Merge branch 'JABAWS_Release_2_5' into develop

[jabaws.git] / binaries / src / jpred / lib / Concise / File.pm

diff --git a/binaries/src/jpred/lib/Concise/File.pm b/binaries/src/jpred/lib/Concise/File.pm
new file mode 100644 (file)
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+++ b/binaries/src/jpred/lib/Concise/File.pm
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+package Concise::File;
+
+use strict;
+use warnings;
+use Carp;
+
+use base qw(Root Read Write Sequence::File);
+use Concise;
+
+# Pass a filehandle
+sub read {
+       my ($self, $fh) = @_;
+
+       while (<$fh>) {
+               chomp;
+
+               next if /^\s*$/;        # Skip blank lines
+               next if /^#/;           # skip comment lines
+#              s/#.*//g;                       # Clear comments
+               
+               my ($head, $field) = split /:/, $_, 2;
+
+               unless (defined $field and defined $head) {
+                       carp "Line $. doesn't match concise file format, skipping";
+                       next;
+               }
+
+               $field =~ s/,$//g;
+               my @fields = split /,/, $field;
+
+               my $new = Concise->new(id => $head);
+               $new->seq(@fields);
+               $self->add_entries($new);
+       }
+}
+
+sub write {
+       my ($self, $fh) = @_;
+
+       for ($self->get_entries) {
+               my $id = $_->id;
+               my @seq = $_->seq;
+
+               my $seq = join ',', @seq;
+               $seq =~ s/,$//;
+
+               print $fh "$id:$seq\n";
+       }
+}
+
+1;
+
+__END__
+
+=head1 NAME
+
+Concise::File - Module to read Concise file
+
+=head1 SYNOPSYS
+
+  # Read a concise file and print the id's in the file
+  $concise = Concise::File->new(read_file => "path_to_file");
+  for ($concise->get_entries) {
+    print $_->id, "\n";
+  }
+
+=head1 DESCRIPTION
+
+This module allows you to read concise files and then get all the information held in the file or to select those entries you want by their IDs.
+
+=head1 METHODS
+
+This module inherits from the Root, Read and Write modules. See these for default methods.
+
+=over
+
+=item $concise->add_entries(@Concise)
+
+Add a list of Concise objects to the Concise::File object.
+
+=item $concise->get_entries
+
+Returns a list of the entries held in the object. These are held as Concise objects.
+
+=item $concise->get_entry_by_id( qr/foo/ )
+
+Get entries dependant upon their IDs and a regex. The argument can either be a regex object or a string to be interpreted as a regex. A list of Concise objects is returned.
+
+=back
+
+=head1 AUTHOR
+
+Jonathan Barber (jon@compbio.dundee.ac.uk)