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This commit was manufactured by cvs2svn to create tag

'after-05-06-merge'.

svn path=/bioperl-live/tags/after-05-06-merge/; revision=1141
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1 parent b7af73a commit a60e2dddaf65b3db378173cac8606e37bccd4f0c nobody committed Jan 27, 2000
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@@ -16,7 +16,7 @@ Bio::AnnSeq - Annotated Sequence
=head1 SYNOPSIS
- $stream = Bio::AnnSeqIO->new(-file => 'my.embl',-format => 'EMBL')
+ $stream = Bio::AnnSeqIO->new(-file 'my.embl',-format => 'EMBL')
foreach $annseq ( $stream->next_annseq() ) {
foreach $feat ( $annseq->all_SeqFeatures() ) {
@@ -26,31 +26,7 @@ Bio::AnnSeq - Annotated Sequence
=head1 DESCRIPTION
-An AnnSeq is a sequence with sequence features placed on them. The
-AnnSeq object is not a Bio::Seq object, but contains one. This is an
-important distinction from other packages which tend to have either a
-single sequence object with features, or an inheritence relationship
-between a "large" and "small" sequence object. In bioperl we have 3
-main players:
-
- Bio::Seq - just the sequence, nothing else.
- Bio::SeqFeature - a location on a sequence, potentially with a sequence.
- and annotation
- Bio::AnnSeq - A sequence and a collection of seqfeatures (an aggregate) with
- its own annotation.
-
-Although bioperl is not tied to file formats heavily, these distrinctions do map to file formats
-sensibly and for some bioinformaticians this might help you:
-
- Bio::Seq - Fasta file of a sequence
- Bio::SeqFeature - A single entry in an EMBL/GenBank/DDBJ feature table
- Bio::AnnSeq - A single EMBL/GenBank/DDBJ entry
-
-By having this split we avoid alot of nasty ciricular references
-(seqfeatures can hold a reference to a sequence without the sequence
-holding a reference to the seqfeature).
-
-Ian Korf really helped in the design of the AnnSeq and SeqFeature system.
+An AnnSeq is a sequence with sequence features placed on them
=head1 FEEDBACK
@@ -74,7 +50,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/
-=head1 AUTHOR - Ewan Birney, inspired by Ian Korf objects
+=head1 AUTHOR - Ewan Birney
Email birney@sanger.ac.uk
@@ -111,8 +87,6 @@ sub _initialize {
my($ann);
my $make = $self->SUPER::_initialize;
$self->{'_as_feat'} = [];
- $self->{'date'} = [];
- $self->{'secondary_accession'} = [];
$ann = new Bio::Annotation;
$self->annotation($ann);
@@ -308,28 +282,6 @@ sub species {
}
}
-=head2 sub_species
-
- Title : sub_species
- Usage :
- Function: Gets or sets the sub_species
- Example : $sub_species = $self->sub_species();
- Returns : Bio::Species object
- Args : Bio::Species object or none;
-
-
-=cut
-
-sub sub_species {
- my ($self, $sub_species) = @_;
-
- if ($sub_species) {
- $self->{'sub_species'} = $sub_species;
- } else {
- return $self->{'sub_species'}
- }
-}
-
=head1 EMBL/GenBank/DDBJ methods
These methods are here to support the EMBL/GenBank/DDBJ format.
@@ -364,70 +316,11 @@ sub division{
}
-=head2 molecule
-
- Title : molecule
- Usage : $obj->molecule($newval)
- Function:
- Returns : type of molecule (DNA, mRNA)
- Args : newvalue (optional)
-
-
-=cut
-
-sub molecule{
- my $obj = shift;
- if( @_ ) {
- my $value = shift;
- $obj->{'molecule'} = $value;
- }
- return $obj->{'molecule'};
-
-}
-
-=head2 add_date
-
- Title : add_date
- Usage : $self->add_domment($ref)
- Function: adds a date
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub add_date{
- my ($self) = shift;
- foreach my $dt ( @_ ) {
- push(@{$self->{'date'}},$dt);
- }
-}
-
-=head2 each_Comment
-
- Title : each_date
- Usage : foreach $dt ( $self->each_date() )
- Function: gets an array of dates
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub each_date{
- my ($self) = @_;
- return @{$self->{'date'}};
-}
-
=head2 accession
Title : accession
Usage : $obj->accession($newval)
- Function: Whilst the underlying sequence object does not
- have an accession, so we need one here. Wont stay
- when we do the reimplementation.
+ Function:
Example :
Returns : value of accession
Args : newvalue (optional)
@@ -444,83 +337,7 @@ sub accession{
}
-=head2 add_secondary_accession
-
- Title : add_secondary_accession
- Usage : $self->add_domment($ref)
- Function: adds a secondary_accession
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub add_secondary_accession{
- my ($self) = shift;
- foreach my $dt ( @_ ) {
- push(@{$self->{'secondary_accession'}},$dt);
- }
-}
-
-=head2 each_Comment
- Title : each_secondary_accession
- Usage : foreach $dt ( $self->each_secondary_accession() )
- Function: gets an array of secondary_accessions
- Example :
- Returns :
- Args :
-
-
-=cut
-
-sub each_secondary_accession{
- my ($self) = @_;
- return @{$self->{'secondary_accession'}};
-}
-
-=head2 sv
-
- Title : sv
- Usage : $obj->sv($newval)
- Function:
- Returns : value of sv
- Args : newvalue (optional)
-
-
-=cut
-
-sub sv{
- my $obj = shift;
- if( @_ ) {
- my $value = shift;
- $obj->{'sv'} = $value;
- }
- return $obj->{'sv'};
-
-}
-
-=head2 keywords
-
- Title : keywords
- Usage : $obj->keywords($newval)
- Function:
- Returns : value of keywords
- Args : newvalue (optional)
-
-
-=cut
-
-sub keywords{
- my $obj = shift;
- if( @_ ) {
- my $value = shift;
- $obj->{'keywords'} = $value;
- }
- return $obj->{'keywords'};
-
-}
View
@@ -21,8 +21,8 @@ Bio::AnnSeqIO - Handler for AnnSeqIO Formats
$in = Bio::AnnSeqIO->new(-file => "inputfilename" , -format => 'Fasta');
$out = Bio::AnnSeqIO->new(-file => ">outputfilename" , -format => 'EMBL');
- while ($seq = $in->next_annseq() ) {
- $out->write_annseq($seq);
+ while $seq ( $in->next_annseq() ) {
+ $out->write_annseq($out);
}
=head1 DESCRIPTION
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