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Simple Naming changes to reflect Bio::Expression::FeatureGroup

svn path=/bioperl-microarray/trunk/; revision=11829
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commit 16981599fb39209b06d069f858e5e1431f094c38 1 parent 04f15d2
crsto authored
30 Bio/Expression/Microarray/Affymetrix/ArrayDesign.pm
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@@ -54,7 +54,7 @@ package Bio::Expression::Microarray::Affymetrix::ArrayDesign;
use strict;
use Bio::Root::Root;
-use Bio::Expression::FeatureSet;
+use Bio::Expression::FeatureGroup;
use Bio::Expression::Microarray::Affymetrix::Feature;
use base qw(Bio::Root::Root);
@@ -120,17 +120,17 @@ sub matrix {
Title : featuregroup
Usage : $self->featuregroup->($featurename);
- Function: get-set method for FeatureSet object
-Returns : a Bio::Expression::FeatureSet object
- Args : A key for a FeatureSet object
+ Function: get-set method for FeatureGroup object
+Returns : a Bio::Expression::FeatureGroup object
+ Args : A key for a FeatureGroup object
=cut
sub featuregroup {
my($self,$arg) = @_;
return $self->{featuregroup}->{$arg} if $self->{featuregroup}->{$arg};
- $self->{featuregroup}->{$arg} = Bio::Expression::FeatureSet->new()
- or $self->throw("Couldn't create a Bio::Expression::FeatureSet: $!");
+ $self->{featuregroup}->{$arg} = Bio::Expression::FeatureGroup->new()
+ or $self->throw("Couldn't create a Bio::Expression::FeatureGroup: $!");
return $self->{featuregroup}->{$arg};
}
@@ -138,17 +138,17 @@ sub featuregroup {
Title : qc_featuregroup
Usage : $self->qc_featuregroup($mode);
- Function: get-set method for quality control FeatureSet object
-Returns : a Bio::Expression::FeatureSet object
- Args : A key for a FeatureSet object
+ Function: get-set method for quality control FeatureGroup object
+Returns : a Bio::Expression::FeatureGroup object
+ Args : A key for a FeatureGroup object
=cut
sub qc_featuregroup {
my($self,$arg) = @_;
return $self->{qcfeaturegroup}->{$arg} if $self->{qcfeaturegroup}->{$arg};
- $self->{qcfeaturegroup}->{$arg} = Bio::Expression::FeatureSet->new()
- or $self->throw("Couldn't create a Bio::Expression::FeatureSet: $!");
+ $self->{qcfeaturegroup}->{$arg} = Bio::Expression::FeatureGroup->new()
+ or $self->throw("Couldn't create a Bio::Expression::FeatureGroup: $!");
#tag it as being a QC featuregroup
$self->{qcfeaturegroup}->{$arg}->is_qc(1);
@@ -160,8 +160,8 @@ sub qc_featuregroup {
Title : each_featuregroup
Usage : @featuregroups = $array->each_featuregroup();
- Function: gets a list of FeatureSet objects
- Returns : returns list of FeatureSet objects
+ Function: gets a list of FeatureGroup objects
+ Returns : returns list of FeatureGroup objects
Args : none
=cut
@@ -179,8 +179,8 @@ sub each_featuregroup {
Title : each_qcfeaturegroup
Usage : @qcfeaturegroups = $array->each_qcfeaturegroup();
- Function: gets a list of quality control FeatureSet objects
- Returns : returns list of quality control FeatureSet objects
+ Function: gets a list of quality control FeatureGroup objects
+ Returns : returns list of quality control FeatureGroup objects
Args : none
=cut
18 Bio/Expression/Microarray/Affymetrix/Mas50TxtArray.pm
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@@ -61,7 +61,7 @@ use lib '/home2/crsto/cvsroot/bioperl-live/';
use strict;
use Bio::Root::Root;
use Bio::Root::IO;
-use Bio::Expression::FeatureSet::FeatureSetMas50;
+use Bio::Expression::FeatureGroup::FeatureGroupMas50;
use IO::File;
use base qw(Bio::Root::Root Bio::Root::IO);
@@ -88,18 +88,18 @@ use Class::MakeMethods::Emulator::MethodMaker
=head2 featuregroup
Title : featuregroup
- Usage : $array->featureset($name);
- Function: get-set method for FeatureSet object
-Returns : a Bio::Expression::FeatureSet object
- Args : A key for a FeatureSet object
+ Usage : $array->featuregroup($name);
+ Function: get-set method for FeatureGroup object
+Returns : a Bio::Expression::FeatureGroup object
+ Args : A key for a FeatureGroup object
=cut
sub featuregroup {
my($self,$arg) = @_;
return $self->{featuregroup}->{$arg} if $self->{featuregroup}->{$arg};
- $self->{featuregroup}->{$arg} = Bio::Expression::FeatureSet::FeatureSetMas50->new()
- or $self->throw("Couldn't create a Bio::Expression::FeatureSet::FeatureSetMas50 $!");
+ $self->{featuregroup}->{$arg} = Bio::Expression::FeatureGroup::FeatureGroupMas50->new()
+ or $self->throw("Couldn't create a Bio::Expression::FeatureGroup::FeatureGroupMas50 $!");
return $self->{featuregroup}->{$arg};
}
@@ -107,8 +107,8 @@ sub featuregroup {
Title : each_featuregroup
Usage : @featuregroups = $array->each_featuregroup();
- Function: iterated through FeatureSet objects
-Returns : a list of Bio::Expression::FeatureSet::FeatureSetMas50 object
+ Function: iterated through FeatureGroup objects
+Returns : a list of Bio::Expression::FeatureGroup::FeatureGroupMas50 object
Args : none
=cut
16 Bio/Expression/Microarray/Affymetrix/dChipArray.pm
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@@ -54,7 +54,7 @@ package Bio::Expression::Microarray::Affymetrix::dChipArray;
use strict;
use Bio::Root::Root;
-use Bio::Expression::FeatureSet;
+use Bio::Expression::FeatureGroup;
use Bio::Expression::Microarray::Affymetrix::Feature;
use base qw(Bio::Root::Root);
@@ -111,17 +111,17 @@ sub init {
Title : featuregroup
Usage : $self->featuregroup->($featurename);
- Function: get-set method for FeatureSet object
- Returns : a Bio::Expression::FeatureSet object
- Args : A key for a FeatureSet object
+ Function: get-set method for FeatureGroup object
+ Returns : a Bio::Expression::FeatureGroup object
+ Args : A key for a FeatureGroup object
=cut
sub featuregroup {
my($self,$arg) = @_;
return $self->{featuregroup}->{$arg} if $self->{featuregroup}->{$arg};
- $self->{featuregroup}->{$arg} = Bio::Expression::FeatureSet->new()
- or $self->throw("Couldn't create a Bio::Expression::FeatureSet: $!");
+ $self->{featuregroup}->{$arg} = Bio::Expression::FeatureGroup->new()
+ or $self->throw("Couldn't create a Bio::Expression::FeatureGroup: $!");
return $self->{featuregroup}->{$arg};
}
@@ -129,8 +129,8 @@ sub featuregroup {
Title : each_featuregroup
Usage : @featuregroups = $array->each_featuregroup();
- Function: gets a list of FeatureSet objects
- Returns : returns list of FeatureSet objects
+ Function: gets a list of FeatureGroup objects
+ Returns : returns list of FeatureGroup objects
Args : none
=cut
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