bsml documentation.

 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    :

to_bsml

 Title   : to_bsml
 Usage   : my $domDoc = $obj->to_bsml(@args)
 Function: Generates an XML structure for one or more Bio::Seq objects.
           If $seqref is an array ref, the XML tree generated will include
           all the sequences in the array.
 Returns : A reference to the XML DOM::Document object generated / modified
 Args    : Argument array in form of -key => val. Recognized keys:

      -seq A Bio::Seq reference, or an array reference of many of them

   -xmldoc Specifies an existing XML DOM document to add the sequences
           to. If included, then only data (no page formatting) will
           be added. If not, a new XML::DOM::Document will be made,
           and will be populated with both  data, as well as
            display elements.

   -nodisp Do not generate  elements, or any children
           thereof, even if -xmldoc is not set.

 -skipfeat If set to 'all', all s will be skipped.  If it is
           a hash reference, any  with a class matching a key
           in the hash will be skipped - for example, to skip 'source'
           and 'score' features, use:

               -skipfeat => { source => 'Y', score => 'Y' }

 -skiptags As above: if set to 'all', no tags are included, and if a
           hash reference, those specific tags will be ignored.

           Skipping some or all tags and features can result in
           noticable speed improvements.

   -nodata If true, then  will not be included.  This may be
           useful if you just want annotations and do not care about
           the raw ACTG information.

   -return Default is 'xml', which will return a reference to the BSML
           XML object. If set to 'seq' will return an array ref of the
            objects added (rather than the whole XML object)

    -close Early BSML browsers will crash if an element *could* have
           children but does not, and is closed as an empty element
           e.g. . If -close is true, then such tags are given
           a comment child to explicitly close them e.g.  . This is default true, set to "0" if you do
           not want this behavior.

 Examples : my $domObj = $stream->to_bsml( -seq => \@fourCoolSequenceObjects,
					   -skipfeat => { source => 1 },
					   );

            # Or add sequences to an existing BSML document:
            $stream->to_bsml( -seq => \@fourCoolSequenceObjects,
			      -skipfeat => { source => 1 },
			      -xmldoc => $myBsmlDocumentInProgress,  );

write_seq

 Title   : write_seq
 Usage   : $obj->write_seq(@args)
 Function: Prints out an XML structure for one or more Bio::Seq objects.
           If $seqref is an array ref, the XML tree generated will include
           all the sequences in the array. This method is fairly simple,
           most of the processing is performed within to_bsml.
 Returns : A reference to the XML object generated / modified
 Args    : Argument array. Recognized keys:

      -seq A Bio::Seq reference, or an array reference of many of them

           Alternatively, the method may be called simply as...

           $obj->write_seq( $bioseq )

           ... if only a single argument is passed, it is assumed that
           it is the sequence object (can also be an array ref of
           many Seq objects )

-printmime If true prints "Content-type: $mimetype\n\n" at top of
document, where $mimetype is the value designated by this
key. For generic XML use text/xml, for BSML use text/x-bsml

   -return This option will be supressed, since the nature of this
           method is to print out the XML document. If you wish to
           retrieve the  objects generated, use the to_bsml
           method directly.

_parse_location

 Title   : _parse_location
 Usage   : $obj->_parse_location($xmlDocument, $parentElem, $SeqFeatureObj)
 Function: Adds  and  children to <$parentElem> based
           on locations / sublocations found in $SeqFeatureObj. If
           sublocations exist, the original location will be ignored.
 Returns : An array ref containing the elements added to the parent.
           These will have already been added to <$parentElem>
 Args    : 0 The DOM::Document being modified
           1 The DOM::Element parent that you want to add to
           2 Reference to the Bio::SeqFeature being analyzed

_parse_bsml_feature

 Title   : _parse_bsml_feature
 Usage   : $obj->_parse_bsml_feature($xmlFeature )
 Function: Will examine the  element provided by $xmlFeature and
           return a generic seq feature.
 Returns : Bio::SeqFeature::Generic
 Args    : 0 XML::DOM::Element  being analyzed.

_parse_bsml_location

 Title   : _parse_bsml_location
 Usage   : $obj->_parse_bsml_feature( $intOrSiteLoc, $gsfObject )
 Function: Will examine the  or  element provided
 Returns : Bio::SeqFeature::Generic
 Args    : 0 XML::DOM::Element  being analyzed.
           1 Optional SeqFeature::Generic to use

_parse_reference

 Title   : _parse_reference
 Usage   : $obj->_parse_reference(@args )
 Function: Makes a new  object from a ::Reference, which is
           then stored in an array provide by -refs. It will be
           appended to the XML tree later.
 Returns : 
 Args    : Argument array. Recognized keys:

      -xml The DOM::Document being modified

   -refobj The Annotation::Reference Object

     -refs An array reference to hold the new  DOM object

       -id Optional. If the XML id for the 'calling' element is
           provided, it will be placed in any  refs
           attribute.

_parse_annotation

 Title   : _parse_annotation
 Usage   : $obj->_parse_annotation(@args )
 Function: Will examine any Annotations found in -obj. Data found in
           ::Comment and ::DBLink structures, as well as Annotation 
           description fields are stored in -desc for later
           generation of s.  objects are generated
           from ::References, and are stored in -refs - these will
           be appended to the XML tree later.
 Returns : 
 Args    : Argument array. Recognized keys:

      -xml The DOM::Document being modified

      -obj Reference to the Bio object being analyzed

    -descr An array reference for holding description text items

     -refs An array reference to hold  DOM objects

       -id Optional. If the XML id for the 'calling' element is
           provided, it will be placed in any  refs
           attribute.

_parse_annotation_old

    Title   : _parse_annotation_old
 Usage   : $obj->_parse_annotation_old(@args)
 Function: As above, but for the old Annotation system.
           Apparently needed because Features are still using the old-style
           annotations?
 Returns : 
 Args    : Argument array. Recognized keys:

      -xml The DOM::Document being modified

      -obj Reference to the Bio object being analyzed

    -descr An array reference for holding description text items

     -refs An array reference to hold  DOM objects

       -id Optional. If the XML id for the 'calling' element is
           provided, it will be placed in any  refs
           attribute.

_add_page

 Title   : _add_page
 Usage   : $obj->_add_page($xmlDocument, $xmlSequenceObject)
 Function: Adds a simple  and  structure for a 
 Returns : a reference to the newly created 
 Args    : 0 The DOM::Document being modified
           1 Reference to the  object

_addel

 Title   : _addel
 Usage   : $obj->_addel($parentElem, 'ChildName',
			{ anAttr => 'someValue', anotherAttr => 'aValue',})
 Function: Add an element with attribute values to a DOM tree
 Returns : a reference to the newly added element
 Args    : 0 The DOM::Element parent that you want to add to
           1 The name of the new child element
           2 Optional hash reference containing 
             attribute name => attribute value assignments

_show_dna

 Title   : _show_dna
 Usage   : $obj->_show_dna($newval)
 Function: (cut-and-pasted directly from embl.pm)
 Returns : value of _show_dna
 Args    : newvalue (optional)

_initialize

 Title   : _initialize
 Usage   : $dom = $obj->_initialize(@args)
 Function: Coppied from embl.pm, and augmented with initialization of the
           XML DOM tree
 Returns : 
 Args    : -file => the XML file to be parsed

_parseparams

 Title   : _parseparams
 Usage   : my $paramHash = $obj->_parseparams(@args)
 Function: Borrowed from Bio::Parse.pm, who borrowed it from CGI.pm
           Lincoln Stein -> Richard Resnick -> here
 Returns : A hash reference of the parameter keys (uppercase) pointing to
           their values.
 Args    : An array of key, value pairs. Easiest to pass values as:
           -key1 => value1, -key2 => value2, etc
           Leading "-" are removed.

_parse_xml

 Title   : _parse_xml
 Usage   : $dom = $obj->_parse_xml($filename)
 Function: uses XML::DOM to construct a DOM tree from the BSML document
 Returns : a reference to the parsed DOM tree
 Args    : 0 Path to the XML file needing to be parsed

Methods code

next_seq

sub next_seq {

    my $self = shift;
    my ($desc);
    my $bioSeq = $self->sequence_factory->create(-verbose =>$self->verbose());
    
    unless (exists $self->{'domtree'}) {
	$self->throw("A BSML document has not yet been parsed.");
	return undef;
    }
    my $dom = $self->{'domtree'};
    my $seqElements = $dom->getElementsByTagName ("Sequence");
    if ($self->{'current_node'} == $seqElements->getLength ) {
	# There are no more <Sequence>s to process
	return undef;
    }
    my $xmlSeq = $seqElements->item($self->{'current_node'});
    
    # Assume that title attribute contains the best display id
    if (my $val = $xmlSeq->getAttribute( "title")) {
       $bioSeq->display_id($val);
   }
    
    # Set the molecule type
    if (my $val = $xmlSeq->getAttribute( "molecule" )) {
	my %mol = ('dna' => 'DNA', 'rna' => 'RNA', 'aa' => 'protein');
	$bioSeq->molecule($mol{ lc($val) });
    }
    
    # Set the accession number
    if (my $val = $xmlSeq->getAttribute( "ic-acckey" )) {
	$bioSeq->accession_number($val);
    }
    
    # Get the sequence data for the element
    if (my $seqData = &FIRSTDATA($xmlSeq->getElementsByTagName("Seq-data")
				 ->item(0) ) ) {
	# Sequence data exists, transfer to the Seq object
	# Remove white space and CRs (not neccesary?)
	$seqData =~ s/[\s\n\r]//g;
	$bioSeq->seq($seqData);
    } elsif (my $import = $xmlSeq->getElementsByTagName("Seq-dataimport")
	     ->item(0) )  {
#>>>>  # What about <Seq-data-import> ??
	
    } elsif (my $val = $xmlSeq->getAttribute("length"))  {
	# No sequence defined, set the length directly
	
#>>>>   # This does not appear to work - length is apparently calculated
	# from the sequence. How to make a "virtual" sequence??? Such
	# creatures are common in BSML...
	$bioSeq->length($val);
    }
   
    my $species = Bio::Species->new();
    my @classification = ();
    
    # Peruse the generic <Attributes> - those that are direct children of
    # the <Sequence> or the <Feature-tables> element
    # Sticky wicket here - data not controlled by schema, could be anything
    my @seqDesc = ();
    my %specs = ('common_name' => 'y', 
		 'genus' => 'y', 
		 'species' => 'y', 
		 'sub_species' => 'y', );
    my %seqMap = (
		  'add_date' => [ 'date' ],
		  'keywords' => [ 'keyword', ],
		  'seq_version' => [ 'version' ],
		  'division' => [ 'division' ],
		  'add_secondary_accession' => ['accession'],
		  'pid' => ['pid'],
		  'primary_id' => [ 'primary.id', 'primary_id' ],
		  );
    my $floppies = &GETFLOPPIES($xmlSeq);
    foreach my $attr (@{$floppies}) {
	# Don't want to get attributes from <Feature> or <Table> elements yet
	my $parent = $attr->getParentNode->getNodeName;
	next unless($parent eq "Sequence" || $parent eq "Feature-tables");
	
	my ($name, $content) = &FLOPPYVALS($attr);
	$name = lc($name);
	if (exists $specs{$name}) { # It looks like part of species...
	    $species->$name($content);
	    next;
	}
	my $value = "";
	# Cycle through the Seq methods:
	foreach my $method (keys %seqMap) {
	    # Cycle through potential matching attributes:
	    foreach my $match (@{$seqMap{$method}}) {
		# If the <Attribute> name matches one of the keys,
		# set $value, unless it has already been set
		$value ||= $content if ($name =~ /$match/i);
	    }
	    if ($value ne "") {
		$bioSeq->$method($value);
		last;
	    }
	}
	next if ($value ne "");

	if ($name =~ /^species$/i) {   # Uh, it's the species designation?
	    if ($content =~ / /) {
		# Assume that a full species name has been provided
		# This will screw up if the last word is the subspecies...
		my @break = split " ", $content;
		@classification = reverse @break;
	    } else {
		$classification[0] = $content;
	    }
	    next;
	}
	if ($name =~ /sub[_ ]?species/i) {  # Should be the subspecies...
	    $species->sub_species( $content );
	    next;
	}
	if ($name =~ /classification/i) {  # Should be species classification
	    # We will assume that there are spaces separating the terms:
	    my @bits = split " ", $content;
	    # Now make sure there is not other cruft as well (eg semi-colons)
	    for my $i (0..$#bits) {
		$bits[$i] =~ /(\w+)/;
		$bits[$i] = $1;
	    }
	    $species->classification( @bits );
	    next;
	}
	if ($name =~ /comment/) {
	    my $com = Bio::Annotation::Comment->new('-text' => $content);
	  #  $bioSeq->annotation->add_Comment($com);
	    $bioSeq->annotation->add_Annotation('comment', $com);
	    next;
	}
	# Description line - collect all descriptions for later assembly
	if ($name =~ /descr/) {
	    push @seqDesc, $content;
	    next;
	}
	# Ok, we have no idea what this attribute is. Dump to SimpleValue
	my $simp = Bio::Annotation::SimpleValue->new( -value => $content);
	$bioSeq->annotation->add_Annotation($name, $simp);
    }
    unless ($#seqDesc < 0) {
	$bioSeq->desc( join "; ", @seqDesc);
    }

#>>>>  This should be modified so that any IDREF associated with the
    # <Reference> is then used to associate the reference with the
    # appropriate Feature
    
    # Extract out <Reference>s associated with the sequence
    my @refs;
    my %tags = (
		-title => "RefTitle",
		-authors => "RefAuthors",
		-location => "RefJournal",
		);
    foreach my $ref ( $xmlSeq->getElementsByTagName ("Reference") ) {
	my %refVals;
	foreach my $tag (keys %tags) {
	    my $rt = &FIRSTDATA($ref->getElementsByTagName($tags{$tag})
				->item(0));
	    $rt =~ s/^[\s\r\n]+//;  # Kill leading space
	    $rt =~ s/[\s\r\n]+$//;  # Kill trailing space
	    $rt =~ s/[\s\r\n]+/ /;  # Collapse internal space runs
	    $refVals{$tag} = $rt;
	}
	my $reference = Bio::Annotation::Reference->new( %refVals );
	
	# Pull out any <Reference> information hidden in <Attributes>
	my %refMap = (
		      comment => [ 'comment', 'remark' ],
		      medline => [ 'medline', ],
		      pubmed => [ 'pubmed' ],
		      start => [ 'start', 'begin' ],
		      end => [ 'stop', 'end' ],
		      );
	my @refCom = ();
	my $floppies = &GETFLOPPIES($ref);
	foreach my $attr (@{$floppies}) {
	    my ($name, $content) = &FLOPPYVALS($attr);
	    my $value = "";
	    # Cycle through the Seq methods:
	    foreach my $method (keys %refMap) {
		# Cycle through potential matching attributes:
		foreach my $match (@{$refMap{$method}}) {
		    # If the <Attribute> name matches one of the keys,
		    # set $value, unless it has already been set
		    $value ||= $content if ($name =~ /$match/i);
		}
		if ($value ne "") {
		    my $str = '$reference->' . $method . "($value)";
		    eval($str);
		    next;
		}
	    }
	    next if ($value ne "");
	    # Don't know what the <Attribute> is, dump it to comments:
	    push @refCom, $name . $nvtoken . $content;
	}
	unless ($#refCom < 0) {
	    # Random stuff was found, tack it to the comment field
	    my $exist = $reference->comment;
	    $exist .= join ", ", @refCom;
	    $reference->comment($exist);
	}
	push @refs, $reference;
    }
    $bioSeq->annotation->add_Annotation('reference'=>$_) foreach @refs;
    
    # Extract the <Feature>s for this <Sequence>
    foreach my $feat ( $xmlSeq->getElementsByTagName("Feature") ) {
	$bioSeq->add_SeqFeature( $self->_parse_bsml_feature($feat) );
    }
    
    $species->classification( @classification );
    $bioSeq->species( $species );
    
# $seq->annotation->add_DBLink(@links);    ->
    
    $self->{'current_node'}++;
    return $bioSeq;

}

GETFLOPPIES

description

sub GETFLOPPIES {

    my $obj = shift;
    
    my @floppies;
    my $attributes = $obj->getElementsByTagName ("Attribute");
    for (my $i = 0; $i < $attributes->getLength; $i++) {
	push @floppies, $attributes->item($i);
    }
    my $qualifiers = $obj->getElementsByTagName ("Qualifier");
    for (my $i = 0; $i < $qualifiers->getLength; $i++) {
	push @floppies, $qualifiers->item($i);
    }
    return\@ floppies;

}

FLOPPYVALS

description

sub FLOPPYVALS {

    my $obj = shift;

    my ($name, $value);
    if      ($obj->getNodeName eq "Attribute") {
	$name  = $obj->getAttribute('name');
	$value = $obj->getAttribute('content');
    } elsif ($obj->getNodeName eq "Qualifier") {
	# Wheras <Attribute>s require both 'name' and 'content' attributes,
	# <Qualifier>s can technically have either blank (and sometimes do)
	my $n =  $obj->getAttribute('value-type');
	$name = $n if ($n ne "");
	my $v =  $obj->getAttribute('value');
	$value = $v if ($v ne "");
    }
    return ($name, $value);

}

FIRSTDATA

description

sub FIRSTDATA {

    my $element = shift;
    return undef unless ($element);

    my $hopefuls = $element->getChildNodes;
    my $data;
    for (my $i = 0; $i < $hopefuls->getLength; $i++) {
	if ($hopefuls->item($i)->getNodeType ==
	  XML::DOM::Node::TEXT_NODE() ) {
	    $data = $hopefuls->item($i)->getNodeValue;
	    last;
	}
    }
    return $data;

}

STRIP

description

sub STRIP {

    my $string = shift;
    $string =~ s/[\s\r\n]+/ /g;
    return $string;

}

to_bsml

sub to_bsml {

    my $self = shift;
    my $args = $self->_parseparams( -close => 1,
				    -return => 'xml',
				    @_);
    $args->{NODISP} ||= $args->{NODISPLAY};
    my $seqref = $args->{SEQ};
    $seqref = (ref($seqref) eq 'ARRAY') ? $seqref : [ $seqref ];

    #############################
    # Basic BSML XML Components #
    #############################
    
    my $xml;
    my ($bsmlElem, $defsElem, $seqsElem, $dispElem);
    if ($args->{XMLDOC}) {
	# The user has provided an existing XML DOM object
	$xml = $args->{XMLDOC};
	unless ($xml->isa("XML::DOM::Document")) {
	    die ('SeqIO::bsml.pm error:\n'.
		 'When calling ->to_bsml( { xmldoc => $myDoc }), $myDoc\n ' .
		 'should be an XML::DOM::Document object, or an object that\n'.
		 'inherits from that class (like BsmlHelper.pm)');
	}
    } else {
	# The user has not provided a new document, make one from scratch
	$xml = XML::DOM::Document->new();
	$xml->setXMLDecl( $xml->createXMLDecl("1.0") );
	my $url = "http://www.labbook.com/dtd/bsml2_2.dtd";
	my $doc = $xml->createDocumentType("Bsml",$url);
	$xml->setDoctype($doc);
	$bsmlElem = $self->_addel( $xml, 'Bsml');
	$defsElem = $self->_addel( $bsmlElem, 'Definitions');
	$seqsElem = $self->_addel( $defsElem, 'Sequences');
	unless ($args->{NODISP}) {
	    $dispElem = $self->_addel( $bsmlElem, 'Display');
	    my $stylElem = $self->_addel( $dispElem, 'Styles');
	    my $style = $self->_addel( $stylElem, 'Style', {
		type => "text/css" });
	    my $styleText = 
		qq(Interval-widget { display : "1"; }\n) .
		    qq(Feature { display-auto : "1"; });
	    $style->appendChild( $xml->createTextNode($styleText) );
	}
    }

    # Establish fundamental BSML elements, if they do not already exist
    $bsmlElem ||= $xml->getElementsByTagName("Bsml")->item(0);
    $defsElem ||= $xml->getElementsByTagName("Definitions")->item(0);
    $seqsElem ||= $xml->getElementsByTagName("Sequences")->item(0);
    
    ###############
    # <Sequences> #
    ###############

    # Map over Bio::Seq to BSML
    my %mol = ('dna' => 'DNA', 'rna' => 'RNA', 'protein' => 'AA');
    my @xmlSequences;

    foreach my $bioSeq (@{$seqref}) {
	my $xmlSeq = $xml->createElement("Sequence");
	my $FTs    = $xml->createElement("Feature-tables");
	
	# Array references to hold <Reference> objects:
	my $seqRefs = []; my $featRefs = [];
	# Array references to hold <Attribute> values (not objects):
	my $seqDesc = [];
	push @{$seqDesc}, ["comment" , "This file generated to BSML 2.2 standards - joins will be collapsed to a single feature enclosing all members of the join"];
	push @{$seqDesc}, ["description" , eval{$bioSeq->desc}];
	foreach my $kwd ( eval{$bioSeq->get_keywords} ) {
	    push @{$seqDesc}, ["keyword" , $kwd];
	}
	push @{$seqDesc}, ["keyword" , eval{$bioSeq->keywords}];
	push @{$seqDesc}, ["version" , eval{$bioSeq->seq_version}];
	push @{$seqDesc}, ["division" , eval{$bioSeq->division}];
	push @{$seqDesc}, ["pid" , eval{$bioSeq->pid}];
#	push @{$seqDesc}, ["bio_object" , ref($bioSeq)];
	push @{$seqDesc}, ["primary_id" , eval{$bioSeq->primary_id}];
	foreach my $dt (eval{$bioSeq->get_dates()} ) {
	    push @{$seqDesc}, ["date" , $dt];
	}
	foreach my $ac (eval{$bioSeq->get_secondary_accessions()} ) {
	    push @{$seqDesc}, ["secondary_accession" , $ac];
	}
	
	# Determine the accession number and a unique identifier
	my $acc = $bioSeq->accession_number eq "unknown" ?
	    "" : $bioSeq->accession_number;
	my $id;
	my $pi = $bioSeq->primary_id;
	if ($pi && $pi !~ /Bio::/) {
	    # Not sure I understand what primary_id is... It sometimes
	    # is a string describing a reference to a BioSeq object...
	    $id = "SEQ" . $bioSeq->primary_id;
	} else {
	    # Nothing useful found, make a new unique ID
	    $id = $acc || ("SEQ-io" . $idcounter->{Sequence}++);
	}
	# print "$id->",ref($bioSeq->primary_id),"\n";
	# An id field with spaces is interpreted as an idref - kill the spaces
	$id =~ s/ /-/g;
	# Map over <Sequence> attributes
	my %attr = ( 'title'         => $bioSeq->display_id,
		     'length'        => $bioSeq->length,
		     'ic-acckey'     => $acc,
		     'id'            => $id,
		     'representation' => 'raw',
		     );
	$attr{molecule} = $mol{ lc($bioSeq->molecule) } if $bioSeq->can('molecule');


	foreach my $a (keys %attr) {
	    $xmlSeq->setAttribute($a, $attr{$a}) if (defined $attr{$a} &&
						     $attr{$a} ne "");
	}
	# Orphaned Attributes:
	$xmlSeq->setAttribute('topology', 'circular') 
	    if ($bioSeq->is_circular);
	# <Sequence> strand, locus
	
	$self->_add_page($xml, $xmlSeq) if ($dispElem);
	################
	# <Attributes> #
	################

	# Check for Bio::Annotations on the * <Sequence> *.
	$self->_parse_annotation( -xml => $xml, -obj => $bioSeq, 
				  -desc => $seqDesc, -refs => $seqRefs);

	# Incorporate species data
	if (ref($bioSeq->species) eq 'Bio::Species') {
	    # Need to peer into Bio::Species ...
	    my @specs = ('common_name', 'genus', 'species', 'sub_species');
	    foreach my $sp (@specs) {
		next unless (my $val = $bioSeq->species()->$sp());
		push @{$seqDesc}, [$sp , $val];
	    }
	    push @{$seqDesc}, ['classification', 
			       (join " ", $bioSeq->species->classification) ];
	    # Species::binomial will return "genus species sub_species" ...
	} elsif (my $val = $bioSeq->species) {
	    # Ok, no idea what it is, just dump it in there...
	    push @{$seqDesc}, ["species", $val];
	}

	# Add the description <Attribute>s for the <Sequence>
	foreach my $seqD (@{$seqDesc}) {
	    $self->_addel($xmlSeq, "Attribute", {
		name => $seqD->[0], content => $seqD->[1]}) if ($seqD->[1]);
	}

	# If sequence references were added, make a Feature-table for them
	unless ($#{$seqRefs} < 0) {
	    my $seqFT = $self->_addel($FTs, "Feature-table", {
		title => "Sequence References", });
	    foreach my $feat (@{$seqRefs}) {
		$seqFT->appendChild($feat);
	    }
	}
	
	# This is the appropriate place to add <Feature-tables>
	$xmlSeq->appendChild($FTs);
	
	#############
	# <Feature> #
	#############	

#>>>>	# Perhaps it is better to loop through top_Seqfeatures?...
#>>>>	# ...however, BSML does not have a hierarchy for Features

	if (defined $args->{SKIPFEAT} &&
	    $args->{SKIPFEAT} eq 'all') {
	    $args->{SKIPFEAT} = { all => 1};
	} else { $args->{SKIPFEAT} ||= {} }
	foreach my $class (keys %{$args->{SKIPFEAT}}) {
	    $args->{SKIPFEAT}{lc($class)} = $args->{SKIPFEAT}{$class};
	}
	# Loop through all the features
	my @features = $bioSeq->all_SeqFeatures();
	if (@features && !$args->{SKIPFEAT}{all}) {
	    my $ft = $self->_addel($FTs, "Feature-table", {
		title => "Features", });
	    foreach my $bioFeat (@features ) {
		my $featDesc = [];
		my $class = lc($bioFeat->primary_tag);
		# The user may have specified to ignore this type of feature
		next if ($args->{SKIPFEAT}{$class});
		my $id = "FEAT-io" . $idcounter->{Feature}++;
		my $xmlFeat = $self->_addel( $ft, 'Feature', {
		    'id' => $id,
		    'class' => $class , 
		    'value-type' => $bioFeat->source_tag });
		# Check for Bio::Annotations on the * <Feature> *.
		$self->_parse_annotation( -xml => $xml, -obj => $bioFeat,
					  -desc => $featDesc, -id => $id,
					  -refs =>$featRefs, );
		# Add the description stuff for the <Feature>
		foreach my $de (@{$featDesc}) {
		    $self->_addel($xmlFeat, "Attribute", {
			name => $de->[0], content => $de->[1]}) if ($de->[1]);
		}
		$self->_parse_location($xml, $xmlFeat, $bioFeat);

		# loop through the tags, add them as <Qualifiers>
		next if (defined $args->{SKIPTAGS} &&
			 $args->{SKIPTAGS} =~ /all/i);
		# Tags can consume a lot of CPU cycles, and can often be
		# rather non-informative, so -skiptags can allow total or
		# selective omission of tags.
		foreach my $tag ($bioFeat->all_tags()) {
		    next if (exists $args->{SKIPTAGS}{$tag});
		    foreach my $val ($bioFeat->each_tag_value($tag)) {
			$self->_addel( $xmlFeat, 'Qualifier', {
			    'value-type' => $tag , 
			    'value' => $val });
		    }
		}
	    }
	}

	##############
	# <Seq-data> #
	##############	
	
	# Add sequence data
	if ( (my $data = $bioSeq->seq) && !$args->{NODATA} ) {
	    my $d = $self->_addel($xmlSeq, 'Seq-data');
	    $d->appendChild( $xml->createTextNode($data) );
	}

	# If references were added, make a Feature-table for them
	unless ($#{$featRefs} < 0) {
	    my $seqFT = $self->_addel($FTs, "Feature-table", {
		title => "Feature References", });
	    foreach my $feat (@{$featRefs}) {
		$seqFT->appendChild($feat);
	    }
	}
	
	# Place the completed <Sequence> tree as a child of <Sequences>
	$seqsElem->appendChild($xmlSeq);
	push @xmlSequences, $xmlSeq;
    }

    # Prevent browser crashes by explicitly closing empty elements:
    if ($args->{CLOSE}) {
	my @problemChild = ('Sequences', 'Sequence', 'Feature-tables', 
			    'Feature-table', 'Screen', 'View',);
	foreach my $kid (@problemChild) {
	    foreach my $prob ($xml->getElementsByTagName($kid)) {
		unless ($prob->hasChildNodes) {
		    $prob->appendChild(
			$xml->createComment(" Must close <$kid> explicitly "));
		}
	    }
	}
    }

    if (defined $args->{RETURN} &&
	$args->{RETURN} =~ /seq/i) {
	return\@ xmlSequences;
    } else {
	return $xml;
    }

}

write_seq

sub write_seq {

    my $self = shift;
    my $args = $self->_parseparams( @_);
    if ($#_ == 0 ) {
	# If only a single value is passed, assume it is the seq object
	unshift @_, "-seq";
    }
    # Build a BSML XML DOM object based on the sequence(s)
    my $xml = $self->to_bsml( @_,
			      -return => undef );
    # Convert to a string
    my $out = $xml->toString;
    # Print after putting a return after each element - more readable
    $out =~ s/>/>\n/g;
    $self->_print("Content-type: " . $args->{PRINTMIME} . "\n\n") 
	if ($args->{PRINTMIME});
    $self->_print( $out );
    # Return the DOM tree in case the user wants to do something with it

    $self->flush if $self->_flush_on_write && defined $self->_fh;
    return $xml;

}

_parse_location

sub _parse_location {

    my $self = shift;
    my ($xml, $xmlFeat, $bioFeat) = @_;
    my $bioLoc = $bioFeat->location;
    my @locations;
    if (ref($bioLoc) =~ /Split/) {
	@locations = $bioLoc->sub_Location;
	# BSML 2.2 does not recognize / support joins. For this reason,
	# we will just use the upper-level location. The line below can
	# be deleted or commented out if/when BSML 3 supports complex
	# interval deffinitions:
	@locations = ($bioLoc);
    } else {
	@locations = ($bioLoc);
    }
    my @added = ();
    
    # Add the site or interval positional information:
    foreach my $loc (@locations) {
	my ($start, $end) = ($loc->start, $loc->end);
	my %locAttr;
	# Strand information is not well described in BSML
	$locAttr{complement} = 1 if ($loc->strand == -1);
	if ($start ne "" && ($start == $end || $end eq "")) {
	    $locAttr{sitepos} = $start;
	    push @added, $self->_addel($xmlFeat,'Site-loc',\%locAttr);
	} elsif ($start ne "" && $end ne "") {
	    if ($start > $end) {
		# The feature is on the complementary strand
		($start, $end) = ($end, $start);
		$locAttr{complement} = 1;
	    }
	    $locAttr{startpos} = $start;
	    $locAttr{endpos} = $end;
	    push @added, $self->_addel($xmlFeat,'Interval-loc',\%locAttr);
	} else {
	    warn "Failure to parse SeqFeature location. Start = '$start' & End = '$end'";
	}
    }
    return\@ added;

}

_parse_bsml_feature

sub _parse_bsml_feature {

    my $self = shift;
    my ($feat) = @_;
    
    my $basegsf = new Bio::SeqFeature::Generic;
       # score
       # frame
       # source_tag

    # Use the class as the primary tag value, if it is present
    if ( my $val = $feat->getAttribute("class") ) {
	$basegsf->primary_tag($val);
    }

    # Positional information is in <Interval-loc>s or <Site-loc>s
    # We need to grab these in order, to try to recreate joins...
    my @locations = ();
    foreach my $kid ($feat->getChildNodes) {
	my $nodeName = $kid->getNodeName;
	next unless ($nodeName eq "Interval-loc" ||
		     $nodeName eq "Site-loc");
	push @locations, $kid;
    }
    if ($#locations == 0) {
	# There is only one location specified
	$self->_parse_bsml_location($locations[0], $basegsf);
    } elsif ($#locations > 0) {
#>>>>   # This is not working, I think the error is somewhere downstream
	# of add_sub_SeqFeature, probably in RangeI::union ?
	# The sub features are added fine, but the EXPANDed parent feature
	# location has a messed up start - Bio::SeqFeature::Generic ref
	# instead of an integer - and an incorrect end  - the end of the first
	# sub feature added, not of the union of all of them.

	# Also, the SeqIO::genbank.pm output is odd - the sub features appear
	# to be listed with the *previous* feature, not this one.

	foreach my $location (@locations) {
	    my $subgsf = $self->_parse_bsml_location($location);
	  #  print "start ", $subgsf->start,"\n";
	  #  print "end ", $subgsf->end,"\n";
	    $basegsf->add_sub_SeqFeature($subgsf, 'EXPAND');
	}
	# print $feat->getAttribute('id'),"\n";
	# print $basegsf->primary_tag,"\n";

    } else {
	# What to do if there are no locations? Nothing needed?
    }
    
    # Look at any <Attribute>s or <Qualifier>s that are present:
    my $floppies = &GETFLOPPIES($feat);
    foreach my $attr (@{$floppies}) {
	my ($name, $content) = &FLOPPYVALS($attr);
	
	if ($name =~ /xref/i) {
	    # Do we want to put these in DBLinks??
	}

	# Don't know what the object is, dump it to a tag:
	$basegsf->add_tag_value(lc($name), $content);
    }

    # Mostly this helps with debugging, but may be of utility...
    # Add a tag holding the BSML id value
    if ( (my $val = $feat->getAttribute('id')) &&
	 !$basegsf->has_tag('bsml-id')) {
	# Decided that this got a little sloppy...
#	$basegsf->add_tag_value("bsml-id", $val);
    }
    return $basegsf;

}

_parse_bsml_location

sub _parse_bsml_location {

    my $self = shift;
    my ($loc, $gsf) = @_;
    
    $gsf ||= new Bio::SeqFeature::Generic;
    my $type = $loc->getNodeName;
    my ($start, $end);
    if ($type eq 'Interval-loc') {
	$start = $loc->getAttribute('startpos');
	$end = $loc->getAttribute('endpos');
    } elsif ($type eq 'Site-loc') {
	$start = $end = $loc->getAttribute('sitepos');
    } else {
	warn "Unknown location type '$type', could not make GSF\n";
	return undef;
    }
    $gsf->start($start);
    $gsf->end($end);

    # BSML does not have an explicit method to set undefined strand
    if (my $s = $loc->getAttribute("complement")) {
	if ($s) {
	    $gsf->strand(-1);
	} else {
	    $gsf->strand(1);
	}
    } else {
	# We're setting "strand nonspecific" here - bad idea?
	# In most cases the user likely meant it to be on the + strand
	$gsf->strand(0);
    }
    
    return $gsf;

}

_parse_reference

sub _parse_reference {

    my $self = shift;
    my $args = $self->_parseparams( @_);
    my ($xml, $ref, $refRef) = ($args->{XML}, $args->{REFOBJ}, $args->{REFS});

    ###############
    # <Reference> #
    ###############

    my $xmlRef = $xml->createElement("Reference");
#>> This may not be the right way to make a BSML dbxref...
    if (my $link = $ref->medline) {
	$xmlRef->setAttribute('dbxref', $link);
    }

    # Make attributes for some of the characteristics
    my %stuff = ( start => $ref->start,
		  end => $ref->end,
		  rp => $ref->rp, 
		  comment => $ref->comment,
		  pubmed => $ref->pubmed,
		  );
    foreach my $s (keys %stuff) {
	$self->_addel($xmlRef, "Attribute", {
	    name => $s, content => $stuff{$s} }) if ($stuff{$s});
    }
    $xmlRef->setAttribute('refs', $args->{ID}) if ($args->{ID});
    # Add the basic information
    # Should probably check for content before creation...
    $self->_addel($xmlRef, "RefAuthors")->
	appendChild( $xml->createTextNode(&STRIP($ref->authors)) );
    $self->_addel($xmlRef, "RefTitle")->
	appendChild( $xml->createTextNode(&STRIP($ref->title)) );
    $self->_addel($xmlRef, "RefJournal")->
	appendChild( $xml->createTextNode(&STRIP($ref->location)) );
    # References will be added later in a <Feature-Table>
    push @{$refRef}, $xmlRef;

}

_parse_annotation

sub _parse_annotation {

    my $self = shift;
    my $args = $self->_parseparams( @_);
    my ($xml, $obj, $descRef, $refRef) = 
	( $args->{XML}, $args->{OBJ}, $args->{DESC}, $args->{REFS} );
    # No good place to put any of this (except for references). Most stuff
    # just gets dumped to <Attribute>s
    my $ann = $obj->annotation;
    return undef unless ($ann);
#	use BMS::Branch; my $debug = BMS::Branch->new( ); warn "$obj :"; $debug->branch($ann);
    unless (ref($ann) =~ /Collection/) {
	# Old style annotation. It seems that Features still use this
	# form of object
	$self->_parse_annotation_old(@_);
	return;
    }

    foreach my $key ($ann->get_all_annotation_keys()) {
	foreach my $thing ($ann->get_Annotations($key)) {
	    if ($key eq 'description') {
		push @{$descRef}, ["description" , $thing->value];
	    } elsif ($key eq 'comment') {
		push @{$descRef}, ["comment" , $thing->text];
	    } elsif ($key eq 'dblink') {
		# DBLinks get dumped to attributes, too
		push @{$descRef}, ["db_xref" ,  $thing->database . ":" 
				   . $thing->primary_id ];
		if (my $com = $thing->comment) {
		    push @{$descRef}, ["link" , $com->text ];
		}
		
	    } elsif ($key eq 'reference') {
		$self->_parse_reference( @_, -refobj => $thing );
	    } elsif (ref($thing) =~ /SimpleValue/) {
		push @{$descRef}, [$key , $thing->value];
	    } else {
		# What is this??
		push @{$descRef}, ["error", "bsml.pm did not understand ".
				   "'$key' = '$thing'" ];
	    }
	}
    }

}

_parse_annotation_old

sub _parse_annotation_old {

    my $self = shift;
    my $args = $self->_parseparams( @_);
    my ($xml, $obj, $descRef, $refRef) = 
	( $args->{XML}, $args->{OBJ}, $args->{DESC}, $args->{REFS} );
    # No good place to put any of this (except for references). Most stuff
    # just gets dumped to <Attribute>s
    if (my $ann = $obj->annotation) {
	push @{$descRef}, ["annotation", $ann->description];
	foreach my $com ($ann->each_Comment) {
	    push @{$descRef}, ["comment" , $com->text];
	}
	
	# Gene names just get dumped to <Attribute name="gene">
	foreach my $gene ($ann->each_gene_name) {
	    push @{$descRef}, ["gene" , $gene];
	}

	# DBLinks get dumped to attributes, too
	foreach my $link ($ann->each_DBLink) {
	    push @{$descRef}, ["db_xref" , 
			       $link->database . ":" . $link->primary_id ];
	    if (my $com = $link->comment) {
		push @{$descRef}, ["link" , $com->text ];
	    }
	}
	
	# References get produced and temporarily held
	foreach my $ref ($ann->each_Reference) {
	    $self->_parse_reference( @_, -refobj => $ref );
	}
    }

}

_add_page

sub _add_page {

    my $self = shift;
    my ($xml, $seq) = @_;
    my $disp = $xml->getElementsByTagName("Display")->item(0);
    my $page = $self->_addel($disp, "Page");
    my ($width, $height) = ( 7.8, 5.5);
    my $screen = $self->_addel($page, "Screen", {
	width => $width, height => $height, });
#    $screen->appendChild($xml->createComment("Must close explicitly"));
    my $view = $self->_addel($page, "View", {
	seqref => $seq->getAttribute('id'),
	title => $seq->getAttribute('title'),
	title1 => "{NAME}",
	title2 => "{LENGTH} {UNIT}",
    });
    $self->_addel($view, "View-line-widget", { 
	shape => 'horizontal',
	hcenter => $width/2 + 0.7,
	'linear-length' => $width - 2,
    });
    $self->_addel($view, "View-axis-widget");
    return $page;

}

_addel

sub _addel {

    my $self = shift;
    my ($root, $name, $attr) = @_;

    # Find the DOM::Document for the parent
    my $doc = $root->getOwnerDocument || $root;
    my $elem = $doc->createElement($name);
    foreach my $a (keys %{$attr}) {
	$elem->setAttribute($a, $attr->{$a});
    }
    $root->appendChild($elem);
    return $elem;

}

_show_dna

sub _show_dna {

   my $obj = shift;
   if( @_ ) {
      my $value = shift;
      $obj->{'_show_dna'} = $value;
    }
    return $obj->{'_show_dna'};

}

_initialize

sub _initialize {

  my($self,@args) = @_;

  $self->SUPER::_initialize(@args);  
  # hash for functions for decoding keys.
  $self->{'_func_ftunit_hash'} = {}; 
  $self->_show_dna(1); # sets this to one by default. People can change it 

  my %param = @args;  # From SeqIO.pm
  @param{ map { lc $_ } keys %param } = values %param; # lowercase keys
  if ( exists $param{-file} && $param{-file} !~ /^>/) {
      # Is it blasphemy to add your own keys to an object in another package?
      # domtree => the parsed DOM tree retruned by XML::DOM
      $self->{'domtree'} = $self->_parse_xml( $param{-file} );
      # current_node => the <Sequence> node next in line for next_seq
      $self->{'current_node'} = 0;
  }
    
  $self->sequence_factory( new Bio::Seq::SeqFactory
			   ( -verbose => $self->verbose(), 
			     -type => 'Bio::Seq::RichSeq')) 
      if( ! defined $self->sequence_factory );

}

_parseparams

sub _parseparams {

    my $self = shift;
    my %hash = ();
    my @param = @_;
    
    # Hacked out from Parse.pm
    # The next few lines strip out the '-' characters which
    # preceed the keys, and capitalizes them.
    for (my $i=0;$i<@param;$i+=2) {
        $param[$i]=~s/^\-//;
        $param[$i]=~tr/a-z/A-Z/;
    }
    pop @param if @param %2;  # not an even multiple
    %hash = @param;
    return\% hash;

}

_parse_xml

sub _parse_xml {

    my $self = shift;
    my $file = shift;
    
    unless (-e $file) {
	$self->throw("Could not parse non-existant XML file '$file'.");
	return undef;
    }
    my $parser = new XML::DOM::Parser;
    my $doc = $parser->parsefile ($file);
    return $doc;

}

DESTROY

description

sub DESTROY {

    my $self = shift;
    # Reports off the net imply that DOM::Parser will memory leak if you
    # do not explicitly dispose of it:
    # http://aspn.activestate.com/ASPN/Mail/Message/perl-xml/788458
    my $dom = $self->{'domtree'};
    # For some reason the domtree can get undef-ed somewhere...
    $dom->dispose if ($dom);

}

General documentation

DEPENDENCIES

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

 XML::DOM

FEEDBACK

Mailing Lists

 User feedback is an integral part of the evolution of this and other
 Bioperl modules. Send your comments and suggestions preferably to one
 of the Bioperl mailing lists.  Your participation is much
 appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://www.bioperl.org/MailList.shtml  - About the mailing lists

Reporting Bugs

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

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

Things Still to Do

 * The module now uses the new Collection.pm system. However,
   Annotations associated with a Feature object still seem to use the
   old system, so parsing with the old methods are included..

 * Generate Seq objects with no sequence data but an assigned
   length. This appears to be an issue with Bio::Seq. It is possible
   (and reasonable) to make a BSML document with features but no
   sequence data.

 * Support . Do not know how commonly this is used.

 * Some features are awaiting implementation in later versions of
   BSML. These include: 

       * Nested feature support

       * Complex feature (ie joins)

       * Unambiguity in strand (ie -1,0,1, not just  'complement' )

       * More friendly dblink structures

 * Location.pm (or RangeI::union?) appears to have a bug when 'expand'
   is used.

 * More intelligent hunting for sequence and feature titles? It is not
   terribly clear where the most appropriate field is located, better
   grepping (eg looking for a reasonable count for spaces and numbers)
   may allow for titles better than "AE008041".

AUTHOR - Charles Tilford

Bristol-Myers Squibb Bioinformatics
Email tilfordc@bms.com
I have developed the BSML specific code for this package, but have used
code from other SeqIO packages for much of the nuts-and-bolts. In particular
I have used code from the embl.pm module either directly or as a framework
for many of the subroutines that are common to SeqIO modules.

INTERNAL METHODS

#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-

 The following methods are used for internal processing, and should probably
 not be accessed by the user.

TESTING SCRIPT