lib/CXGN/Chado/FeatureLoc.pm

   1
   2 =head1 NAME
   3
   4 CXGN::Chado::FeatureLoc - a database wrapper class for the Chado featureloc table
   5
   6 =head1 DESCRIPTION
   7
   8 The featureloc table is used to map features onto other features, for example, exons on genomic sequence, or domains on proteins. The meaning of the database fields in the featureloc table has been reverse engineered to mean the following:
   9
  10 =over 4
  11
  12 =item featureloc_id: primary key
  13
  14 =item feature_id: the feature that is being mapped (let's called f1)
  15
  16 =item srcfeature_id: the feature we're mapping on (let's call it f2)
  17
  18 =item fmin: the start coordinate of f1 on f2
  19
  20 =item is_fmin_partial: is f2 truncated?
  21
  22 =item fmax: the end coordinate of f1 on f2
  23
  24 =item is_fmax_partial: is f2 truncated?
  25
  26 =item strand: either -1,-2,-3,1,2,3
  27
  28 =item phase: the phase for protein coding exons
  29
  30 =item residue_info: this is possibly used for snps (?)
  31
  32 =item locgroup:
  33
  34 =item rank:
  35
  36 =back
  37
  38 =head1 AUTHOR
  39
  40 Lukas Mueller <lam87@cornell.edu>
  41
  42 =head1 METHODS
  43
  44 This class implements the following methods:
  45
  46 =cut
  47
  48
  49
  50 use strict;
  51
  52 package CXGN::Chado::FeatureLoc;
  53
  54 use CXGN::DB::Object;
  55
  56 use base "CXGN::DB::Object";
  57
  58
  59 =head2 new
  60
  61  Usage:
  62  Desc:
  63  Ret:
  64  Args:
  65  Side Effects:
  66  Example:
  67
  68 =cut
  69
  70
  71 sub new {
  72     my $class = shift;
  73     my $dbh = shift;
  74     my $id = shift;
  75     my $self = $class->SUPER::new($dbh);
  76
  77     if ($id) {
  78         $self->set_featureloc_id($id);
  79         $self->fetch();
  80     }
  81
  82     return $self;
  83 }
  84
  85 =head2 fetch
  86
  87  Usage:
  88  Desc:
  89  Ret:
  90  Args:
  91  Side Effects:
  92  Example:
  93
  94 =cut
  95
  96
  97
  98 sub fetch {
  99     my $self = shift;
 100     my $query = "SELECT featureloc_id, feature_id, srcfeature_id, fmin, is_fmin_partial, famx, is_fmax_partial, strand, phase, residue_info, locgroup, rank FROM
 101 featureloc WHERE featureloc_id=?";
 102     my $sth = $self->get_dbh()->prepare($query);
 103     $sth->execute($self->get_featureloc_id());
 104     my ($featureloc_id, $feature_id, $srcfeature_id, $fmin, $is_fmin_partial, $fmax, $is_fmax_partial, $strand, $phase, $residue_info, $locgroup, $rank) = $sth->fetchrow_array();
 105     $self->set_featureloc_id($featureloc_id);
 106     $self->set_feature_id($feature_id);
 107     $self->set_scrfeature_id($srcfeature_id);
 108     $self->set_fmin($fmin);
 109     $self->set_is_fmin_partial($is_fmin_partial);
 110     $self->set_fmax($fmax);
 111     $self->set_is_fmax_partial($is_fmax_partial);
 112     $self->set_strand($strand);
 113     $self->set_phase($phase);
 114     $self->set_residue_info($residue_info);
 115     $self->set_locgroup($locgroup);
 116     $self->set_rank($rank);
 117 }
 118
 119 =head2 store
 120
 121  Usage:
 122  Desc:
 123  Ret:
 124  Args:
 125  Side Effects:
 126  Example:
 127
 128 =cut
 129
 130
 131 sub store {
 132     my $self = shift;
 133     if ($self->get_featureloc_id()) {
 134         my $query = "UPDATE featureloc SET
 135                        feature_id=?, srcfeature_id=?, fmin=?, is_fmin_partial=?, fmax=?, is_fmax_partial=?, strand=?, phase=?, residue_info=?, locgroup=?, rank=? WHERE featureloc_id=?";
 136         my $sth = $self->get_dbh()->prepare($query);
 137         $sth->execute($self->get_feature_id(),
 138                       $self->get_srcfeature_id(),
 139                       $self->get_fmin(),
 140                       $self->get_is_fmin_partial(),
 141                       $self->get_fmax(),
 142                       $self->get_is_fmax_partial(),
 143                       $self->get_strand(),
 144                       $self->get_phase(),
 145                       $self->get_residue_info(),
 146                       $self->get_locgroup(),
 147                       $self->get_rank(),
 148                       $self->get_featureloc_id(),
 149                       );
 150         return $self->get_featureloc_id();
 151     }
 152     else {
 153         my $query = "INSERT INTO featureloc (feature_id, srcfeature_id, fmin, is_fmin_partial, fmax, is_fmax_partial, strand, phase, residue_info, locgroup, rank) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)";
 154         my $sth = $self->get_dbh()->prepare($query);
 155         $sth->execute( $self->get_feature_id(),
 156                        $self->get_srcfeature_id(),
 157                        $self->get_fmin(),
 158                        $self->get_is_fmin_partial(),
 159                        $self->get_fmax(),
 160                        $self->get_is_fmax_partial(),
 161                        $self->get_strand(),
 162                        $self->get_phase(),
 163                        $self->get_residue_info(),
 164                        $self->get_locgroup(),
 165                        $self->get_rank()
 166                        );
 167         my $id = $self->get_currval("featureloc_featureloc_id_seq");
 168         $self->set_featureloc_id($id);
 169         return $id;
 170     }
 171 }
 172
 173 =head2 accessors get_featureloc_id, set_featureloc_id
 174
 175  Usage:
 176  Desc:
 177  Property
 178  Side Effects:
 179  Example:
 180
 181 =cut
 182
 183 sub get_featureloc_id {
 184   my $self = shift;
 185   return $self->{featureloc_id};
 186 }
 187
 188 sub set_featureloc_id {
 189   my $self = shift;
 190   $self->{featureloc_id} = shift;
 191 }
 192
 193 =head2 accessors get_feature_id, set_feature_id
 194
 195  Usage:
 196  Desc:
 197  Property
 198  Side Effects:
 199  Example:
 200
 201 =cut
 202
 203 sub get_feature_id {
 204   my $self = shift;
 205   return $self->{feature_id};
 206 }
 207
 208 sub set_feature_id {
 209   my $self = shift;
 210   $self->{feature_id} = shift;
 211 }
 212
 213 =head2 accessors get_srcfeature_id, set_srcfeature_id
 214
 215  Usage:
 216  Desc:
 217  Property
 218  Side Effects:
 219  Example:
 220
 221 =cut
 222
 223 sub get_srcfeature_id {
 224   my $self = shift;
 225   return $self->{srcfeature_id};
 226 }
 227
 228 sub set_srcfeature_id {
 229   my $self = shift;
 230   $self->{srcfeature_id} = shift;
 231 }
 232
 233 =head2 accessors get_fmin, set_fmin
 234
 235  Usage:
 236  Desc:
 237  Property
 238  Side Effects:
 239  Example:
 240
 241 =cut
 242
 243 sub get_fmin {
 244   my $self = shift;
 245   return $self->{fmin};
 246 }
 247
 248 sub set_fmin {
 249   my $self = shift;
 250   $self->{fmin} = shift;
 251 }
 252
 253 =head2 accessors get_is_fmin_partial, set_is_fmin_partial
 254
 255  Usage:
 256  Desc:
 257  Property
 258  Side Effects:
 259  Example:
 260
 261 =cut
 262
 263 sub get_is_fmin_partial {
 264   my $self = shift;
 265   if (!exists($self->{is_fmin_partial}) || !defined($self->{is_fmin_partial})) {
 266       $self->{is_fmin_partial}='f';
 267   }
 268   return $self->{is_fmin_partial};
 269 }
 270
 271 sub set_is_fmin_partial {
 272   my $self = shift;
 273   $self->{is_fmin_partial} = shift;
 274 }
 275
 276 =head2 accessors get_fmax, set_fmax
 277
 278  Usage:
 279  Desc:
 280  Property
 281  Side Effects:
 282  Example:
 283
 284 =cut
 285
 286 sub get_fmax {
 287   my $self = shift;
 288   return $self->{fmax};
 289 }
 290
 291 sub set_fmax {
 292   my $self = shift;
 293   $self->{fmax} = shift;
 294 }
 295
 296 =head2 accessors get_is_fmax_partial, set_is_fmax_partial
 297
 298  Usage:
 299  Desc:
 300  Property
 301  Side Effects:
 302  Example:
 303
 304 =cut
 305
 306 sub get_is_fmax_partial {
 307   my $self = shift;
 308   if (!exists($self->{is_fmax_partial})||!defined($self->{is_fmax_partial})) {
 309       $self->{is_fmax_partial}='f';
 310   }
 311   return $self->{is_fmax_partial};
 312 }
 313
 314 sub set_is_fmax_partial {
 315   my $self = shift;
 316   $self->{is_fmax_partial} = shift;
 317 }
 318
 319 =head2 accessors get_strand, set_strand
 320
 321  Usage:
 322  Desc:
 323  Property
 324  Side Effects:
 325  Example:
 326
 327 =cut
 328
 329 sub get_strand {
 330   my $self = shift;
 331   return $self->{strand};
 332 }
 333
 334 sub set_strand {
 335   my $self = shift;
 336   $self->{strand} = shift;
 337 }
 338
 339 =head2 accessors get_phase, set_phase
 340
 341  Usage:
 342  Desc:
 343  Property
 344  Side Effects:
 345  Example:
 346
 347 =cut
 348
 349 sub get_phase {
 350   my $self = shift;
 351   return $self->{phase};
 352 }
 353
 354 sub set_phase {
 355   my $self = shift;
 356   $self->{phase} = shift;
 357 }
 358
 359 =head2 accessors get_residue_info, set_residue_info
 360
 361  Usage:
 362  Desc:
 363  Property
 364  Side Effects:
 365  Example:
 366
 367 =cut
 368
 369 sub get_residue_info {
 370   my $self = shift;
 371   return $self->{residue_info};
 372 }
 373
 374 sub set_residue_info {
 375   my $self = shift;
 376   $self->{residue_info} = shift;
 377 }
 378
 379 =head2 accessors get_locgroup, set_locgroup
 380
 381  Usage:
 382  Desc:
 383  Property
 384  Side Effects:
 385  Example:
 386
 387 =cut
 388
 389 sub get_locgroup {
 390   my $self = shift;
 391   if (!exists($self->{locgroup}) || !defined($self->{locgroup})) {
 392       $self->{locgroup}=0;
 393   }
 394   return $self->{locgroup};
 395 }
 396
 397 sub set_locgroup {
 398   my $self = shift;
 399   $self->{locgroup} = shift;
 400 }
 401
 402 =head2 accessors get_rank, set_rank
 403
 404  Usage:
 405  Desc:
 406  Property
 407  Side Effects:
 408  Example:
 409
 410 =cut
 411
 412 sub get_rank {
 413   my $self = shift;
 414   if (!exists($self->{rank}) || !defined($self->{rank})) {
 415       $self->{rank} = 0;
 416   }
 417   return $self->{rank};
 418 }
 419
 420 sub set_rank {
 421   my $self = shift;
 422   $self->{rank} = shift;
 423 }
 424
 425
 426
 427 return 1;