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Updated method names to follow Bio::SeqFeature::Generic convention an…
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…d provided aliasess
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@fangly
fangly committed Mar 5, 2012
1 parent 11f497c commit b2140a4
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Showing 2 changed files with 90 additions and 88 deletions.
172 changes: 87 additions & 85 deletions Bio/SeqFeature/Computation.pm
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Expand Up @@ -18,16 +18,18 @@ Bio::SeqFeature::Computation - Computation SeqFeature
=head1 SYNOPSIS
$feat = Bio::SeqFeature::Computation->new(
-start => 10, -end => 100,
-strand => -1, -primary => 'repeat',
-program_name => 'GeneMark',
-program_date => '12-5-2000',
-program_version => 'x.y',
-database_name => 'Arabidopsis',
-database_date => '12-dec-2000',
-computation_id => 2231,
-score => { no_score => 334 } );
-start => 10,
-end => 100,
-strand => -1,
-primary => 'repeat',
-program_name => 'GeneMark',
-program_date => '12-5-2000',
-program_version => 'x.y',
-database_name => 'Arabidopsis',
-database_date => '12-dec-2000',
-computation_id => 2231,
-score => { no_score => 334 }
);
=head1 DESCRIPTION
Expand All @@ -42,10 +44,6 @@ subseqfeatures is now a hash which contains arrays of seqfeatures
Both the score and subSeqfeature methods can be called in exactly the same
way, the value's will be stored as a 'default' score or subseqfeature.
=cut

#'

=head1 FEEDBACK
=head2 Mailing Lists
Expand Down Expand Up @@ -79,6 +77,7 @@ web:
=head1 AUTHOR - Ewan Birney, Mark Fiers
Ewan Birney E<lt>birney@sanger.ac.ukE<gt>
Mark Fiers E<lt>m.w.e.j.fiers@plant.wag-ur.nlE<gt>
=head1 DEVELOPERS
Expand All @@ -102,27 +101,25 @@ package Bio::SeqFeature::Computation;
use strict;

use base qw(Bio::SeqFeature::Generic);

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

my $self = $class->SUPER::new(@args);


my ( $computation_id,
$program_name, $program_date, $program_version,
$database_name, $database_date, $database_version) =
$self->_rearrange([qw(COMPUTATION_ID
PROGRAM_NAME
PROGRAM_DATE
PROGRAM_VERSION
DATABASE_NAME
DATABASE_DATE
DATABASE_VERSION
)],@args);

$program_name && $self->program_name($program_name);
$program_date && $self->program_date($program_date);
my ( $computation_id, $program_name, $program_date, $program_version,
$database_name, $database_date, $database_version) =
$self->_rearrange([qw( COMPUTATION_ID
PROGRAM_NAME
PROGRAM_DATE
PROGRAM_VERSION
DATABASE_NAME
DATABASE_DATE
DATABASE_VERSION )],@args);

$program_name && $self->program_name($program_name);
$program_date && $self->program_date($program_date);
$program_version && $self->program_version($program_version);
$database_name && $self->database_name($database_name);
$database_date && $self->database_date($database_date);
Expand Down Expand Up @@ -179,7 +176,7 @@ sub add_score_value {
$comp_obj->score($value)
Function: Returns the 'default' score or sets the 'default' score
This method exist for compatibility options
It would equal ($comp_obj->each_score_value('default'))[0];
It would equal ($comp_obj->each_score_value('default'))[0];
Returns : A value
Args : (optional) a new value for the 'default' score
Expand All @@ -190,17 +187,17 @@ sub score {
my @v;
if (defined $value) {

if( ref($value) =~ /HASH/i ) {
while( my ($t,$val) = each %{ $value } ) {
$self->add_score_value($t,$val);
}
} else {
@v = $value;
$self->add_score_value('default', $value);
}
if( ref($value) =~ /HASH/i ) {
while( my ($t,$val) = each %{ $value } ) {
$self->add_score_value($t,$val);
}
} else {
@v = $value;
$self->add_score_value('default', $value);
}

} else {
@v = $self->each_score_value('default');
@v = $self->each_score_value('default');
}
return $v[0];
}
Expand Down Expand Up @@ -424,19 +421,19 @@ sub database_version {

}

=head2 sub_SeqFeature_type
=head2 get_SeqFeature_type
Title : sub_SeqFeature_type
Usage : $sub_SeqFeature_type = $feat->sub_SeqFeature_type()
$feat->sub_SeqFeature_type($sub_SeqFeature_type)
Function: sub_SeqFeature_type is automatically set when adding
a sub_computation (sub_SeqFeature) to a computation object
Returns : sub_SeqFeature_type (string)
Title : get_SeqFeature_type
Usage : $SeqFeature_type = $feat->get_SeqFeature_type()
$feat->get_SeqFeature_type($SeqFeature_type)
Function: Get SeqFeature type which is automatically set when adding
a computation (SeqFeature) to a computation object
Returns : SeqFeature_type (string)
Args : none if get, the new value if set
=cut

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

if (defined($value)) {
Expand All @@ -445,78 +442,78 @@ sub sub_SeqFeature_type {
return $self->{'_gsf_sub_SeqFeature_type'};
}

=head2 all_sub_SeqFeature_types
=head2 get_all_SeqFeature_types
Title : all_Sub_SeqFeature_types
Usage : @all_sub_seqfeature_types = $comp->all_Sub_SeqFeature_types();
Title : get_all_SeqFeature_types
Usage : @all_SeqFeature_types = $comp->get_all_SeqFeature_types();
Function: Returns an array with all subseqfeature types
Returns : An array
Args : none
=cut

sub all_sub_SeqFeature_types {
sub get_all_SeqFeature_types {
my ($self) = @_;
return keys ( %{$self->{'gsf_sub_hash'}} );
}

=head2 sub_SeqFeature
=head2 get_SeqFeatures
Title : sub_SeqFeature('sub_feature_type')
Usage : @feats = $feat->sub_SeqFeature();
@feats = $feat->sub_SeqFeature('sub_feature_type');
Title : get_SeqFeatures('feature_type')
Usage : @feats = $feat->get_SeqFeatures();
@feats = $feat->get_SeqFeatures('feature_type');
Function: Returns an array of sub Sequence Features of a specific
type or, if the type is ommited, all sub Sequence Features
Returns : An array
Args : (optional) a sub_SeqFeature type (ie exon, pattern)
Args : (optional) a SeqFeature type (ie exon, pattern)
=cut

sub sub_SeqFeature {
sub get_SeqFeatures {
my ($self, $ssf_type) = @_;
my (@return_array) = ();
if ($ssf_type eq '') {
#return all sub_SeqFeatures
#return all SeqFeatures
foreach (keys ( %{$self->{'gsf_sub_hash'}} )){
push @return_array, @{$self->{'gsf_sub_hash'}->{$_}};
push @return_array, @{$self->{'gsf_sub_hash'}->{$_}};
}
return @return_array;
} else {
if (defined ($self->{'gsf_sub_hash'}->{$ssf_type})) {
return @{$self->{'gsf_sub_hash'}->{$ssf_type}};
return @{$self->{'gsf_sub_hash'}->{$ssf_type}};
} else {
$self->warn("$ssf_type is not a valid sub SeqFeature type");
}
}
}

=head2 add_sub_SeqFeature
=head2 add_SeqFeature
Title : add_sub_SeqFeature
Usage : $feat->add_sub_SeqFeature($subfeat);
$feat->add_sub_SeqFeature($subfeat,'sub_seqfeature_type')
$feat->add_sub_SeqFeature($subfeat,'EXPAND')
$feat->add_sub_SeqFeature($subfeat,'EXPAND','sub_seqfeature_type')
Title : add_SeqFeature
Usage : $feat->add_SeqFeature($subfeat);
$feat->add_SeqFeature($subfeat,'seqfeature_type')
$feat->add_SeqFeature($subfeat,'EXPAND')
$feat->add_SeqFeature($subfeat,'EXPAND','seqfeature_type')
Function: adds a SeqFeature into a specific 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 parents start/end/strand will
be adjusted so that it grows to accommodate the new
subFeature,
optionally a sub_seqfeature type can be defined.
optionally a seqfeature type can be defined.
Returns : nothing
Args : An object which has the SeqFeatureI interface
: (optional) 'EXPAND'
: (optional) 'sub_SeqFeature_type'
(optional) 'EXPAND'
(optional) 'SeqFeature_type'
=cut

sub add_sub_SeqFeature{
sub add_SeqFeature{
my ($self,$feat,$var1, $var2) = @_;
$var1 = '' unless( defined $var1);
$var2 = '' unless( defined $var2);
my ($expand, $ssf_type) = ('', $var1 . $var2);
my ($expand, $ssf_type) = ('', $var1 . $var2);
$expand = 'EXPAND' if ($ssf_type =~ s/EXPAND//);

if ( !$feat->isa('Bio::SeqFeatureI') ) {
Expand All @@ -527,7 +524,7 @@ sub add_sub_SeqFeature{
$self->_expand_region($feat);
} else {
if ( !$self->contains($feat) ) {
$self->throw("$feat is not contained within parent feature, and expansion is not valid");
$self->throw("$feat is not contained within parent feature, and expansion is not valid");
}
}

Expand All @@ -536,28 +533,26 @@ sub add_sub_SeqFeature{
if (!(defined ($self->{'gsf_sub_hash'}->{$ssf_type}))) {
@{$self->{'gsf_sub_hash'}->{$ssf_type}} = ();
}
$feat->sub_SeqFeature_type($ssf_type);
$feat->get_SeqFeature_type($ssf_type);
push @{$self->{'gsf_sub_hash'}->{$ssf_type}}, $feat;
}

=head2 flush_sub_SeqFeature
=head2 remove_SeqFeatures
Title : flush_sub_SeqFeature
Usage : $sf->flush_sub_SeqFeature
$sf->flush_sub_SeqFeature('sub_SeqFeature_type');
Function: Removes all sub SeqFeature or all sub SeqFeatures
of a specified type
(if you want to remove a more specific subset, take
an array of them all, flush them, and add
back only the guys you want)
Title : remove_SeqFeatures
Usage : $sf->remove_SeqFeatures
$sf->remove_SeqFeatures('SeqFeature_type');
Function: Removes all sub SeqFeature or all sub SeqFeatures of a specified type
(if you want to remove a more specific 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 {
sub remove_SeqFeatures {
my ($self, $ssf_type) = @_;
if ($ssf_type) {
if ((defined ($self->{'gsf_sub_hash'}->{$ssf_type}))) {
Expand All @@ -568,8 +563,15 @@ sub flush_sub_SeqFeature {
} else {
$self->{'_gsf_sub_hash'} = {}; # zap the complete hash implicitly.
}
}
}


# Aliases to better match Bio::SeqFeature function names
*sub_SeqFeature_type = \&get_SeqFeature_type;
*all_sub_SeqFeature_types = \&get_all_SeqFeature_types;
*sub_SeqFeature = \&get_SeqFeatures;
*add_sub_SeqFeature = \&add_SeqFeature;
*flush_sub_SeqFeatures = \&remove_SeqFeatures;
*flush_sub_SeqFeature = \&remove_SeqFeatures;

1;
6 changes: 3 additions & 3 deletions t/SeqFeature/Computation.t
View file
Expand Up @@ -7,7 +7,7 @@ BEGIN {
use lib '.';
use Bio::Root::Test;

test_begin(-tests => 11);
test_begin(-tests => 12);

use_ok('Bio::SeqFeature::Computation');
}
Expand All @@ -28,8 +28,8 @@ ok $comp_obj2 = Bio::SeqFeature::Computation->new(
-end => 10,
);

ok $comp_obj1->add_sub_SeqFeature($comp_obj2, 'exon');
ok @sft = $comp_obj1->all_sub_SeqFeature_types();
ok $comp_obj1->add_SeqFeature($comp_obj2, 'exon');
ok @sft = $comp_obj1->get_all_SeqFeature_types();

is $sft[0], 'exon', 'sft[0] is exon';

Expand Down

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