Merge branch 'JABAWS_Release_2_5' into develop

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

diff --git a/binaries/src/jpred/lib/Profile/Generic.pm b/binaries/src/jpred/lib/Profile/Generic.pm
new file mode 100644 (file)
index 0000000..cb8cf7b
--- /dev/null
+++ b/binaries/src/jpred/lib/Profile/Generic.pm
@@ -0,0 +1,49 @@
+package Profile::Generic;
+
+use strict;
+use warnings;
+use base qw(Profile);
+
+=head1 NAME
+
+Profile::Generic
+
+=head1 DESCRIPTION
+
+Reads in a generic profile, where each position is represented by a line, and each piece of information is white space deliminated.
+
+=head1 INHERITS
+
+Profile.
+
+=head1 METHODS
+
+=head2 $obj->read($filehandle)
+
+Reads in the profile contained in the file.
+
+=cut
+
+sub read {
+       my ($self, $fh) = @_;
+       while (<$fh>) {
+               chomp;
+               $self->add_pos(split);
+       }
+}
+
+=head2 $obj->write($filehandle);
+
+Writes WS seperated profile, with each position on each line.
+
+=cut
+
+sub write {
+       my ($self, $fh) = @_;
+
+       while ((my @data = $self->get_pos) > 1) {
+               print $fh " ".join("  ", @data), "\n";
+       }
+}
+
+1;