# interpro.pm,v 1.5 2004/12/08 11:46:41 heikki Exp
#
# BioPerl module for interpro
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

interpro - DESCRIPTION of Object

=head1 SYNOPSIS

  # do not call this module directly. Use Bio::SeqIO

=head1 DESCRIPTION

Bio::SeqIO::interpro will parse interpro scan XML (version 1.2) and
create Bio::SeqFeature::Generic objects based on the contents of the
XML document.

Bio::SeqIO::Interpro will also attach the annotation given in the XML
file to the 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/MailList.shtml  - 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.bioperl.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 interpro;
use vars qw(@ISA);
use strict;

# Object preamble - inherits from Bio::Root::Root

use Bio::Root::Root;


@ISA = qw(Bio::Root::Root );

=head2 new

 Title   : new
 Usage   : my $obj = new interpro();
 Function: Builds a new interpro object 
 Returns : an instance of interpro
 Args    :


=cut

sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  return $self;
}

1;
#

package Bio::SeqIO::interpro;
use vars qw(@ISA);
use strict;

use Bio::SeqIO;
use Bio::SeqFeature::Generic;
use XML::DOM;
use XML::DOM::XPath;
use Bio::Seq::SeqFactory;
use Bio::Annotation::Collection;
use Bio::Annotation::DBLink;
use Data::Dumper;

@ISA = 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

=head1 METHODS

=cut

=head2 next_seq

 Title   : next_seq
 Usage   : my $bioSeqObj = $stream->next_seq
 Function: Retrieves the next sequence from a SeqIO::interpro stream.
 Returns : A reference to 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 the 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 undef 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');
  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);

#      $self->warn(join '*', map { $_->getAttribute('score') } @locnodes);

        my @seqFeatures = map { Bio::SeqFeature::Generic->new(
                               -start => $_->getAttribute('start'), 
                               -end => $_->getAttribute('end'), 
                               -score => $_->getAttribute('score'), 
                               -source_tag => 'IPRscan',
                               -primary_tag => 'region',
  #                            -source_tag => $interproNodes[$interpn]->getAttribute('id'), 
                               -display_name => $interproNodes[$interpn]->getAttribute('name'),
                               -seq_id => $protein_node->getAttribute('id'),
                                ),
        } @locNodes;
        foreach my $seqFeature (@seqFeatures){
          #my $annotationCollection = Bio::Annotation::Collection->new;
          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)
        }
        $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;
}

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 );
}

sub sequence_factory {
  my $self = shift;
  my $val = shift;

  $self->{'sequence_factory'} = $val if defined($val);
  return $self->{'sequence_factory'};
}

sub xml_parser {
  my $self = shift;
  my $val = shift;

  $self->{'xml_parser'} = $val if defined($val);
  return $self->{'xml_parser'};
}

sub parse_xml {
  my ($self,$xml) = @_;
  $self->dom( $self->xml_parser->parse($xml) );
  return 1;
}

sub dom {
  my $self = shift;
  my $val = shift;

  $self->{'dom'} = $val if defined($val);
  return $self->{'dom'};
}


1;
