Bio/SeqFeatureI.pm

   1 #
   2 # BioPerl module for Bio::SeqFeatureI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Ewan Birney <birney@ebi.ac.uk>
   7 #
   8 # Copyright Ewan Birney
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::SeqFeatureI - Abstract interface of a Sequence Feature
  17
  18 =head1 SYNOPSIS
  19
  20     # get a seqfeature somehow, eg, from a Sequence with Features attached
  21
  22     foreach $feat ( $seq->get_SeqFeatures() ) {
  23        print "Feature from ", $feat->start, "to ",
  24                $feat->end, " Primary tag  ", $feat->primary_tag,
  25                   ", produced by ", $feat->source_tag(), "\n";
  26
  27        if( $feat->strand == 0 ) {
  28                     print "Feature applicable to either strand\n";
  29        } else {
  30           print "Feature on strand ", $feat->strand,"\n"; # -1,1
  31        }
  32
  33        print "feature location is ",$feat->start, "..",
  34           $feat->end, " on strand ", $feat->strand, "\n";
  35        print "easy utility to print locations in GenBank/EMBL way ",
  36           $feat->location->to_FTstring(), "\n";
  37
  38        foreach $tag ( $feat->get_all_tags() ) {
  39                     print "Feature has tag ", $tag, " with values, ",
  40                       join(' ',$feat->get_tag_values($tag)), "\n";
  41        }
  42             print "new feature\n" if $feat->has_tag('new');
  43             # features can have sub features
  44             my @subfeat = $feat->get_SeqFeatures();
  45          }
  46
  47 =head1 DESCRIPTION
  48
  49 This interface is the functions one can expect for any Sequence
  50 Feature, whatever its implementation or whether it is a more complex
  51 type (eg, a Gene). This object does not actually provide any
  52 implementation, it just provides the definitions of what methods one can
  53 call. See Bio::SeqFeature::Generic for a good standard implementation
  54 of this object
  55
  56 =head1 FEEDBACK
  57
  58 User feedback is an integral part of the evolution of this and other
  59 Bioperl modules. Send your comments and suggestions preferably to one
  60 of the Bioperl mailing lists.  Your participation is much appreciated.
  61
  62   bioperl-l@bioperl.org                  - General discussion
  63   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  64
  65 =head2 Support
  66
  67 Please direct usage questions or support issues to the mailing list:
  68
  69 I<bioperl-l@bioperl.org>
  70
  71 rather than to the module maintainer directly. Many experienced and
  72 reponsive experts will be able look at the problem and quickly
  73 address it. Please include a thorough description of the problem
  74 with code and data examples if at all possible.
  75
  76 =head2 Reporting Bugs
  77
  78 Report bugs to the Bioperl bug tracking system to help us keep track
  79 the bugs and their resolution.  Bug reports can be submitted via the
  80 web:
  81
  82   https://github.com/bioperl/bioperl-live/issues
  83
  84 =head1 APPENDIX
  85
  86 The rest of the documentation details each of the object
  87 methods. Internal methods are usually preceded with a _
  88
  89 =cut
  90
  91
  92 # Let the code begin...
  93
  94
  95 package Bio::SeqFeatureI;
  96 use vars qw($HasInMemory);
  97 use strict;
  98 BEGIN {
  99     eval { require Bio::DB::InMemoryCache };
 100     if( $@ ) { $HasInMemory = 0 }
 101     else { $HasInMemory = 1 }
 102 }
 103
 104 use Bio::Seq;
 105
 106 use Carp;
 107
 108 use base qw(Bio::RangeI);
 109
 110 =head1 Bio::SeqFeatureI specific methods
 111
 112 New method interfaces.
 113
 114 =cut
 115
 116 =head2 get_SeqFeatures
 117
 118  Title   : get_SeqFeatures
 119  Usage   : @feats = $feat->get_SeqFeatures();
 120  Function: Returns an array of sub Sequence Features
 121  Returns : An array
 122  Args    : none
 123
 124 =cut
 125
 126 sub get_SeqFeatures{
 127    my ($self,@args) = @_;
 128
 129    $self->throw_not_implemented();
 130 }
 131
 132 =head2 display_name
 133
 134  Title   : display_name
 135  Usage   : $name = $feat->display_name()
 136  Function: Returns the human-readable name of the feature for displays.
 137  Returns : a string
 138  Args    : none
 139
 140 =cut
 141
 142 sub display_name {
 143     shift->throw_not_implemented();
 144 }
 145
 146 =head2 primary_tag
 147
 148  Title   : primary_tag
 149  Usage   : $tag = $feat->primary_tag()
 150  Function: Returns the primary tag for a feature,
 151            eg 'exon'
 152  Returns : a string
 153  Args    : none
 154
 155
 156 =cut
 157
 158 sub primary_tag{
 159    my ($self,@args) = @_;
 160
 161    $self->throw_not_implemented();
 162
 163 }
 164
 165 =head2 source_tag
 166
 167  Title   : source_tag
 168  Usage   : $tag = $feat->source_tag()
 169  Function: Returns the source tag for a feature,
 170            eg, 'genscan'
 171  Returns : a string
 172  Args    : none
 173
 174
 175 =cut
 176
 177 sub source_tag{
 178    my ($self,@args) = @_;
 179
 180    $self->throw_not_implemented();
 181 }
 182
 183 =head2 has_tag
 184
 185  Title   : has_tag
 186  Usage   : $tag_exists = $self->has_tag('some_tag')
 187  Function:
 188  Returns : TRUE if the specified tag exists, and FALSE otherwise
 189  Args    :
 190
 191 =cut
 192
 193 sub has_tag{
 194    my ($self,@args) = @_;
 195
 196    $self->throw_not_implemented();
 197
 198 }
 199
 200 =head2 get_tag_values
 201
 202  Title   : get_tag_values
 203  Usage   : @values = $self->get_tag_values('some_tag')
 204  Function:
 205  Returns : An array comprising the values of the specified tag.
 206  Args    : a string
 207
 208 throws an exception if there is no such tag
 209
 210 =cut
 211
 212 sub get_tag_values {
 213     shift->throw_not_implemented();
 214 }
 215
 216 =head2 get_tagset_values
 217
 218  Title   : get_tagset_values
 219  Usage   : @values = $self->get_tagset_values(qw(label transcript_id product))
 220  Function:
 221  Returns : An array comprising the values of the specified tags, in order of tags
 222  Args    : An array of strings
 223
 224 does NOT throw an exception if none of the tags are not present
 225
 226 this method is useful for getting a human-readable label for a
 227 SeqFeatureI; not all tags can be assumed to be present, so a list of
 228 possible tags in preferential order is provided
 229
 230 =cut
 231
 232 # interface + abstract method
 233 sub get_tagset_values {
 234     my ($self, @args) = @_;
 235     my @vals = ();
 236     foreach my $arg (@args) {
 237         if ($self->has_tag($arg)) {
 238             push(@vals, $self->get_tag_values($arg));
 239         }
 240     }
 241     return @vals;
 242 }
 243
 244 =head2 get_all_tags
 245
 246  Title   : get_all_tags
 247  Usage   : @tags = $feat->get_all_tags()
 248  Function: gives all tags for this feature
 249  Returns : an array of strings
 250  Args    : none
 251
 252
 253 =cut
 254
 255 sub get_all_tags{
 256     shift->throw_not_implemented();
 257 }
 258
 259 =head2 attach_seq
 260
 261  Title   : attach_seq
 262  Usage   : $sf->attach_seq($seq)
 263  Function: Attaches a Bio::Seq object to this feature. This
 264            Bio::Seq object is for the *entire* sequence: ie
 265            from 1 to 10000
 266
 267            Note that it is not guaranteed that if you obtain a feature from
 268            an object in bioperl, it will have a sequence attached. Also,
 269            implementors of this interface can choose to provide an empty
 270            implementation of this method. I.e., there is also no guarantee
 271            that if you do attach a sequence, seq() or entire_seq() will not
 272            return undef.
 273
 274            The reason that this method is here on the interface is to enable
 275            you to call it on every SeqFeatureI compliant object, and
 276            that it will be implemented in a useful way and set to a useful
 277            value for the great majority of use cases. Implementors who choose
 278            to ignore the call are encouraged to specifically state this in
 279            their documentation.
 280
 281  Example :
 282  Returns : TRUE on success
 283  Args    : a Bio::PrimarySeqI compliant object
 284
 285
 286 =cut
 287
 288 sub attach_seq {
 289     shift->throw_not_implemented();
 290 }
 291
 292 =head2 seq
 293
 294  Title   : seq
 295  Usage   : $tseq = $sf->seq()
 296  Function: returns the truncated sequence (if there is a sequence attached)
 297            for this feature
 298  Example :
 299  Returns : sub seq (a Bio::PrimarySeqI compliant object) on attached sequence
 300            bounded by start & end, or undef if there is no sequence attached
 301  Args    : none
 302
 303
 304 =cut
 305
 306 sub seq {
 307     shift->throw_not_implemented();
 308 }
 309
 310 =head2 entire_seq
 311
 312  Title   : entire_seq
 313  Usage   : $whole_seq = $sf->entire_seq()
 314  Function: gives the entire sequence that this seqfeature is attached to
 315  Example :
 316  Returns : a Bio::PrimarySeqI compliant object, or undef if there is no
 317            sequence attached
 318  Args    : none
 319
 320
 321 =cut
 322
 323 sub entire_seq {
 324     shift->throw_not_implemented();
 325 }
 326
 327
 328 =head2 seq_id
 329
 330  Title   : seq_id
 331  Usage   : $obj->seq_id($newval)
 332  Function: There are many cases when you make a feature that you
 333            do know the sequence name, but do not know its actual
 334            sequence. This is an attribute such that you can store
 335            the ID (e.g., display_id) of the sequence.
 336
 337            This attribute should *not* be used in GFF dumping, as
 338            that should come from the collection in which the seq
 339            feature was found.
 340  Returns : value of seq_id
 341  Args    : newvalue (optional)
 342
 343
 344 =cut
 345
 346 sub seq_id {
 347     shift->throw_not_implemented();
 348 }
 349
 350 =head2 gff_string
 351
 352  Title   : gff_string
 353  Usage   : $str = $feat->gff_string;
 354            $str = $feat->gff_string($gff_formatter);
 355  Function: Provides the feature information in GFF format.
 356
 357            The implementation provided here returns GFF2 by default. If you
 358            want a different version, supply an object implementing a method
 359            gff_string() accepting a SeqFeatureI object as argument. E.g., to
 360            obtain GFF1 format, do the following:
 361
 362                 my $gffio = Bio::Tools::GFF->new(-gff_version => 1);
 363                 $gff1str = $feat->gff_string($gff1io);
 364
 365  Returns : A string
 366  Args    : Optionally, an object implementing gff_string().
 367
 368
 369 =cut
 370
 371 sub gff_string{
 372    my ($self,$formatter) = @_;
 373
 374    $formatter = $self->_static_gff_formatter unless $formatter;
 375    return $formatter->gff_string($self);
 376 }
 377
 378 my $static_gff_formatter = undef;
 379
 380 =head2 _static_gff_formatter
 381
 382  Title   : _static_gff_formatter
 383  Usage   :
 384  Function:
 385  Example :
 386  Returns :
 387  Args    :
 388
 389
 390 =cut
 391
 392 sub _static_gff_formatter{
 393    my ($self,@args) = @_;
 394    require Bio::Tools::GFF; # on the fly inclusion -- is this better?
 395    if( !defined $static_gff_formatter ) {
 396        $static_gff_formatter = Bio::Tools::GFF->new('-gff_version' => 2);
 397    }
 398    return $static_gff_formatter;
 399 }
 400
 401
 402 =head1 Decorating methods
 403
 404 These methods have an implementation provided by Bio::SeqFeatureI,
 405 but can be validly overwritten by subclasses
 406
 407 =head2 spliced_seq
 408
 409   Title   : spliced_seq
 410
 411   Usage   : $seq = $feature->spliced_seq()
 412             $seq = $feature_with_remote_locations->spliced_seq($db_for_seqs)
 413
 414   Function: Provides a sequence of the feature which is the most
 415             semantically "relevant" feature for this sequence. A default
 416             implementation is provided which for simple cases returns just
 417             the sequence, but for split cases, loops over the split location
 418             to return the sequence. In the case of split locations with
 419             remote locations, eg
 420
 421             join(AB000123:5567-5589,80..1144)
 422
 423             in the case when a database object is passed in, it will attempt
 424             to retrieve the sequence from the database object, and "Do the right thing",
 425             however if no database object is provided, it will generate the correct
 426             number of N's (DNA) or X's (protein, though this is unlikely).
 427
 428             This function is deliberately "magical" attempting to second guess
 429             what a user wants as "the" sequence for this feature.
 430
 431             Implementing classes are free to override this method with their
 432             own magic if they have a better idea what the user wants.
 433
 434   Args    : [optional]
 435             -db        A L<Bio::DB::RandomAccessI> compliant object if
 436                        one needs to retrieve remote seqs.
 437             -nosort    boolean if the locations should not be sorted
 438                        by start location.  This may occur, for instance,
 439                        in a circular sequence where a gene span starts
 440                        before the end of the sequence and ends after the
 441                        sequence start. Example : join(15685..16260,1..207)
 442                                            (default = if sequence is_circular(), 1, otherwise 0)
 443                         -phase     truncates the returned sequence based on the
 444                                            intron phase (0,1,2).
 445
 446   Returns : A L<Bio::PrimarySeqI> object
 447
 448 =cut
 449
 450 sub spliced_seq {
 451     my $self = shift;
 452         my @args = @_;
 453         my ($db, $nosort, $phase) =
 454            $self->_rearrange([qw(DB NOSORT PHASE)], @args);
 455
 456         # set no_sort based on the parent sequence status
 457         if ($self->entire_seq->is_circular) {
 458                 $nosort = 1;
 459         }
 460
 461         # (added 7/7/06 to allow use old API (with warnings)
 462         my $old_api = (!(grep {$_ =~ /(?:nosort|db|phase)/} @args)) ? 1 : 0;
 463         if (@args && $old_api) {
 464                 $self->warn(q(API has changed; please use '-db' or '-nosort' ).
 465                      qq(for args. See POD for more details.));
 466                 $db = shift @args if @args;
 467                 $nosort = shift @args if @args;
 468                 $phase = shift @args if @args;
 469         };
 470
 471         if (defined($phase) && ($phase < 0 || $phase > 2)) {
 472             $self->warn("Phase must be 0,1, or 2.  Setting phase to 0...");
 473             $phase = 0;
 474         }
 475
 476         if( $db && ref($db) && ! $db->isa('Bio::DB::RandomAccessI') ) {
 477         $self->warn("Must pass in a valid Bio::DB::RandomAccessI object".
 478                     " for access to remote locations for spliced_seq");
 479         $db = undef;
 480     } elsif( defined $db && $HasInMemory &&
 481             $db->isa('Bio::DB::InMemoryCache') ) {
 482         $db = Bio::DB::InMemoryCache->new(-seqdb => $db);
 483     }
 484
 485     if( ! $self->location->isa("Bio::Location::SplitLocationI") ) {
 486         if ($phase) {
 487             $self->debug("Subseq start: ",$phase+1,"\tend: ",$self->end,"\n");
 488             my $seqstr = substr($self->seq->seq, $phase);
 489             my $out = Bio::Seq->new( -id => $self->entire_seq->display_id
 490                                 . "_spliced_feat",
 491                          -seq => $seqstr);
 492             return $out;
 493         } else {
 494             return $self->seq(); # nice and easy!
 495         }
 496     }
 497
 498     # redundant test, but the above ISA is probably not ideal.
 499     if( ! $self->location->isa("Bio::Location::SplitLocationI") ) {
 500         $self->throw("not atomic, not split, yikes, in trouble!");
 501     }
 502
 503     my $seqstr = '';
 504     my $seqid = $self->entire_seq->display_id;
 505     # This is to deal with reverse strand features
 506     # so we are really sorting features 5' -> 3' on their strand
 507     # i.e. rev strand features will be sorted largest to smallest
 508     # as this how revcom CDSes seem to be annotated in genbank.
 509     # Might need to eventually allow this to be programable?
 510     # (can I mention how much fun this is NOT! --jason)
 511
 512     my ($mixed,$mixedloc, $fstrand) = (0);
 513
 514     if( $self->isa('Bio::Das::SegmentI') &&
 515         ! $self->absolute ) {
 516         $self->warn("Calling spliced_seq with a Bio::Das::SegmentI which does have absolute set to 1 -- be warned you may not be getting things on the correct strand");
 517     }
 518
 519     my @locset = $self->location->each_Location;
 520     my @locs;
 521     if( ! $nosort ) {
 522         @locs = map { $_->[0] }
 523         # sort so that most negative is first basically to order
 524         # the features on the opposite strand 5'->3' on their strand
 525         # rather than they way most are input which is on the fwd strand
 526
 527         sort { $a->[1] <=> $b->[1] } # Yes Tim, Schwartzian transformation
 528         map {
 529             $fstrand = $_->strand unless defined $fstrand;
 530             $mixed = 1 if defined $_->strand && $fstrand != $_->strand;
 531             if( defined $_->seq_id ) {
 532                 $mixedloc = 1 if( $_->seq_id ne $seqid );
 533             }
 534             [ $_, $_->start * ($_->strand || 1)];
 535         } @locset;
 536
 537         if ( $mixed ) {
 538             $self->warn("Mixed strand locations, spliced seq using the input order rather than trying to sort");
 539             @locs = @locset;
 540         }
 541     } else {
 542         # use the original order instead of trying to sort
 543         @locs = @locset;
 544         $fstrand = $locs[0]->strand;
 545     }
 546
 547     foreach my $loc ( @locs ) {
 548         if( ! $loc->isa("Bio::Location::Atomic") ) {
 549             $self->throw("Can only deal with one level deep locations");
 550         }
 551         my $called_seq;
 552         if( $fstrand != $loc->strand ) {
 553             $self->warn("feature strand is different from location strand!");
 554         }
 555         # deal with remote sequences
 556
 557         if( defined $loc->seq_id &&
 558             $loc->seq_id ne $seqid ) {
 559             if( defined $db ) {
 560                 my $sid = $loc->seq_id;
 561                 $sid =~ s/\.\d+$//g;
 562                 eval {
 563                     $called_seq = $db->get_Seq_by_acc($sid);
 564                 };
 565                 if( $@ ) {
 566                     $self->warn("In attempting to join a remote location, sequence $sid was not in database. Will provide padding N's. Full exception \n\n$@");
 567                     $called_seq = undef;
 568                 }
 569             } else {
 570                 $self->warn( "cannot get remote location for ".$loc->seq_id ." without a valid Bio::DB::RandomAccessI database handle (like Bio::DB::GenBank)");
 571                 $called_seq = undef;
 572             }
 573             if( !defined $called_seq ) {
 574                 $seqstr .= 'N' x $self->length;
 575                 next;
 576             }
 577         } else {
 578             $called_seq = $self->entire_seq;
 579         }
 580
 581     # does the called sequence make sense? Bug 1780
 582     if ($called_seq->length < $loc->end) {
 583         my $accession = $called_seq->accession;
 584         my $end = $loc->end;
 585         my $length = $called_seq->length;
 586         my $orig_id = $self->seq_id; # originating sequence
 587         my ($locus) = $self->get_tagset_values("locus_tag");
 588         $self->throw("Location end ($end) exceeds length ($length) of ".
 589                      "called sequence $accession.\nCheck sequence version used in ".
 590                      "$locus locus-tagged SeqFeature in $orig_id.");
 591     }
 592
 593         if( $self->isa('Bio::Das::SegmentI') ) {
 594             my ($s,$e) = ($loc->start,$loc->end);
 595                 # $called_seq is Bio::DB::GFF::RelSegment, as well as its subseq();
 596                 # Bio::DB::GFF::RelSegment::seq() returns a Bio::PrimarySeq, and using seq()
 597                 # in turn returns a string.  Confused?
 598             $seqstr .= $called_seq->subseq($s,$e)->seq()->seq();
 599         } else {
 600             # If guide_strand is defined, assemble the sequence first and revcom later if needed,
 601             # if its not defined, apply revcom immediately to proper locations
 602             if (defined $self->location->guide_strand) {
 603                 $seqstr .= $called_seq->subseq($loc->start,$loc->end);
 604             } else {
 605                 my $strand = defined ($loc->strand) ? ($loc->strand) : 0;
 606                 if ($strand == -1) {
 607                     $seqstr .= $called_seq->trunc($loc->start,$loc->end)->revcom->seq;
 608                 } else {
 609                     $seqstr .= $called_seq->subseq($loc->start,$loc->end);
 610                 }
 611             }
 612         }
 613     }
 614     # Use revcom only after the whole sequence has been assembled
 615     my $guide_strand = defined ($self->location->guide_strand) ? ($self->location->guide_strand) : 0;
 616     if ($guide_strand == -1) {
 617         my $seqstr_obj = Bio::Seq->new(-seq => $seqstr);
 618         $seqstr = $seqstr_obj->revcom->seq;
 619     }
 620
 621     if (defined($phase)) {
 622         $seqstr = substr($seqstr, $phase);
 623     }
 624
 625     my $out = Bio::Seq->new( -id => $self->entire_seq->display_id
 626                                     . "_spliced_feat",
 627                              -seq => $seqstr);
 628
 629     return $out;
 630 }
 631
 632 =head2 location
 633
 634  Title   : location
 635  Usage   : my $location = $seqfeature->location()
 636  Function: returns a location object suitable for identifying location
 637            of feature on sequence or parent feature
 638  Returns : Bio::LocationI object
 639  Args    : none
 640
 641
 642 =cut
 643
 644 sub location {
 645    my ($self) = @_;
 646
 647    $self->throw_not_implemented();
 648 }
 649
 650
 651 =head2 primary_id
 652
 653  Title   : primary_id
 654  Usage   : $obj->primary_id($newval)
 655  Function:
 656  Example :
 657  Returns : value of primary_id (a scalar)
 658  Args    : on set, new value (a scalar or undef, optional)
 659
 660 Primary ID is a synonym for the tag 'ID'
 661
 662 =cut
 663
 664 sub primary_id{
 665     my $self = shift;
 666     # note from cjm@fruitfly.org:
 667     # I have commented out the following 2 lines:
 668
 669     #return $self->{'primary_id'} = shift if @_;
 670     #return $self->{'primary_id'};
 671
 672     #... and replaced it with the following; see
 673     # http://bioperl.org/pipermail/bioperl-l/2003-December/014150.html
 674     # for the discussion that lead to this change
 675
 676     if (@_) {
 677         if ($self->has_tag('ID')) {
 678             $self->remove_tag('ID');
 679         }
 680         $self->add_tag_value('ID', shift);
 681     }
 682     my ($id) = $self->get_tagset_values('ID');
 683     return $id;
 684 }
 685
 686 sub generate_unique_persistent_id {
 687     # DEPRECATED - us IDHandler
 688     my $self = shift;
 689     require Bio::SeqFeature::Tools::IDHandler;
 690     Bio::SeqFeature::Tools::IDHandler->new->generate_unique_persistent_id($self);
 691 }
 692
 693
 694 =head2 phase
 695
 696  Title   : phase
 697  Usage   : $obj->phase($newval)
 698  Function: get/set this feature's phase.
 699  Example :
 700  Returns : undef if no phase is set,
 701            otherwise 0, 1, or 2 (the only valid values for phase)
 702  Args    : on set, the new value
 703
 704 Most features do not have or need a defined phase.
 705
 706 For features representing a CDS, the phase indicates where the feature
 707 begins with reference to the reading frame.  The phase is one of the
 708 integers 0, 1, or 2, indicating the number of bases that should be
 709 removed from the beginning of this feature to reach the first base of
 710 the next codon. In other words, a phase of "0" indicates that the next
 711 codon begins at the first base of the region described by the current
 712 line, a phase of "1" indicates that the next codon begins at the
 713 second base of this region, and a phase of "2" indicates that the
 714 codon begins at the third base of this region. This is NOT to be
 715 confused with the frame, which is simply start modulo 3.
 716
 717 For forward strand features, phase is counted from the start
 718 field. For reverse strand features, phase is counted from the end
 719 field.
 720
 721 =cut
 722
 723 sub phase {
 724     my $self = shift;
 725     if( @_ ) {
 726         $self->remove_tag('phase') if $self->has_tag('phase');
 727         my $newphase = shift;
 728         $self->throw("illegal phase value '$newphase', phase must be either undef, 0, 1, or 2")
 729             unless !defined $newphase || $newphase == 0 || $newphase == 1 || $newphase == 2;
 730         $self->add_tag_value('phase', $newphase );
 731         return $newphase;
 732     }
 733
 734     return $self->has_tag('phase') ? ($self->get_tag_values('phase'))[0] : undef;
 735 }
 736
 737
 738 =head1 Bio::RangeI methods
 739
 740 These methods are inherited from RangeI and can be used
 741 directly from a SeqFeatureI interface. Remember that a
 742 SeqFeature is-a RangeI, and so wherever you see RangeI you
 743 can use a feature ($r in the below documentation).
 744
 745 =cut
 746
 747 =head2 start()
 748
 749  See L<Bio::RangeI>
 750
 751 =head2 end()
 752
 753  See L<Bio::RangeI>
 754
 755 =head2 strand()
 756
 757  See L<Bio::RangeI>
 758
 759 =head2 overlaps()
 760
 761  See L<Bio::RangeI>
 762
 763 =head2 contains()
 764
 765  See L<Bio::RangeI>
 766
 767 =head2 equals()
 768
 769  See L<Bio::RangeI>
 770
 771 =head2 intersection()
 772
 773  See L<Bio::RangeI>
 774
 775 =head2 union()
 776
 777  See L<Bio::RangeI>
 778
 779 =cut
 780
 781 1;