Merge branch 'JABAWS_Release_2_5' into develop

[jabaws.git] / binaries / src / jpred / lib / Profile / Scanps / Result.pm

diff --git a/binaries/src/jpred/lib/Profile/Scanps/Result.pm b/binaries/src/jpred/lib/Profile/Scanps/Result.pm
new file mode 100644 (file)
index 0000000..90be61d
--- /dev/null
+++ b/binaries/src/jpred/lib/Profile/Scanps/Result.pm
@@ -0,0 +1,54 @@
+package Profile::Scanps::Result;
+
+use strict;
+use warnings;
+use Carp;
+use base qw(Profile::Generic);
+use Scanps::Result;
+
+sub read {
+       my ($self, $fh) = @_;
+       my $scanps = Scanps::Result->new($fh);
+
+       # Get third, or last iteration, which ever is smaller
+       my $it = $scanps->iterations - 1;
+       $it > 2 and $it = 2; # iterations is zero based
+       my @positions = $scanps->profile($it);
+
+       for (@positions) {
+               my (undef, @data) = split /\s+/, $_;
+               $self->add_pos(@data[0..22]);
+       }
+}
+
+sub write {
+       my ($self, $fh) = @_;
+
+       while ((my @data = $self->get_pos) > 1) {
+               print $fh map({ sprintf "%2.5f ", 1 / (1 + exp(-$_/100)) } @data), "\n";
+               #print $fh join(" ", map  $_ / 100 } @data), "\n";
+               #print $fh join(" ", @data), "\n";
+       }
+}
+
+1;
+
+__END__
+
+=head1 NAME
+
+Profile::Scanps::Result - Reads a profile from a Scanps result file
+
+=head1 DESCRIPTION
+
+Reads the profile that can be provided at the end of a Scanps file.
+
+=head1 INHERITANCE
+
+Inherits from Profile and Generic modules.
+
+=head1 METHODS
+
+=head2 read()
+
+=cut