Bio-EnsEMBL
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lib/Bio/EnsEMBL/SeqFeature.pm  view on Meta::CPAN 


=head1 DESCRIPTION

Do not use this module if you can avoid it. It has been replaced by
Bio::EnsEMBL::Feature.  This module has a long history of usage but has
become very bloated, and quite unweildy.  It was decided to replace
it completely with a smaller, light-weight feature class rather than
attempting to refactor this class, and maintain strict backwards
compatibility.

Part of the complexity of this class was in its extensive
inheritance. As an example the following is a simplified inheritance
heirarchy that was present for Bio::EnsEMBL::DnaAlignFeature:

  Bio::EnsEMBL::DnaAlignFeature
  Bio::EnsEMBL::BaseAlignFeature
  Bio::EnsEMBL::FeaturePair
  Bio::EnsEMBL::SeqFeature
  Bio::SeqFeatureI
  Bio::RangeI
  Bio::Root::RootI

The new Bio::EnsEMBL::Feature class is much shorter, and hopefully much
easier to understand and maintain.

=head1 METHODS

=cut


# Let the code begin...


package Bio::EnsEMBL::SeqFeature;
$Bio::EnsEMBL::SeqFeature::VERSION = '114.0.0';
use vars qw(@ISA);
use strict;


use Bio::EnsEMBL::Analysis;

use Bio::EnsEMBL::Utils::Argument qw(rearrange);

sub new {
  my($caller,@args) = @_;

  my $self = {};

  if(ref $caller) {
    bless $self, ref $caller;
  } else {
    bless $self, $caller;
  }

  $self->{'_gsf_tag_hash'} = {};
  $self->{'_gsf_sub_array'} = [];
  $self->{'_parse_h'} = {};
  $self->{'_is_splittable'} = 0;

  my ($start,$end,$strand,$frame,$score,$analysis,$seqname, $source_tag,
      $primary_tag, $percent_id, $p_value, $phase, $end_phase) =

      &rearrange([qw(START
                            END
                            STRAND
                            FRAME
                            SCORE
                            ANALYSIS
                            SEQNAME
                            SOURCE_TAG
                            PRIMARY_TAG
                            PERCENT_ID
                            P_VALUE
                            PHASE
                            END_PHASE
                            )],@args);

  #  $gff_string && $self->_from_gff_string($gff_string);

  if ( defined $analysis  && $analysis ne "")   { $self->analysis($analysis)};
  if ( defined ($start) && $start ne "" )       { $self->start($start)};
  if ( defined ($end )  && $end   ne "" )       { $self->end($end)}
  if ( defined $strand  && $strand ne "")       { $self->strand($strand)}
  if ( defined $frame  && $frame ne "")         { $self->frame($frame)}
  if ( defined $score  && $score ne "")         { $self->score($score)}
  if ( defined $seqname && $seqname ne "")      { $self->seqname($seqname)};
  if ( defined $percent_id && $percent_id ne ""){ $self->percent_id($percent_id)};
  if ( defined $p_value && $p_value ne "")      { $self->p_value($p_value)};
  if ( defined $phase && $phase ne "")          { $self->phase($phase)};
  if ( defined $end_phase && $end_phase ne "")  { $self->end_phase($end_phase)};

  return $self; # success - we hope!

}






=head2 start

 Title   : start
 Usage   : $start = $feat->start
           $feat->start(20)
 Function: Get/set on the start coordinate of the feature
 Returns : integer
 Args    : none


=cut

sub start{
    my ($self,$value) = @_;

    if (defined($value)) {
        if ($value !~ /^\-?\d+/ ) {
        $self->throw("$value is not a valid start");
    }
	
    $self->{'_gsf_start'} = $value
   }

    return $self->{'_gsf_start'};

}

=head2 end

 Title   : end
 Usage   : $end = $feat->end
           $feat->end($end)
 Function: get/set on the end coordinate of the feature
 Returns : integer
 Args    : none


=cut

sub end{
    my ($self,$value) = @_;

    if (defined($value)) {
        if( $value !~ /^\-?\d+/ ) {
            $self->throw("[$value] is not a valid end");
        }

lib/Bio/EnsEMBL/SeqFeature.pm  view on Meta::CPAN 



=cut

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

    $self->vthrow("Seqname not defined in feature")     unless defined($self->seqname);
    $self->vthrow("start not defined in feature")       unless defined($self->start);
    $self->vthrow("end not defined in feature")         unless defined($self->end);
    $self->vthrow("strand not defined in feature")      unless defined($self->strand);
    $self->vthrow("score not defined in feature")       unless defined($self->score);
    $self->vthrow("analysis not defined in feature")    unless defined($self->analysis);

    if ($self->end < $self->start) {
      $self->vthrow("End coordinate < start coordinate");
    }

}



sub vthrow {
    my ($self,$message) = @_;

    print(STDERR "Error validating feature [$message]\n");
    print(STDERR "   Seqname     : [" . $self->{_seqname} . "]\n");
    print(STDERR "   Start       : [" . $self->{_gsf_start} . "]\n");
    print(STDERR "   End         : [" . $self->{_gsf_end} . "]\n");
    print(STDERR "   Strand      : [" .
        ((defined ($self->{_gsf_strand})) ? $self->{_gsf_strand} : "undefined") . "]\n");

    print(STDERR "   Score       : [" . $self->{_gsf_score} . "]\n");

    print(STDERR "   Analysis    : [" . $self->{_analysis}->dbID . "]\n");

    $self->throw("Invalid feature - see dump on STDERR");
}


=head2 validate_prot_feature

 Title   : validate_prot_feature
 Usage   :
 Function:
 Example :
 Returns :
 Args    :


=cut

# Shouldn't this go as "validate" into Pro_SeqFeature?
sub validate_prot_feature{
    my ($self,$num) = @_;
    $self->throw("Seqname not defined in feature")     unless defined($self->seqname);
    $self->throw("start not defined in feature")       unless defined($self->start);
    $self->throw("end not defined in feature")         unless defined($self->end);
    if ($num == 1) {
        $self->throw("score not defined in feature")       unless defined($self->score);
        $self->throw("percent_id not defined in feature") unless defined($self->percent_id);
        $self->throw("evalue not defined in feature") unless defined($self->p_value);
    }
    $self->throw("analysis not defined in feature")    unless defined($self->analysis);
}



# These methods are specified in the SeqFeatureI interface but we don't want
# people to store data in them.  These are just here in order to keep
# existing code working


=head2 has_tag

 Title   : has_tag
 Usage   : $value = $self->has_tag('some_tag')
 Function: Returns the value of the tag (undef if
           none)
 Returns :
 Args    :


=cut

sub has_tag{
   my ($self,$tag) = (shift, shift);

   return exists $self->{'_gsf_tag_hash'}->{$tag};
}

=head2 add_tag_value

 Title   : add_tag_value
 Usage   : $self->add_tag_value('note',"this is a note");
 Returns : nothing
 Args    : tag (string) and value (any scalar)


=cut

sub add_tag_value{
   my ($self,$tag,$value) = @_;

   if( !defined $self->{'_gsf_tag_hash'}->{$tag} ) {
       $self->{'_gsf_tag_hash'}->{$tag} = [];
   }

   push(@{$self->{'_gsf_tag_hash'}->{$tag}},$value);
}

=head2 each_tag_value

 Title   : each_tag_value
 Usage   :
 Function:
 Example :
 Returns :
 Args    :

lib/Bio/EnsEMBL/SeqFeature.pm  view on Meta::CPAN 

               $end = $feat->end;
           }

           $self->start($start);
           $self->end($end);

       }
   } else {
     if( !defined($feat->start()) || !defined($feat->end()) ||
         !defined($self->start())  || !defined($self->end())) {
       $self->throw( "This SeqFeature and the sub_SeqFeature must define".
                     " start and end.");
     }
     if($feat->start() > $feat->end() || $self->start() > $self->end()) {
       $self->throw("This SeqFeature and the sub_SeqFeature must have " .
                    "start that is less than or equal to end.");
     }
     if($feat->start() < $self->start() || $feat->end() > $self->end() ) {
       $self->throw("$feat is not contained within parent feature, " .
                    "and expansion is not valid");
     }
   }

   push(@{$self->{'_gsf_sub_array'}},$feat);

}

=head2 flush_sub_SeqFeature

 Title   : flush_sub_SeqFeature
 Usage   : $sf->flush_sub_SeqFeature
 Function: Removes all sub SeqFeature
           (if you want to remove only a subset, take
            an array of them all, flush them, and add
            back only the guys you want)
 Example :
 Returns : none
 Args    : none


=cut

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

   $self->{'_gsf_sub_array'} = []; # zap the array implicitly.
}


sub id {
    my ($self,$value) = @_;

    if (defined($value)) {
        $self->{_id} = $value;
    }

    return $self->{_id};

}

=head2 percent_id

 Title   : percent_id
 Usage   : $pid = $feat->percent_id()
           $feat->percent_id($pid)
 Function: get/set on percentage identity information
 Returns : float
 Args    : none if get, the new value if set

=cut

sub percent_id {
    my ($self,$value) = @_;

    if (defined($value))
    {
            $self->{_percent_id} = $value;
    }

    return $self->{_percent_id};
}

=head2 p_value

 Title   : p_value
 Usage   : $p_val = $feat->p_value()
           $feat->p_value($p_val)
 Function: get/set on p value information
 Returns : float
 Args    : none if get, the new value if set

=cut

sub p_value {
    my ($self,$value) = @_;

    if (defined($value))
    {
            $self->{_p_value} = $value;
    }

    return $self->{_p_value};
}

=head2 phase

 Title   : phase
 Usage   : $phase = $feat->phase()
           $feat->phase($phase)
 Function: get/set on start phase of predicted exon feature
 Returns : [0,1,2]
 Args    : none if get, 0,1 or 2 if set.

=cut

sub phase {
    my ($self, $value) = @_;

    if (defined($value) )
    {
        $self->throw("Valid values for Phase are [0,1,2]") if ($value < 0 || $value > 2);
            $self->{_phase} = $value;
    }

    return $self->{_phase};
}

=head2 end_phase

 Title   : end_phase
 Usage   : $end_phase = $feat->end_phase()
           $feat->end_phase($end_phase)
 Function: returns end_phase based on phase and length of feature
 Returns : [0,1,2]
 Args    : none if get, 0,1 or 2 if set.

=cut

sub end_phase {
   my ($self, $value) = @_;



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