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featureset -> featuregroup

svn path=/bioperl-microarray/trunk/; revision=11836
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allenday
allenday committed Sep 8, 2003
1 parent e231d5e commit fb81a047bb2999ac92a81411476f3103cf4dcc79
@@ -92,40 +92,40 @@ sub matrix {
return $self->{matrix}->[ $args[1] ][ $args[0] ];
}
-sub featureset {
+sub featuregroup {
my($self,$arg) = @_;
- return $self->{featureset}->{$arg} if $self->{featureset}->{$arg};
- $self->{featureset}->{$arg} = Bio::Expression::FeatureSet->new()
+ return $self->{featuregroup}->{$arg} if $self->{featureset}->{$arg};
+ $self->{featuregroup}->{$arg} = Bio::Expression::FeatureSet->new()
or $self->throw("Couldn't create a Bio::Expression::FeatureSet: $!");
- return $self->{featureset}->{$arg};
+ return $self->{featuregroup}->{$arg};
}
-sub qcfeatureset {
+sub qcfeaturegroup {
my($self,$arg) = @_;
- return $self->{qcfeatureset}->{$arg} if $self->{qcfeatureset}->{$arg};
- $self->{qcfeatureset}->{$arg} = Bio::Expression::FeatureSet->new()
+ return $self->{qcfeaturegroup}->{$arg} if $self->{qcfeatureset}->{$arg};
+ $self->{qcfeaturegroup}->{$arg} = Bio::Expression::FeatureSet->new()
or $self->throw("Couldn't create a Bio::Expression::FeatureSet: $!");
- #tag it as being a QC featureset
- $self->{qcfeatureset}->{$arg}->is_qc(1);
+ #tag it as being a QC featuregroup
+ $self->{qcfeaturegroup}->{$arg}->is_qc(1);
- return $self->{qcfeatureset}->{$arg};
+ return $self->{qcfeaturegroup}->{$arg};
}
-sub each_featureset {
+sub each_featuregroup {
my $self = shift;
my @return = ();
- foreach my $p (sort keys %{$self->{featureset}}){
- push @return, $self->{featureset}->{$p};
+ foreach my $p (sort keys %{$self->{featuregroup}}){
+ push @return, $self->{featuregroup}->{$p};
}
return @return;
}
-sub each_qcfeatureset {
+sub each_qcfeaturegroup {
my $self = shift;
my @return = ();
- foreach my $p (sort keys %{$self->{qcfeatureset}}){
- push @return, $self->{qcfeatureset}->{$p};
+ foreach my $p (sort keys %{$self->{qcfeaturegroup}}){
+ push @return, $self->{qcfeaturegroup}->{$p};
}
return @return;
}
@@ -154,12 +154,12 @@ sub load_data {
elsif($self->mode =~ /^QC/){
return if /^CellHeader/;
- my $featureset = $self->qcfeatureset($self->mode);
+ my $featuregroup = $self->qcfeatureset($self->mode);
my($type) = $_ =~ /Type=(.+)/;
- $featureset->type($type) and return if $type;
- $featureset->id($self->mode) if $self->mode;
+ $featuregroup->type($type) and return if $type;
+ $featuregroup->id($self->mode) if $self->mode;
my($feature,$attrs) = $_ =~ /Cell(\d+)=(.+)/;
return unless $attrs;
@@ -179,21 +179,21 @@ sub load_data {
my $feature = Bio::Expression::Microarray::Affymetrix::Feature->new( %featureparams );
$self->matrix($attrs[UNIT_X],$attrs[UNIT_Y],\$feature);
- $featureset->add_feature($feature);
+ $featuregroup->add_feature($feature);
}
elsif($self->mode =~ /^Unit(\d+)_Block/){
return if /^Block|Num|Start|Stop|CellHeader/;
- my $featureset;
+ my $featuregroup;
my($name) = $_ =~ /^Name=(.+)/;
if($name){
- $featureset = $self->featureset($name);
- $featureset->id($name);
+ $featuregroup = $self->featureset($name);
+ $featuregroup->id($name);
$self->_temp_name($name);
return;
} else {
- $featureset = $self->featureset($self->_temp_name);
+ $featuregroup = $self->featureset($self->_temp_name);
}
my($feature,$attrs) = $_ =~ /Cell(\d+)=(.+)/;
@@ -223,7 +223,7 @@ sub load_data {
}
my $feature = Bio::Expression::Microarray::Affymetrix::Feature->new( %featureparams );
- $featureset->add_feature($feature);
+ $featuregroup->add_feature($feature);
$self->matrix($attrs[UNIT_X],$attrs[UNIT_Y],\$feature);
}
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