Browse files

move Bio::Expression completely into bioperl-microarray

  • Loading branch information...
1 parent ee2f86e commit ee0fc180b7be18b01cb8d6c94653a82803ec9fa9 Chris Fields committed Jun 25, 2010
View
17 .gitignore
@@ -0,0 +1,17 @@
+*~
+.tmp
+*#
+.#*
+*(Autosaved)blib*
+Build
+Build.bat
+_build*
+pm_to_blib*
+*.tar.gz
+.lwpcookies
+cover_db
+pod2htm*.tmp
+.emacs.*
+blib*
+*.bak
+MYMETA.yml
View
184 Bio/Expression/Contact.pm
@@ -0,0 +1,184 @@
+# $Id$
+#
+# BioPerl module for Bio::Expression::Contact
+#
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
+#
+# Cared for by Allen Day <allenday@ucla.edu>
+#
+# Copyright Allen Day
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Expression::Contact - DESCRIPTION of Object
+
+=head1 SYNOPSIS
+
+Give standard usage here
+
+=head1 DESCRIPTION
+
+Describe the object here
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to
+the Bioperl mailing list. Your participation is much appreciated.
+
+ bioperl-l@bioperl.org - General discussion
+ http://bioperl.org/wiki/Mailing_lists - About the mailing lists
+
+=head2 Support
+
+Please direct usage questions or support issues to the mailing list:
+
+I<bioperl-l@bioperl.org>
+
+rather than to the module maintainer directly. Many experienced and
+reponsive experts will be able look at the problem and quickly
+address it. Please include a thorough description of the problem
+with code and data examples if at all possible.
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+of the bugs and their resolution. Bug reports can be submitted via
+the web:
+
+ http://bugzilla.open-bio.org/
+
+=head1 AUTHOR - Allen Day
+
+Email allenday@ucla.edu
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::Expression::Contact;
+use strict;
+use base qw(Bio::Root::Root);
+
+=head2 new()
+
+ Usage : my $obj = Bio::Expression::Contact->new();
+ Function: Builds a new Bio::Expression::Contact object
+ Returns : an instance of Bio::Expression::Contact
+ Args :
+
+
+=cut
+
+sub new {
+ my($class,@args) = @_;
+
+ my $self = $class->SUPER::new(@args);
+ $self->_initialize(@args);
+ return $self;
+}
+
+=head2 _initialize()
+
+ Usage : $obj->_initialize(%arg);
+ Function: Internal method to initialize a new Bio::Expression::Contact object
+ Returns : true on success
+ Args : passed through to new()
+
+=cut
+
+sub _initialize {
+ my($self,%arg) = @_;
+
+ foreach my $arg (keys %arg){
+ my $marg = $arg;
+ $marg =~ s/^-//;
+ $self->$marg($arg{$arg}) if $self->can($marg);
+ }
+
+ return 1;
+}
+
+=head2 source()
+
+ Usage : $obj->source($newval)
+ Function:
+ Example :
+ Returns : value of source (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub source {
+ my($self,$val) = @_;
+ $self->{'source'} = $val if defined($val);
+ return $self->{'source'};
+}
+
+=head2 accession()
+
+ Usage : $obj->accession($newval)
+ Function:
+ Example :
+ Returns : value of accession (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub accession {
+ my($self,$val) = @_;
+ $self->{'accession'} = $val if defined($val);
+ return $self->{'accession'};
+}
+
+=head2 name()
+
+ Usage : $obj->name($newval)
+ Function:
+ Example :
+ Returns : value of name (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub name {
+ my($self,$val) = @_;
+ $self->{'name'} = $val if defined($val);
+ return $self->{'name'};
+}
+
+=head2 db()
+
+ Usage : $obj->db($newval)
+ Function:
+ Example :
+ Returns : value of db (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub db {
+ my($self,$val) = @_;
+ $self->{'db'} = $val if defined($val);
+ return $self->{'db'};
+}
+
+
+1;
View
342 Bio/Expression/DataSet.pm
@@ -0,0 +1,342 @@
+# $Id$
+#
+# BioPerl module for Bio::Expression::DataSet
+#
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
+#
+# Cared for by Allen Day <allenday@ucla.edu>
+#
+# Copyright Allen Day
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Expression::DataSet - DESCRIPTION of Object
+
+=head1 SYNOPSIS
+
+Give standard usage here
+
+=head1 DESCRIPTION
+
+Describe the object here
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to
+the Bioperl mailing list. Your participation is much appreciated.
+
+ bioperl-l@bioperl.org - General discussion
+ http://bioperl.org/wiki/Mailing_lists - About the mailing lists
+
+=head2 Support
+
+Please direct usage questions or support issues to the mailing list:
+
+I<bioperl-l@bioperl.org>
+
+rather than to the module maintainer directly. Many experienced and
+reponsive experts will be able look at the problem and quickly
+address it. Please include a thorough description of the problem
+with code and data examples if at all possible.
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+of the bugs and their resolution. Bug reports can be submitted via
+the web:
+
+ http://bugzilla.open-bio.org/
+
+=head1 AUTHOR - Allen Day
+
+Email allenday@ucla.edu
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::Expression::DataSet;
+use strict;
+use base qw(Bio::Root::Root);
+
+=head2 new()
+
+ Usage : my $obj = Bio::Expression::DataSet->new();
+ Function: Builds a new Bio::Expression::DataSet object
+ Returns : an instance of Bio::Expression::DataSet
+ Args :
+
+
+=cut
+
+sub new {
+ my($class,@args) = @_;
+
+ my $self = $class->SUPER::new(@args);
+ $self->_initialize(@args);
+ return $self;
+}
+
+=head2 _initialize()
+
+ Usage : $obj->_initialize(%arg);
+ Function: Internal method to initialize a new Bio::Expression::DataSet object
+ Returns : true on success
+ Args : passed through to new()
+
+=cut
+
+sub _initialize {
+ my($self,%arg) = @_;
+
+ foreach my $arg (keys %arg){
+ my $marg = $arg;
+ $marg =~ s/^-//;
+ $self->$marg($arg{$arg}) if $self->can($marg);
+ }
+
+ return 1;
+}
+
+=head2 accession()
+
+ Usage : $obj->accession($newval)
+ Function:
+ Example :
+ Returns : value of accession (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub accession {
+ my($self,$val) = @_;
+ $self->{'accession'} = $val if defined($val);
+ return $self->{'accession'};
+}
+
+=head2 name()
+
+ Usage :
+ Function:
+ Example :
+ Returns :
+ Args :
+
+
+=cut
+
+sub name {
+ my($self,$val) = @_;
+ $self->_load();
+ $self->{'db'} = $val if defined($val);
+ return $self->{'db'};
+}
+
+=head2 db()
+
+ Usage : $obj->db($newval)
+ Function:
+ Example :
+ Returns : value of db (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub db {
+ my($self,$val) = @_;
+ $self->{'db'} = $val if defined($val);
+ return $self->{'db'};
+}
+
+=head2 pubmed_id()
+
+ Usage : $obj->pubmed_id($newval)
+ Function:
+ Example :
+ Returns : value of pubmed_id (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub pubmed_id {
+ my($self,$val) = @_;
+ $self->_load();
+ $self->{'pubmed_id'} = $val if defined($val);
+ return $self->{'pubmed_id'};
+}
+
+=head2 web_link()
+
+ Usage : $obj->web_link($newval)
+ Function:
+ Example :
+ Returns : value of web_link (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub web_link {
+ my($self,$val) = @_;
+ $self->_load();
+ $self->{'web_link'} = $val if defined($val);
+ return $self->{'web_link'};
+}
+
+=head2 contact()
+
+ Usage : $obj->contact($newval)
+ Function:
+ Example :
+ Returns : value of contact (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub contact {
+ my($self,$val) = @_;
+ $self->_load();
+ $self->{'contact'} = $val if defined($val);
+ return $self->{'contact'};
+}
+
+=head2 samples()
+
+ Usage : $obj->samples($newval)
+ Function:
+ Example :
+ Returns : value of samples (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub samples {
+ my($self,$val) = @_;
+ $self->_load();
+ $self->{'samples'} = $val if defined($val);
+ return $self->{'samples'};
+}
+
+=head2 description()
+
+ Usage : $obj->description($newval)
+ Function:
+ Example :
+ Returns : value of description (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub description {
+ my($self,$val) = @_;
+ $self->_load();
+ $self->{'description'} = $val if defined($val);
+ return $self->{'description'};
+}
+
+=head2 design()
+
+ Usage : $obj->design($newval)
+ Function:
+ Example :
+ Returns : value of design (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub design {
+ my($self,$val) = @_;
+ $self->_load();
+ $self->{'design'} = $val if defined($val);
+ return $self->{'design'};
+}
+
+=head2 design_description()
+
+ Usage : $obj->design_description($newval)
+ Function:
+ Example :
+ Returns : value of design_description (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub design_description {
+ my($self,$val) = @_;
+ $self->_load();
+ $self->{'design_description'} = $val if defined($val);
+ return $self->{'design_description'};
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+=head2 get_samples()
+
+ Usage :
+ Function:
+ Example :
+ Returns :
+ Args :
+
+
+=cut
+
+sub get_samples {
+ my ($self,@args) = @_;
+ if ( $self->samples() ) {
+ return @{ $self->samples() };
+ }
+ else {
+ return ();
+ }
+}
+
+
+
+
+
+
+
+sub _load {
+ my $self = shift;
+ if ( $self->{'_load'} ) {
+ return 1;
+ }
+ $self->{'_load'}++;
+ $self->db->fill_dataset( $self );
+ return $self->{'_load'};
+}
+
+1;
View
297 Bio/Expression/FeatureGroup.pm
@@ -0,0 +1,297 @@
+# $Id$
+# BioPerl module for Bio::Expression::FeatureGroup
+#
+# Copyright Allen Day <allenday@ucla.edu>, Stanley Nelson <snelson@ucla.edu>
+# Human Genetics, UCLA Medical School, University of California, Los Angeles
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Expression::FeatureGroup - a set of DNA/RNA features. ISA
+Bio::Expression::FeatureI
+
+=head1 SYNOPSIS
+
+#
+
+=head1 DESCRIPTION
+
+A set of DNA/RNA features.
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to one
+of the Bioperl mailing lists. Your participation is much appreciated.
+
+ bioperl-l@bioperl.org - General discussion
+ http://bioperl.org/wiki/Mailing_lists - About the mailing lists
+
+=head2 Support
+
+Please direct usage questions or support issues to the mailing list:
+
+I<bioperl-l@bioperl.org>
+
+rather than to the module maintainer directly. Many experienced and
+reponsive experts will be able look at the problem and quickly
+address it. Please include a thorough description of the problem
+with code and data examples if at all possible.
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+the bugs and their resolution. Bug reports can be submitted via the
+web:
+
+ http://bugzilla.open-bio.org/
+
+=head1 AUTHOR
+
+Allen Day E<lt>allenday@ucla.eduE<gt>
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object
+methods. Internal methods are usually preceded with a _
+
+=cut
+
+# Let the code begin...
+package Bio::Expression::FeatureGroup;
+
+use strict;
+
+use base qw(Bio::Root::Root Bio::Expression::FeatureI);
+use vars qw($DEBUG);
+
+=head2 new
+
+ Title : new
+ Usage : $featuregroup = Bio::Expression::FeatureGroup->new(%args);
+ Function: create a new featuregroup object
+ Returns : a Bio::Expression::FeatureGroup object
+ Args : an optional hash of parameters to be used in initialization:
+ -id -- the featuregroup ID
+ -type -- the featuregroup type
+
+=cut
+
+sub new {
+ my($class,@args) = @_;
+ my $self = bless {}, $class;
+ $self->_initialize(@args);
+ return $self;
+}
+
+=head2 _initialize
+
+ Title : _initialize
+ Usage : $featuregroup->_initialize(@args);
+ Function: initialize the featuregroup object
+ Returns : nothing
+ Args : @args
+
+=cut
+
+sub _initialize{
+ my ($self,@args) = @_;
+ my %param = @args;
+
+ $self->type($param{-type});
+ $self->id($param{-id} );
+
+ $self->SUPER::_initialize(@args);
+ $DEBUG = 1 if( ! defined $DEBUG && $self->verbose > 0);
+}
+
+=head2 type
+
+ Title : type
+ Usage : $featuregroup->type($optional_arg);
+ Function: get/set the type of the featuregroup
+ Comments: this is probably going to be a string like
+ "quality control", "mismatch blah blah", etc.
+ Returns : the featuregroup type
+ Args : a new value for the featuregroup type
+
+=cut
+
+sub type {
+ my $self = shift;
+ $self->{type} = shift if @_;
+ return $self->{type};
+}
+
+=head2 id
+
+ Title : id
+ Usage : $featuregroup->id($optional_arg);
+ Function: get/set the id of the featuregroup
+ Returns : the featuregroup id
+ Args : a new value for the featuregroup id
+
+=cut
+
+sub id {
+ my $self = shift;
+ $self->{id} = shift if @_;
+ return $self->{id};
+}
+
+
+=head2 standard_deviation
+
+ Title : standard_deviation
+ Usage : $featuregroup->standard_deviation($optional_arg);
+ Function: get/set the standard deviation of the featuregroup value
+ Returns : the featuregroup standard deviation
+ Args : a new value for the featuregroup standard deviation
+ Notes : this method does no calculation, it merely holds a value
+
+=cut
+
+sub standard_deviation {
+ my $self = shift;
+ $self->{standard_deviation} = shift if @_;
+ return $self->{standard_deviation};
+}
+
+=head2 quantitation
+
+ Title : quantitation
+ Usage : $featuregroup->quantitation($optional_arg);
+ Function: get/set the quantitation of the featuregroup
+ Returns : the featuregroup's quantitated value
+ Args : a new value for the featuregroup's quantitated value
+ Notes : this method does no calculation, it merely holds a value
+
+=cut
+
+sub quantitation {
+ my $self = shift;
+ $self->{quantitation} = shift if @_;
+ return $self->{quantitation};
+}
+
+=head2 quantitation_units
+
+ Title : quantitation_units
+ Usage : $featuregroup->quantitation_units($optional_arg);
+ Function: get/set the quantitation units of the featuregroup
+ Returns : the featuregroup's quantitated value units
+ Args : a new value for the featuregroup's quantitated value units
+
+=cut
+
+sub quantitation_units {
+ my $self = shift;
+ $self->{quantitation_units} = shift if @_;
+ return $self->{quantitation_units};
+}
+
+=head2 presence
+
+ Title : presence
+ Usage : $featuregroup->presence($optional_arg);
+ Function: get/set the presence call of the featuregroup
+ Returns : the featuregroup's presence call
+ Args : a new value for the featuregroup's presence call
+
+=cut
+
+sub presence {
+ my $self = shift;
+ $self->{presence} = shift if @_;
+ return $self->{presence};
+}
+
+=head2 add_feature
+
+ Title : add_feature
+ Usage : $feature_copy = $featuregroup->add_feature($feature);
+ Function: add a feature to the featuregroup
+ Returns : see this_feature()
+ Args : a Bio::Expression::FeatureI compliant object
+
+=cut
+
+sub add_feature {
+ my($self,@args) = @_;
+ foreach my $feature (@args){
+ $self->throw('Features must be Bio::Expression::FeatureI compliant') unless $feature->isa('Bio::Expression::FeatureI');
+ push @{$self->{features}}, $feature;
+ }
+
+ return $self->{features} ? $self->{features}->[-1] : undef;
+}
+
+=head2 this_feature
+
+ Title : this_feature
+ Usage : $feature = $featuregroup->this_feature
+ Function: access the last feature added to the featuregroup
+ Returns : the last feature added to the featuregroup
+ Args : none
+
+=cut
+
+sub this_feature {
+ my $self = shift;
+ return $self->{features} ? $self->{features}->[-1] : undef;
+}
+
+=head2 each_feature
+
+ Title : each_feature
+ Usage : @features = $featuregroup->each_feature
+ Function: returns a list of Bio::Expression::FeatureI compliant
+ objects
+ Returns : a list of objects
+ Args : none
+
+=cut
+
+sub each_feature {
+ my $self = shift;
+ return @{$self->{features}} if defined($self->{features});
+ return ();
+}
+
+=head2 each_feature_quantitation
+
+ Title : each_feature_quantitation
+ Usage : @featurequantitions = $featuregroup->each_feature_quantitation;
+ Function: returns an list of quantitations of the features in the featuregroup
+ Returns : a list of numeric values
+ Args : none
+
+=cut
+
+sub each_feature_quantitation {
+ my $self = shift;
+ my @values = ();
+ push @values, $_->value foreach $self->each_feature;
+ return @values;
+}
+
+=head2 is_qc
+
+ Title : is_qc
+ Usage : $is_quality_control = $featuregroup->is_qc
+ Function: get/set whether or not the featuregroup is used for quality control purposes
+ Returns : a boolean (equivalent)
+ Args : a new value
+
+=cut
+
+sub is_qc {
+ my $self = shift;
+ $self->{is_qc} = shift if defined @_;
+ return $self->{is_qc};
+}
+
+1;
View
37 Bio/Expression/FeatureGroup/FeatureGroupMas50.pm
@@ -0,0 +1,37 @@
+# Let the code begin...
+package Bio::Expression::FeatureGroup::FeatureGroupMas50;
+
+# $Id$
+
+=head1 NAME
+
+Bio::Expression::FeatureGroup::FeatureGroupMas50 - utility class for Mas50 FeatureGroup
+
+=cut
+
+use strict;
+
+use base qw(Bio::Expression::FeatureGroup);
+use vars qw($DEBUG);
+
+use Class::MakeMethods::Emulator::MethodMaker
+ get_set => [qw(
+
+ probe_set_name stat_pairs stat_pairs_used
+ signal detection detection_p_value
+ stat_common_pairs signal_log_ratio
+ signal_log_ratio_low
+ signal_log_ratio_high change change_p_value
+ positive negative pairs pairs_used
+ pairs_inavg pos_fraction log_avg
+ pos_neg avg_diff abs_call inc dec
+ inc_ratio dec_ratio pos_change
+ neg_change inc_dec dpos_dneg_ratio
+ log_avg_ratio_change diff_call
+ avg_diff_change b_a fold_change
+ sort_score
+
+ )],
+;
+
+1;
View
131 Bio/Expression/FeatureI.pm
@@ -0,0 +1,131 @@
+# $Id$
+# BioPerl module for Bio::Expression::FeatureI
+#
+# Copyright Allen Day <allenday@ucla.edu>, Stan Nelson <snelson@ucla.edu>
+# Human Genetics, UCLA Medical School, University of California, Los Angeles
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Expression::FeatureI - an interface class for DNA/RNA features
+
+=head1 SYNOPSIS
+
+Do not use this module directly
+
+=head1 DESCRIPTION
+
+This provides a standard bioperl interface class for representing
+DNA and RNA features. It cannot be instantiated directly, but serves
+as an abstract base class for implementors.
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to one
+of the Bioperl mailing lists. Your participation is much appreciated.
+
+ bioperl-l@bioperl.org - General discussion
+ http://bioperl.org/wiki/Mailing_lists - About the mailing lists
+
+=head2 Support
+
+Please direct usage questions or support issues to the mailing list:
+
+I<bioperl-l@bioperl.org>
+
+rather than to the module maintainer directly. Many experienced and
+reponsive experts will be able look at the problem and quickly
+address it. Please include a thorough description of the problem
+with code and data examples if at all possible.
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+the bugs and their resolution. Bug reports can be submitted via the
+web:
+
+ http://bugzilla.open-bio.org/
+
+=head1 AUTHOR
+
+Allen Day E<lt>allenday@ucla.eduE<gt>
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object
+methods. Internal methods are usually preceded with a _
+
+=cut
+
+# Let the code begin...
+package Bio::Expression::FeatureI;
+
+use strict;
+use Bio::Root::RootI;
+
+use base qw(Bio::Root::RootI Bio::PrimarySeqI);
+use vars qw($DEBUG);
+
+=head2 quantitation()
+
+ Title : value
+ Usage : $val = $ftr->quantitation()
+ Function: get/set the feature's quantitation
+ Returns : A numeric value
+ Args : a new numeric value (optional)
+
+=cut
+
+sub quantitation {
+ shift->throw_not_implemented();
+}
+
+=head2 quantitation_units()
+
+ Title : quantitation_units
+ Usage : $units = $ftr->quantitation_units()
+ Function: get/set the units of the feature's quantitation
+ Returns : A string or undef
+ Args : a new string (optional)
+
+=cut
+
+sub quantitation_units {
+ shift->throw_not_implemented();
+}
+
+=head2 standard_deviation()
+
+ Title : standard_deviation
+ Usage : $std_dev = $ftr->standard_deviation()
+ Function: get/set the feature's standard deviation of quantitation()
+ Returns : A numeric value
+ Args : a new numeric value (optional)
+ Comments: no calculation is done here
+
+=cut
+
+sub standard_deviation {
+ shift->throw_not_implemented();
+}
+
+=head2 sample_count()
+
+ Title : sample_count
+ Usage : $sample_count = $ftr->sample_count()
+ Function: get/set the number of samples used to calculate
+ quantitation()
+ Returns : An integer
+ Args : a new integer (optional)
+
+=cut
+
+sub sample_count {
+ shift->throw_not_implemented();
+}
+
+1;
View
37 Bio/Expression/FeatureSet/FeatureSetMas50.pm
@@ -0,0 +1,37 @@
+# Let the code begin...
+package Bio::Expression::FeatureSet::FeatureSetMas50;
+
+# $Id$
+
+=head1 NAME
+
+Bio::Expression::FeatureSet::FeatureSetMas50 - utility class for Mas50 FeatureSet
+
+=cut
+
+use strict;
+
+use base qw(Bio::Expression::FeatureSet);
+use vars qw($DEBUG);
+
+use Class::MakeMethods::Emulator::MethodMaker
+ get_set => [qw(
+
+ probe_set_name stat_pairs stat_pairs_used
+ signal detection detection_p-value
+ stat_common_pairs signal_log_ratio
+ signal_log_ratio_low
+ signal_log_ratio_high change change_p-value
+ positive negative pairs pairs_used
+ pairs_inavg pos_fraction log_avg
+ pos_neg avg_diff abs_call inc dec
+ inc_ratio dec_ratio pos_change
+ neg_change inc_dec dpos-dneg_ratio
+ log_avg_ratio_change diff_call
+ avg_diff_change b_a fold_change
+ sort_score
+
+ )],
+;
+
+1;
View
260 Bio/Expression/Platform.pm
@@ -0,0 +1,260 @@
+# $Id$
+#
+# BioPerl module for Bio::Expression::Platform
+#
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
+#
+# Cared for by Allen Day <allenday@ucla.edu>
+#
+# Copyright Allen Day
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Expression::Platform - DESCRIPTION of Object
+
+=head1 SYNOPSIS
+
+Give standard usage here
+
+=head1 DESCRIPTION
+
+Describe the object here
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to
+the Bioperl mailing list. Your participation is much appreciated.
+
+ bioperl-l@bioperl.org - General discussion
+ http://bioperl.org/wiki/Mailing_lists - About the mailing lists
+
+=head2 Support
+
+Please direct usage questions or support issues to the mailing list:
+
+I<bioperl-l@bioperl.org>
+
+rather than to the module maintainer directly. Many experienced and
+reponsive experts will be able look at the problem and quickly
+address it. Please include a thorough description of the problem
+with code and data examples if at all possible.
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+of the bugs and their resolution. Bug reports can be submitted via
+the web:
+
+ http://bugzilla.open-bio.org/
+
+=head1 AUTHOR - Allen Day
+
+Email allenday@ucla.edu
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::Expression::Platform;
+use strict;
+use base qw(Bio::Root::Root);
+use Bio::DB::Taxonomy;
+
+=head2 new()
+
+ Usage : my $obj = Bio::Expression::Platform->new();
+ Function: Builds a new Bio::Expression::Platform object
+ Returns : an instance of Bio::Expression::Platform
+ Args :
+
+=cut
+
+sub new {
+ my($class,@args) = @_;
+
+ my $self = $class->SUPER::new(@args);
+ $self->_initialize(@args);
+ return $self;
+}
+
+=head2 _initialize()
+
+ Usage : $obj->_initialize(%arg);
+ Function: Internal method to initialize a new Bio::Expression::Platform object
+ Returns : true on success
+ Args : passed through to new()
+
+=cut
+
+sub _initialize {
+ my($self,%arg) = @_;
+
+ foreach my $arg (keys %arg){
+ my $marg = $arg;
+ $marg =~ s/^-//;
+ $self->$marg($arg{$arg}) if $self->can($marg);
+ }
+
+ $self->taxdb( Bio::DB::Taxonomy->new(-source => 'entrez') );
+ return 1;
+}
+
+
+
+=head2 get_datasets()
+
+ Usage :
+ Function:
+ Example :
+ Returns :
+ Args :
+
+=cut
+
+sub get_datasets {
+ my ($self,@args) = @_;
+ my $db = $self->db();
+
+ my @datasets = $db->get_datasets( $self );
+
+ return @datasets;
+}
+
+=head2 accession()
+
+ Usage : $obj->accession($newval)
+ Function:
+ Example :
+ Returns : value of accession (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub accession {
+ my($self,$val) = @_;
+ $self->{'accession'} = $val if defined($val);
+ return $self->{'accession'};
+}
+
+=head2 name()
+
+ Usage : $obj->name($newval)
+ Function:
+ Example :
+ Returns : value of name (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub name {
+ my($self,$val) = @_;
+ $self->{'name'} = $val if defined($val);
+ return $self->{'name'};
+}
+
+=head2 taxon()
+
+ Usage : $obj->taxon()
+ Function:
+ Example :
+ Returns : A Bio::Taxonomy::Node object
+ Args : none
+
+
+=cut
+
+sub taxon {
+ my($self) = @_;
+ if ( ! $self->{'taxon'} ) {
+ $self->{'taxon'} = $self->taxdb->get_Taxonomy_Node( $self->_taxon_id() );
+ }
+ return $self->{'taxon'};
+}
+
+=head2 contact()
+
+ Usage : $obj->contact($newval)
+ Function:
+ Example :
+ Returns : a Bio::Expression::Contact object
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub contact {
+ my($self,$val) = @_;
+ $self->{'contact'} = $val if defined($val);
+ return $self->{'contact'};
+}
+
+=head2 db()
+
+ Usage : $obj->db($newval)
+ Function:
+ Example :
+ Returns : value of db (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub db {
+ my($self,$val) = @_;
+ $self->{'db'} = $val if defined($val);
+ return $self->{'db'};
+}
+
+=head2 _taxon_id()
+
+ Usage : $obj->_taxon_id($newval)
+ Function:
+ Example :
+ Returns : value of _taxon_id (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub _taxon_id {
+ my($self,$val) = @_;
+ $self->{'_taxon_id'} = $val if defined($val);
+ return $self->{'_taxon_id'};
+}
+
+=head2 taxdb()
+
+ Usage : $obj->taxdb($newval)
+ Function:
+ Example :
+ Returns : a Bio::DB::Taxonomy object
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub taxdb {
+ my($self,$val) = @_;
+ $self->{'taxdb'} = $val if defined($val);
+ return $self->{'taxdb'};
+}
+
+
+
+1;
View
71 Bio/Expression/ProbeI.pm
@@ -0,0 +1,71 @@
+# $Id$
+# BioPerl module for Bio::Expression::ProbeI
+#
+# Copyright Allen Day <allenday@ucla.edu>, Stan Nelson <snelson@ucla.edu>
+# Human Genetics, UCLA Medical School, University of California, Los Angeles
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Expression::ProbeI - an interface class for DNA/RNA probes
+
+=head1 SYNOPSIS
+
+Do not use this module directly
+
+=head1 DESCRIPTION
+
+This class ISA Bio::Expression::FeatureI, nothing more.
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to
+the Bioperl mailing list. Your participation is much appreciated.
+
+ bioperl-l@bioperl.org - General discussion
+ http://bioperl.org/wiki/Mailing_lists - About the mailing lists
+
+=head2 Support
+
+Please direct usage questions or support issues to the mailing list:
+
+I<bioperl-l@bioperl.org>
+
+rather than to the module maintainer directly. Many experienced and
+reponsive experts will be able look at the problem and quickly
+address it. Please include a thorough description of the problem
+with code and data examples if at all possible.
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+of the bugs and their resolution. Bug reports can be submitted via
+the web:
+
+ http://bugzilla.open-bio.org/
+
+=head1 AUTHOR
+
+Allen Day E<lt>allenday@ucla.eduE<gt>
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object
+methods. Internal methods are usually preceded with a _
+
+=cut
+
+# Let the code begin...
+package Bio::Expression::ProbeI;
+
+use strict;
+use Bio::Root::Root;
+
+use base qw(Bio::Expression::FeatureI);
+use vars qw($DEBUG);
+
+1;
View
253 Bio/Expression/Sample.pm
@@ -0,0 +1,253 @@
+# $Id$
+#
+# BioPerl module for Bio::Expression::Sample
+#
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
+#
+# Cared for by Allen Day <allenday@ucla.edu>
+#
+# Copyright Allen Day
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Expression::Sample - DESCRIPTION of Object
+
+=head1 SYNOPSIS
+
+Give standard usage here
+
+=head1 DESCRIPTION
+
+Describe the object here
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to
+the Bioperl mailing list. Your participation is much appreciated.
+
+ bioperl-l@bioperl.org - General discussion
+ http://bioperl.org/wiki/Mailing_lists - About the mailing lists
+
+=head2 Support
+
+Please direct usage questions or support issues to the mailing list:
+
+I<bioperl-l@bioperl.org>
+
+rather than to the module maintainer directly. Many experienced and
+reponsive experts will be able look at the problem and quickly
+address it. Please include a thorough description of the problem
+with code and data examples if at all possible.
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+of the bugs and their resolution. Bug reports can be submitted via
+the web:
+
+ http://bugzilla.open-bio.org/
+
+=head1 AUTHOR - Allen Day
+
+Email allenday@ucla.edu
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::Expression::Sample;
+use strict;
+use base qw(Bio::Root::Root);
+
+=head2 new()
+
+ Usage : my $obj = Bio::Expression::Sample->new();
+ Function: Builds a new Bio::Expression::Sample object
+ Returns : an instance of Bio::Expression::Sample
+ Args :
+
+
+=cut
+
+sub new {
+ my($class,@args) = @_;
+
+ my $self = $class->SUPER::new(@args);
+ $self->_initialize(@args);
+ return $self;
+}
+
+=head2 _initialize()
+
+ Usage : $obj->_initialize(%arg);
+ Function: Internal method to initialize a new Bio::Expression::Sample object
+ Returns : true on success
+ Args : passed through to new()
+
+=cut
+
+sub _initialize {
+ my($self,%arg) = @_;
+
+ foreach my $arg (keys %arg){
+ my $marg = $arg;
+ $marg =~ s/^-//;
+ $self->$marg($arg{$arg}) if $self->can($marg);
+ }
+
+ return 1;
+}
+
+=head2 accession()
+
+ Usage : $obj->accession($newval)
+ Function:
+ Example :
+ Returns : value of accession (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub accession {
+ my($self,$val) = @_;
+ $self->{'accession'} = $val if defined($val);
+ return $self->{'accession'};
+}
+
+=head2 dataset()
+
+ Usage : $obj->dataset($newval)
+ Function:
+ Example :
+ Returns : value of dataset (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub dataset {
+ my($self,$val) = @_;
+ $self->{'dataset'} = $val if defined($val);
+ return $self->{'dataset'};
+}
+
+=head2 db()
+
+ Usage : $obj->db($newval)
+ Function:
+ Example :
+ Returns : value of db (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub db {
+ my($self,$val) = @_;
+ $self->{'db'} = $val if defined($val);
+ return $self->{'db'};
+}
+
+
+
+
+
+
+=head2 name()
+
+ Usage : $obj->name($newval)
+ Function:
+ Example :
+ Returns : value of name (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub name {
+ my($self,$val) = @_;
+ $self->_load();
+ $self->{'name'} = $val if defined($val);
+ return $self->{'name'};
+}
+
+=head2 source_name()
+
+ Usage : $obj->source_name($newval)
+ Function:
+ Example :
+ Returns : value of source_name (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub source_name {
+ my($self,$val) = @_;
+ $self->_load();
+ $self->{'source_name'} = $val if defined($val);
+ return $self->{'source_name'};
+}
+
+=head2 description()
+
+ Usage : $obj->description($newval)
+ Function:
+ Example :
+ Returns : value of description (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub description {
+ my($self,$val) = @_;
+ $self->_load();
+ $self->{'description'} = $val if defined($val);
+ return $self->{'description'};
+}
+
+=head2 treatment_description()
+
+ Usage : $obj->treatment_description($newval)
+ Function:
+ Example :
+ Returns : value of treatment_description (a scalar)
+ Args : on set, new value (a scalar or undef, optional)
+
+
+=cut
+
+sub treatment_description {
+ my($self,$val) = @_;
+ $self->_load();
+ $self->{'treatment_description'} = $val if defined($val);
+ return $self->{'treatment_description'};
+}
+
+sub _load {
+ my $self = shift;
+ if ( $self->{'_load'} ) {
+ return 1;
+ }
+ $self->{'_load'}++;
+ $self->db->fill_sample( $self );
+ return $self->{'_load'};
+}
+
+1;
View
937 Makefile
@@ -0,0 +1,937 @@
+# This Makefile is for the Bio extension to perl.
+#
+# It was generated automatically by MakeMaker version
+# 6.56 (Revision: 65600) from the contents of
+# Makefile.PL. Don't edit this file, edit Makefile.PL instead.
+#
+# ANY CHANGES MADE HERE WILL BE LOST!
+#
+# MakeMaker ARGV: ()
+#
+
+# MakeMaker Parameters:
+
+# ABSTRACT => q[Bioperl Toolkit - Addendum for microarray data]
+# AUTHOR => q[Bioperl Team (bioperl-l@bioperl.org)]
+# BUILD_REQUIRES => { }
+# DIR => []
+# DISTNAME => q[bioperl-microarray]
+# NAME => q[Bio]
+# PREREQ_PM => { }
+# VERSION => q[0.1]
+# dist => { DIST_DEFAULT=>q[all tardist], COMPRESS=>q[gzip -9f], SUFFIX=>q[.gz] }
+# realclean => { FILES=>q[] }
+
+# --- MakeMaker post_initialize section:
+
+
+# --- MakeMaker const_config section:
+
+# These definitions are from config.sh (via /opt/perl512/lib/5.12.1/darwin-thread-multi-2level/Config.pm).
+# They may have been overridden via Makefile.PL or on the command line.
+AR = ar
+CC = cc
+CCCDLFLAGS =
+CCDLFLAGS =
+DLEXT = bundle
+DLSRC = dl_dlopen.xs
+EXE_EXT =
+FULL_AR = /usr/bin/ar
+LD = env MACOSX_DEPLOYMENT_TARGET=10.3 cc
+LDDLFLAGS = -bundle -undefined dynamic_lookup -L/usr/local/lib -L/opt/local/lib -fstack-protector
+LDFLAGS = -fstack-protector -L/usr/local/lib -L/opt/local/lib
+LIBC = /usr/lib/libc.dylib
+LIB_EXT = .a
+OBJ_EXT = .o
+OSNAME = darwin
+OSVERS = 10.3.0
+RANLIB = ranlib
+SITELIBEXP = /opt/perl512/lib/site_perl/5.12.1
+SITEARCHEXP = /opt/perl512/lib/site_perl/5.12.1/darwin-thread-multi-2level
+SO = dylib
+VENDORARCHEXP =
+VENDORLIBEXP =
+
+
+# --- MakeMaker constants section:
+AR_STATIC_ARGS = cr
+DIRFILESEP = /
+DFSEP = $(DIRFILESEP)
+NAME = Bio
+NAME_SYM = Bio
+VERSION = 0.1
+VERSION_MACRO = VERSION
+VERSION_SYM = 0_1
+DEFINE_VERSION = -D$(VERSION_MACRO)=\"$(VERSION)\"
+XS_VERSION = 0.1
+XS_VERSION_MACRO = XS_VERSION
+XS_DEFINE_VERSION = -D$(XS_VERSION_MACRO)=\"$(XS_VERSION)\"
+INST_ARCHLIB = blib/arch
+INST_SCRIPT = blib/script
+INST_BIN = blib/bin
+INST_LIB = blib/lib
+INST_MAN1DIR = blib/man1
+INST_MAN3DIR = blib/man3
+MAN1EXT = 1
+MAN3EXT = 3
+INSTALLDIRS = site
+DESTDIR =
+PREFIX = $(SITEPREFIX)
+PERLPREFIX = /opt/perl512
+SITEPREFIX = /opt/perl512
+VENDORPREFIX =
+INSTALLPRIVLIB = /opt/perl512/lib/5.12.1
+DESTINSTALLPRIVLIB = $(DESTDIR)$(INSTALLPRIVLIB)
+INSTALLSITELIB = /opt/perl512/lib/site_perl/5.12.1
+DESTINSTALLSITELIB = $(DESTDIR)$(INSTALLSITELIB)
+INSTALLVENDORLIB =
+DESTINSTALLVENDORLIB = $(DESTDIR)$(INSTALLVENDORLIB)
+INSTALLARCHLIB = /opt/perl512/lib/5.12.1/darwin-thread-multi-2level
+DESTINSTALLARCHLIB = $(DESTDIR)$(INSTALLARCHLIB)
+INSTALLSITEARCH = /opt/perl512/lib/site_perl/5.12.1/darwin-thread-multi-2level
+DESTINSTALLSITEARCH = $(DESTDIR)$(INSTALLSITEARCH)
+INSTALLVENDORARCH =
+DESTINSTALLVENDORARCH = $(DESTDIR)$(INSTALLVENDORARCH)
+INSTALLBIN = /opt/perl512/bin
+DESTINSTALLBIN = $(DESTDIR)$(INSTALLBIN)
+INSTALLSITEBIN = /opt/perl512/bin
+DESTINSTALLSITEBIN = $(DESTDIR)$(INSTALLSITEBIN)
+INSTALLVENDORBIN =
+DESTINSTALLVENDORBIN = $(DESTDIR)$(INSTALLVENDORBIN)
+INSTALLSCRIPT = /opt/perl512/bin
+DESTINSTALLSCRIPT = $(DESTDIR)$(INSTALLSCRIPT)
+INSTALLSITESCRIPT = /opt/perl512/bin
+DESTINSTALLSITESCRIPT = $(DESTDIR)$(INSTALLSITESCRIPT)
+INSTALLVENDORSCRIPT =
+DESTINSTALLVENDORSCRIPT = $(DESTDIR)$(INSTALLVENDORSCRIPT)
+INSTALLMAN1DIR = /opt/perl512/man/man1
+DESTINSTALLMAN1DIR = $(DESTDIR)$(INSTALLMAN1DIR)
+INSTALLSITEMAN1DIR = /opt/perl512/man/man1
+DESTINSTALLSITEMAN1DIR = $(DESTDIR)$(INSTALLSITEMAN1DIR)
+INSTALLVENDORMAN1DIR =
+DESTINSTALLVENDORMAN1DIR = $(DESTDIR)$(INSTALLVENDORMAN1DIR)
+INSTALLMAN3DIR = /opt/perl512/man/man3
+DESTINSTALLMAN3DIR = $(DESTDIR)$(INSTALLMAN3DIR)
+INSTALLSITEMAN3DIR = /opt/perl512/man/man3
+DESTINSTALLSITEMAN3DIR = $(DESTDIR)$(INSTALLSITEMAN3DIR)
+INSTALLVENDORMAN3DIR =
+DESTINSTALLVENDORMAN3DIR = $(DESTDIR)$(INSTALLVENDORMAN3DIR)
+PERL_LIB = /opt/perl512/lib/5.12.1
+PERL_ARCHLIB = /opt/perl512/lib/5.12.1/darwin-thread-multi-2level
+LIBPERL_A = libperl.a
+FIRST_MAKEFILE = Makefile
+MAKEFILE_OLD = Makefile.old
+MAKE_APERL_FILE = Makefile.aperl
+PERLMAINCC = $(CC)
+PERL_INC = /opt/perl512/lib/5.12.1/darwin-thread-multi-2level/CORE
+PERL = /opt/perl512/bin/perl
+FULLPERL = /opt/perl512/bin/perl
+ABSPERL = $(PERL)
+PERLRUN = $(PERL)
+FULLPERLRUN = $(FULLPERL)
+ABSPERLRUN = $(ABSPERL)
+PERLRUNINST = $(PERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
+FULLPERLRUNINST = $(FULLPERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
+ABSPERLRUNINST = $(ABSPERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
+PERL_CORE = 0
+PERM_DIR = 755
+PERM_RW = 644
+PERM_RWX = 755
+
+MAKEMAKER = /opt/perl512/lib/5.12.1/ExtUtils/MakeMaker.pm
+MM_VERSION = 6.56
+MM_REVISION = 65600
+
+# FULLEXT = Pathname for extension directory (eg Foo/Bar/Oracle).
+# BASEEXT = Basename part of FULLEXT. May be just equal FULLEXT. (eg Oracle)
+# PARENT_NAME = NAME without BASEEXT and no trailing :: (eg Foo::Bar)
+# DLBASE = Basename part of dynamic library. May be just equal BASEEXT.
+MAKE = make
+FULLEXT = Bio
+BASEEXT = Bio
+PARENT_NAME =
+DLBASE = $(BASEEXT)
+VERSION_FROM =
+OBJECT =
+LDFROM = $(OBJECT)
+LINKTYPE = dynamic
+BOOTDEP =
+
+# Handy lists of source code files:
+XS_FILES =
+C_FILES =
+O_FILES =
+H_FILES =
+MAN1PODS =
+MAN3PODS = Bio/Expression/Microarray/Affymetrix/Array.pm \
+ Bio/Expression/Microarray/Affymetrix/ArrayDesign.pm \
+ Bio/Expression/Microarray/Affymetrix/CelArray.pm \
+ Bio/Expression/Microarray/Affymetrix/Data.pm \
+ Bio/Expression/Microarray/Affymetrix/Feature.pm \
+ Bio/Expression/Microarray/Affymetrix/Mas50TxtArray.pm \
+ Bio/Expression/Microarray/Affymetrix/dChipArray.pm \
+ Bio/Expression/Microarray/Affymetrix/dChipXLS.pm \
+ Bio/Expression/Microarray/FeatureI.pm \
+ Bio/Expression/MicroarrayIO.pm \
+ Bio/Expression/MicroarrayIO/affymetrix.pm \
+ Bio/Expression/MicroarrayIO/dchipxls.pm \
+ Bio/Expression/MicroarrayIO/mas50txt.pm
+
+# Where is the Config information that we are using/depend on
+CONFIGDEP = $(PERL_ARCHLIB)$(DFSEP)Config.pm $(PERL_INC)$(DFSEP)config.h
+
+# Where to build things
+INST_LIBDIR = $(INST_LIB)
+INST_ARCHLIBDIR = $(INST_ARCHLIB)
+
+INST_AUTODIR = $(INST_LIB)/auto/$(FULLEXT)
+INST_ARCHAUTODIR = $(INST_ARCHLIB)/auto/$(FULLEXT)
+
+INST_STATIC =
+INST_DYNAMIC =
+INST_BOOT =
+
+# Extra linker info
+EXPORT_LIST =
+PERL_ARCHIVE =
+PERL_ARCHIVE_AFTER =
+
+
+TO_INST_PM = Bio/Expression/Microarray/Affymetrix/Array.pm \
+ Bio/Expression/Microarray/Affymetrix/ArrayDesign.pm \
+ Bio/Expression/Microarray/Affymetrix/CelArray.pm \
+ Bio/Expression/Microarray/Affymetrix/Changes.txt \
+ Bio/Expression/Microarray/Affymetrix/Data.pm \
+ Bio/Expression/Microarray/Affymetrix/Feature.pm \
+ Bio/Expression/Microarray/Affymetrix/Mas50Data.pm \
+ Bio/Expression/Microarray/Affymetrix/Mas50TxtArray.pm \
+ Bio/Expression/Microarray/Affymetrix/dChipArray.pm \
+ Bio/Expression/Microarray/Affymetrix/dChipXLS.pm \
+ Bio/Expression/Microarray/ArrayI.pm \
+ Bio/Expression/Microarray/DataI.pm \
+ Bio/Expression/Microarray/FeatureI.pm \
+ Bio/Expression/MicroarrayI.pm \
+ Bio/Expression/MicroarrayIO.pm \
+ Bio/Expression/MicroarrayIO/affymetrix.pm \
+ Bio/Expression/MicroarrayIO/dchipxls.pm \
+ Bio/Expression/MicroarrayIO/mas50txt.pm
+
+PM_TO_BLIB = Bio/Expression/MicroarrayI.pm \
+ $(INST_LIB)/Bio/Expression/MicroarrayI.pm \
+ Bio/Expression/Microarray/Affymetrix/Mas50Data.pm \
+ $(INST_LIB)/Bio/Expression/Microarray/Affymetrix/Mas50Data.pm \
+ Bio/Expression/MicroarrayIO/dchipxls.pm \
+ $(INST_LIB)/Bio/Expression/MicroarrayIO/dchipxls.pm \
+ Bio/Expression/Microarray/Affymetrix/dChipXLS.pm \
+ $(INST_LIB)/Bio/Expression/Microarray/Affymetrix/dChipXLS.pm \
+ Bio/Expression/MicroarrayIO/mas50txt.pm \
+ $(INST_LIB)/Bio/Expression/MicroarrayIO/mas50txt.pm \
+ Bio/Expression/Microarray/Affymetrix/dChipArray.pm \
+ $(INST_LIB)/Bio/Expression/Microarray/Affymetrix/dChipArray.pm \
+ Bio/Expression/MicroarrayIO/affymetrix.pm \
+ $(INST_LIB)/Bio/Expression/MicroarrayIO/affymetrix.pm \
+ Bio/Expression/Microarray/Affymetrix/Array.pm \
+ $(INST_LIB)/Bio/Expression/Microarray/Affymetrix/Array.pm \
+ Bio/Expression/Microarray/Affymetrix/CelArray.pm \
+ $(INST_LIB)/Bio/Expression/Microarray/Affymetrix/CelArray.pm \
+ Bio/Expression/Microarray/FeatureI.pm \
+ $(INST_LIB)/Bio/Expression/Microarray/FeatureI.pm \
+ Bio/Expression/Microarray/Affymetrix/Data.pm \
+ $(INST_LIB)/Bio/Expression/Microarray/Affymetrix/Data.pm \
+ Bio/Expression/Microarray/DataI.pm \
+ $(INST_LIB)/Bio/Expression/Microarray/DataI.pm \
+ Bio/Expression/Microarray/Affymetrix/Feature.pm \
+ $(INST_LIB)/Bio/Expression/Microarray/Affymetrix/Feature.pm \
+ Bio/Expression/Microarray/Affymetrix/Changes.txt \
+ $(INST_LIB)/Bio/Expression/Microarray/Affymetrix/Changes.txt \
+ Bio/Expression/Microarray/ArrayI.pm \
+ $(INST_LIB)/Bio/Expression/Microarray/ArrayI.pm \
+ Bio/Expression/Microarray/Affymetrix/ArrayDesign.pm \
+ $(INST_LIB)/Bio/Expression/Microarray/Affymetrix/ArrayDesign.pm \
+ Bio/Expression/MicroarrayIO.pm \
+ $(INST_LIB)/Bio/Expression/MicroarrayIO.pm \
+ Bio/Expression/Microarray/Affymetrix/Mas50TxtArray.pm \
+ $(INST_LIB)/Bio/Expression/Microarray/Affymetrix/Mas50TxtArray.pm
+
+
+# --- MakeMaker platform_constants section:
+MM_Unix_VERSION = 6.56
+PERL_MALLOC_DEF = -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc
+
+
+# --- MakeMaker tool_autosplit section:
+# Usage: $(AUTOSPLITFILE) FileToSplit AutoDirToSplitInto
+AUTOSPLITFILE = $(ABSPERLRUN) -e 'use AutoSplit; autosplit($$ARGV[0], $$ARGV[1], 0, 1, 1)' --
+
+
+
+# --- MakeMaker tool_xsubpp section:
+
+
+# --- MakeMaker tools_other section:
+SHELL = /bin/sh
+CHMOD = chmod
+CP = cp
+MV = mv
+NOOP = $(TRUE)
+NOECHO = @
+RM_F = rm -f
+RM_RF = rm -rf
+TEST_F = test -f
+TOUCH = touch
+UMASK_NULL = umask 0
+DEV_NULL = > /dev/null 2>&1
+MKPATH = $(ABSPERLRUN) -MExtUtils::Command -e 'mkpath' --
+EQUALIZE_TIMESTAMP = $(ABSPERLRUN) -MExtUtils::Command -e 'eqtime' --
+FALSE = false
+TRUE = true
+ECHO = echo
+ECHO_N = echo -n
+UNINST = 0
+VERBINST = 0
+MOD_INSTALL = $(ABSPERLRUN) -MExtUtils::Install -e 'install([ from_to => {@ARGV}, verbose => '\''$(VERBINST)'\'', uninstall_shadows => '\''$(UNINST)'\'', dir_mode => '\''$(PERM_DIR)'\'' ]);' --
+DOC_INSTALL = $(ABSPERLRUN) -MExtUtils::Command::MM -e 'perllocal_install' --
+UNINSTALL = $(ABSPERLRUN) -MExtUtils::Command::MM -e 'uninstall' --
+WARN_IF_OLD_PACKLIST = $(ABSPERLRUN) -MExtUtils::Command::MM -e 'warn_if_old_packlist' --
+MACROSTART =
+MACROEND =
+USEMAKEFILE = -f
+FIXIN = $(ABSPERLRUN) -MExtUtils::MY -e 'MY->fixin(shift)' --
+
+
+# --- MakeMaker makemakerdflt section:
+makemakerdflt : all
+ $(NOECHO) $(NOOP)
+
+
+# --- MakeMaker dist section:
+TAR = COPY_EXTENDED_ATTRIBUTES_DISABLE=1 COPYFILE_DISABLE=1 tar
+TARFLAGS = cvf
+ZIP = zip
+ZIPFLAGS = -r
+COMPRESS = gzip -9f
+SUFFIX = .gz
+SHAR = shar
+PREOP = $(NOECHO) $(NOOP)
+POSTOP = $(NOECHO) $(NOOP)
+TO_UNIX = $(NOECHO) $(NOOP)
+CI = ci -u
+RCS_LABEL = rcs -Nv$(VERSION_SYM): -q
+DIST_CP = best
+DIST_DEFAULT = all tardist
+DISTNAME = bioperl-microarray
+DISTVNAME = bioperl-microarray-0.1
+
+
+# --- MakeMaker macro section:
+
+
+# --- MakeMaker depend section:
+
+
+# --- MakeMaker cflags section:
+
+
+# --- MakeMaker const_loadlibs section:
+
+
+# --- MakeMaker const_cccmd section:
+
+
+# --- MakeMaker post_constants section:
+
+
+# --- MakeMaker pasthru section:
+
+PASTHRU = LIBPERL_A="$(LIBPERL_A)"\
+ LINKTYPE="$(LINKTYPE)"\
+ PREFIX="$(PREFIX)"
+
+
+# --- MakeMaker special_targets section:
+.SUFFIXES : .xs .c .C .cpp .i .s .cxx .cc $(OBJ_EXT)
+
+.PHONY: all config static dynamic test linkext manifest blibdirs clean realclean disttest distdir
+
+
+
+# --- MakeMaker c_o section:
+
+
+# --- MakeMaker xs_c section:
+
+
+# --- MakeMaker xs_o section:
+
+
+# --- MakeMaker top_targets section:
+all :: pure_all manifypods
+ $(NOECHO) $(NOOP)
+
+
+pure_all :: config pm_to_blib subdirs linkext
+ $(NOECHO) $(NOOP)
+
+subdirs :: $(MYEXTLIB)
+ $(NOECHO) $(NOOP)
+
+config :: $(FIRST_MAKEFILE) blibdirs
+ $(NOECHO) $(NOOP)
+
+help :
+ perldoc ExtUtils::MakeMaker
+
+
+# --- MakeMaker blibdirs section:
+blibdirs : $(INST_LIBDIR)$(DFSEP).exists $(INST_ARCHLIB)$(DFSEP).exists $(INST_AUTODIR)$(DFSEP).exists $(INST_ARCHAUTODIR)$(DFSEP).exists $(INST_BIN)$(DFSEP).exists $(INST_SCRIPT)$(DFSEP).exists $(INST_MAN1DIR)$(DFSEP).exists $(INST_MAN3DIR)$(DFSEP).exists
+ $(NOECHO) $(NOOP)
+
+# Backwards compat with 6.18 through 6.25
+blibdirs.ts : blibdirs
+ $(NOECHO) $(NOOP)
+
+$(INST_LIBDIR)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_LIBDIR)
+ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_LIBDIR)
+ $(NOECHO) $(TOUCH) $(INST_LIBDIR)$(DFSEP).exists
+
+$(INST_ARCHLIB)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_ARCHLIB)
+ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_ARCHLIB)
+ $(NOECHO) $(TOUCH) $(INST_ARCHLIB)$(DFSEP).exists
+
+$(INST_AUTODIR)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_AUTODIR)
+ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_AUTODIR)
+ $(NOECHO) $(TOUCH) $(INST_AUTODIR)$(DFSEP).exists
+
+$(INST_ARCHAUTODIR)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_ARCHAUTODIR)
+ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_ARCHAUTODIR)
+ $(NOECHO) $(TOUCH) $(INST_ARCHAUTODIR)$(DFSEP).exists
+
+$(INST_BIN)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_BIN)
+ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_BIN)
+ $(NOECHO) $(TOUCH) $(INST_BIN)$(DFSEP).exists
+
+$(INST_SCRIPT)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_SCRIPT)
+ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_SCRIPT)
+ $(NOECHO) $(TOUCH) $(INST_SCRIPT)$(DFSEP).exists
+
+$(INST_MAN1DIR)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_MAN1DIR)
+ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_MAN1DIR)
+ $(NOECHO) $(TOUCH) $(INST_MAN1DIR)$(DFSEP).exists
+
+$(INST_MAN3DIR)$(DFSEP).exists :: Makefile.PL
+ $(NOECHO) $(MKPATH) $(INST_MAN3DIR)
+ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_MAN3DIR)
+ $(NOECHO) $(TOUCH) $(INST_MAN3DIR)$(DFSEP).exists
+
+
+
+# --- MakeMaker linkext section:
+
+linkext :: $(LINKTYPE)
+ $(NOECHO) $(NOOP)
+
+
+# --- MakeMaker dlsyms section:
+
+
+# --- MakeMaker dynamic section:
+
+dynamic :: $(FIRST_MAKEFILE) $(INST_DYNAMIC) $(INST_BOOT)
+ $(NOECHO) $(NOOP)
+
+
+# --- MakeMaker dynamic_bs section:
+
+BOOTSTRAP =
+
+
+# --- MakeMaker dynamic_lib section:
+
+
+# --- MakeMaker static section:
+
+## $(INST_PM) has been moved to the all: target.
+## It remains here for awhile to allow for old usage: "make static"
+static :: $(FIRST_MAKEFILE) $(INST_STATIC)
+ $(NOECHO) $(NOOP)
+
+
+# --- MakeMaker static_lib section:
+
+
+# --- MakeMaker manifypods section:
+
+POD2MAN_EXE = $(PERLRUN) "-MExtUtils::Command::MM" -e pod2man "--"
+POD2MAN = $(POD2MAN_EXE)
+
+
+manifypods : pure_all \
+ Bio/Expression/MicroarrayIO/dchipxls.pm \
+ Bio/Expression/Microarray/Affymetrix/dChipXLS.pm \
+ Bio/Expression/Microarray/Affymetrix/Feature.pm \
+ Bio/Expression/MicroarrayIO/mas50txt.pm \
+ Bio/Expression/Microarray/Affymetrix/dChipArray.pm \
+ Bio/Expression/MicroarrayIO/affymetrix.pm \
+ Bio/Expression/Microarray/Affymetrix/Array.pm \
+ Bio/Expression/Microarray/Affymetrix/CelArray.pm \
+ Bio/Expression/Microarray/Affymetrix/ArrayDesign.pm \
+ Bio/Expression/Microarray/FeatureI.pm \
+ Bio/Expression/MicroarrayIO.pm \
+ Bio/Expression/Microarray/Affymetrix/Mas50TxtArray.pm \
+ Bio/Expression/Microarray/Affymetrix/Data.pm
+ $(NOECHO) $(POD2MAN) --section=3 --perm_rw=$(PERM_RW) \
+ Bio/Expression/MicroarrayIO/dchipxls.pm $(INST_MAN3DIR)/Bio::Expression::MicroarrayIO::dchipxls.$(MAN3EXT) \
+ Bio/Expression/Microarray/Affymetrix/dChipXLS.pm $(INST_MAN3DIR)/Bio::Expression::Microarray::Affymetrix::dChipXLS.$(MAN3EXT) \
+ Bio/Expression/Microarray/Affymetrix/Feature.pm $(INST_MAN3DIR)/Bio::Expression::Microarray::Affymetrix::Feature.$(MAN3EXT) \
+ Bio/Expression/MicroarrayIO/mas50txt.pm $(INST_MAN3DIR)/Bio::Expression::MicroarrayIO::mas50txt.$(MAN3EXT) \
+ Bio/Expression/Microarray/Affymetrix/dChipArray.pm $(INST_MAN3DIR)/Bio::Expression::Microarray::Affymetrix::dChipArray.$(MAN3EXT) \
+ Bio/Expression/MicroarrayIO/affymetrix.pm $(INST_MAN3DIR)/Bio::Expression::MicroarrayIO::affymetrix.$(MAN3EXT) \
+ Bio/Expression/Microarray/Affymetrix/Array.pm $(INST_MAN3DIR)/Bio::Expression::Microarray::Affymetrix::Array.$(MAN3EXT) \
+ Bio/Expression/Microarray/Affymetrix/CelArray.pm $(INST_MAN3DIR)/Bio::Expression::Microarray::Affymetrix::CelArray.$(MAN3EXT) \
+ Bio/Expression/Microarray/Affymetrix/ArrayDesign.pm $(INST_MAN3DIR)/Bio::Expression::Microarray::Affymetrix::ArrayDesign.$(MAN3EXT) \
+ Bio/Expression/Microarray/FeatureI.pm $(INST_MAN3DIR)/Bio::Expression::Microarray::FeatureI.$(MAN3EXT) \
+ Bio/Expression/MicroarrayIO.pm $(INST_MAN3DIR)/Bio::Expression::MicroarrayIO.$(MAN3EXT) \
+ Bio/Expression/Microarray/Affymetrix/Mas50TxtArray.pm $(INST_MAN3DIR)/Bio::Expression::Microarray::Affymetrix::Mas50TxtArray.$(MAN3EXT) \
+ Bio/Expression/Microarray/Affymetrix/Data.pm $(INST_MAN3DIR)/Bio::Expression::Microarray::Affymetrix::Data.$(MAN3EXT)
+
+
+
+
+# --- MakeMaker processPL section:
+
+
+# --- MakeMaker installbin section:
+
+
+# --- MakeMaker subdirs section:
+
+# none
+
+# --- MakeMaker clean_subdirs section:
+clean_subdirs :
+ $(NOECHO) $(NOOP)
+
+
+# --- MakeMaker clean section:
+
+# Delete temporary files but do not touch installed files. We don't delete
+# the Makefile here so a later make realclean still has a makefile to use.
+
+clean :: clean_subdirs
+ - $(RM_F) \
+ *$(LIB_EXT) core \
+ core.[0-9] $(INST_ARCHAUTODIR)/extralibs.all \
+ core.[0-9][0-9] $(BASEEXT).bso \
+ pm_to_blib.ts core.[0-9][0-9][0-9][0-9] \
+ $(BASEEXT).x $(BOOTSTRAP) \
+ perl$(EXE_EXT) tmon.out \
+ *$(OBJ_EXT) pm_to_blib \
+ $(INST_ARCHAUTODIR)/extralibs.ld blibdirs.ts \
+ core.[0-9][0-9][0-9][0-9][0-9] *perl.core \
+ core.*perl.*.? $(MAKE_APERL_FILE) \
+ perl $(BASEEXT).def \
+ core.[0-9][0-9][0-9] mon.out \
+ lib$(BASEEXT).def perlmain.c \
+ perl.exe so_locations \
+ $(BASEEXT).exp
+ - $(RM_RF) \
+ blib
+ - $(MV) $(FIRST_MAKEFILE) $(MAKEFILE_OLD) $(DEV_NULL)
+
+
+# --- MakeMaker realclean_subdirs section:
+realclean_subdirs :
+ $(NOECHO) $(NOOP)
+
+
+# --- MakeMaker realclean section:
+# Delete temporary files (via clean) and also delete dist files
+realclean purge :: clean realclean_subdirs
+ - $(RM_F) \
+ $(MAKEFILE_OLD) $(FIRST_MAKEFILE)
+ - $(RM_RF) \
+ $(DISTVNAME)
+
+
+# --- MakeMaker metafile section:
+metafile : create_distdir
+ $(NOECHO) $(ECHO) Generating META.yml
+ $(NOECHO) $(ECHO) '--- #YAML:1.0' > META_new.yml
+ $(NOECHO) $(ECHO) 'name: bioperl-microarray' >> META_new.yml
+ $(NOECHO) $(ECHO) 'version: 0.1' >> META_new.yml
+ $(NOECHO) $(ECHO) 'abstract: Bioperl Toolkit - Addendum for microarray data' >> META_new.yml
+ $(NOECHO) $(ECHO) 'author:' >> META_new.yml
+ $(NOECHO) $(ECHO) ' - Bioperl Team (bioperl-l@bioperl.org)' >> META_new.yml
+ $(NOECHO) $(ECHO) 'license: unknown' >> META_new.yml
+ $(NOECHO) $(ECHO) 'distribution_type: module' >> META_new.yml
+ $(NOECHO) $(ECHO) 'configure_requires:' >> META_new.yml
+ $(NOECHO) $(ECHO) ' ExtUtils::MakeMaker: 0' >> META_new.yml
+ $(NOECHO) $(ECHO) 'build_requires:' >> META_new.yml
+ $(NOECHO) $(ECHO) ' ExtUtils::MakeMaker: 0' >> META_new.yml
+ $(NOECHO) $(ECHO) 'requires: {}' >> META_new.yml
+ $(NOECHO) $(ECHO) 'no_index:' >> META_new.yml
+ $(NOECHO) $(ECHO) ' directory:' >> META_new.yml
+ $(NOECHO) $(ECHO) ' - t' >> META_new.yml
+ $(NOECHO) $(ECHO) ' - inc' >> META_new.yml
+ $(NOECHO) $(ECHO) 'generated_by: ExtUtils::MakeMaker version 6.56' >> META_new.yml
+ $(NOECHO) $(ECHO) 'meta-spec:' >> META_new.yml
+ $(NOECHO) $(ECHO) ' url: http://module-build.sourceforge.net/META-spec-v1.4.html' >> META_new.yml
+ $(NOECHO) $(ECHO) ' version: 1.4' >> META_new.yml
+ -$(NOECHO) $(MV) META_new.yml $(DISTVNAME)/META.yml
+
+
+# --- MakeMaker signature section:
+signature :
+ cpansign -s
+
+
+# --- MakeMaker dist_basics section:
+distclean :: realclean distcheck
+ $(NOECHO) $(NOOP)
+
+distcheck :
+ $(PERLRUN) "-MExtUtils::Manifest=fullcheck" -e fullcheck
+
+skipcheck :
+ $(PERLRUN) "-MExtUtils::Manifest=skipcheck" -e skipcheck
+
+manifest :
+ $(PERLRUN) "-MExtUtils::Manifest=mkmanifest" -e mkmanifest
+
+veryclean : realclean
+ $(RM_F) *~ */*~ *.orig */*.orig *.bak */*.bak *.old */*.old
+
+
+
+# --- MakeMaker dist_core section:
+
+dist : $(DIST_DEFAULT) $(FIRST_MAKEFILE)
+ $(NOECHO) $(ABSPERLRUN) -l -e 'print '\''Warning: Makefile possibly out of date with $(VERSION_FROM)'\''' \
+ -e ' if -e '\''$(VERSION_FROM)'\'' and -M '\''$(VERSION_FROM)'\'' < -M '\''$(FIRST_MAKEFILE)'\'';' --
+
+tardist : $(DISTVNAME).tar$(SUFFIX)
+ $(NOECHO) $(NOOP)
+
+uutardist : $(DISTVNAME).tar$(SUFFIX)
+ uuencode $(DISTVNAME).tar$(SUFFIX) $(DISTVNAME).tar$(SUFFIX) > $(DISTVNAME).tar$(SUFFIX)_uu
+
+$(DISTVNAME).tar$(SUFFIX) : distdir
+ $(PREOP)
+ $(TO_UNIX)
+ $(TAR) $(TARFLAGS) $(DISTVNAME).tar $(DISTVNAME)
+ $(RM_RF) $(DISTVNAME)
+ $(COMPRESS) $(DISTVNAME).tar
+ $(POSTOP)
+
+zipdist : $(DISTVNAME).zip
+ $(NOECHO) $(NOOP)
+
+$(DISTVNAME).zip : distdir
+ $(PREOP)
+ $(ZIP) $(ZIPFLAGS) $(DISTVNAME).zip $(DISTVNAME)
+ $(RM_RF) $(DISTVNAME)
+ $(POSTOP)
+
+shdist : distdir
+ $(PREOP)
+ $(SHAR) $(DISTVNAME) > $(DISTVNAME).shar
+ $(RM_RF) $(DISTVNAME)
+ $(POSTOP)
+
+
+# --- MakeMaker distdir section:
+create_distdir :
+ $(RM_RF) $(DISTVNAME)
+ $(PERLRUN) "-MExtUtils::Manifest=manicopy,maniread" \
+ -e "manicopy(maniread(),'$(DISTVNAME)', '$(DIST_CP)');"
+
+distdir : create_distdir distmeta
+ $(NOECHO) $(NOOP)
+
+
+
+# --- MakeMaker dist_test section:
+disttest : distdir
+ cd $(DISTVNAME) && $(ABSPERLRUN) Makefile.PL
+ cd $(DISTVNAME) && $(MAKE) $(PASTHRU)
+ cd $(DISTVNAME) && $(MAKE) test $(PASTHRU)
+
+
+
+# --- MakeMaker dist_ci section:
+
+ci :
+ $(PERLRUN) "-MExtUtils::Manifest=maniread" \
+ -e "@all = keys %{ maniread() };" \
+ -e "print(qq{Executing $(CI) @all\n}); system(qq{$(CI) @all});" \
+ -e "print(qq{Executing $(RCS_LABEL) ...\n}); system(qq{$(RCS_LABEL) @all});"
+
+
+# --- MakeMaker distmeta section:
+distmeta : create_distdir metafile
+ $(NOECHO) cd $(DISTVNAME) && $(ABSPERLRUN) -MExtUtils::Manifest=maniadd -e 'eval { maniadd({q{META.yml} => q{Module meta-data (added by MakeMaker)}}) } ' \
+ -e ' or print "Could not add META.yml to MANIFEST: $${'\''@'\''}\n"' --
+
+
+
+# --- MakeMaker distsignature section:
+distsignature : create_distdir
+ $(NOECHO) cd $(DISTVNAME) && $(ABSPERLRUN) -MExtUtils::Manifest=maniadd -e 'eval { maniadd({q{SIGNATURE} => q{Public-key signature (added by MakeMaker)}}) } ' \
+ -e ' or print "Could not add SIGNATURE to MANIFEST: $${'\''@'\''}\n"' --
+ $(NOECHO) cd $(DISTVNAME) && $(TOUCH) SIGNATURE
+ cd $(DISTVNAME) && cpansign -s
+
+
+
+# --- MakeMaker install section:
+
+install :: pure_install doc_install
+ $(NOECHO) $(NOOP)
+
+install_perl :: pure_perl_install doc_perl_install
+ $(NOECHO) $(NOOP)
+
+install_site :: pure_site_install doc_site_install
+ $(NOECHO) $(NOOP)
+
+install_vendor :: pure_vendor_install doc_vendor_install
+ $(NOECHO) $(NOOP)
+
+pure_install :: pure_$(INSTALLDIRS)_install
+ $(NOECHO) $(NOOP)
+
+doc_install :: doc_$(INSTALLDIRS)_install
+ $(NOECHO) $(NOOP)
+
+pure__install : pure_site_install
+ $(NOECHO) $(ECHO) INSTALLDIRS not defined, defaulting to INSTALLDIRS=site
+
+doc__install : doc_site_install
+ $(NOECHO) $(ECHO) INSTALLDIRS not defined, defaulting to INSTALLDIRS=site
+
+pure_perl_install :: all
+ $(NOECHO) $(MOD_INSTALL) \
+ read $(PERL_ARCHLIB)/auto/$(FULLEXT)/.packlist \
+ write $(DESTINSTALLARCHLIB)/auto/$(FULLEXT)/.packlist \
+ $(INST_LIB) $(DESTINSTALLPRIVLIB) \
+ $(INST_ARCHLIB) $(DESTINSTALLARCHLIB) \
+ $(INST_BIN) $(DESTINSTALLBIN) \
+ $(INST_SCRIPT) $(DESTINSTALLSCRIPT) \
+ $(INST_MAN1DIR) $(DESTINSTALLMAN1DIR) \
+ $(INST_MAN3DIR) $(DESTINSTALLMAN3DIR)
+ $(NOECHO) $(WARN_IF_OLD_PACKLIST) \
+ $(SITEARCHEXP)/auto/$(FULLEXT)
+
+
+pure_site_install :: all
+ $(NOECHO) $(MOD_INSTALL) \
+ read $(SITEARCHEXP)/auto/$(FULLEXT)/.packlist \
+ write $(DESTINSTALLSITEARCH)/auto/$(FULLEXT)/.packlist \
+ $(INST_LIB) $(DESTINSTALLSITELIB) \
+ $(INST_ARCHLIB) $(DESTINSTALLSITEARCH) \
+ $(INST_BIN) $(DESTINSTALLSITEBIN) \
+ $(INST_SCRIPT) $(DESTINSTALLSITESCRIPT) \
+ $(INST_MAN1DIR) $(DESTINSTALLSITEMAN1DIR) \
+ $(INST_MAN3DIR) $(DESTINSTALLSITEMAN3DIR)
+ $(NOECHO) $(WARN_IF_OLD_PACKLIST) \
+ $(PERL_ARCHLIB)/auto/$(FULLEXT)
+
+pure_vendor_install :: all
+ $(NOECHO) $(MOD_INSTALL) \
+ read $(VENDORARCHEXP)/auto/$(FULLEXT)/.packlist \
+ write $(DESTINSTALLVENDORARCH)/auto/$(FULLEXT)/.packlist \
+ $(INST_LIB) $(DESTINSTALLVENDORLIB) \
+ $(INST_ARCHLIB) $(DESTINSTALLVENDORARCH) \
+ $(INST_BIN) $(DESTINSTALLVENDORBIN) \
+ $(INST_SCRIPT) $(DESTINSTALLVENDORSCRIPT) \
+ $(INST_MAN1DIR) $(DESTINSTALLVENDORMAN1DIR) \
+ $(INST_MAN3DIR) $(DESTINSTALLVENDORMAN3DIR)
+
+doc_perl_install :: all
+ $(NOECHO) $(ECHO) Appending installation info to $(DESTINSTALLARCHLIB)/perllocal.pod
+ -$(NOECHO) $(MKPATH) $(DESTINSTALLARCHLIB)
+ -$(NOECHO) $(DOC_INSTALL) \
+ "Module" "$(NAME)" \
+ "installed into" "$(INSTALLPRIVLIB)" \
+ LINKTYPE "$(LINKTYPE)" \
+ VERSION "$(VERSION)" \
+ EXE_FILES "$(EXE_FILES)" \
+ >> $(DESTINSTALLARCHLIB)/perllocal.pod
+
+doc_site_install :: all
+ $(NOECHO) $(ECHO) Appending installation info to $(DESTINSTALLARCHLIB)/perllocal.pod
+ -$(NOECHO) $(MKPATH) $(DESTINSTALLARCHLIB)
+ -$(NOECHO) $(DOC_INSTALL) \
+ "Module" "$(NAME)" \
+ "installed into" "$(INSTALLSITELIB)" \
+ LINKTYPE "$(LINKTYPE)" \
+ VERSION "$(VERSION)" \
+ EXE_FILES "$(EXE_FILES)" \
+ >> $(DESTINSTALLARCHLIB)/perllocal.pod
+
+doc_vendor_install :: all
+ $(NOECHO) $(ECHO) Appending installation info to $(DESTINSTALLARCHLIB)/perllocal.pod
+ -$(NOECHO) $(MKPATH) $(DESTINSTALLARCHLIB)
+ -$(NOECHO) $(DOC_INSTALL) \
+ "Module" "$(NAME)" \
+ "installed into" "$(INSTALLVENDORLIB)" \
+ LINKTYPE "$(LINKTYPE)" \
+ VERSION "$(VERSION)" \
+ EXE_FILES "$(EXE_FILES)" \
+ >> $(DESTINSTALLARCHLIB)/perllocal.pod
+
+
+uninstall :: uninstall_from_$(INSTALLDIRS)dirs
+ $(NOECHO) $(NOOP)
+
+uninstall_from_perldirs ::
+ $(NOECHO) $(UNINSTALL) $(PERL_ARCHLIB)/auto/$(FULLEXT)/.packlist
+
+uninstall_from_sitedirs ::
+ $(NOECHO) $(UNINSTALL) $(SITEARCHEXP)/auto/$(FULLEXT)/.packlist
+
+uninstall_from_vendordirs ::
+ $(NOECHO) $(UNINSTALL) $(VENDORARCHEXP)/auto/$(FULLEXT)/.packlist
+
+
+# --- MakeMaker force section:
+# Phony target to force checking subdirectories.
+FORCE :
+ $(NOECHO) $(NOOP)
+
+
+# --- MakeMaker perldepend section:
+
+
+# --- MakeMaker makefile section:
+# We take a very conservative approach here, but it's worth it.
+# We move Makefile to Makefile.old here to avoid gnu make looping.
+$(FIRST_MAKEFILE) : Makefile.PL $(CONFIGDEP)
+ $(NOECHO) $(ECHO) "Makefile out-of-date with respect to $?"
+ $(NOECHO) $(ECHO) "Cleaning current config before rebuilding Makefile..."
+ -$(NOECHO) $(RM_F) $(MAKEFILE_OLD)
+ -$(NOECHO) $(MV) $(FIRST_MAKEFILE) $(MAKEFILE_OLD)
+ - $(MAKE) $(USEMAKEFILE) $(MAKEFILE_OLD) clean $(DEV_NULL)
+ $(PERLRUN) Makefile.PL
+ $(NOECHO) $(ECHO) "==> Your Makefile has been rebuilt. <=="
+ $(NOECHO) $(ECHO) "==> Please rerun the $(MAKE) command. <=="
+ $(FALSE)
+
+
+
+# --- MakeMaker staticmake section:
+
+# --- MakeMaker makeaperl section ---
+MAP_TARGET = perl
+FULLPERL = /opt/perl512/bin/perl
+
+$(MAP_TARGET) :: static $(MAKE_APERL_FILE)
+ $(MAKE) $(USEMAKEFILE) $(MAKE_APERL_FILE) $@
+
+$(MAKE_APERL_FILE) : $(FIRST_MAKEFILE) pm_to_blib
+ $(NOECHO) $(ECHO) Writing \"$(MAKE_APERL_FILE)\" for this $(MAP_TARGET)
+ $(NOECHO) $(PERLRUNINST) \
+ Makefile.PL DIR= \
+ MAKEFILE=$(MAKE_APERL_FILE) LINKTYPE=static \
+ MAKEAPERL=1 NORECURS=1 CCCDLFLAGS=
+
+
+# --- MakeMaker test section:
+
+TEST_VERBOSE=0
+TEST_TYPE=test_$(LINKTYPE)
+TEST_FILE = test.pl
+TEST_FILES = t/*.t
+TESTDB_SW = -d
+
+testdb :: testdb_$(LINKTYPE)
+
+test :: $(TEST_TYPE) subdirs-test
+
+subdirs-test ::
+ $(NOECHO) $(NOOP)
+
+
+test_dynamic :: pure_all
+ PERL_DL_NONLAZY=1 $(FULLPERLRUN) "-MExtUtils::Command::MM" "-e" "test_harness($(TEST_VERBOSE), '$(INST_LIB)', '$(INST_ARCHLIB)')" $(TEST_FILES)
+
+testdb_dynamic :: pure_all
+ PERL_DL_NONLAZY=1 $(FULLPERLRUN) $(TESTDB_SW) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE)
+
+test_ : test_dynamic
+
+test_static :: test_dynamic
+testdb_static :: testdb_dynamic
+