Bio/Map/Clone.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Map::clone
   4 #
   5 # Cared for by Sendu Bala <bix@sendu.me.uk>
   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::Clone - An central map object representing a clone
  16
  17 =head1 SYNOPSIS
  18
  19    # get the clone object of $clone from the Bio::Map::Clone
  20    my $cloneobj = $physical->get_cloneobj($clone);
  21
  22    # acquire all the markers that hit this clone
  23    foreach my $marker ($cloneobj->each_markerid()) {
  24        print "   +++$marker\n";
  25    }
  26
  27 See L<Bio::Map::Position> and L<Bio::Map::PositionI> for more information.
  28
  29 =head1 DESCRIPTION
  30
  31 This object handles the notion of a clone. This clone will
  32 have a name and a position in a map.
  33
  34 This object is intended to be used by a map parser like fpc.pm.
  35
  36 =head1 FEEDBACK
  37
  38 =head2 Mailing Lists
  39
  40 User feedback is an integral part of the evolution of this and other
  41 Bioperl modules. Send your comments and suggestions preferably to
  42 the Bioperl mailing list.  Your participation is much appreciated.
  43
  44   bioperl-l@bioperl.org                  - General discussion
  45   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  46
  47 =head2 Reporting Bugs
  48
  49 Report bugs to the Bioperl bug tracking system to help us keep track
  50 of the bugs and their resolution. Bug reports can be submitted via the
  51 web:
  52
  53   http://bugzilla.open-bio.org/
  54
  55 =head1 AUTHOR - Gaurav Gupta
  56
  57 Email gaurav@genome.arizona.edu
  58
  59 =head1 CONTRIBUTORS
  60
  61 Sendu Bala  bix@sendu.me.uk
  62
  63 =head1 PROJECT LEADERS
  64
  65 Jamie Hatfield      jamie@genome.arizona.edu
  66 Dr. Cari Soderlund  cari@genome.arizona.edu
  67
  68 =head1 PROJECT DESCRIPTION
  69
  70 The project was done in Arizona Genomics Computational Laboratory (AGCoL)
  71 at University of Arizona.
  72
  73 This work was funded by USDA-IFAFS grant #11180 titled "Web Resources for
  74 the Computation and Display of Physical Mapping Data".
  75
  76 For more information on this project, please refer:
  77   http://www.genome.arizona.edu
  78
  79 =head1 APPENDIX
  80
  81 The rest of the documentation details each of the object methods.
  82 Internal methods are usually preceded with a _
  83
  84 =cut
  85
  86 # Let the code begin...
  87
  88 package Bio::Map::Clone;
  89 use strict;
  90 use Bio::Map::Position;
  91
  92 use base qw(Bio::Root::Root Bio::Map::MappableI);
  93
  94 =head2 new
  95
  96  Title   : new
  97  Usage   : my $clone = Bio::Map::Clone->new
  98                       (
  99                        -name    => $clone,
 100                        -markers => \@markers,
 101                        -contig  => $contig,
 102                        -type    => $type,
 103                        -bands   => $bands,
 104                        -gel     => $gel,
 105                        -group   => $group,
 106                        -remark  => $remark,
 107                        -fpnumber=> $fp_number,
 108                        -sequencetype  => $seq_type,
 109                        -sequencestatus=> $seq_status,
 110                        -fpcremark => $fpc_remark,
 111                        -matche    => \@ematch,
 112                        -matcha    => \@amatch,
 113                        -matchp    => \@pmatch,
 114                        -range     => Bio::Range->new(-start => $startrange,
 115                                                      -end   => $endrange)
 116                        );
 117  Function: Initialize a new Bio::Map::Clone object
 118            Most people will not use this directly but get Clones
 119            through L<Bio::MapIO::fpc>
 120  Returns : L<Bio::Map::Clone> object
 121  Args    :   -name => marker name string,
 122              -markers => array ref of markers,
 123              -contig  => contig name string,
 124              -type    => type string,
 125              -bands   => band string,
 126              -gel     => gel string,
 127              -group   => group name string,
 128              -remark  => remark string,
 129              -fpnumber=> FP number string,
 130              -sequencetype  => seq type string,
 131              -sequencestatus=> seq status string,
 132              -fpcremark => FPC remark,
 133              -matche    => array ref,
 134              -matcha    => array ref,
 135              -matchp    => array ref,
 136              -range     => L<Bio::Range> object,
 137
 138 =cut
 139
 140 sub new {
 141    my ($class,@args) = @_;
 142    my $self= $class->SUPER::new(@args);
 143
 144    my ($name,$markers,$contig,$type,$bands,$gel,$group,
 145        $remark,$fpnumber,$seqtype,$seqstatus,$fpcremark,
 146        $matche,$matcha,$matchp,
 147        $range) = $self->_rearrange([qw(NAME  MARKERS CONTIG TYPE
 148                                        BANDS GEL GROUP REMARK FPNUMBER
 149                                        SEQUENCETYPE SEQUENCESTATUS
 150                                        FPCREMARK MATCHE MATCHA MATCHP
 151                                        RANGE)],@args);
 152
 153    $self->name($name)                  if defined $name;
 154    $self->markers($markers)            if defined $markers;
 155    $self->contigid($contig)            if defined $contig;
 156    $self->type($type)                  if defined $type;
 157    $self->bands($bands)                if defined $bands;
 158    $self->gel($gel)                    if defined $gel;
 159    $self->group($group)                if defined $group;
 160    $self->remark($remark)              if defined $remark;
 161    $self->fp_number($fpnumber)         if defined $fpnumber;
 162    $self->sequence_type($seqtype)     if defined $seqtype;
 163    $self->sequence_status($seqstatus) if defined $seqstatus;
 164    $self->fpc_remark($fpcremark)       if defined $fpcremark;
 165    $self->range($range)                if defined $range;
 166
 167    $self->set_match('approx', $matcha) if defined $matcha;
 168    $self->set_match('pseudo', $matchp) if defined $matchp;
 169    $self->set_match('exact',  $matche) if defined $matche;
 170
 171    return $self;
 172 }
 173
 174 =head1 Access Methods
 175
 176 These methods let you get and set the member variables
 177
 178 =head2 name
 179
 180  Title   : name
 181  Usage   : my $name = $cloneobj->name();
 182  Function: Get/set the name for this Clone
 183  Returns : scalar representing the current name of this clone
 184  Args    : none to get, OR string to set
 185
 186 =cut
 187
 188 sub name {
 189     my ($self) = shift;
 190     return $self->{'_name'} = shift if @_;
 191     return $self->{'_name'};
 192 }
 193
 194 =head2 type
 195
 196  Title   : type
 197  Usage   : my $type = $cloneobj->type();
 198  Function: Get/set the type for this clone
 199  Returns : scalar representing the current type of this clone
 200  Args    : none to get, OR string to set
 201
 202 =cut
 203
 204 sub type {
 205     my ($self) = shift;
 206     return $self->{'_type'} = shift if @_;
 207     return $self->{'_type'};
 208 }
 209
 210 =head2 range
 211
 212  Title   : range
 213  Usage   : my $range = $cloneobj->range();
 214  Function: Get/set the range of the contig that this clone covers
 215  Returns : Bio::Range representing the current range of this contig,
 216            start and end of the contig can be thus found using:
 217            my $start = $contigobj->range()->start();
 218            my $end   = $contigobj->range()->end();
 219  Args    : none to get, OR Bio::Range to set
 220
 221 =cut
 222
 223 sub range {
 224     my ($self) = shift;
 225     return $self->{'_range'} = shift if @_;
 226     return $self->{'_range'};
 227 }
 228
 229 =head2 match
 230
 231  Title   : match
 232  Usage   : @eclone = $cloneobj->match('exact');
 233            @aclone = $cloneobj->match('approximate');
 234            @pclone = $cloneobj->match('pseudo');
 235  Function: get all matching clones
 236  Returns : list
 237  Args    : scalar representing the type of clone to be
 238            queried.
 239
 240 =cut
 241
 242 sub match {
 243   my ($self,$type) = @_;
 244
 245   $type = "_match" . lc(substr($type, 0, 1));
 246   return @{$self->{$type} || []};
 247 }
 248
 249 =head2 each_match
 250
 251  Title   : each_match
 252  Function: Synonym of the match() method.
 253
 254 =cut
 255
 256 *each_match = \&match;
 257
 258 =head2 set_match
 259
 260  Title   : set_match
 261  Usage   : $clone->set_match($type,$values);
 262  Function: Set the Matches per type
 263  Returns : None
 264  Args    : type (one of 'exact' 'approx' 'pseudo')
 265            array ref of match values
 266
 267 =cut
 268
 269 sub set_match{
 270    my ($self,$type,$val) = @_;
 271    $type = "_match" . lc(substr($type, 0, 1));
 272    $self->{$type} = $val;
 273 }
 274
 275 =head2 gel
 276
 277  Title   : gel
 278  Usage   : $clonegel = $cloneobj->gel();
 279  Function: Get/set the gel number for this clone
 280  Returns : scalar representing the gel number of this clone
 281  Args    : none to get, OR string to set
 282
 283 =cut
 284
 285 sub gel {
 286     my ($self) = shift;
 287     return $self->{'_gel'} = shift if @_;
 288     return $self->{'_gel'};
 289 }
 290
 291 =head2 remark
 292
 293  Title   : remark
 294  Usage   : $cloneremark = $cloneobj->remark();
 295  Function: Get/set the remark for this clone
 296  Returns : scalar representing the current remark of this clone
 297  Args    : none to get, OR string to set
 298
 299 =cut
 300
 301 sub remark {
 302     my ($self) = shift;
 303     return $self->{'_remark'} = shift if @_;
 304     return $self->{'_remark'};
 305 }
 306
 307 =head2 fp_number
 308
 309  Title   : fp_number
 310  Usage   : $clonefpnumber = $cloneobj->fp_number();
 311  Function: Get/set the fp number for this clone
 312  Returns : scalar representing the fp number of this clone
 313  Args    : none to get, OR string to set
 314
 315 =cut
 316
 317 sub fp_number {
 318     my ($self) = shift;
 319     return $self->{'_fpnumber'} = shift if @_;
 320     return $self->{'_fpnumber'};
 321 }
 322
 323 =head2 sequence_type
 324
 325  Title   : sequence_type
 326  Usage   : $cloneseqtype = $cloneobj->sequence_type();
 327  Function: Get/set the sequence type for this clone
 328  Returns : scalar representing the sequence type of this clone
 329  Args    : none to get, OR string to set
 330
 331 =cut
 332
 333 sub sequence_type {
 334     my ($self) = shift;
 335     return $self->{'_sequencetype'} = shift if @_;
 336     return $self->{'_sequencetype'};
 337 }
 338
 339 =head2 sequence_status
 340
 341  Title   : sequence_status
 342  Usage   : $cloneseqstatus = $cloneobj->sequence_status();
 343  Function: Get/set the sequence status for this clone
 344  Returns : scalar representing the sequence status of this clone
 345  Args    : none to get, OR string to set
 346
 347 =cut
 348
 349 sub sequence_status {
 350     my ($self) = shift;
 351     return $self->{'_sequencestatus'} = shift if @_;
 352     return $self->{'_sequencestatus'};
 353 }
 354
 355 =head2 fpc_remark
 356
 357  Title   : fpc_remark
 358  Usage   : $clonefpcremark = $cloneobj->fpc_remark();
 359  Function: Get/set the fpc remark for this clone
 360  Returns : scalar representing the fpc remark of this clone
 361  Args    : none to get, OR string to set
 362
 363 =cut
 364
 365 sub fpc_remark {
 366     my ($self) = shift;
 367     return $self->{'_fpcremark'} = shift if @_;
 368     return $self->{'_fpcremark'};
 369 }
 370
 371 =head2 bands
 372
 373  Title   : bands
 374  Usage   : @clonebands = $cloneobj->bands();
 375  Function: Get/set the bands for this clone
 376  Returns : liat representing the band of this clone, if
 377            readcor = 1 while creating the MapIO object and the
 378            .cor exists
 379  Args    : none to get, OR string to set
 380
 381 =cut
 382
 383 sub bands {
 384     my ($self) = shift;
 385     return $self->{'_bands'} = shift if @_;
 386     return $self->{'_bands'};
 387 }
 388
 389 =head2 group
 390
 391  Title   : group
 392  Usage   : $cloneobj->group($chrno);
 393  Function: Get/set the group number for this clone.
 394            This is a generic term, used for Linkage-Groups as well as for
 395            Chromosomes.
 396  Returns : scalar representing the group number of this clone
 397  Args    : none to get, OR string to set
 398
 399 =cut
 400
 401 sub group {
 402     my ($self) = shift;
 403     return $self->{'_group'} = shift if @_;
 404     return $self->{'_group'};
 405 }
 406
 407 =head2 contigid
 408
 409  Title   : contigid
 410  Usage   : my $ctg = $cloneobj->contigid();
 411  Function: Get/set the contig this clone belongs to
 412  Returns : scalar representing the contig
 413  Args    : none to get, OR string to set
 414
 415 =cut
 416
 417 sub contigid {
 418     my ($self) = shift;
 419     $self->{'_contig'} = shift if @_;
 420     return $self->{'_contig'} || 0;
 421 }
 422
 423 =head2 each_markerid
 424
 425  Title   : each_markerid
 426  Usage   : @markers = $cloneobj->each_markerid();
 427  Function: retrieves all the elements in a map unordered
 428  Returns : list of strings (ids)
 429  Args    : none
 430
 431  *** This only supplies the ids set with the set_markers method ***
 432  *** It has nothing to do with actual Bio::Map::MarkerI objects ***
 433
 434 =cut
 435
 436 sub each_markerid {
 437   my ($self,$value) = @_;
 438   return @{$self->{"_markers"}};
 439 }
 440
 441 =head2 set_markers
 442
 443  Title   : markers
 444  Usage   : $obj->set_markers($newval)
 445  Function: Set list of Marker ids (arrayref)
 446  Returns : None
 447  Args    : arrayref of strings (ids)
 448
 449  *** This only sets a list of ids ***
 450  *** It has nothing to do with actual Bio::Map::MarkerI objects ***
 451
 452 =cut
 453
 454 sub set_markers {
 455     my ($self,$markers) = @_;
 456     if( defined $markers && ref($markers) =~ /ARRAY/ ) {
 457         $self->{'_markers'} = $markers;
 458     }
 459 }
 460
 461 1;