← Back to branch summary

~ubuntu-branches/ubuntu/raring/bioperl/raring

« back to all changes in this revision

Viewing changes to Bio/Matrix/PSM/Psm.pm

  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2008-03-18 14:44:57 UTC
  • mfrom: (4 hardy)
  • mto: This revision was merged to the branch mainline in revision 6.
  • Revision ID: james.westby@ubuntu.com-20080318144457-1jjoztrvqwf0gruk
http://bugs.debian.org/448890
* debian/control:
  - Removed MIA Matt Hope (dopey) from the Uploaders field.
    Thank you for your work, Matt. I hope you are doing well.
  - Downgraded some recommended package to the 'Suggests' priority,
    according to the following discussion on Upstream's mail list.
    http://bioperl.org/pipermail/bioperl-l/2008-March/027379.html
    (Closes: #448890)
* debian/copyright converted to machine-readable format.

Show diffs side-by-side

added added

removed removed

Lines of Context:
Bio/Matrix/PSM/Psm.pm
1
1
#---------------------------------------------------------
2
 
# $Id: Psm.pm,v 1.4 2003/10/25 15:00:57 heikki Exp $
 
2
# $Id: Psm.pm,v 1.14.4.1 2006/10/02 23:10:22 sendu Exp $
3
3
 
4
4
#ISA SiteMatrix, HAS InstanceSite
5
5
 
83
83
 to one of the Bioperl mailing lists.
84
84
Your participation is much appreciated.
85
85
 
86
 
  bioperl-l@bioperl.org                 - General discussion
87
 
  http://bio.perl.org/MailList.html             - About the mailing lists
 
86
  bioperl-l@bioperl.org                  - General discussion
 
87
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
88
88
 
89
89
=head2 Reporting Bugs
90
90
 
91
91
Report bugs to the Bioperl bug tracking system to help us keep track
92
 
 the bugs and their resolution.
93
 
 Bug reports can be submitted via email or the web:
 
92
the bugs and their resolution.  Bug reports can be submitted via the
 
93
web:
94
94
 
95
 
  bioperl-bugs@bio.perl.org
96
 
  http://bugzilla.bioperl.org/
 
95
  http://bugzilla.open-bio.org/
97
96
 
98
97
=head1 AUTHOR - Stefan Kirov
99
98
 
115
114
 
116
115
# Let the code begin...
117
116
package Bio::Matrix::PSM::Psm;
118
 
use Bio::Root::Root;
119
 
use Bio::Root::IO;
120
 
use Bio::Matrix::PSM::SiteMatrix;
121
117
use Bio::Matrix::PSM::InstanceSite;
122
 
use Bio::Matrix::PSM::PsmI;
123
 
use vars qw(@ISA);
124
118
use strict;
125
119
 
126
 
@ISA=qw( Bio::Matrix::PSM::SiteMatrix Bio::Root::Root Bio::Matrix::PSM::PsmI);
 
120
use base qw(Bio::Matrix::PSM::SiteMatrix Bio::Matrix::PSM::PsmI Bio::Annotation::Collection);
127
121
 
128
122
@Bio::Matrix::PSM::Psm::HEADER = qw(e_val sites IC width);
129
123
 
149
143
    my ($caller,@args) = @_;
150
144
    my $class = ref($caller) || $caller;
151
145
    my $self = $class->SUPER::new(@args);
 
146
    $self->{'_annotation'} = {};  #Init from Annotation::Collection
 
147
    $self->_typemap(Bio::Annotation::TypeManager->new()); #same
152
148
    ($self->{instances})=$self->_rearrange(['INSTANCES'], @args);
153
149
    return $self;
154
150
}
196
192
 
197
193
sub header {
198
194
    my $self = shift;
199
 
    return undef if ($self->{end});
 
195
    return  if ($self->{end});
200
196
    my %header;
201
197
    if (@_) {my $key=shift; return $self->{$key}; }
202
198
    foreach my $key (@Bio::Matrix::PSM::Psm::HEADER) {
225
221
                                                -pC=>$self->{probC},
226
222
                                                -pG=>$self->{probG},
227
223
                                                -pT=>$self->{probT},
 
224
                                                -lA=>$self->{logA},
 
225
                                                -lC=>$self->{logC},
 
226
                                                -lG=>$self->{logG},
 
227
                                                -lT=>$self->{logT},
228
228
                                                -IC=>$self->{IC},
229
229
                                                -e_val=>$self->{e_val},
230
230
                                                -id=>$self->{id});