lib/CXGN/Insitu/Probe.pm

   1
   2 =head1 NAME
   3
   4
   5 =cut
   6
   7 ##
   8
   9 use strict;
  10
  11 package CXGN::Insitu::Probe;
  12
  13 use CXGN::Insitu::Experiment;
  14
  15 use base qw / CXGN::Insitu::DB /;
  16
  17 =head2 new
  18
  19  Usage:
  20  Desc:
  21  Ret:
  22  Args:
  23  Side Effects:
  24  Example:
  25
  26 =cut
  27
  28 sub new {
  29     my $class = shift;
  30     my $dbh = shift;
  31     my $id = shift;
  32
  33     my $self = $class->SUPER::new($dbh);
  34
  35     if ($id) {
  36         $self->set_probe_id($id);
  37         $self->fetch_probe();
  38     }
  39
  40     return $self;
  41 }
  42
  43 =head2 fetch_probe
  44
  45  Usage:
  46  Desc:
  47  Ret:
  48  Args:
  49  Side Effects:
  50  Example:
  51
  52 =cut
  53
  54 sub fetch_probe {
  55     my $self = shift;
  56     my $query = "SELECT probe_id,
  57                         name,
  58                         sequence,
  59                         clone,
  60                         link_desc,
  61                         link,
  62                         dbxref_type_id,
  63                         identifier,
  64                         primer1,
  65                         primer1_seq,
  66                         primer2,
  67                         primer2_seq,
  68                         user_id
  69                    FROM insitu.probe
  70                   WHERE insitu.probe.probe_id=?";
  71     my $sth = $self->get_dbh()->prepare($query);
  72     $sth->execute($self->get_probe_id());
  73     my ($probe_id, $name, $sequence, $clone, $link_desc, $link, $dbxref_type_id, $identifier, $primer1,
  74         $primer1_seq, $primer2, $primer2_seq, $user_id) =
  75             $sth->fetchrow_array();
  76     $self->set_probe_id($probe_id);
  77     $self->set_name($name);
  78     $self->set_sequence($sequence);
  79     $self->set_clone($clone);
  80     $self->set_link_desc($link_desc);
  81     $self->set_link($link);
  82     $self->set_dbxref_type_id($dbxref_type_id);
  83     $self->set_identifier($identifier);
  84     $self->set_primer1($primer1);
  85     $self->set_primer1_seq($primer1_seq);
  86     $self->set_primer2($primer2);
  87     $self->set_primer2_seq($primer2_seq);
  88     $self->set_user_id($user_id);
  89 }
  90
  91 sub store {
  92     my $self = shift;
  93     if ($self->get_probe_id()) {
  94         my $query = "UPDATE insitu.probe SET
  95                         name=?,
  96                         sequence=?,
  97                         clone=?,
  98                         link_desc=?,
  99                         link=?,
 100                         dbxref_type_id=?,
 101                         identifier =?,
 102                         primer1 = ?,
 103                         primer1_seq = ?,
 104                         primer2 = ?,
 105                         primer2_seq = ?,
 106                         user_id=?
 107                      WHERE
 108                         probe_id=?";
 109         my $sth = $self->get_dbh()->prepare($query);
 110         $sth->execute($self->get_name(),
 111                       $self->get_sequence(),
 112                       $self->get_clone(),
 113                       $self->get_link_desc(),
 114                       $self->get_link(),
 115                       $self->get_dbxref_type_id(),
 116                       $self->get_identifier(),
 117                       $self->get_primer1(),
 118                       $self->get_primer1_seq(),
 119                       $self->get_primer2(),
 120                       $self->get_primer2_seq(),
 121                       $self->get_user_id(),
 122                       $self->get_probe_id()
 123                       );
 124         return $self->get_probe_id();
 125     }
 126     else {
 127         my $query = "INSERT INTO insitu.probe (
 128                        name, sequence, clone, link_desc, link, dbxref_type_id, identifier, primer1, primer1_seq, primer2, primer2_seq, user_id
 129                      ) VALUES (
 130                        ?, ?, ?, ?, ?, ?, ?,?,?,?,?,?)";
 131         my $sth = $self->get_dbh()->prepare($query);
 132         $sth->execute($self->get_name(),
 133                       $self->get_sequence(),
 134                       $self->get_clone(),
 135                       $self->get_link_desc(),
 136                       $self->get_link(),
 137                       $self->get_dbxref_type_id(),
 138                       $self->get_identifier(),
 139                       $self->get_primer1(),
 140                       $self->get_primer1_seq(),
 141                       $self->get_primer2(),
 142                       $self->get_primer2_seq(),
 143                       $self->get_user_id(),
 144                       );
 145         return $self->get_dbh()->last_insert_id("probe");
 146     }
 147 }
 148
 149 sub delete {
 150     my $self = shift;
 151
 152     if (!$self->get_probe_id()) { # can't delete if not in db
 153         return 1;
 154     }
 155     if ($self->get_experiments()) { # can't delete if has experiments
 156         return 2;
 157     }
 158     my $query = "UPDATE insitu.probe SET
 159                         obsolete='t'
 160                   WHERE probe.probe_id =?";
 161     my $sth = $self->get_dbh()->prepare($query);
 162     $sth->execute($self->get_probe_id());
 163
 164     return 0;
 165 }
 166
 167 =head2 get_probe_id
 168
 169  Usage:
 170  Desc:
 171  Ret:
 172  Args:
 173  Side Effects:
 174  Example:
 175
 176 =cut
 177
 178 sub get_probe_id {
 179   my $self=shift;
 180   return $self->{probe_id};
 181
 182 }
 183
 184 =head2 set_probe_id
 185
 186  Usage:
 187  Desc:
 188  Ret:
 189  Args:
 190  Side Effects:
 191  Example:
 192
 193 =cut
 194
 195 sub set_probe_id {
 196   my $self=shift;
 197   $self->{probe_id}=shift;
 198 }
 199
 200
 201
 202 =head2 get_name
 203
 204  Usage:
 205  Desc:
 206  Ret:
 207  Args:
 208  Side Effects:
 209  Example:
 210
 211 =cut
 212
 213 sub get_name {
 214   my $self=shift;
 215   return $self->{name};
 216
 217 }
 218
 219 =head2 set_name
 220
 221  Usage:
 222  Desc:
 223  Ret:
 224  Args:
 225  Side Effects:
 226  Example:
 227
 228 =cut
 229
 230 sub set_name {
 231   my $self=shift;
 232   $self->{name}=shift;
 233 }
 234
 235 =head2 get_sequence
 236
 237  Usage:
 238  Desc:
 239  Ret:
 240  Args:
 241  Side Effects:
 242  Example:
 243
 244 =cut
 245
 246 sub get_sequence {
 247   my $self=shift;
 248   return $self->{sequence};
 249
 250 }
 251
 252 =head2 set_sequence
 253
 254  Usage:
 255  Desc:
 256  Ret:
 257  Args:
 258  Side Effects:
 259  Example:
 260
 261 =cut
 262
 263 sub set_sequence {
 264   my $self=shift;
 265   $self->{sequence}=shift;
 266 }
 267
 268 =head2 get_clone
 269
 270  Usage:
 271  Desc:
 272  Ret:
 273  Args:
 274  Side Effects:
 275  Example:
 276
 277 =cut
 278
 279 sub get_clone {
 280   my $self=shift;
 281   return $self->{clone};
 282
 283 }
 284
 285 =head2 set_clone
 286
 287  Usage:
 288  Desc:
 289  Ret:
 290  Args:
 291  Side Effects:
 292  Example:
 293
 294 =cut
 295
 296 sub set_clone {
 297   my $self=shift;
 298   $self->{clone}=shift;
 299 }
 300
 301 =head2 get_link_desc
 302
 303  Usage:
 304  Desc:
 305  Ret:
 306  Args:
 307  Side Effects:
 308  Example:
 309
 310 =cut
 311
 312 sub get_link_desc {
 313   my $self=shift;
 314   return $self->{link_desc};
 315
 316 }
 317
 318 =head2 set_link_desc
 319
 320  Usage:
 321  Desc:
 322  Ret:
 323  Args:
 324  Side Effects:
 325  Example:
 326
 327 =cut
 328
 329 sub set_link_desc {
 330   my $self=shift;
 331   $self->{link_desc}=shift;
 332 }
 333
 334 =head2 get_link
 335
 336  Usage:
 337  Desc:
 338  Ret:
 339  Args:
 340  Side Effects:
 341  Example:
 342
 343 =cut
 344
 345 sub get_link {
 346   my $self=shift;
 347   return $self->{link};
 348
 349 }
 350
 351 =head2 set_link
 352
 353  Usage:
 354  Desc:
 355  Ret:
 356  Args:
 357  Side Effects:
 358  Example:
 359
 360 =cut
 361
 362 sub set_link {
 363   my $self=shift;
 364   $self->{link}=shift;
 365 }
 366
 367 =head2 get_dbxref_type_id
 368
 369  Usage:
 370  Desc:
 371  Ret:
 372  Args:
 373  Side Effects:
 374  Example:
 375
 376 =cut
 377
 378 sub get_dbxref_type_id {
 379   my $self=shift;
 380   return $self->{dbxref_type_id};
 381
 382 }
 383
 384 =head2 set_dbxref_type_id
 385
 386  Usage:
 387  Desc:
 388  Ret:
 389  Args:
 390  Side Effects:
 391  Example:
 392
 393 =cut
 394
 395 sub set_dbxref_type_id {
 396   my $self=shift;
 397   $self->{dbxref_type_id}=shift;
 398 }
 399
 400
 401 =head2 get_identifier
 402
 403  Usage:
 404  Desc:
 405  Ret:
 406  Args:
 407  Side Effects:
 408  Example:
 409
 410 =cut
 411
 412 sub get_identifier {
 413   my $self=shift;
 414   return $self->{identifier};
 415
 416 }
 417
 418 =head2 set_identifier
 419
 420  Usage:
 421  Desc:
 422  Ret:
 423  Args:
 424  Side Effects:
 425  Example:
 426
 427 =cut
 428
 429 sub set_identifier {
 430   my $self=shift;
 431   $self->{identifier}=shift;
 432 }
 433
 434 =head2 get_primer1
 435
 436  Usage:
 437  Desc:
 438  Ret:
 439  Args:
 440  Side Effects:
 441  Example:
 442
 443 =cut
 444
 445 sub get_primer1 {
 446   my $self=shift;
 447   return $self->{primer1};
 448
 449 }
 450
 451 =head2 set_primer1
 452
 453  Usage:
 454  Desc:
 455  Ret:
 456  Args:
 457  Side Effects:
 458  Example:
 459
 460 =cut
 461
 462 sub set_primer1 {
 463   my $self=shift;
 464   $self->{primer1}=shift;
 465 }
 466
 467 =head2 get_primer1_seq
 468
 469  Usage:
 470  Desc:
 471  Ret:
 472  Args:
 473  Side Effects:
 474  Example:
 475
 476 =cut
 477
 478 sub get_primer1_seq {
 479   my $self=shift;
 480   return $self->{primer1_seq};
 481
 482 }
 483
 484 =head2 set_primer1_seq
 485
 486  Usage:
 487  Desc:
 488  Ret:
 489  Args:
 490  Side Effects:
 491  Example:
 492
 493 =cut
 494
 495 sub set_primer1_seq {
 496   my $self=shift;
 497   $self->{primer1_seq}=shift;
 498 }
 499
 500 =head2 get_primer2
 501
 502  Usage:
 503  Desc:
 504  Ret:
 505  Args:
 506  Side Effects:
 507  Example:
 508
 509 =cut
 510
 511 sub get_primer2 {
 512   my $self=shift;
 513   return $self->{primer2};
 514
 515 }
 516
 517 =head2 set_primer2
 518
 519  Usage:
 520  Desc:
 521  Ret:
 522  Args:
 523  Side Effects:
 524  Example:
 525
 526 =cut
 527
 528 sub set_primer2 {
 529   my $self=shift;
 530   $self->{primer2}=shift;
 531 }
 532
 533 =head2 get_primer2_seq
 534
 535  Usage:
 536  Desc:
 537  Ret:
 538  Args:
 539  Side Effects:
 540  Example:
 541
 542 =cut
 543
 544 sub get_primer2_seq {
 545   my $self=shift;
 546   return $self->{primer2_seq};
 547
 548 }
 549
 550 =head2 set_primer2_seq
 551
 552  Usage:
 553  Desc:
 554  Ret:
 555  Args:
 556  Side Effects:
 557  Example:
 558
 559 =cut
 560
 561 sub set_primer2_seq {
 562   my $self=shift;
 563   $self->{primer2_seq}=shift;
 564 }
 565
 566
 567
 568 =head2 get_antibody
 569
 570  Usage:
 571  Desc:
 572  Ret:
 573  Args:
 574  Side Effects:
 575  Example:
 576
 577 =cut
 578
 579 sub get_antibody {
 580   my $self=shift;
 581   return $self->{antibody};
 582
 583 }
 584
 585 =head2 set_antibody
 586
 587  Usage:
 588  Desc:
 589  Ret:
 590  Args:
 591  Side Effects:
 592  Example:
 593
 594 =cut
 595
 596 sub set_antibody {
 597   my $self=shift;
 598   $self->{antibody}=shift;
 599 }
 600
 601 =head2 get_comments
 602
 603  Usage:
 604  Desc:
 605  Ret:
 606  Args:
 607  Side Effects:
 608  Example:
 609
 610 =cut
 611
 612 sub get_comments {
 613   my $self=shift;
 614   return $self->{comments};
 615
 616 }
 617
 618 =head2 set_comments
 619
 620  Usage:
 621  Desc:
 622  Ret:
 623  Args:
 624  Side Effects:
 625  Example:
 626
 627 =cut
 628
 629 sub set_comments {
 630   my $self=shift;
 631   $self->{comments}=shift;
 632 }
 633
 634
 635
 636
 637 =head2 get_user_id
 638
 639  Usage:
 640  Desc:
 641  Ret:
 642  Args:
 643  Side Effects:
 644  Example:
 645
 646 =cut
 647
 648 sub get_user_id {
 649   my $self=shift;
 650   return $self->{user_id};
 651
 652 }
 653
 654 =head2 set_user_id
 655
 656  Usage:
 657  Desc:
 658  Ret:
 659  Args:
 660  Side Effects:
 661  Example:
 662
 663 =cut
 664
 665 sub set_user_id {
 666   my $self=shift;
 667   $self->{user_id}=shift;
 668 }
 669
 670 =head2 get_experiments
 671
 672  Usage:
 673  Desc:
 674  Ret:
 675  Args:
 676  Side Effects:
 677  Example:
 678
 679 =cut
 680
 681 sub get_experiments {
 682     my $self = shift;
 683     my $query = "SELECT experiment_id
 684                    FROM insitu.experiment
 685                    JOIN insitu.probe
 686                   USING (probe_id)
 687                   WHERE probe.probe_id=?";
 688
 689     my $sth = $self->get_dbh()->prepare($query);
 690     $sth->execute($self->get_probe_id());
 691     my @experiments = ();
 692     while (my ($experiment_id) = $sth->fetchrow_array()) {
 693         print STDERR "Instantiating experiment with id = $experiment_id\n";
 694         my $experiment = CXGN::Insitu::Experiment->new($self->get_dbh(),$experiment_id);
 695         push @experiments, $experiment;
 696         print STDERR "experiment: ".$experiment->get_experiment_id()."\n";
 697     }
 698     return @experiments;
 699 }
 700
 701
 702
 703
 704 # =head2 as_html
 705
 706 #  Usage:
 707 #  Desc:
 708 #  Ret:
 709 #  Args:
 710 #  Side Effects:
 711 #  Example:
 712
 713 # =cut
 714
 715 # sub as_html {
 716 #     my $self = shift;
 717
 718 #     print
 719 #       "Name: ". $self->get_name() ."<br />".
 720 #       "Sequence: ".$self->get_sequence()."<br />".
 721 #       "Link: ".$self->get_link()."<br />\n";
 722
 723 # }
 724
 725 =head2 get_all_probes
 726
 727  Usage:
 728  Desc:         static function that retrieves two lists,
 729                one with probe names and one with probe ids.
 730  Ret:          ($names_array_ref, $ids_array_ref)
 731  Args:
 732  Side Effects: none
 733  Example:
 734
 735 =cut
 736
 737 sub get_all_probes {
 738     my $dbh=shift;
 739     my $query = "SELECT probe_id, name
 740                    FROM insitu.probe";
 741     my $sth = $dbh->prepare($query);
 742
 743     $sth->execute();
 744     my @names = ();
 745     my @ids = ();
 746     while (my ($probe_id, $name) = $sth->fetchrow_array()) {
 747         push @names, $name;
 748         push @ids, $probe_id;
 749     }
 750     return (\@names, \@ids);
 751 }
 752
 753
 754
 755 return 1;