1311 =cut
1312
1313 sub get_offset_text_color {
1314     my $self = shift;
1315     #if (!exists($self->{offset_text_color})) { @{$self->{offset_text_color}}=(); }
1316     return $self->get_offset_label()->get_text_color();
1317     #return @{$self->{offset_text_color}};
1318 }
1319
1320 =head2 function set_offset_text_color()
1321
1322   Sets the color of the offset scale text, if enabled.
1323
1324 =cut
1325
1326 sub set_offset_text_color {
1327     my $self = shift;
1328     $self->get_offset_label()->set_text_color(@_);
1329 }
1330
1331 =head2 function get_text_color()
1332
1333  gets the color of the label text.
1334
1335 =cut
1336
1337
1338 sub get_text_color {
1339     my $self = shift;
1340     return $self->get_label()->get_text_color();
1341 }
1342
1343 =head2 function set_text_color()
1344
1345  sets the color of the label text.
1346
1347 =cut
1348
1349 sub set_text_color {
1350     my $self = shift;
1351     $self->get_label()->set_text_color(@_);
1352
1353 }
1354
1355 =head2 accessors get_order_in_loc(), set_order_in_loc()
1356
1357   Synopsis:     I think this is deprecated...
1358   Arguments:
1359   Returns:
1360   Side effects:
1361   Description:
1362
1363 =cut
1364
1365 sub get_order_in_loc {
1366     my $self=shift;
1367     return $self->{order_in_loc};
1368 }
1369
1370 sub set_order_in_loc {
1371     my $self=shift;
1372     $self->{order_in_loc}=shift;
1373 }
1374
1375
1376 =head2 functions get_location_subscript(), set_location_subscript()
1377
1378   Synopsis:     sets the location subscript of this marker position
1379   Arguments:    setter: a subscript, usually "a".."c" or similar
1380   Returns:      getter: the current subscript
1381   Side effects: the subscript will be rendered on the map,
1382                 added to the marker name. The CXGN::Cview::Marker function
1383                 get_name() will also include the subscript, whereas
1384                 get_marker_name() will not.
1385   Description:
1386
1387 =cut
1388
1389 sub get_location_subscript {
1390     my $self=shift;
1391     return $self->{location_subscript};
1392 }
1393
1394 sub set_location_subscript {
1395     my $self=shift;
1396     $self->{location_subscript}=shift;
1397 }
1398
1399 =head2 accessors get_loc_type(), set_loc_type()
1400
1401   Synopsis:
1402   Arguments:
1403   Returns:
1404   Side effects:
1405   Description:
1406
1407 =cut
1408
1409 sub get_loc_type {
1410     my $self=shift;
1411     return $self->{loc_type};
1412 }
1413
1414 sub set_loc_type {
1415     my $self=shift;
1416     $self->{loc_type}=shift;
1417 }
1418
1419 =head2 accessors get_loc_order(), set_loc_order()
1420
1421   Synopsis:     I think this is deprecated.
1422   Arguments:
1423   Returns:
1424   Side effects:
1425   Description:
1426
1427 =cut
1428
1429 sub get_loc_order {
1430     my $self=shift;
1431     return $self->{loc_order};
1432 }
1433
1434 sub set_loc_order {
1435     my $self=shift;
1436     $self->{loc_order}=shift;
1437 }
1438
1439 =head2 has_range
1440
1441  Usage:        my $flag = $m->has_range()
1442  Desc:         returns true if the marker has a range defined
1443                (usually using set_north_range() and set_south_range())
1444                false otherwise.
1445  Side Effects: none
1446  Example:
1447
1448 =cut
1449
1450 sub has_range {
1451     my $self = shift;
1452     if ( ($self->get_end() - $self->get_start()) >  12) { return 1;}
1453     return 0;
1454 }
1455
1456 1;