Bio/Map/FPCMarker.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Map::fpcmarker
   4 #
   5 # Cared for by Gaurav Gupta <gaurav@genome.arizona.edu>
   6 #
   7 # Copyright Gaurav Gupta
   8 #
   9 # You may distribute this module under the same terms as perl itself
  10
  11 # POD documentation - main docs before the code
  12
  13 =head1 NAME
  14
  15 Bio::Map::FPCMarker - An central map object representing a marker
  16
  17 =head1 SYNOPSIS
  18
  19    # get the marker object of $marker from the Bio::Map::FPCMarker
  20    my $markerobj = $physical->get_markerobj($marker);
  21
  22    # acquire all the clones that hit this marker
  23    foreach my $clone ($markerobj->each_cloneid()) {
  24        print "   +++$clone\n";
  25    }
  26
  27    # find the position of this marker in $contig
  28    print "Position in contig $contig"," = ",$markerobj->position($contig),
  29          "\n";
  30
  31    # find the group of the marker
  32    print "Group : ",$markerobj->group();
  33
  34
  35 See L<Bio::Map::Position> and L<Bio::Map::PositionI> for more information.
  36
  37 =head1 DESCRIPTION
  38
  39 This object handles the notion of a marker.
  40 This object is intended to be used by a map parser like fpc.pm.
  41
  42 =head1 FEEDBACK
  43
  44 =head2 Mailing Lists
  45
  46 User feedback is an integral part of the evolution of this and other
  47 Bioperl modules. Send your comments and suggestions preferably to
  48 the Bioperl mailing list.  Your participation is much appreciated.
  49
  50   bioperl-l@bioperl.org                  - General discussion
  51   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  52
  53 =head2 Reporting Bugs
  54
  55 Report bugs to the Bioperl bug tracking system to help us keep track
  56 of the bugs and their resolution. Bug reports can be submitted via the
  57 web:
  58
  59   http://bugzilla.open-bio.org/
  60
  61 =head1 AUTHOR - Gaurav Gupta
  62
  63 Email gaurav@genome.arizona.edu
  64
  65 =head1 CONTRIBUTORS
  66
  67 Sendu Bala  bix@sendu.me.uk
  68
  69 =head1 PROJECT LEADERS
  70
  71 Jamie Hatfield      jamie@genome.arizona.edu
  72 Dr. Cari Soderlund  cari@genome.arizona.edu
  73
  74 =head1 PROJECT DESCRIPTION
  75
  76 The project was done in Arizona Genomics Computational Laboratory (AGCoL)
  77 at University of Arizona.
  78
  79 This work was funded by USDA-IFAFS grant #11180 titled "Web Resources for
  80 the Computation and Display of Physical Mapping Data".
  81
  82 For more information on this project, please refer:
  83   http://www.genome.arizona.edu
  84
  85 =head1 APPENDIX
  86
  87 The rest of the documentation details each of the object methods.
  88 Internal methods are usually preceded with a _
  89
  90 =cut
  91
  92 # Let the code begin...
  93
  94 package Bio::Map::FPCMarker;
  95 use strict;
  96 use Bio::Map::Position;
  97 use Time::Local;
  98
  99 use base qw(Bio::Root::Root Bio::Map::MappableI);
 100
 101 =head2 new
 102
 103  Title   : new
 104  Usage   : my $clone = Bio::Map::FPCMarker->new
 105                       (
 106                        -name    => $marker,
 107                        -type    => $type,
 108                        -global  => $global,
 109                        -frame   => $frame,
 110                        -group   => $group,
 111                        -subgroup=> $subgroup,
 112                        -anchor  => $anchor,
 113                        -clones  => \%clones,
 114                        -contigs => \%contigs,
 115                        -position => \%markerpos,
 116                -remark => $remark
 117                        );
 118
 119  Function: Initialize a new Bio::Map::FPCMarker object
 120            Most people will not use this directly but get Markers
 121            through L<Bio::MapIO::fpc>
 122  Returns : L<Bio::Map::FPCMarker> object
 123  Args    : -name     => marker name string,
 124                -type     => type string,
 125                -global   => global position for marker,
 126                -frame    => boolean if marker is framework or placement,
 127                -group    => group number for marker,
 128                -subgroup => subgroup number of marker,
 129                -anchor   => boolean if marker is anchored,
 130                -clones   => all the clone elements in map (hashref),
 131                -contigs  => all the contig elements (hasref),
 132                -position => mapping of marker names to map position (hasref),
 133            -remark   => remarks, separated by newlines
 134
 135 =cut
 136
 137 sub new {
 138    my ($class,@args) = @_;
 139    my $self= $class->SUPER::new(@args);
 140
 141    my ($name,$type,$global,$frame,$group,
 142        $subgroup, $anchor, $clones,$contigs,
 143        $positions, $remark) = $self->_rearrange([qw(NAME TYPE GLOBAL FRAME
 144                                            GROUP SUBGROUP ANCHOR
 145                                            CLONES CONTIGS POSITIONS REMARK)],@args);
 146
 147    $self->name($name)                  if defined $name;
 148    $self->type($type)                  if defined $type;
 149    $self->global($global)              if defined $global;
 150    $self->group($group)                if defined $group;
 151    $self->subgroup($group)             if defined $subgroup;
 152    $self->anchor($anchor)              if defined $anchor;
 153    $self->remark($remark)              if defined $remark;
 154
 155    $self->set_clones($clones)          if defined $clones;
 156    $self->set_contigs($contigs)        if defined $contigs;
 157    $self->set_positions($positions)    if defined $positions;
 158
 159    return $self;
 160 }
 161
 162 =head1 Access Methods
 163
 164 These methods let you get and set the member variables
 165
 166 =head2 name
 167
 168  Title   : name
 169  Usage   : my $name = $markerobj->name();
 170  Function: Get/set the name for this marker
 171  Returns : scalar representing the current name of this marker
 172  Args    : none to get, OR string to set
 173
 174 =cut
 175
 176 sub name {
 177     my ($self) = shift;
 178     return $self->{'_name'} = shift if @_;
 179     return $self->{'_name'};
 180 }
 181
 182 =head2 type
 183
 184  Title   : type
 185  Usage   : my $type = $markerobj->type();
 186  Function: Get/set the type for this marker
 187  Returns : scalar representing the current type of this marker
 188  Args    : none to get, OR string to set
 189
 190 =cut
 191
 192 sub type {
 193     my ($self) = shift;
 194     return $self->{'_type'} = shift if @_;
 195     return $self->{'_type'};
 196 }
 197
 198 =head2 global
 199
 200  Title   : global
 201  Usage   : my $type = $markerobj->global();
 202  Function: Get/set the global position for this marker
 203  Returns : scalar representing the current global position of this marker
 204  Args    : none to get, OR string to set
 205
 206 =cut
 207
 208 sub global {
 209     my ($self) = shift;
 210     return $self->{'_global'} = shift if @_;
 211     return $self->{'_global'};
 212 }
 213
 214 =head2 anchor
 215
 216  Title   : anchor
 217  Usage   : my $anchor = $markerobj->anchor();
 218  Function: indicate if the Marker is anchored or not (True | False)
 219  Returns : scalar representing the anchor (1 | 0) for this marker
 220  Args    : none to get, OR 1|0 to set
 221
 222 =cut
 223
 224 sub anchor {
 225     my ($self) = shift;
 226     return $self->{'_anchor'} = shift if @_;
 227     return $self->{'_anchor'};
 228 }
 229
 230 =head2 framework
 231
 232  Title   : framework
 233  Usage   : $frame = $markerobj->framework();
 234  Function: indicate if the Marker is framework or placement (1 | 0)
 235  Returns : scalar representing if the marker is framework
 236            (1 if framework, 0 if placement)
 237  Args    : none to get, OR 1|0 to set
 238
 239 =cut
 240
 241 sub framework {
 242     my ($self) = shift;
 243     return $self->{'_frame'} = shift if @_;
 244     return $self->{'_frame'};
 245 }
 246
 247 =head2 group
 248
 249  Title   : group
 250  Usage   : $grpno = $markerobj->group();
 251  Function: Get/set the group number for this marker. This is a generic term,
 252            used for Linkage-Groups as well as for Chromosomes.
 253  Returns : scalar representing the group number of this marker
 254  Args    : none to get, OR string to set
 255
 256 =cut
 257
 258 sub group {
 259     my ($self) = shift;
 260     $self->{'_group'} = shift if @_;
 261     return $self->{'_group'} || 0;
 262 }
 263
 264 =head2 subgroup
 265
 266  Title   : subgroup
 267  Usage   : $subgroup = $marker->subgroup();
 268  Function: Get/set the subgroup for this marker. This is a generic term:
 269            subgroup here could represent subgroup of a Chromosome or of a
 270            Linkage Group. The user must take care of which subgroup he/she is
 271            querying for.
 272  Returns : scalar representing the subgroup of this marker
 273  Args    : none to get, OR string to set
 274
 275 =cut
 276
 277 sub subgroup {
 278     my ($self) = shift;
 279     $self->{'_subgroup'} = shift if @_;
 280     return $self->{'_subgroup'} || 0;
 281 }
 282
 283 =head2 position
 284
 285  Title   : position
 286  Usage   : $markerpos = $markerobj->position($ctg);
 287  Function: get the position of the marker in the contig
 288  Returns : scalar representing the position of the markernumber of
 289            the contig
 290  Args    : $ctg is necessary to look for the position of the marker
 291            in that contig.
 292
 293  *** This has nothing to do with an actual Bio::Map::PositionI object ***
 294
 295 =cut
 296
 297 sub position {
 298     my ($self,$ctg) = @_;
 299     return 0 unless defined $ctg;
 300
 301     return 0 unless( defined $self->{'_position'} &&
 302                      defined $self->{'_position'}{$ctg});
 303     return $self->{'_position'}{$ctg};
 304 }
 305
 306 =head2 remark
 307
 308  Title   : remark
 309  Usage   : $markerremark = $markerobj->remark();
 310  Function: get the remarks for this marker
 311  Returns : scalar of newline-separated markers
 312  Args    : none
 313
 314 =cut
 315
 316 sub remark {
 317     my ($self) = shift;
 318     return $self->{'_remark'} = shift if @_;
 319     return $self->{'_remark'};
 320 }
 321
 322 =head2 each_cloneid
 323
 324  Title   : each_cloneid
 325  Usage   : my @clones  = $map->each_cloneid();
 326  Function: retrieves all the clone ids in a map unordered
 327  Returns : list of strings (ids)
 328  Args    : none
 329
 330  *** This only supplies the ids set with the set_clones method ***
 331  *** It has nothing to do with actual Bio::Map::MappableI objects ***
 332
 333 =cut
 334
 335 sub each_cloneid {
 336     my ($self) = @_;
 337     return $self->_each_element('clones');
 338 }
 339
 340 =head2 each_contigid
 341
 342  Title   : each_contigid
 343  Usage   : my @contigs = $map->each_contigid();
 344  Function: retrieves all the contig ids in a map unordered
 345  Returns : list of strings (ids)
 346  Args    : none
 347
 348  *** This only supplies the ids set with the set_contigs method ***
 349  *** It has nothing to do with actual Bio::Map::MapI objects ***
 350
 351 =cut
 352
 353 sub each_contigid {
 354     my ($self) = @_;
 355     return $self->_each_element('contigs');
 356 }
 357
 358 sub _each_element{
 359     my ($self, $type) = @_;
 360
 361     $type = 'clones' unless defined $type;
 362     $type = lc("_$type");
 363
 364     return keys %{$self->{$type} || {}};
 365 }
 366
 367 =head2 set_clones
 368
 369  Title   : set_clones
 370  Usage   : $marker->set_clones(\%clones)
 371  Function: Set the clone ids hashref
 372  Returns : None
 373  Args    : Hashref of clone ids
 374
 375  *** This only sets a hash of ids ***
 376  *** It has nothing to do with actual Bio::Map::MappableI objects ***
 377
 378 =cut
 379
 380 sub set_clones{
 381    my ($self,$clones) = @_;
 382    if( defined $clones && ref($clones) =~ /HASH/ ) {
 383        $self->{'_clones'} = $clones;
 384    }
 385 }
 386
 387 =head2 set_contigs
 388
 389  Title   : set_contigs
 390  Usage   : $marker->set_contigs(\%contigs)
 391  Function: Set the contig ids hashref
 392  Returns : None
 393  Args    : Hashref of contig ids
 394
 395  *** This only sets a hash of ids ***
 396  *** It has nothing to do with actual Bio::Map::MapI objects ***
 397
 398 =cut
 399
 400 sub set_contigs{
 401    my ($self,$contigs) = @_;
 402    if( defined $contigs && ref($contigs) =~ /HASH/ ) {
 403        $self->{'_contigs'} = $contigs;
 404    }
 405 }
 406
 407 =head2 set_positions
 408
 409  Title   : set_positions
 410  Usage   : $marker->set_positions(\%markerpos)
 411  Function: Set the positions hashref
 412  Returns : None
 413  Args    : Hashref of marker positions
 414
 415  *** This only sets a hash of numbers ***
 416  *** It has nothing to do with actual Bio::Map::PositionI objects ***
 417
 418 =cut
 419
 420 sub set_positions{
 421    my ($self,$pos) = @_;
 422    if( defined $pos && ref($pos) =~ /HASH/ ) {
 423        $self->{'_positions'} = $pos;
 424    }
 425 }
 426
 427 1;