Merge branch 'JABAWS_Release_2_5' into develop

[jabaws.git] / binaries / src / jpred / lib / PSIBLAST / PSSM.pm

diff --git a/binaries/src/jpred/lib/PSIBLAST/PSSM.pm b/binaries/src/jpred/lib/PSIBLAST/PSSM.pm
new file mode 100644 (file)
index 0000000..6093d20
--- /dev/null
+++ b/binaries/src/jpred/lib/PSIBLAST/PSSM.pm
@@ -0,0 +1,149 @@
+package PSIBLAST::PSSM;
+
+use strict;
+use warnings;
+use Carp;
+
+use base qw(Root Read Write);
+
+sub read {
+       my ($self, $fh) = @_;
+
+       local $/ = "\n";
+
+       my $xsum = 0;
+       while (my $line = <$fh>) {
+               if ($line =~ /^\s{11}A  R  N  D  C  Q  E/) {
+                       while ($line = <$fh>) {
+                               chomp;
+                               last if $line =~ /^\s*$/;
+
+                               my @pssm = split /\s+/, $line;
+
+                               my @data;
+                               for (@pssm[3..22]) {
+                                       push @data, sprintf "%2.8f", 1 / (1 + (exp(- $_)));
+                                       $xsum += $_;
+                               }
+
+                               $self->add_pos(@data);
+                       }
+               }
+       }
+
+}
+
+sub add_pos {
+       my ($self, @data) = @_;
+
+       @data == 20 or croak "add_pos passed wrong length array";
+
+       push @{ $self->{__PACKAGE__."pos"} }, \@data;
+}
+
+{
+       my $i = 0;
+
+       sub get_pos {
+               my ($self) = @_;
+
+               if (defined (my $foo = $self->get_num_pos($i++))) {
+                       return $foo
+               }
+               else {
+                       $i = 0;
+                       return undef;
+               }
+       }
+}
+
+sub seq {
+       my ($self, $data) = @_;
+
+       if ($data) {
+               confess "Not passed ARRAY" unless ref $data eq 'ARRAY';
+               $self->add_pos(@{ $data });
+       }
+       else {
+               my $size = $self->get_pos_size - 1;
+               $size or return ();
+               return map { $self->get_num_pos($_) } 0..$size;
+       }
+}
+
+sub get_num_pos {
+       my ($self, $pos) = @_;
+       confess "No positions passed to get_num_pos" unless defined $pos;
+       return undef unless exists $self->{__PACKAGE__."pos"};
+       return ${ $self->{__PACKAGE__."pos"} }[$pos];
+}
+
+sub get_pos_size {
+       my ($self) = @_;
+       exists $self->{__PACKAGE__."pos"} ?
+               return scalar @{ $self->{__PACKAGE__."pos"} } :
+               0;
+}
+
+sub write {
+       my ($self, $fh) = @_;
+       while (my $pos = $self->get_pos) {
+               print $fh join(" ", @{$pos}), "\n"
+       }
+}
+
+1;
+
+__END__
+
+=head1 NAME
+
+PSIBLAST::PSSM - Read PSIBLAST PSSM files
+
+=head1 EXAMPLE
+
+ my $pssm = PSIBLAST::PSSM->new;
+ $pssm->read_file("data.pssm");
+
+ for ($pssm->seq) {
+       print join(" ", @{$_}), "\n";
+ }
+
+=head1 DESCRIPTION
+
+Class for reading PSIBLAST PSSM files, subclasses the Root, Read and Write classes.
+
+=head1 METHODS
+
+=head2 my $pssm = PSIBLAST::PSSM->new()
+
+Create the object. See Root module for details.
+
+=head2 $pssm->read_file("path_to_file");
+
+Read in a PSIBLAST PSSM file. See Read module for other methods.
+
+=head2 $pssm->add_pos(@data);
+
+Adds data from PSIBLAST PSSM.
+
+=head2 $pssm->get_pos;
+
+Itterator for returning the data for each position loaded in the object.
+
+=head2 $pssm->write;
+
+Prints the PSSM file for use by Jnet.
+
+=head2 $pssm->seq([ @data ] );
+  $data = $pssm->seq;
+
+Gah! Deprecated.
+
+=head1 SEE ALSO
+
+Root, Read and Write modules.
+
+=head1 AUTHOR
+
+Jonathan Barber <jon@compbio.dundee.ac.uk>