Translation.pm 27.8 KB
Newer Older
1 2
=head1 LICENSE

3
  Copyright (c) 1999-2010 The European Bioinformatics Institute and
4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <ensembl-dev@ebi.ac.uk>.

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.

=cut
Ewan Birney's avatar
Ewan Birney committed
20 21 22

=head1 NAME

23 24
Bio::EnsEMBL::Translation - A class representing the translation of a
transcript
Ewan Birney's avatar
Ewan Birney committed
25 26 27

=head1 SYNOPSIS

Patrick Meidl's avatar
Patrick Meidl committed
28 29 30 31 32 33 34 35 36 37 38 39
  my $translation = Bio::EnsEMBL::Translation->new(
    -START_EXON => $exon1,
    -END_EXON   => $exon2,
    -SEQ_START  => 98,
    -SEQ_END    => 39
  );

  # stable ID setter
  $translation->stable_id('ENSP00053458');

  # get start and end position in start/end exons
  my $start = $translation->start;
40
  my $end   = $translation->end;
41

Ewan Birney's avatar
Ewan Birney committed
42 43
=head1 DESCRIPTION

44
A Translation object defines the CDS and UTR regions of a Transcript
45
through the use of start_Exon/end_Exon, and start/end attributes.
Ewan Birney's avatar
Ewan Birney committed
46 47 48 49

=cut


50 51
package Bio::EnsEMBL::Translation;

Ewan Birney's avatar
Ewan Birney committed
52 53 54
use vars qw($AUTOLOAD @ISA);
use strict;

55 56
use Scalar::Util qw(weaken);

57 58
use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
Ewan Birney's avatar
Ewan Birney committed
59

60
use Bio::EnsEMBL::Storable;
Ewan Birney's avatar
Ewan Birney committed
61

62
@ISA = qw(Bio::EnsEMBL::Storable);
Ewan Birney's avatar
Ewan Birney committed
63 64


65 66 67 68 69 70 71 72 73 74 75 76 77 78 79
=head2 new

  Arg [-START_EXON] : The Exon object in which the translation (CDS) starts
  Arg [-END_EXON]   : The Exon object in which the translation (CDS) ends
  Arg [-SEQ_START]  : The offset in the start_Exon indicating the start
                      position of the CDS.
  Arg [-SEQ_END]    : The offset in the end_Exon indicating the end
                      position of the CDS.
  Arg [-STABLE_ID]  : The stable identifier for this Translation
  Arg [-VERSION]    : The version of the stable identifier
  Arg [-DBID]       : The internal identifier of this Translation
  Arg [-ADAPTOR]    : The TranslationAdaptor for this Translation
  Arg [-SEQ]        : Manually sets the peptide sequence of this translation.
                      May be useful if this translation is not stored in
                      a database.
80 81
  Arg [-CREATED_DATE]: the date the translation was created
  Arg [-MODIFIED_DATE]: the date the translation was modified
82 83 84 85 86 87 88 89 90
  Example    : my $tl = Bio::EnsEMBL::Translation->new
                   (-START_EXON => $ex1,
                    -END_EXON   => $ex2,
                    -SEQ_START  => 98,
                    -SEQ_END    => 39);
  Description: Constructor.  Creates a new Translation object
  Returntype : Bio::EnsEMBL::Translation
  Exceptions : none
  Caller     : general
91
  Status     : Stable
92 93 94

=cut

95
sub new {
Graham McVicker's avatar
Graham McVicker committed
96
  my $caller = shift;
97

Graham McVicker's avatar
Graham McVicker committed
98
  my $class = ref($caller) || $caller;
Ewan Birney's avatar
Ewan Birney committed
99

100
  my ( $start_exon, $end_exon, $seq_start, $seq_end,
101
       $stable_id, $version, $dbID, $adaptor, $seq,
102 103 104 105
       $created_date, $modified_date ) =
	   rearrange( [ "START_EXON", "END_EXON", "SEQ_START", "SEQ_END",
			"STABLE_ID", "VERSION", "DBID", "ADAPTOR",
			"SEQ", "CREATED_DATE", "MODIFIED_DATE" ], @_ );
106 107 108

  my $self = bless {
		    'start_exon' => $start_exon,
109 110 111 112 113 114 115
		    'end_exon'   => $end_exon,
		    'adaptor'    => $adaptor,
		    'dbID'       => $dbID,
		    'start'      => $seq_start,
		    'end'        => $seq_end,
		    'stable_id'  => $stable_id,
		    'version'    => $version,
116 117
		    'created_date' => $created_date,
		    'modified_date' => $modified_date,
118
        'seq'        => $seq
119 120 121
		   }, $class;

  return $self;
Ewan Birney's avatar
Ewan Birney committed
122 123
}

124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141
=head2 new_fast

  Arg [1]    : hashref to be blessed
  Description: Construct a new Bio::EnsEMBL::Translation using the hashref.
  Exceptions : none
  Returntype : Bio::EnsEMBL::Translation
  Caller     : general, subclass constructors
  Status     : Stable

=cut


sub new_fast {
  my $class = shift;
  my $hashref = shift;
  return bless $hashref, $class;
}

142 143 144 145 146 147 148
sub transcript {
  my ( $self, $transcript ) = @_;

  if ( defined($transcript) ) {

    $self->{'transcript'} = $transcript;

149 150
    weaken($self->{'transcript'});

151 152 153 154 155 156 157 158 159 160 161 162 163 164
  } elsif ( !defined( $self->{'transcript'} ) ) {
    my $adaptor = $self->{'adaptor'};
    if ( !defined($adaptor) ) {
      throw("Adaptor is not set.");
    }

    my $dbID = $self->{'dbID'};
    if ( !defined($dbID) ) {
      throw("dbID is not set.");
    }

    $self->{'transcript'} =
      $adaptor->db()->get_TranscriptAdaptor()
      ->fetch_by_translation_id($dbID);
165 166

    weaken($self->{'transcript'});
167 168 169 170 171
  }

  return $self->{'transcript'};
}

Ewan Birney's avatar
Ewan Birney committed
172 173 174

=head2 start

Patrick Meidl's avatar
Patrick Meidl committed
175 176 177 178 179
  Arg [1]    : (optional) int $start - start position to set
  Example    : $translation->start(17);
  Description: Getter/setter for the value of start, which is a position within
               the exon given by start_Exon.

180 181
               If you need genomic coordinates, use the genomic_start()
               method.
Patrick Meidl's avatar
Patrick Meidl committed
182 183 184 185
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable
Ewan Birney's avatar
Ewan Birney committed
186 187 188 189 190 191 192

=cut

sub start{
   my $obj = shift;
   if( @_ ) {
      my $value = shift;
Laura Clarke's avatar
 
Laura Clarke committed
193
      
Ewan Birney's avatar
Ewan Birney committed
194 195 196 197 198 199 200
      $obj->{'start'} = $value;
    }
    return $obj->{'start'};

}


201 202
=head2 end

Patrick Meidl's avatar
Patrick Meidl committed
203 204 205 206
  Arg [1]    : (optional) int $end - end position to set
  Example    : $translation->end(8);
  Description: Getter/setter for the value of end, which is a position within
               the exon given by end_Exon.
207

208 209
               If you need genomic coordinates, use the genomic_end()
               method.
Patrick Meidl's avatar
Patrick Meidl committed
210 211 212 213
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable
214 215 216 217 218 219 220

=cut

sub end {
   my $self = shift;
   if( @_ ) {
      my $value = shift;
Laura Clarke's avatar
 
Laura Clarke committed
221
      
222 223 224 225 226 227 228
      $self->{'end'} = $value;
    }
    return $self->{'end'};

}


Graham McVicker's avatar
Graham McVicker committed
229
=head2 start_Exon
230

Patrick Meidl's avatar
Patrick Meidl committed
231 232 233 234 235 236 237 238 239
  Arg [1]    : (optional) Bio::EnsEMBL::Exon - start exon to assign
  Example    : $translation->start_Exon($exon1);
  Description: Getter/setter for the value of start_Exon, which denotes the
               exon at which translation starts (and within this exon, at the
               position indicated by start, see above).
  Returntype : Bio::EnsEMBL::Exon
  Exceptions : thrown on wrong argument type
  Caller     : general
  Status     : Stable
Ewan Birney's avatar
Ewan Birney committed
240 241 242

=cut

Graham McVicker's avatar
Graham McVicker committed
243
sub start_Exon {
244
   my $self = shift;
245

Ewan Birney's avatar
Ewan Birney committed
246 247
   if( @_ ) {
      my $value = shift;
248
      if( !ref $value || !$value->isa('Bio::EnsEMBL::Exon') ) {
249
         throw("Got to have an Exon object, not a $value");
250 251
      }
      $self->{'start_exon'} = $value;
Ewan Birney's avatar
Ewan Birney committed
252
    }
253
   return $self->{'start_exon'};
Ewan Birney's avatar
Ewan Birney committed
254 255 256
}


Graham McVicker's avatar
Graham McVicker committed
257
=head2 end_Exon
258

Patrick Meidl's avatar
Patrick Meidl committed
259 260 261 262 263 264 265 266 267
  Arg [1]    : (optional) Bio::EnsEMBL::Exon - start exon to assign
  Example    : $translation->start_Exon($exon1);
  Description: Getter/setter for the value of end_Exon, which denotes the
               exon at which translation ends (and within this exon, at the
               position indicated by end, see above).
  Returntype : Bio::EnsEMBL::Exon
  Exceptions : thrown on wrong argument type
  Caller     : general
  Status     : Stable
Ewan Birney's avatar
Ewan Birney committed
268 269 270

=cut

Graham McVicker's avatar
Graham McVicker committed
271
sub end_Exon {
272
   my $self = shift;
Ewan Birney's avatar
Ewan Birney committed
273 274
   if( @_ ) {
      my $value = shift;
275
      if( !ref $value || !$value->isa('Bio::EnsEMBL::Exon') ) {
276
         throw("Got to have an Exon object, not a $value");
277 278
      }
      $self->{'end_exon'} = $value;
279
    } 
Ewan Birney's avatar
Ewan Birney committed
280

281
    return $self->{'end_exon'};
Ewan Birney's avatar
Ewan Birney committed
282 283
}

284 285
=head2 cdna_start

Andreas Kusalananda Kähäri's avatar
Andreas Kusalananda Kähäri committed
286 287
    Arg  [1]    : (optional) Bio::EnsEMBL::Transcript $transcript
                  The transcript which this is a translation of.
288 289 290
    Example     : $translation_cdna_start = $translation->cdna_start();
    Description : Returns the start position of the translation in cDNA
                  coordinates.
Andreas Kusalananda Kähäri's avatar
Andreas Kusalananda Kähäri committed
291 292 293
                  If no transcript is given, the method will use
                  TranscriptAdaptor->fetch_by_translation_id() to locate
                  the correct transcript.
294 295 296 297 298 299 300 301 302 303 304 305 306 307
    Return type : Integer
    Exceptions  : Throws if the given (optional) argument is not a
                  transcript.
    Caller      : General
    Status      : At Risk (Under Development)

=cut

sub cdna_start {
    my $self = shift;
    my ($transcript) = @_;

    if ( defined $transcript
         && (    !ref $transcript
Andreas Kusalananda Kähäri's avatar
Andreas Kusalananda Kähäri committed
308 309
              || !$transcript->isa('Bio::EnsEMBL::Transcript') ) )
    {
310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334
        throw("Argument is not a transcript");
    }

    if ( !exists $self->{'cdna_start'} ) {
        if ( !defined $transcript ) {
            # We were not given a transcript, get the transcript out of
            # the database.

            my $transcript_adaptor =
              $self->adaptor()->db()->get_TranscriptAdaptor();

            $transcript =
              $transcript_adaptor->fetch_by_translation_id(
                                                        $self->dbID() );
        }

        $self->{'cdna_start'} =
          $self->start_Exon()->cdna_coding_start($transcript);
    }

    return $self->{'cdna_start'};
} ## end sub cdna_start

=head2 cdna_end

Andreas Kusalananda Kähäri's avatar
Andreas Kusalananda Kähäri committed
335 336
    Arg  [1]    : (optional) Bio::EnsEMBL::Transcript $transcript
                  The transcript which this is a translation of.
337 338 339
    Example     : $translation_cdna_end = $translation->cdna_end();
    Description : Returns the end position of the translation in cDNA
                  coordinates.
Andreas Kusalananda Kähäri's avatar
Andreas Kusalananda Kähäri committed
340 341 342
                  If no transcript is given, the method will use
                  TranscriptAdaptor->fetch_by_translation_id() to locate
                  the correct transcript.
343 344 345 346 347 348 349 350 351 352 353 354 355 356
    Return type : Integer
    Exceptions  : Throws if the given (optional) argument is not a
                  transcript.
    Caller      : General
    Status      : At Risk (Under Development)

=cut

sub cdna_end {
    my $self = shift;
    my ($transcript) = @_;

    if ( defined $transcript
         && (    !ref $transcript
Andreas Kusalananda Kähäri's avatar
Andreas Kusalananda Kähäri committed
357 358
              || !$transcript->isa('Bio::EnsEMBL::Transcript') ) )
    {
359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439
        throw("Argument is not a transcript");
    }

    if ( !exists $self->{'cdna_end'} ) {
        if ( !defined $transcript ) {
            # We were not given a transcript, get the transcript out of
            # the database.

            my $transcript_adaptor =
              $self->adaptor()->db()->get_TranscriptAdaptor();

            $transcript =
              $transcript_adaptor->fetch_by_translation_id(
                                                        $self->dbID() );
        }

        $self->{'cdna_end'} =
          $self->end_Exon()->cdna_coding_end($transcript);
    }

    return $self->{'cdna_end'};
} ## end sub cdna_end

=head2 genomic_start

    Args        : None
    Example     : $translation_genomic_start =
                      $translation->genomic_start();
    Description : Returns the start position of the translation in
                  genomic coordinates on the forward strand.
    Return type : Integer
    Exceptions  : None
    Caller      : General
    Status      : At Risk (Under Development)

=cut

sub genomic_start {
    my $self = shift;

    if ( !exists $self->{'genomic_start'} ) {
        if ( $self->start_Exon()->strand() >= 0 ) {
            $self->{'genomic_start'} =
              $self->start_Exon()->start() + ( $self->start() - 1 );
        } else {
            $self->{'genomic_start'} =
              $self->end_Exon()->end() - ( $self->end() - 1 );
        }
    }

    return $self->{'genomic_start'};
}

=head2 genomic_end

    Args        : None
    Example     : $translation_genomic_end = $translation->genomic_end();
    Description : Returns the end position of the translation in genomic
                  coordinates on the forward strand.
    Return type : Integer
    Exceptions  : None
    Caller      : General
    Status      : At Risk (Under Development)

=cut

sub genomic_end {
    my $self = shift;

    if ( !exists $self->{'genomic_end'} ) {
        if ( $self->end_Exon()->strand() >= 0 ) {
            $self->{'genomic_end'} =
              $self->end_Exon()->start() + ( $self->end() - 1 );
        } else {
            $self->{'genomic_end'} =
              $self->start_Exon()->end() - ( $self->start() - 1 );
        }
    }

    return $self->{'genomic_end'};
}
Ewan Birney's avatar
Ewan Birney committed
440

441
=head2 version
442

Patrick Meidl's avatar
Patrick Meidl committed
443 444 445
  Arg [1]    : (optional) string $version - version to set
  Example    : $translation->version(2);
  Description: Getter/setter for attribute version
446 447 448
  Returntype : string
  Exceptions : none
  Caller     : general
449
  Status     : Stable
Ewan Birney's avatar
Ewan Birney committed
450 451 452

=cut

453
sub version {
454
   my $self = shift;
455 456
  $self->{'version'} = shift if( @_ );
  return $self->{'version'};
Ewan Birney's avatar
Ewan Birney committed
457
}
458 459


460
=head2 stable_id
Graham McVicker's avatar
Graham McVicker committed
461

Patrick Meidl's avatar
Patrick Meidl committed
462 463 464
  Arg [1]    : (optional) string $stable_id - stable ID to set
  Example    : $translation->stable_id('ENSP0059890');
  Description: Getter/setter for attribute stable_id
465 466 467
  Returntype : string
  Exceptions : none
  Caller     : general
468
  Status     : Stable
469 470 471

=cut

472
sub stable_id {
473
   my $self = shift;
474 475
  $self->{'stable_id'} = shift if( @_ );
  return $self->{'stable_id'};
476 477
}

478 479
=head2 created_date

Patrick Meidl's avatar
Patrick Meidl committed
480 481 482
  Arg [1]    : (optional) string $created_date - created date to set
  Example    : $translation->created_date('2007-01-10 20:52:00');
  Description: Getter/setter for attribute created date
483 484 485 486 487 488 489
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut 

490 491 492 493 494 495 496
sub created_date {
  my $self = shift;
  $self->{'created_date'} = shift if ( @_ );
  return $self->{'created_date'};
}


497 498
=head2 modified_date

Patrick Meidl's avatar
Patrick Meidl committed
499 500 501
  Arg [1]    : (optional) string $modified_date - modification date to set
  Example    : $translation->modified_date('2007-01-10 20:52:00');
  Description: Getter/setter for attribute modified date
502 503 504 505 506 507 508
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut 

509 510 511 512 513 514
sub modified_date {
  my $self = shift;
  $self->{'modified_date'} = shift if ( @_ );
  return $self->{'modified_date'};
}

515

Graham McVicker's avatar
Graham McVicker committed
516

517 518
=head2 transform

Patrick Meidl's avatar
Patrick Meidl committed
519 520 521 522
  Arg [1]    : hashref $old_new_exon_map
               a hash that maps old to new exons for a whole gene
  Description: maps start end end exon according to mapping table.
              If an exon is not mapped, just keep the old one.
523
  Returntype: none
Patrick Meidl's avatar
Patrick Meidl committed
524 525
  Exceptions : none
  Caller     : Transcript->transform() 
526
  Status     : Stable
527 528 529 530 531 532 533

=cut

sub transform {
  my $self = shift;
  my $href_exons = shift;

Graham McVicker's avatar
Graham McVicker committed
534 535
  my $start_exon = $self->start_Exon();
  my $end_exon = $self->end_Exon();
536

Arne Stabenau's avatar
Arne Stabenau committed
537 538
  if ( exists $href_exons->{$start_exon} ) {
    $self->start_Exon($href_exons->{$start_exon});
539 540
  } else {
    # do nothing, the start exon wasnt mapped
541 542
  }

Arne Stabenau's avatar
Arne Stabenau committed
543 544
  if ( exists $href_exons->{$end_exon} ) {
    $self->end_Exon($href_exons->{$end_exon});
545 546
  } else { 
    # do nothing, the end exon wasnt mapped
547 548 549
  }
}

550 551 552

=head2 get_all_DBEntries

Patrick Meidl's avatar
Patrick Meidl committed
553 554
  Arg [1]    : (optional) $ex_db_exp - external db name
  Example    : @dbentries = @{$translation->get_all_DBEntries()};
555 556 557 558 559 560 561 562 563
  Description: Retrieves DBEntries (xrefs) for this translation.  

               This method will attempt to lazy-load DBEntries from a
               database if an adaptor is available and no DBEntries are present
               on the translation (i.e. they have not already been added or 
               loaded).
  Returntype : list reference to Bio::EnsEMBL::DBEntry objects
  Exceptions : none
  Caller     : get_all_DBLinks, TranslationAdaptor::store
564
  Status     : Stable
565 566 567 568 569

=cut

sub get_all_DBEntries {
  my $self = shift;
570
  my $ex_db_exp = shift;
Ian Longden's avatar
Ian Longden committed
571
  my $ex_db_type = shift;
572 573 574 575 576 577

  my $cache_name = "dbentries";

  if(defined($ex_db_exp)){
    $cache_name .= $ex_db_exp;
  }
Ian Longden's avatar
Ian Longden committed
578 579
  if(defined($ex_db_type)){
    $cache_name .= $ex_db_type;
580
  }
581

Patrick Meidl's avatar
Patrick Meidl committed
582
  # if not cached, retrieve all of the xrefs for this gene
583
  if(!defined $self->{$cache_name}) {
584 585
    my $adaptor = $self->adaptor();
    my $dbID    = $self->dbID();
Graham McVicker's avatar
Graham McVicker committed
586 587

    return [] if(!$adaptor || !$dbID);
588
    $self->{$cache_name} =
Ian Longden's avatar
Ian Longden committed
589
      $self->adaptor->db->get_DBEntryAdaptor->fetch_all_by_Translation($self, $ex_db_exp, $ex_db_type);
590 591
  }

592
  $self->{$cache_name} ||= [];
593

594
  return $self->{$cache_name};
595 596 597 598 599 600 601
}


=head2 add_DBEntry

  Arg [1]    : Bio::EnsEMBL::DBEntry $dbe
               The dbEntry to be added
Patrick Meidl's avatar
Patrick Meidl committed
602 603 604 605
  Example    : $translation->add_DBEntry($xref);
  Description: Associates a DBEntry with this translation. Note that adding
               DBEntries will prevent future lazy-loading of DBEntries for this
               translation (see get_all_DBEntries).
606 607 608
  Returntype : none
  Exceptions : thrown on incorrect argument type
  Caller     : general
609
  Status     : Stable
610 611 612 613 614 615 616 617

=cut

sub add_DBEntry {
  my $self = shift;
  my $dbe = shift;

  unless($dbe && ref($dbe) && $dbe->isa('Bio::EnsEMBL::DBEntry')) {
618
    throw('Expected DBEntry argument');
619 620 621 622 623 624 625
  }

  $self->{'dbentries'} ||= [];
  push @{$self->{'dbentries'}}, $dbe;
}


Stephen Keenan's avatar
Stephen Keenan committed
626 627
=head2 get_all_DBLinks

628 629 630
  Arg [1]    : see get_all_DBEntries
  Example    : see get_all_DBEntries
  Description: This is here for consistancy with the Transcript and Gene 
Patrick Meidl's avatar
Patrick Meidl committed
631
               classes. It is a synonym for the get_all_DBEntries method.
632 633 634
  Returntype : see get_all_DBEntries
  Exceptions : none
  Caller     : general
635
  Status     : Stable
Stephen Keenan's avatar
Stephen Keenan committed
636 637 638 639 640

=cut

sub get_all_DBLinks {
  my $self = shift;
641
  return $self->get_all_DBEntries(@_);
Stephen Keenan's avatar
Stephen Keenan committed
642 643
}

644

645 646 647 648 649 650 651 652 653 654
=head2 get_all_ProteinFeatures

  Arg [1]    : (optional) string $logic_name
               The analysis logic_name of the features to retrieve.  If not
               specified, all features are retrieved instead.
  Example    : $features = $self->get_all_ProteinFeatures('PFam');
  Description: Retrieves all ProteinFeatures associated with this 
               Translation. If a logic_name is specified, only features with 
               that logic_name are returned.  If no logic_name is provided all
               associated protein_features are returned.
655 656 657

               ProteinFeatures are lazy-loaded from the database unless they
               added manually to the Translation or had already been loaded.
658 659 660
  Returntype : Bio::EnsEMBL::ProteinFeature
  Exceptions : none
  Caller     : general
661
  Status     : Stable
662 663 664 665 666 667 668 669 670 671

=cut

sub get_all_ProteinFeatures {
  my $self = shift;
  my $logic_name = shift;

  if(!$self->{'protein_features'}) {
    my $adaptor = $self->adaptor();
    my $dbID    = $self->dbID();
672 673

    return [] if (!$adaptor || !$dbID);
674 675 676 677 678 679 680 681 682

    my %hash;
    $self->{'protein_features'} = \%hash;

    my $pfa = $adaptor->db()->get_ProteinFeatureAdaptor();
    my $name;
    foreach my $f (@{$pfa->fetch_all_by_translation_id($dbID)}) {
      my $analysis = $f->analysis();
      if($analysis) {
683
        $name = lc($f->analysis->logic_name());
684
      } else {
685 686
        warning("ProteinFeature has no attached analysis\n");
        $name = '';
687 688 689 690 691 692
      }
      $hash{$name} ||= [];
      push @{$hash{$name}}, $f;
    }
  }

Patrick Meidl's avatar
Patrick Meidl committed
693
  # a specific type of protein feature was requested
694 695 696 697 698
  if(defined($logic_name)) {
    $logic_name = lc($logic_name);
    return $self->{'protein_features'}->{$logic_name} || [];
  }

699
  my @features = ();
700

Patrick Meidl's avatar
Patrick Meidl committed
701
  # all protein features were requested
702 703 704 705 706 707 708 709 710 711 712 713 714 715
  foreach my $type (keys %{$self->{'protein_features'}}) {
    push @features, @{$self->{'protein_features'}->{$type}};
  }

  return \@features;    
}


=head2 get_all_DomainFeatures

  Example    : @domain_feats = @{$translation->get_all_DomainFeatures};
  Description: A convenience method which retrieves all protein features
               that are considered to be 'Domain' features.  Features which
               are 'domain' features are those with analysis logic names:
Patrick Meidl's avatar
Patrick Meidl committed
716 717
               'pfscan', 'scanprosite', 'superfamily', 'pfam', 'prints',
               'smart', 'pirsf', 'tigrfam'.
718 719 720
  Returntype : listref of Bio::EnsEMBL::ProteinFeatures
  Exceptions : none
  Caller     : webcode (protview)
721
  Status     : Stable
722 723 724 725 726 727 728 729

=cut

sub get_all_DomainFeatures{
 my ($self) = @_;

 my @features;

730 731 732
 my @types = ('pfscan',      #profile (prosite or pfam motifs)
              'scanprosite', #prosite
              'superfamily',
733
              'pfam',
734 735 736
              'smart',
              'tigrfam',
              'pirsf',
737 738 739 740 741 742 743 744 745
              'prints');

 foreach my $type (@types) {
   push @features, @{$self->get_all_ProteinFeatures($type)};
 }

 return \@features;
}

746

747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777
=head2 add_ProteinFeature

  Arg [1]    : Bio::EnsEMBL::ProteinFeature $pf
               The ProteinFeature to be added
  Example    : $translation->add_ProteinFeature($pf);
  Description: Associates a ProteinFeature with this translation. Note that
               adding ProteinFeatures will prevent future lazy-loading of
               ProteinFeatures for this translation (see
               get_all_ProteinFeatures).
  Returntype : none
  Exceptions : thrown on incorrect argument type
  Caller     : general
  Status     : Stable

=cut

sub add_ProteinFeature {
  my $self = shift;
  my $pf = shift;

  unless ($pf && ref($pf) && $pf->isa('Bio::EnsEMBL::ProteinFeature')) {
    throw('Expected ProteinFeature argument');
  }

  my $analysis = $pf->analysis;
  throw("ProteinFeature has no attached Analysis.") unless $analysis;

  push @{ $self->{'protein_features'}->{$analysis->logic_name} }, $pf;
}


778 779 780 781
=head2 display_id

  Example    : print $translation->display_id();
  Description: This method returns a string that is considered to be
782 783 784
               the 'display' identifier. For translations this is (depending on
               availability and in this order) the stable Id, the dbID or an
               empty string.
785 786 787
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
788
  Status     : Stable
789 790 791 792 793

=cut

sub display_id {
  my $self = shift;
794
  return $self->{'stable_id'} || $self->dbID || '';
795 796 797
}


798 799 800 801 802 803 804 805
=head2 length

  Example    : print "Peptide length =", $translation->length();
  Description: Retrieves the length of the peptide sequence (i.e. number of
               amino acids) represented by this Translation object.
  Returntype : int
  Exceptions : none
  Caller     : webcode (protview etc.)
806
  Status     : Stable
807 808 809

=cut

Web Admin's avatar
Web Admin committed
810
sub length {
811 812
  my $self = shift;
  my $seq = $self->seq();
Web Admin's avatar
testing  
Web Admin committed
813

814
  return ($seq) ? CORE::length($seq) : 0;
815 816 817 818 819 820 821 822 823
}


=head2 seq

  Example    : print $translation->seq();
  Description: Retrieves a string representation of the peptide sequence
               of this Translation.  This retrieves the transcript from the
               database and gets its sequence, or retrieves the sequence which
Patrick Meidl's avatar
Patrick Meidl committed
824
               was set via the constructor.
825 826 827 828
  Returntype : string
  Exceptions : warning if the sequence is not set and cannot be retrieved from
               the database.
  Caller     : webcode (protview etc.)
829
  Status     : Stable
830 831 832 833

=cut

sub seq {
Andreas Kusalananda Kähäri's avatar
Andreas Kusalananda Kähäri committed
834
  my ( $self, $sequence ) = @_;
835

Andreas Kusalananda Kähäri's avatar
Andreas Kusalananda Kähäri committed
836
  if ( defined($sequence) ) {
837

Andreas Kusalananda Kähäri's avatar
Andreas Kusalananda Kähäri committed
838
    $self->{'seq'} = $sequence;
839

Andreas Kusalananda Kähäri's avatar
Andreas Kusalananda Kähäri committed
840
  } elsif ( !defined( $self->{'seq'} ) ) {
841

842
    my $transcript = $self->transcript();
Andreas Kusalananda Kähäri's avatar
Andreas Kusalananda Kähäri committed
843

844 845 846
    my $canonical_translation = $transcript->translation();
    my $is_alternative =
      ( $canonical_translation->stable_id() ne $self->stable_id() );
Andreas Kusalananda Kähäri's avatar
Andreas Kusalananda Kähäri committed
847

848 849 850 851
    if ($is_alternative) {
      # To deal with non-canonical (alternative) translations, subsitute
      # the canonical translation in the transcript with $self for a
      # while.
Andreas Kusalananda Kähäri's avatar
Andreas Kusalananda Kähäri committed
852

853 854 855 856
      $transcript->translation($self);
    }

    my $seq = $transcript->translate();
Andreas Kusalananda Kähäri's avatar
Andreas Kusalananda Kähäri committed
857 858 859
    if ( defined($seq) ) {
      $self->{'seq'} = $seq->seq();
    }
860

861 862 863 864 865 866 867
    if ($is_alternative) {
      # Reinstate the real canonical translation.

      $transcript->translation($canonical_translation);
    }

  } ## end elsif ( !defined( $self->...))
Andreas Kusalananda Kähäri's avatar
Andreas Kusalananda Kähäri committed
868 869 870

  if ( !defined( $self->{'seq'} ) ) {
    return '';    # Empty string
871
  }
Andreas Kusalananda Kähäri's avatar
Andreas Kusalananda Kähäri committed
872 873 874 875

  return $self->{'seq'};

} ## end sub seq
876

Patrick Meidl's avatar
Patrick Meidl committed
877

878 879 880 881
=head2 get_all_Attributes

  Arg [1]    : optional string $attrib_code
               The code of the attribute type to retrieve values for.
882
  Example    : ($sc_attr) = @{$tl->get_all_Attributes('_selenocysteine')};
883
               @tl_attributes = @{$translation->get_all_Attributes()};
884 885
  Description: Gets a list of Attributes of this translation.
               Optionally just get Attrubutes for given code.
886
               Recognized attribute "_selenocysteine"
887 888 889 890
  Returntype : listref Bio::EnsEMBL::Attribute
  Exceptions : warning if translation does not have attached adaptor and 
               attempts lazy load.
  Caller     : general, modify_translation
891
  Status     : Stable
892 893 894 895 896 897 898 899 900 901 902 903 904

=cut

sub get_all_Attributes {
  my $self = shift;
  my $attrib_code = shift;

  if( ! exists $self->{'attributes' } ) {
    if(!$self->adaptor() ) {
#      warning('Cannot get attributes without an adaptor.');
      return [];
    }

905 906
    my $aa = $self->adaptor->db->get_AttributeAdaptor();
    $self->{'attributes'} = $aa->fetch_all_by_Translation( $self );
907 908 909
  }

  if( defined $attrib_code ) {
910
    my @results = grep { uc($_->code()) eq uc($attrib_code) }
911 912 913 914 915 916 917 918 919 920
    @{$self->{'attributes'}};
    return \@results;
  } else {
    return $self->{'attributes'};
  }
}


=head2 add_Attributes

Patrick Meidl's avatar
Patrick Meidl committed
921 922
  Arg [1..N] : Bio::EnsEMBL::Attribute $attribute
               Attributes to add.
923
  Example    : $translation->add_Attributes($selenocysteine_attribute);
924
  Description: Adds an Attribute to the Translation. Usefull to 
925
               do _selenocysteine.
926 927
               If you add an attribute before you retrieve any from database, 
               lazy load will be disabled.
928
  Returntype : none
929
  Exceptions : throw on incorrect arguments
930
  Caller     : general
931
  Status     : Stable
932 933 934 935 936 937 938 939 940 941 942 943 944

=cut

sub add_Attributes {
  my $self = shift;
  my @attribs = @_;

  if( ! exists $self->{'attributes'} ) {
    $self->{'attributes'} = [];
  }

  for my $attrib ( @attribs ) {
    if( ! $attrib->isa( "Bio::EnsEMBL::Attribute" )) {
945
      throw( "Argument to add_Attribute must be a Bio::EnsEMBL::Attribute" );
946 947
    }
    push( @{$self->{'attributes'}}, $attrib );
948
    $self->{seq}=undef;
949 950 951
  }
}

Patrick Meidl's avatar
Patrick Meidl committed
952

953
=head2 get_all_SeqEdits
954

955 956 957 958 959 960
  Example    : my @seqeds = @{$transcript->get_all_SeqEdits()};
  Description: Retrieves all post transcriptional sequence modifications for
               this transcript.
  Returntype : Bio::EnsEMBL::SeqEdit
  Exceptions : none
  Caller     : spliced_seq()
961
  Status     : Stable
962 963 964

=cut

965
sub get_all_SeqEdits {
966 967
  my $self = shift;

968
  my @seqeds;
969

970 971
  my $attribs;
  
972
  my @edits = ('initial_met', '_selenocysteine', 'amino_acid_sub');
973 974 975 976
  

  foreach my $edit(@edits){
    $attribs = $self->get_all_Attributes($edit);
977

978 979 980 981
    # convert attributes to SeqEdit objects
    foreach my $a (@$attribs) {
      push @seqeds, Bio::EnsEMBL::SeqEdit->new(-ATTRIB => $a);
    }
982 983 984
  }
  return \@seqeds;
}
Patrick Meidl's avatar
Patrick Meidl committed
985
  
986 987 988

=head2 modify_translation

Patrick Meidl's avatar
Patrick Meidl committed
989
  Arg [1]    : Bio::Seq $peptide 
990 991
  Example    : my $seq = Bio::Seq->new(-SEQ => $dna)->translate();
               $translation->modify_translation($seq);
992
  Description: Applies sequence edits such as selenocysteines to the Bio::Seq 
993
               peptide thats passed in
994
  Returntype : Bio::Seq
Patrick Meidl's avatar
Patrick Meidl committed
995
  Exceptions : none
996
  Caller     : Bio::EnsEMBL::Transcript->translate
997
  Status     : Stable
998 999 1000 1001

=cut

sub modify_translation {
1002
  my ( $self, $seq ) = @_;
1003

1004
  my @seqeds = @{ $self->get_all_SeqEdits() };
1005

1006 1007 1008
  # Sort in reverse order to avoid complication of adjusting
  # downstream edits.
  @seqeds = sort { $b->start() <=> $a->start() } @seqeds;
1009

1010
  # Apply all edits.
1011 1012
  my $peptide = $seq->seq();
  foreach my $se (@seqeds) {
1013
    $se->apply_edit( \$peptide );
1014
  }
1015

1016
  $seq->seq($peptide);
1017 1018 1019 1020 1021

  return $seq;
}


1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037
=head2 temporary_id

  Description: DEPRECATED This method should not be needed. Use dbID,
               stable_id or something else.

=cut

sub temporary_id {
   my $self = shift;
   deprecate( "I cant see what a temporary_id is good for, please use " .
               "dbID or stableID or\n try without an id." );
  $self->{'temporary_id'} = shift if( @_ );
  return $self->{'temporary_id'};
}


1038 1039 1040
=head2 get_all_DASFactories

  Function  : Retrieves a listref of registered DAS objects
Patrick Meidl's avatar
Patrick Meidl committed
1041 1042
  Returntype: DAS objects
  Exceptions: none
1043
  Caller    : webcode
Patrick Meidl's avatar
Patrick Meidl committed
1044 1045
  Example   : $dasref = $prot->get_all_DASFactories;
  Status    : Stable
1046 1047 1048 1049 1050 1051 1052 1053 1054

=cut

sub get_all_DASFactories {
   my $self = shift;
   return [ $self->adaptor()->db()->_each_DASFeatureFactory ];
}


1055 1056 1057 1058 1059 1060 1061 1062 1063
=head2 get_all_DAS_Features

  Example    : $features = $prot->get_all_DAS_Features;
  Description: Retreives a hash reference to a hash of DAS feature
               sets, keyed by the DNS, NOTE the values of this hash
               are an anonymous array containing:
                (1) a pointer to an array of features;
                (2) a pointer to the DAS stylesheet
  Returntype : hashref of Bio::SeqFeatures
Patrick Meidl's avatar
Patrick Meidl committed
1064
  Exceptions : none
1065
  Caller     : webcode
1066
  Status     : Stable
1067 1068 1069 1070

=cut

sub get_all_DAS_Features{
Patrick Meidl's avatar
Patrick Meidl committed
1071
  my $self = shift;
1072 1073 1074

  my $db = $self->adaptor->db;
  my $GeneAdaptor = $db->get_GeneAdaptor;
1075
  my $Gene = $GeneAdaptor->fetch_by_translation_stable_id($self->stable_id) || return;
1076
  my $slice = $Gene->feature_Slice;
1077 1078
 
  return $self->SUPER::get_all_DAS_Features($slice);
1079 1080
}

1081

1082
1;