Merge branch 'JABAWS_Release_2_5' into develop

[jabaws.git] / binaries / src / jpred / lib / HMMER / Profile / Jnet.pm

diff --git a/binaries/src/jpred/lib/HMMER/Profile/Jnet.pm b/binaries/src/jpred/lib/HMMER/Profile/Jnet.pm
new file mode 100644 (file)
index 0000000..febc73d
--- /dev/null
+++ b/binaries/src/jpred/lib/HMMER/Profile/Jnet.pm
@@ -0,0 +1,80 @@
+package HMMER::Profile::Jnet;
+
+use strict;
+use warnings;
+use Carp;
+
+use base qw(HMMER::Profile Write);
+
+sub read {
+       my ($self, $fh) = @_;
+
+       local $/ = "\n";
+
+       while (my $line = <$fh>) {
+               chomp $line;
+               my @data = split / /, $line;
+               croak "HMMER::Profile::Jnet: Wrong number of data items in ".$self->path." at line $." if @data != 24;
+               $self->add_line(@data);
+       }
+}
+
+sub jnet {
+       my ($self) = @_;
+       my @data;
+       for ($self->get_line) {
+               # This provides the same output as for hmm2profile
+               push @data, [
+                       map {
+                               sprintf "%2.5f", 1 / (1 + (exp(-($_ / 100))));
+                       } @{$_}
+               ];
+       }
+       @data;
+}
+
+sub write {
+       my ($self, $fh) = @_;
+
+       #die "Sorry, I don't think you mean to use this function. If you do, remove this line";
+
+       for ($self->jnet) {
+               print $fh join(" ", @{$_}), "\n";
+       }
+}
+
+*seq = *jnet;
+
+1;
+
+__END__
+
+=head1 NAME
+
+HMMER::Profile::Jnet - Read in the data output from HMMER::Profile::jnet()
+
+=head1 DESCRIPTION
+
+Reads the output of the HMMER::Profile::jnet() function.
+
+=head1 METHODS
+
+=head2 my $prof = HMMER::Profile::Jnet->new;
+
+Create a new object.
+
+=head2 $prof->read_file($path_to_file);
+
+Read in the data.
+
+=head2 my @data = $prof->seq
+
+Returns an AoA of the numbers.
+
+=head1 SEE ALSO
+
+Packages Root, Read, Sequence and HMMER::Profile.
+
+=head1 AUTHOR
+
+Jonathan Barber <jon@compbio.dundee.ac.uk>