Merge branch 'JABAWS_Release_2_5' into develop

[jabaws.git] / binaries / src / jpred / lib / SOV.pm

diff --git a/binaries/src/jpred/lib/SOV.pm b/binaries/src/jpred/lib/SOV.pm
new file mode 100644 (file)
index 0000000..40e0383
--- /dev/null
+++ b/binaries/src/jpred/lib/SOV.pm
@@ -0,0 +1,111 @@
+package SOV;
+
+=head1 NAME
+
+SOV - Parses output for CASP SOV program.
+
+=head1 DESCRIPTION
+
+Class for parsing SOV output.
+
+=head1 METHODS
+
+Inherits from Read and Root.
+
+=cut
+
+use base qw(Root Read);
+
+=head2 q3()
+
+Access q3 information. Returns SOV::Types object.
+
+=head2 sov(), sov_0(), sov_50()
+
+As for q3()
+
+=cut
+
+sub q3 {
+       if ($_[1]) { $_[0]->{q3} = $_[1] }
+       else { return defined $_[0]->{q3} ? $_[0]->{q3} : undef }
+}
+
+sub sov_0 {
+       if ($_[1]) { $_[0]->{sov_0} = $_[1] }
+       else { return defined $_[0]->{sov_0} ? $_[0]->{sov_0} : undef }
+}
+
+sub sov_50 {
+       if ($_[1]) { $_[0]->{sov_50} = $_[1] }
+       else { return defined $_[0]->{sov_50} ? $_[0]->{sov_50} : undef }
+}
+
+sub sov {
+       if ($_[1]) { $_[0]->{sov} = @_[1] }
+       else { return defined $_[0]->{sov} ? $_[0]->{sov} : undef }
+}
+
+sub read {
+       my ($self, $fh) = @_;
+
+       local $/ = "\n";
+       local $_;
+
+       # Get to the SOV and Q3 results
+       while (<$fh>) { last if /^\s-{22}/ }
+
+       while (<$fh>) {
+               chomp;
+               if (s/^\s*Q3\s*:\s*//) {
+                       $self->q3(to_struct(split / +/, $_))
+               }
+               elsif (s/^\s*SOV\s*:\s*//) {
+                       $self->sov(to_struct(split / +/, $_))
+               }
+               elsif (s/^\s*SOV.*0].*:\s*//) {
+                       $self->sov_0(to_struct(split / +/, $_))
+               }
+               elsif (s/^\s*SOV.*50%.*:\s*//) {
+                       $self->sov_50(to_struct(split / +/, $_))
+               }
+       }
+
+}
+
+sub to_struct ($$$$) {
+       map { $_ > 1 ? $_ /= 100 : $_ } @_;
+       my $new = SOV::Types->new(
+               all => +shift,
+               helix => +shift,
+               sheet => +shift,
+               coil => +shift
+       );
+}
+
+=head1 SOV::Types
+
+Object that stores prediction information
+
+=head1 METHODS
+
+=head2 all(), helix(), sheet(), coil()
+
+Accessors for accuracy of different types of secondary structure.
+
+=cut
+
+use Class::Struct SOV::Types => [
+       all => '$', 
+       helix => '$',
+       sheet => '$',
+       coil => '$'
+];
+
+=head1 AUTHOR
+
+Jonathan Barber <jon@compbio.dundee.ac.uk>
+
+=cut
+
+1;