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# $Id: interpro.pm,v 1.9.4.2 2006/10/16 17:08:16 sendu Exp $
#
# BioPerl module for interpro
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
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=head1 NAME
Bio::SeqIO::interpro - InterProScan XML input/output stream 
=head1 SYNOPSIS
  # do not call this module directly, use Bio::SeqIO
  use strict;
  use Bio::SeqIO;
  my $io = Bio::SeqIO->new(-format => "interpro",
                           -file   => $interpro_file);
  while (my $seq = $io->next_seq) {
    # use the Sequence object
  }
=head1 DESCRIPTION
L<Bio::SeqIO::interpro> will parse Interpro scan XML (version 1.2) and
create L<Bio::SeqFeature::Generic> objects based on the contents of the
XML document.
L<Bio::SeqIO::interpro> will also attach the annotation given in the XML
file to the L<Bio::SeqFeature::Generic> objects that it creates.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
  http://bugzilla.open-bio.org/
=head1 AUTHOR - Jared Fox
Email jaredfox@ucla.edu
=head1 CONTRIBUTORS
Allen Day allenday@ucla.edu
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::SeqIO::interpro;
use strict;
use Bio::SeqFeature::Generic;
use XML::DOM;
use Bio::Seq::SeqFactory;
use Bio::Annotation::Collection;
use Bio::Annotation::DBLink;
use base qw(Bio::SeqIO);
my $idcounter = {};  # Used to generate unique id values
my $nvtoken = ": ";  # The token used if a name/value pair has to be stuffed
                     # into a single line
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=head2 next_seq
 Title   : next_seq
 Usage   : my $seqobj = $stream->next_seq
 Function: Retrieves the next sequence from a SeqIO::interpro stream.
 Returns : A Bio::Seq::RichSeq object
 Args    : 
=cut
sub next_seq {
        my $self = shift;
        my ($desc);
        my $bioSeq = $self->_sequence_factory->create(-verbose =>$self->verbose());
        my $zinc = "(\"zincins\")";
        my $wing = "\"Winged helix\"";
        my $finger = "\"zinc finger\"";
        my $xml_fragment = undef;
        while(my $line = $self->_readline()){
                my $where = index($line, $zinc);
                my $wherefinger = index($line, $finger);
                my $finishedline = $line;
                my $wingwhere = index($line, $wing);
                # the interpro XML is not fully formed, so we need to convert the 
                # extra double quotes and ampersands into appropriate XML chracter codes
                if($where > 0){
                        my @linearray = split /$zinc/, $line;
                        $finishedline = join "&quot;zincins&quot;", $linearray[0], $linearray[2];
                }
                if(index($line, "&") > 0){
                        my @linearray = split /&/, $line;
                        $finishedline = join "&amp;", $linearray[0], $linearray[1];
                }
                if($wingwhere > 0){
                        my @linearray = split /$wing/, $line;
                        $finishedline = join "&quot;Winged helix&quot;", $linearray[0], $linearray[1];
                }
                $xml_fragment .= $finishedline;
                last if $finishedline =~ m!</protein>!;
        }
        return unless $xml_fragment =~ /<protein/;
        $self->_parse_xml($xml_fragment);
        my $dom = $self->_dom;
        my ($protein_node) = $dom->findnodes('/protein');
        my @interproNodes = $protein_node->findnodes('/protein/interpro');
        my @DBNodes = $protein_node->findnodes('/protein/interpro/match');
        for(my $interpn=0; $interpn<scalar(@interproNodes); $interpn++){
                my $ipnlevel = join "", "/protein/interpro[", $interpn + 1, "]";
                my @matchNodes = $protein_node->findnodes($ipnlevel);
                for(my $match=0; $match<scalar(@matchNodes); $match++){
                        my $matlevel = join "", "/protein/interpro[", $interpn+1, "]/match[", 
                          $match+1, "]/location";
                        my @locNodes = $protein_node->findnodes($matlevel);
                        my @seqFeatures = map { Bio::SeqFeature::Generic->new(
                  -start => $_->getAttribute('start'), 
                                                -end => $_->getAttribute('end'), 
                  -score => $_->getAttribute('score'), 
                  -source_tag => 'IPRscan',
                  -primary_tag => 'region',
                  -display_name => $interproNodes[$interpn]->getAttribute('name'),
                  -seq_id => $protein_node->getAttribute('id') ),
                                        } @locNodes;
                        foreach my $seqFeature (@seqFeatures){
                                my $annotation1 = Bio::Annotation::DBLink->new;
                                $annotation1->database($matchNodes[$match]->getAttribute('dbname'));
                                $annotation1->primary_id($matchNodes[$match]->getAttribute('id'));
                                $annotation1->comment($matchNodes[$match]->getAttribute('name'));
                                $seqFeature->annotation->add_Annotation('dblink',$annotation1);
                                 
                                my $annotation2 = Bio::Annotation::DBLink->new;
                                $annotation2->database('INTERPRO');
                                $annotation2->primary_id($interproNodes[$interpn]->getAttribute('id'));
                                $annotation2->comment($interproNodes[$interpn]->getAttribute('name'));
                                $seqFeature->annotation->add_Annotation('dblink',$annotation2);
                                # Bug 1908 (enhancement)
                                my $annotation3  = Bio::Annotation::DBLink->new;
                                $annotation3->database($DBNodes[$interpn]->getAttribute('dbname'));
                                $annotation3->primary_id($DBNodes[$interpn]->getAttribute('id'));
                                $annotation3->comment($DBNodes[$interpn]->getAttribute('name'));
                                $seqFeature->annotation->add_Annotation('dblink',$annotation3);
                        }
                        $bioSeq->add_SeqFeature(@seqFeatures);
                }
        }
        my $accession = $protein_node->getAttribute('id');
        my $displayname = $protein_node->getAttribute('name');
        $bioSeq->accession($accession);
        $bioSeq->display_name($displayname);
        return $bioSeq;
}
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=head2 _initialize
 Title   : _initialize
 Usage   : 
 Function: 
 Returns :
 Args    :
=cut
sub _initialize {
  my($self,@args) = @_;
  $self->SUPER::_initialize(@args);
  # hash for functions for decoding keys.
  $self->{'_func_ftunit_hash'} = {}; 
  my %param = @args;  # From SeqIO.pm
  @param{ map { lc $_ } keys %param } = values %param; # lowercase keys
  my $line = undef;
  # fast forward to first <protein/> record.
  while($line = $self->_readline()){
    if($line =~ /<protein/){
      $self->_pushback($line);
      last;
    }
  }
  $self->_xml_parser( XML::DOM::Parser->new() );
  $self->_sequence_factory( new Bio::Seq::SeqFactory
                           ( -verbose => $self->verbose(),
                             -type => 'Bio::Seq::RichSeq'))
    if ( ! defined $self->sequence_factory );
}
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=head2 _sequence_factory
 Title   : _sequence_factory
 Usage   : 
 Function: 
 Returns :
 Args    :
=cut
sub _sequence_factory {
  my $self = shift;
  my $val = shift;
  $self->{'sequence_factory'} = $val if defined($val);
  return $self->{'sequence_factory'};
}
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=head2 _xml_parser
 Title   : _xml_parser
 Usage   : 
 Function: 
 Returns :
 Args    :
=cut
sub _xml_parser {
  my $self = shift;
  my $val = shift;
  $self->{'xml_parser'} = $val if defined($val);
  return $self->{'xml_parser'};
}
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=head2 _parse_xml
 Title   : _parse_xml
 Usage   : 
 Function: 
 Returns :
 Args    :
=cut
sub _parse_xml {
  my ($self,$xml) = @_;
  $self->_dom( $self->_xml_parser->parse($xml) );
  return 1;
}
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=head2 _dom
 Title   : _dom
 Usage   : 
 Function: 
 Returns :
 Args    :
=cut
sub _dom {
  my $self = shift;
  my $val = shift;
  $self->{'dom'} = $val if defined($val);
  return $self->{'dom'};
}
1;
__END__