Bio::SeqIO::bsml_sax - BSML sequence input/output stream using SAX

 It is probably best not to use this object directly, but rather go
 through the SeqIO handler system. To read a BSML file:

    $stream = Bio::SeqIO->new( -file => $filename, -format => 'bsml');

    while ( my $bioSeqObj = $stream->next_seq() ) {
	# do something with $bioSeqObj
    }

 To write a Seq object to the current file handle in BSML XML format:

    $stream->write_seq( -seq => $seqObj);

 If instead you would like a XML::DOM object containing the BSML, use:

    my $newXmlObject = $stream->to_bsml( -seq => $seqObj);

 In addition to parts of the Bio:: hierarchy, this module uses:

 XML::SAX

 This object can transform Bio::Seq objects to and from BSML (XML)
 flatfiles.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

 Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution. Bug reports can be submitted via the
 web:

  https://redmine.open-bio.org/projects/bioperl/

 Title   : next_seq
 Usage   : my $bioSeqObj = $stream->next_seq
 Function: Retrieves the next sequence from a SeqIO::bsml stream.
 Returns : A reference to a Bio::Seq::RichSeq object
 Args    :

# BioPerl module for Bio::SeqIO::bsml_sax
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Jason Stajich
#

package Bio::SeqIO::bsml_sax;
use vars qw($Default_Source);
use strict;

use Bio::SeqFeature::Generic;
use Bio::Species;
use XML::SAX;
use Bio::Seq::SeqFactory;
use Bio::Annotation::Collection;
use Bio::Annotation::Comment;
use Bio::Annotation::Reference;
use Bio::Annotation::DBLink;

use base qw(Bio::SeqIO XML::SAX::Base);

$Default_Source = 'BSML';

sub _initialize {
    my ($self) = shift;
    $self->SUPER::_initialize(@_);
    $self->{'_parser'} = XML::SAX::ParserFactory->parser('Handler' => $self);
    if( ! defined $self->sequence_factory ) {
	$self->sequence_factory(Bio::Seq::SeqFactory->new
				(-verbose => $self->verbose(),
				 -type => 'Bio::Seq::RichSeq'));
    }
    return;
}

sub next_seq {
    my $self = shift;
    if( @{$self->{'_seendata'}->{'_seqs'} || []} ||
	eof($self->_fh)) {
	return shift @{$self->{'_seendata'}->{'_seqs'}};
    }
    $self->{'_parser'}->parse_file($self->_fh);
    return shift @{$self->{'_seendata'}->{'_seqs'}};
}

# XML::SAX::Base methods

sub start_document {
    my ($self,$doc) = @_;
    $self->{'_seendata'} = {'_seqs'    => [],
			    '_authors' => [],
			    '_feats'   => [] };
    $self->SUPER::start_document($doc);
}

sub end_document {
    my ($self,$doc) = @_;
    $self->SUPER::end_document($doc);
}


sub start_element {
    my ($self,$ele) = @_;
    my $name = uc($ele->{'LocalName'});
    my $attr = $ele->{'Attributes'};
    my $seqid = defined $self->{'_seendata'}->{'_seqs'}->[-1] ?
	$self->{'_seendata'}->{'_seqs'}->[-1]->display_id : undef;
    for my $k ( keys %$attr ) {
	$attr->{uc $k} = $attr->{$k};
	delete $attr->{$k};
    }
    if( $name eq 'BSML' ) {

    } elsif( $name eq 'DEFINITIONS' ) {
    } elsif( $name eq 'SEQUENCES' ) {

    } elsif( $name eq 'SEQUENCE' ) {
	my ($id,$acc,$title,
	    $desc,$length,$topology,
	    $mol) =  map { $attr->{'{}'.$_}->{'Value'} } qw(ID IC-ACCKEY
							    TITLE COMMENT
							    LENGTH
							    TOPOLOGY
							    MOLECULE);
	push @{$self->{'_seendata'}->{'_seqs'}},
	$self->sequence_factory->create
	    (
	     -display_id          => $id,
	     -accession_number    => $acc,
	     -description         => $desc,
	     -length              => $length,
	     -is_circular         => ($topology =~ /^linear$/i) ? 0 : 1,
	     -molecule            => $mol,
	     );

    } elsif( $name eq 'FEATURE-TABLES' ) {
    } elsif( $name eq 'ATTRIBUTE' ) {
	my $curseq = $self->{'_seendata'}->{'_seqs'}->[-1];
	my ($name,$content) = map { $attr->{'{}'.$_}->{'Value'} } qw(NAME CONTENT);
	if($name =~ /^version$/i ) {
	    my ($version);
	    if($content =~ /^[^\.]+\.(\d+)/) {
		$version = $1;
	    } else { $version = $content }
	    $curseq->seq_version($version);
	} elsif( $name eq 'organism-species') {
	    my ($genus,$species,$subsp) = split(/\s+/,$content,3);
	    $curseq->species(Bio::Species->new(-sub_species => $subsp,
					       -classification =>
					       [$species,$genus]));
	} elsif( $name eq 'organism-classification' ) {
	    my (@class) =(split(/\s*;\s*/,$content),$curseq->species->species);
	    $curseq->species->classification([reverse @class]);
	} elsif( $name eq 'database-xref' ) {
	    my ($db,$id) = split(/:/,$content);
	    $curseq->annotation->add_Annotation('dblink',
					      Bio::Annotation::DBLink->new
						( -database  => $db,
						  -primary_id=> $id));
	} elsif( $name eq 'date-created' ||
		 $name eq 'date-last-updated' ) {
	    $curseq->add_date($content);
	}
    } elsif( $name eq 'FEATURE' ) {
	my ($id,$class,$type,$title,$display_auto)
	    =  map { $attr->{'{}'.$_}->{'Value'} } qw(ID CLASS VALUE-TYPE
						      TITLE DISPLAY-AUTO);

	push @{$self->{'_seendata'}->{'_feats'}},
	Bio::SeqFeature::Generic->new
	    ( -seq_id      => $self->{'_seendata'}->{'_seqs'}->[-1]->display_id,
	      -source_tag  => $Default_Source,
	      -primary_tag => $type,
	      -tag => {'ID'    => $id,
		   });

    } elsif( $name eq 'QUALIFIER') {
	my ($type,$value) =  map { $attr->{'{}'.$_}->{'Value'} } qw(VALUE-TYPE
								    VALUE);
	my $curfeat = $self->{'_seendata'}->{'_feats'}->[-1];
	$curfeat->add_tag_value($type,$value);
    } elsif( $name eq 'INTERVAL-LOC' ) {
	my $curfeat = $self->{'_seendata'}->{'_feats'}->[-1];
	my ($start,$end,$strand) =
	    map { $attr->{'{}'.$_}->{'Value'} } qw(STARTPOS
						   ENDPOS
						   COMPLEMENT);

	$curfeat->start($start);
	$curfeat->end($end);
	$curfeat->strand(-1) if($strand);
    } elsif( $name eq 'REFERENCE' ) {
	push @{$self->{'_seendata'}->{'_annot'}},
	Bio::Annotation::Reference->new();
    }

    push @{$self->{'_state'}}, $name;
    $self->SUPER::start_element($ele);
}

sub end_element {
    my ($self,$ele) = @_;
    pop @{$self->{'_state'}};
    my $name = uc $ele->{'LocalName'};
    my $curseq = $self->{'_seendata'}->{'_seqs'}->[-1];
    if( $name eq 'REFERENCE') {
	my $ref = pop @{$self->{'_seendata'}->{'_annot'}};
	$curseq->annotation->add_Annotation('reference',$ref);
    } elsif( $name eq 'FEATURE' ) {
	my $feat = pop @{$self->{'_seendata'}->{'_feats'}};
	$curseq->add_SeqFeature($feat);
    }
    $self->SUPER::end_element($ele);
}

sub characters {
    my ($self,$data) = @_;
    if( ! @{$self->{'_state'}} ) {
	$self->warn("Calling characters with no previous start_element call. Ignoring data");
    } else {
	my $curseq = $self->{'_seendata'}->{'_seqs'}->[-1];
	my $curfeat = $self->{'_seendata'}->{'_feats'}->[-1];
	my $curannot = $self->{'_seendata'}->{'_annot'}->[-1];
	my $name = $self->{'_state'}->[-1];
	if( $name eq 'REFAUTHORS' ) {
	    $curannot->authors($data->{'Data'});
	} elsif( $name eq 'REFTITLE') {
	    $curannot->title($data->{'Data'});
	} elsif( $name eq 'REFJOURNAL') {
	    $curannot->location($data->{'Data'});
	} elsif( $name eq 'SEQ-DATA') {
	    $data->{'Data'} =~ s/\s+//g;
	    $curseq->seq($data->{'Data'});
	}
    }
    $self->SUPER::characters($data);
}

1;