Bio
FeatureHolderI
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Summary
Bio::FeatureHolderI - the base interface an object with features must implement
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
use Bio::SeqIO;
# get a feature-holding object somehow: for example, Bio::SeqI objects
# have features
my $seqio = Bio::SeqIO->new(-fh => \*STDIN, -format => 'genbank');
while (my $seq = $seqio->next_seq()) {
# $seq is-a Bio::FeatureHolderI, hence:
my @feas = $seq->get_SeqFeatures();
# each element is-a Bio::SeqFeatureI
foreach my $fea (@feas) {
# do something with the feature objects
}
}
Description
This is the base interface that all feature-holding objects must
implement.
Popular feature-holders are for instance
Bio::Seq objects. Since
Bio::SeqFeatureI defines a sub_SeqFeature() method, most
Bio::SeqFeatureI implementations like
Bio::SeqFeature::Generic will
implement the feature holder interface as well.
Methods
Methods description
Usage :
Function: Get the feature objects held by this feature holder.
Example :
Returns : an array of Bio::SeqFeatureI implementing objects
Args : none
At some day we may want to expand this method to allow for a feature
filter to be passed in. |
Usage : $feat->add_SeqFeature($subfeat);
$feat->add_SeqFeature($subfeat,'EXPAND')
Function: adds a SeqFeature into the subSeqFeature array.
with no 'EXPAND' qualifer, subfeat will be tested
as to whether it lies inside the parent, and throw
an exception if not.
If EXPAND is used, the parent''s start/end/strand will
be adjusted so that it grows to accommodate the new
subFeature
Example :
Returns : nothing
Args : a Bio::SeqFeatureI object |
Usage : $obj->remove_SeqFeatures
Function: Removes all sub SeqFeatures. If you want to remove only a subset,
remove that subset from the returned array, and add back the rest.
Returns : The array of Bio::SeqFeatureI implementing sub-features that was
deleted from this feature.
Args : none |
Title : feature_count
Usage : $obj->feature_count()
Function: Return the number of SeqFeatures attached to a feature holder.
This is before flattening a possible sub-feature tree.
We provide a default implementation here that just counts
the number of objects returned by get_SeqFeatures().
Implementors may want to override this with a more
efficient implementation.
Returns : integer representing the number of SeqFeatures
Args : None
At some day we may want to expand this method to allow for a feature
filter to be passed in.
Our default implementation allows for any number of additional
arguments and will pass them on to get_SeqFeatures(). I.e., in order to
support filter arguments, just support them in get_SeqFeatures(). |
Title : get_all_SeqFeatures
Usage :
Function: Get the flattened tree of feature objects held by this
feature holder. The difference to get_SeqFeatures is that
the entire tree of sub-features will be flattened out.
We provide a default implementation here, so implementors
don''t necessarily need to implement this method.
Example :
Returns : an array of Bio::SeqFeatureI implementing objects
Args : none
At some day we may want to expand this method to allow for a feature
filter to be passed in.
Our default implementation allows for any number of additional
arguments and will pass them on to any invocation of
get_SeqFeatures(), wherever a component of the tree implements
FeatureHolderI. I.e., in order to support filter arguments, just
support them in get_SeqFeatures(). |
Methods code
sub get_SeqFeatures
{ shift->throw_not_implemented(); } | sub add_SeqFeature
{ shift->throw_not_implemented(); } | sub remove_SeqFeatures
{ shift->throw_not_implemented(); } | sub feature_count
{ return scalar(shift->get_SeqFeatures(@_)); } | sub get_all_SeqFeatures
{ my $self = shift;
my @flatarr;
foreach my $feat ( $self->get_SeqFeatures(@_) ){
push(@flatarr,$feat);
&_add_flattened_SeqFeatures(\@flatarr,$feat,@_);
}
my %seen = ();
my @uniq_flatarr = ();
foreach my $feat (@flatarr) {
push(@uniq_flatarr, $feat) unless $seen{$feat}++;
}
return @uniq_flatarr;} | sub _add_flattened_SeqFeatures
{ my ($arrayref,$feat,@args) = @_;
my @subs = ();
if($feat->isa("Bio::FeatureHolderI")) {
@subs = $feat->get_SeqFeatures(@args);
} elsif($feat->isa("Bio::SeqFeatureI")) {
@subs = $feat->sub_SeqFeature();
} else {
confess ref($feat)." is neither a FeatureHolderI nor a SeqFeatureI. ".
"Don't know how to flatten.";
}
foreach my $sub (@subs) {
push(@$arrayref,$sub);
&_add_flattened_SeqFeatures($arrayref,$sub);
}} | sub set_ParentIDs_from_hierarchy()
{
my $self = shift;
require "Bio/SeqFeature/Tools/IDHandler.pm";
Bio::SeqFeature::Tools::IDHandler->new->set_ParentIDs_from_hierarchy($self); } | | create_hierarchy_from_ParentIDs() | description | prev | next | Top |
sub create_hierarchy_from_ParentIDs()
{
my $self = shift;
require "Bio/SeqFeature/Tools/IDHandler.pm";
Bio::SeqFeature::Tools::IDHandler->new->create_hierarchy_from_ParentIDs($self);
}
1; } | General documentation
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web:
http://bugzilla.open-bio.org/
Email hlapp at gmx.net
Steffen Grossmann [SG], grossman-at-molgen.mpg.de
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _