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POD update: no mention of add_seqfeatures(@feats)
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@fangly
fangly committed Mar 7, 2012
1 parent 5ad8e23 commit d0584ca
Showing 1 changed file with 25 additions and 39 deletions.
64 changes: 25 additions & 39 deletions Bio/Seq.pm
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Expand Up @@ -353,7 +353,6 @@ See L<Bio::PrimarySeq> for more details on PrimarySeq objects.
# one can also add features
$seqobj->add_SeqFeature($feat) # returns 1 if successful
$seqobj->add_SeqFeature(@features) # returns 1 if successful
# sub features. For complex join() statements, the feature
# is one sequence feature with many sub SeqFeatures
Expand Down Expand Up @@ -534,6 +533,7 @@ sub new {
return $self;
}


=head1 PrimarySeq interface
Expand Down Expand Up @@ -589,13 +589,13 @@ sub seq {
0 otherwise.
Args : The sequence string to be validated.
=cut

sub validate_seq {
return shift->primary_seq()->validate_seq(@_);
}


=head2 length
Title : length
Expand All @@ -611,9 +611,8 @@ sub length {
return shift->primary_seq()->length(@_);
}

=head1 Methods from the Bio::PrimarySeqI interface

=cut
=head1 Methods from the Bio::PrimarySeqI interface
=head2 subseq
Expand All @@ -635,6 +634,7 @@ sub subseq {
return shift->primary_seq()->subseq(@_);
}


=head2 display_id
Title : display_id
Expand All @@ -658,15 +658,13 @@ sub subseq {
Returns : A string
Args : None or a new id
=cut

sub display_id {
return shift->primary_seq->display_id(@_);
}



=head2 accession_number
Title : accession_number
Expand All @@ -686,13 +684,13 @@ sub display_id {
Returns : A string
Args : None or an accession number
=cut

sub accession_number {
return shift->primary_seq->accession_number(@_);
}


=head2 desc
Title : desc
Expand All @@ -702,13 +700,13 @@ sub accession_number {
Returns : The description
Args : The description or none
=cut

sub desc {
return shift->primary_seq->desc(@_);
}


=head2 primary_id
Title : primary_id
Expand All @@ -729,7 +727,6 @@ sub desc {
Returns : A string
Args : None or an id, or undef to unset the primary id.
=cut

sub primary_id {
Expand All @@ -748,6 +745,7 @@ sub primary_id {
return shift->primary_seq->primary_id(@_);
}


=head2 can_call_new
Title : can_call_new
Expand All @@ -769,13 +767,13 @@ sub primary_id {
Returns : 1 or 0
Args : None
=cut

sub can_call_new {
return 1;
}


=head2 alphabet
Title : alphabet
Expand All @@ -791,7 +789,6 @@ sub can_call_new {
has to guess.
Args : optional string to set : 'dna' | 'rna' | 'protein'
=cut

sub alphabet {
Expand All @@ -800,6 +797,7 @@ sub alphabet {
return $self->primary_seq->alphabet();
}


=head2 is_circular
Title : is_circular
Expand All @@ -817,8 +815,6 @@ sub is_circular {

=head1 Methods for Bio::IdentifiableI compliance
=cut

=head2 object_id
Title : object_id
Expand All @@ -830,13 +826,13 @@ sub is_circular {
This is aliased to accession_number().
Returns : A scalar
=cut

sub object_id {
return shift->accession_number(@_);
}


=head2 version
Title : version
Expand Down Expand Up @@ -871,6 +867,7 @@ sub authority {
return shift->primary_seq()->authority(@_);
}


=head2 namespace
Title : namespace
Expand All @@ -881,16 +878,14 @@ sub authority {
Returns : A scalar
=cut

sub namespace{
return shift->primary_seq()->namespace(@_);
}

=head1 Methods for Bio::DescribableI compliance

=cut
=head1 Methods for Bio::DescribableI compliance
=head2 display_name
Expand Down Expand Up @@ -931,9 +926,8 @@ sub description {
return shift->desc(@_);
}

=head1 Methods for implementing Bio::AnnotatableI

=cut
=head1 Methods for implementing Bio::AnnotatableI
=head2 annotation
Expand Down Expand Up @@ -962,6 +956,7 @@ sub annotation {
return $obj->{'_annotation'};
}


=head1 Methods for delegating Bio::AnnotationCollectionI
=head2 get_Annotations()
Expand All @@ -976,6 +971,7 @@ sub annotation {

sub get_Annotations { shift->annotation->get_Annotations(@_); }


=head2 add_Annotation()
Usage : $seq->add_Annotation('reference',$object);
Expand All @@ -1001,6 +997,7 @@ sub get_Annotations { shift->annotation->get_Annotations(@_); }

sub add_Annotation { shift->annotation->add_Annotation(@_) }


=head2 remove_Annotations()
Usage : $seq->remove_Annotations()
Expand All @@ -1016,6 +1013,7 @@ sub add_Annotation { shift->annotation->add_Annotation(@_) }

sub remove_Annotations { shift->annotation->remove_Annotations(@_) }


=head2 get_num_of_annotations()
Usage : my $count = $seq->get_num_of_annotations()
Expand All @@ -1030,6 +1028,7 @@ sub remove_Annotations { shift->annotation->remove_Annotations(@_) }
sub get_num_of_annotations { shift->annotation->get_num_of_annotations(@_) }
sub num_Annotations { shift->get_num_of_annotations }; #DWYM


=head1 Methods to implement Bio::FeatureHolderI
This includes methods for retrieving, adding, and removing features.
Expand Down Expand Up @@ -1058,7 +1057,6 @@ This includes methods for retrieving, adding, and removing features.
Returns : an array of Bio::SeqFeatureI implementing objects
Args : [optional] scalar string (feature tag)
=cut

sub get_SeqFeatures{
Expand All @@ -1076,6 +1074,7 @@ sub get_SeqFeatures{
}
}


=head2 get_all_SeqFeatures
Title : get_all_SeqFeatures
Expand All @@ -1092,7 +1091,6 @@ sub get_SeqFeatures{
Returns : An array of Bio::SeqFeatureI implementing objects.
Args : None
=cut

# this implementation is inherited from FeatureHolderI
Expand All @@ -1105,7 +1103,6 @@ sub get_SeqFeatures{
Returns : integer representing the number of SeqFeatures
Args : None
=cut

sub feature_count {
Expand All @@ -1118,19 +1115,17 @@ sub feature_count {
}
}


=head2 add_SeqFeature
Title : add_SeqFeature
Usage : $seq->add_SeqFeature($feat);
$seq->add_SeqFeature(@feat);
Function: Adds the given feature object (or each of an array of feature
objects to the feature array of this
Function: Adds the given feature object to the feature array of this
sequence. The object passed is required to implement the
Bio::SeqFeatureI interface.
Returns : 1 on success
Args : A Bio::SeqFeatureI implementing object, or an array of such objects.
=cut

sub add_SeqFeature {
Expand All @@ -1152,6 +1147,7 @@ sub add_SeqFeature {
return 1;
}


=head2 remove_SeqFeatures
Title : remove_SeqFeatures
Expand All @@ -1164,7 +1160,6 @@ sub add_SeqFeature {
Returns : The array of Bio::SeqFeatureI objects removed from this seq.
Args : None
=cut

sub remove_SeqFeatures {
Expand All @@ -1176,8 +1171,8 @@ sub remove_SeqFeatures {
return @feats;
}

=head1 Methods provided in the Bio::PrimarySeqI interface

=head1 Methods provided in the Bio::PrimarySeqI interface
These methods are inherited from the PrimarySeq interface
and work as one expects, building new Bio::Seq objects
Expand Down Expand Up @@ -1213,9 +1208,6 @@ dealing with this is welcome to give it a go.
Returns : A new (fresh) Bio::Seq object
Args : None
=cut

=head2 trunc
Title : trunc
Expand All @@ -1226,9 +1218,6 @@ dealing with this is welcome to give it a go.
Returns : A fresh Seq object
Args : A Seq object
=cut

=head2 id
Title : id
Expand All @@ -1237,7 +1226,6 @@ dealing with this is welcome to give it a go.
Returns : value of display_id()
Args : [optional] value to update display_id
=cut

sub id {
Expand All @@ -1247,7 +1235,6 @@ sub id {

=head1 Seq only methods
These methods are specific to the Bio::Seq object, and not
found on the Bio::PrimarySeq object
Expand All @@ -1260,7 +1247,6 @@ found on the Bio::PrimarySeq object
Returns : PrimarySeq object
Args : None or PrimarySeq object
=cut

sub primary_seq {
Expand All @@ -1284,6 +1270,7 @@ sub primary_seq {

}


=head2 species
Title : species
Expand All @@ -1305,9 +1292,8 @@ sub species {
}
}

=head1 Internal methods

=cut
# Internal methods follow...

# keep AUTOLOAD happy
sub DESTROY { }
Expand Down

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