Merge branch 'JABAWS_Release_2_5' into develop

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

diff --git a/binaries/src/jpred/lib/Profile/Jnet.pm b/binaries/src/jpred/lib/Profile/Jnet.pm
new file mode 100644 (file)
index 0000000..0feb34d
--- /dev/null
+++ b/binaries/src/jpred/lib/Profile/Jnet.pm
@@ -0,0 +1,65 @@
+package Profile::Jnet;
+
+use strict;
+use warnings;
+use Carp;
+use UNIVERSAL qw(isa);
+
+use base qw(Profile);
+use lib '..';
+use Utils qw(profile);
+
+sub read {
+       my ($self, $fh) = @_;
+
+       local $/ = "\n";
+
+       while (<$fh>) {
+               chomp;
+               $self->add_pos(split);
+       }
+}
+
+=head2 $prof->jpred_profile(@Sequence) 
+
+Creates a PSIBLAST like profile for Jpred.
+
+=cut
+
+sub jpred_profile {
+       my ($self, @seqs) = @_;
+       croak "Not passed Sequence objects" if grep { not isa $_, 'Sequence' } @seqs;
+       $self->_check_seq_length(@seqs) or croak "Not passed sequences of equal length\n";
+
+       my @profile = profile( map { join "", $_->seqs } @seqs );
+
+       for (@profile) {
+               $self->add_pos(@{$_});
+       }
+}
+
+=for private
+
+=head2 _check_seq_length(@Sequence);
+
+Checks that we've been passed PSISEQ objects and that they are the same length. Returns undef if their not and warns, otherwise returns the length of the sequence.
+
+=cut
+
+sub _check_seq_length {
+       undef = shift @_;
+
+       my %lengths;
+       for (@_) {
+               $lengths{ $_->seq } = 1;
+       }
+
+       if (keys %lengths != 1) {
+               warn "The sequences are of different lengths";
+               return undef;
+       }
+
+       return (keys %lengths)[0];
+}
+
+1;