tag fourth (and hopefully last) alpha

[bioperl-live.git] / branch-1-6 / Bio / SeqIO / chadoxml.pm

# $Id$
#
# BioPerl module for Bio::SeqIO::chadoxml
#
# Peili Zhang   <peili@morgan.harvard.edu>
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::SeqIO::chadoxml - chadoxml sequence output stream

=head1 SYNOPSIS

It is probably best not to use this object directly, but
rather go through the SeqIO handler system:

    $writer = Bio::SeqIO->new(-file => ">chado.xml",
                              -format => 'chadoxml');

    # assume you already have Sequence or SeqFeature objects
    $writer->write_seq($seq_obj);

    #after writing all seqs
    $writer->close_chadoxml();



=head1 DESCRIPTION

This object can transform Bio::Seq objects to chadoxml flat
file databases (for chadoxml DTD, see
http://gmod.cvs.sourceforge.net/gmod/schema/chado/dat/chado.dtd).

This is currently a write-only module.

    $seqio = Bio::SeqIO->new(-file => '>outfile.xml',
                             -format => 'chadoxml'
                             -suppress_residues => 1,
                             -allow_residues => 'chromosome',
                             );

    # we have a Bio::Seq object $seq which is a gene located on
    # chromosome arm 'X', to be written out to chadoxml
    # before converting to chadoxml, $seq object B<must> be transformed
    # so that all the coordinates in $seq are against the source
    # feature to be passed into Bio::SeqIO::chadoxml->write_seq()
    # -- chromosome arm X in the example below.

    $seqio->write_seq(-seq=>$seq,
                      -genus   => 'Homo',
                      -species => 'sapiens',
                      -seq_so_type=>'gene',
                      -src_feature=>'X',
                      -src_feat_type=>'chromosome_arm',
                        -nounflatten=>1,
                      -is_analysis=>'true',
                      -data_source=>'GenBank');

The chadoxml output of Bio::SeqIO::chadoxml-E<gt>write_seq() method can be
passed to the loader utility in XORT package
(http://gmod.cvs.sourceforge.net/gmod/schema/XMLTools/XORT/)
to be loaded into chado.

This object is currently implemented to work with sequence and
annotation data from whole genome projects deposited in GenBank. It
may not be able to handle all different types of data from all
different sources.

In converting a Bio::Seq object into chadoxml, a top-level feature is
created to represent the object and all sequence features inside the
Bio::Seq object are treated as subfeatures of the top-level
feature. The Bio::SeqIO::chadoxml object calls
Bio::SeqFeature::Tools::Unflattener to unflatten the flat feature list
contained in the subject Bio::Seq object, to build gene model
containment hierarchy conforming to chado central dogma model: gene
--E<gt> mRNA --E<gt> exons and protein.

Destination of data in the subject Bio::Seq object $seq is as following:

    *$seq->display_id:  name of the top-level feature;

    *$seq->accession_number: if defined, uniquename and
                 feature_dbxref of the top-level
                 feature if not defined,
                 $seq->display_id is used as the
                 uniquename of the top-level feature;

    *$seq->molecule: transformed to SO type, used as the feature
            type of the top-level feature if -seq_so_type
            argument is supplied, use the supplied SO type
            as the feature type of the top-level feature;

    *$seq->species: organism of the top-level feature;

    *$seq->seq: residues of the top-level feature;

    *$seq->is_circular, $seq->division: feature_cvterm;

    *$seq->keywords, $seq->desc, comments: featureprop;

    *references: pub and feature_pub;
        medline/pubmed ids: pub_dbxref;
        comments: pubprop;

    *feature "source" span: featureloc for top-level feature;

    *feature "source" db_xref: feature_dbxref for top-level feature;

    *feature "source" other tags: featureprop for top-level feature;

    *subfeature 'symbol' or 'label' tag: feature uniquename, if
                     none of these is present, the chadoxml object
                     generates feature uniquenames as:
                     <gene>-<feature_type>-<span>
                     (e.g. foo-mRNA--1000..3000);

    *gene model: feature_relationship built based on the
                     containment hierarchy;

    *feature span: featureloc;

    *feature accession numbers: feature_dbxref;

    *feature tags (except db_xref, symbol and gene): featureprop;

Things to watch out for:

    *chado schema change: this version works with the chado
                               version tagged chado_1_01 in GMOD CVS.

    *feature uniquenames: especially important if using XORT
                              loader to do incremental load into
                              chado. may need pre-processing of the
                              source data to put the correct
                              uniquenames in place.

    *pub uniquenames: chadoxml->write_seq() has the FlyBase policy
                          on pub uniquenames hard-coded, it assigns
                          pub uniquenames in the following way: for
                          journals and books, use ISBN number; for
                          published papers, use MEDLINE ID; for
                          everything else, use FlyBase unique
                          identifier FBrf#. need to modify the code to
                          implement your policy. look for the comments
                          in the code.

    *for pubs possibly existing in chado but with no knowledge of
         its uniquename:put "op" as "match", then need to run the
                        output chadoxml through a special filter that
                        talks to chado database and tries to find the
                        pub by matching with the provided information
                        instead of looking up by the unique key. after
                        matching, the filter also resets the "match"
                        operation to either "force" (default), or
                        "lookup", or "insert", or "update". the
                        "match" operation is for a special FlyBase use
                        case. please modify to work according to your
                        rules.

    *chado initialization for loading:

        cv & cvterm: in the output chadoxml, all cv's and
                             cvterm's are lookup only. Therefore,
                             before using XORT loader to load the
                             output into chado, chado must be
                             pre-loaded with all necessary CVs and
                             CVterms, including "SO" , "property
                             type", "relationship type", "pub type",
                             "pubprop type", "pub relationship type",
                             "sequence topology", "GenBank feature
                             qualifier", "GenBank division". A pub by
                             the uniquename 'nullpub' of type 'null
                             pub' needs to be inserted.

=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 one
of the Bioperl mailing lists.  Your participation is much appreciated.

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

=head2 Support 

Please direct usage questions or support issues to the mailing list:

I<bioperl-l@bioperl.org>

rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.

=head2 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 the web:

  http://bugzilla.bioperl.org

=head1 AUTHOR - Peili Zhang

Email peili@morgan.harvard.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::chadoxml;
use strict;
use English;

use Carp;
use Data::Dumper;
use XML::Writer;
use IO::File;
use IO::Handle;
use Bio::Seq;
use Bio::Seq::RichSeq;
use Bio::SeqIO::FTHelper;
use Bio::Species;
use Bio::Seq::SeqFactory;
use Bio::Factory::SequenceStreamI;
use Bio::SeqFeature::Generic;
use Bio::Annotation::Collection;
use Bio::Annotation::Comment;
use Bio::Annotation::Reference;
use Bio::Annotation::DBLink;
use Bio::SeqFeature::Tools::Unflattener;

#global variables
undef(my %finaldatahash); #data from Bio::Seq object stored in a hash
undef(my %datahash); #data from Bio::Seq object stored in a hash

my $chadotables = 'feature featureprop feature_relationship featureloc feature_cvterm cvterm cv feature_pub pub pub_dbxref pub_author author pub_relationship pubprop feature_dbxref dbxref db synonym feature_synonym';

my %fkey = (
    "cvterm.cv_id"          => "cv",
        "cvterm.dbxref_id"              => "dbxref",
    "dbxref.db_id"          => "db",
    "feature.type_id"       => "cvterm",
    "feature.organism_id"       => "organism",
    "feature.dbxref_id"         => "dbxref",
    "featureprop.type_id"       => "cvterm",
    "feature_pub.pub_id"        => "pub",
    "feature_cvterm.cvterm_id"  => "cvterm",
    "feature_cvterm.pub_id"     => "pub",
        "feature_cvterm.feature_id"     => "feature",
    "feature_dbxref.dbxref_id"  => "dbxref",
    "feature_relationship.object_id"    => "feature",
    "feature_relationship.subject_id"   => "feature",
    "feature_relationship.type_id"  => "cvterm",
    "featureloc.srcfeature_id"  => "feature",
    "pub.type_id"           => "cvterm",
    "pub_dbxref.dbxref_id"      => "dbxref",
    "pub_author.author_id"      => "author",
    "pub_relationship.obj_pub_id"   => "pub",
    "pub_relationship.subj_pub_id"  => "pub",
    "pub_relationship.type_id"  => "cvterm",
    "pubprop.type_id"       => "cvterm",
        "feature_synonym.feature_id"    => "feature",
        "feature_synonym.synonym_id"    => "synonym",
        "feature_synonym.pub_id"        => "pub",
        "synonym.type_id"               => "cvterm",
);

my %cv_name = (
        'relationship'                  => 'relationship',
        'sequence'                      => 'sequence',
        'feature_property'              => 'feature_property',
);

my %feattype_args2so = (
    "aberr"             => "aberration_junction",
#   "conflict"          => "sequence_difference",
#   "polyA_signal"          => "polyA_signal_sequence",
    "variation"         => "sequence_variant",
    "mutation1"         => "point_mutation",        #for single-base mutation
    "mutation2"         => "sequence_variant",      #for multi-base mutation
    "rescue"            => "rescue_fragment",
#   "rfrag"             => "restriction_fragment",
    "protein_bind"          => "protein_binding_site",
    "misc_feature"          => "region",
#   "prim_transcript"       => "primary_transcript",
    "CDS"               => "polypeptide",
    "reg_element"           => "regulatory_region",
    "seq_variant"           => "sequence_variant",
    "mat_peptide"           => "mature_peptide",
    "sig_peptide"           => "signal_peptide",
);

undef(my %organism);

use base qw(Bio::SeqIO);

sub _initialize {

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

    $self->SUPER::_initialize(%args);
    unless( defined $self->sequence_factory ) {
        $self->sequence_factory(Bio::Seq::SeqFactory->new
                                (-verbose => $self->verbose(),
                                 -type => 'Bio::Seq::RichSeq'));
    }
    #optional arguments that can be passed in
    $self->suppress_residues($args{'-suppress_residues'})
        if defined $args{'-suppress_residues'};

    $self->allow_residues($args{'-allow_residues'})
        if defined $args{'-allow_residues'};
    return;
}

=head2 write_seq

 Title   : write_seq
 Usage   : $stream->write_seq(-seq=>$seq, -seq_so_type=>$seqSOtype,
                  -src_feature=>$srcfeature,
                  -src_feat_type=>$srcfeattype,
                  -nounflatten=>0 or 1,
                  -is_analysis=>'true' or 'false',
                  -data_source=>$datasource)
 Function: writes the $seq object (must be seq) into chadoxml.
 Returns : 1 for success and 0 for error
 Args     : A Bio::Seq object $seq, optional $seqSOtype, $srcfeature,
            $srcfeattype, $nounflatten, $is_analysis and $data_source.

When $srcfeature (a string, the uniquename of the source feature) is given, the
location and strand information of the top-level feature against the source
feature will be derived from the sequence feature called 'source' of the $seq
object, a featureloc record is generated for the top -level feature on
$srcfeature. when $srcfeature is given, $srcfeattype must also be present. All
feature coordinates in $seq should be against $srcfeature. $seqSOtype is the
optional SO term to use as the type of the top-level feature. For example, a
GenBank data file for a Drosophila melanogaster genome scaffold has the molecule
type of "DNA", when converting to chadoxml, a $seqSOtype argument of
"golden_path_region" can be supplied to save the scaffold as a feature of type
"golden_path_region" in chadoxml, instead of "DNA". a feature with primary tag
of 'source' must be present in the sequence feature list of $seq, to decribe the
whole sequence record.

In the current implementation:

=over 3

=item *

non-mRNA records

A top-level feature of type $seq-E<gt>alphabet is generated for the whole GenBank
record, features listed are unflattened for DNA records to build gene model
feature graph, and for the other types of records all features in $seq are
treated as subfeatures of the top-level feature.

=item *

mRNA records

If a 'gene' feature is present, it B<must> have a /symbol or /label tag to
contain the uniquename of the gene. a top-level feature of type 'gene' is
generated. the mRNA is written as a subfeature of the top-level gene feature,
and the other sequence features listed in $seq are treated as subfeatures of the
mRNA feature.

=back

=cut

sub write_seq {
    my $usage = <<EOUSAGE;
Bio::SeqIO::chadoxml->write_seq()
Usage   : \$stream->write_seq(-seq=>\$seq,
                  -seq_so_type=>\$SOtype,
                  -src_feature=>\$srcfeature,
                  -src_feat_type=>\$srcfeattype,
                  -nounflatten=>0 or 1,
                              -is_analysis=>'true' or 'false',
                              -data_source=>\$datasource)
Args    : \$seq     : a Bio::Seq object
      \$SOtype  : the SO term to use as the feature type of
                      the \$seq record, optional
      \$srcfeature  : unique name of the source feature, a string
              containing at least one alphabetical letter
              (a-z, A-Z), optional
      \$srcfeattype : feature type of \$srcfeature. one of SO terms.
              optional
      when \$srcfeature is given, \$srcfeattype becomes mandatory,
      \$datasource  : source of the sequence annotation data,
              e.g. 'GenBank' or 'GFF'.
EOUSAGE

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

    my ($seq, $seq_so_type, $srcfeature, $srcfeattype, $nounflatten, $isanalysis, $datasource, $genus, $species) =
       $self->_rearrange([qw(SEQ
                 SEQ_SO_TYPE
                 SRC_FEATURE
                 SRC_FEAT_TYPE
                 NOUNFLATTEN
                 IS_ANALYSIS
                 DATA_SOURCE
                                 GENUS
                                 SPECIES
                 )],
                  @args);
    #print "$seq_so_type, $srcfeature, $srcfeattype\n";

    if( !defined $seq ) {
        $self->throw("Attempting to write with no seq!");
    }

    if( ! ref $seq || ! $seq->isa('Bio::Seq::RichSeqI') ) {
       ## FIXME $self->warn(" $seq is not a RichSeqI compliant module. Attempting to dump, but may fail!");
    }

        # try to get the srcfeature from the seqFeature object
        # for this to work, the user has to pass in the srcfeature type
        if (!$srcfeature) {
            if ($seq->can('seq_id')) {
                $srcfeature=$seq->seq_id if ($seq->seq_id ne $seq->display_name);
            }    
        }

    #$srcfeature, when provided, should contain at least one alphabetical letter
    if (defined $srcfeature)
    {
        if ($srcfeature =~ /[a-zA-Z]/)
        {
        chomp($srcfeature);
        } else {
        $self->throw( $usage );
        }

        #check for mandatory $srcfeattype
        if (! defined $srcfeattype)
        {
        $self->throw( $usage );
        #$srcfeattype must be a string of non-whitespace characters
        } else {
        if ($srcfeattype =~ /\S+/) {
            chomp($srcfeattype);
        } else {
            $self->throw( $usage );
        }
        }
    }

    # variables local to write_seq()
        my $div = undef;
    my $hkey = undef;
    undef(my @top_featureprops);
        undef(my @featuresyns);
        undef(my @top_featurecvterms);
    my $name = $seq->display_id if $seq->can('display_id');
        $name = $seq->display_name  if $seq->can('display_name');
    undef(my @feature_cvterms);
    undef(my %sthash);
    undef(my %dvhash);
    undef(my %h1);
    undef(my %h2);
    my $temp = undef;
    my $ann = undef;
    undef(my @references);
    undef(my @feature_pubs);
    my $ref = undef;
    my $location = undef;
    my $fbrf = undef;
    my $journal = undef;
    my $issue = undef;
    my $volume = undef;
    my $volumeissue = undef;
    my $pages = undef;
    my $year = undef;
    my $pubtype = undef;
#   my $miniref= undef;
    my $uniquename = undef;
    my $refhash = undef;
    my $feat = undef;
    my $tag = undef;
    my $tag_cv = undef;
    my $ftype = undef;
    my $subfeatcnt = undef;
    undef(my @top_featrels);
    undef (my %srcfhash);

    local($^W) = 0; # supressing warnings about uninitialized fields.

        if (!$name && $seq->can('attributes') ) {
            ($name) = $seq->attributes('Alias'); 
        }

    if ($seq->can('accession_number') && defined $seq->accession_number && $seq->accession_number ne 'unknown') {
        $uniquename = $seq->accession_number;
    } elsif ($seq->can('accession') && defined $seq->accession && $seq->accession ne 'unknown') {
        $uniquename = $seq->accession;
    } elsif ($seq->can('attributes')) {
                ($uniquename) = $seq->attributes('load_id');
        } else {
        $uniquename = $name;
    }
        my $len = $seq->length();
    if ($len == 0) {
        $len = undef;
    }

    undef(my $gb_type);
    if (!$seq->can('molecule') || ! defined ($gb_type = $seq->molecule()) ) {
        $gb_type = $seq->can('alphabet') ? $seq->alphabet : 'DNA';
    }
    $gb_type = 'DNA' if $ftype eq 'dna';
    $gb_type = 'RNA' if $ftype eq 'rna';

    if(length $seq_so_type > 0) {
        if (defined $seq_so_type) {
            $ftype = $seq_so_type;
        }
            elsif ($seq->type) {
                    $ftype = ($seq->type =~ /(.*):/)
                             ? $1
                             : $seq->type;
            }
        else {
            $ftype = $gb_type;
        }
    }
    else {
        $ftype = $gb_type;
    }

    my %ftype_hash = $self->return_ftype_hash($ftype);

        if ($species) {
            %organism = ("genus"=>$genus, "species" => $species);
        }
        else {
        my $spec = $seq->species();
        if (!defined $spec) {
        $self->throw("$seq does not know what organism it is from, which is required by chado. cannot proceed!\n");
        } else {
        %organism = ("genus"=>$spec->genus(), "species" => $spec->species());
        }
        }

        my $residues;
        if (!$self->suppress_residues ||
            ($self->suppress_residues && $self->allow_residues eq $ftype)) {
            $residues = $seq->seq->isa('Bio::PrimarySeq') 
                        ? $seq->seq->seq 
                        : $seq->seq;
        }
        else {
            $residues = '';
        }

    #set is_analysis flag for gene model features
    undef(my $isanal);
    if ($ftype eq 'gene' || $ftype eq 'mRNA' || $ftype eq 'exon' || $ftype eq 'protein' || $ftype eq 'polypeptide') {
        $isanal = $isanalysis;
        $isanal = 'false' if !defined $isanal;
    }

    %datahash = (
        "name"      => $name,
        "uniquename"    => $uniquename,
        "seqlen"    => $len,
        "residues"  => $residues,
        "type_id"   => \%ftype_hash,
        "organism_id"   => \%organism,
        "is_analysis"   => $isanal || 'false',
        );

        if (defined $srcfeature) {
                %srcfhash = $self->_srcf_hash($srcfeature,
                                              $srcfeattype,
                                              \%organism);
              
                my ($phase,$strand);
                if ($seq->can('phase')) {
                    $phase = $seq->phase;
                } 

                if ($seq->can('strand')) {
                    $strand = $seq->strand;
                }
                my %fl = (
                                "srcfeature_id" => \%srcfhash,
                                "fmin"          => $seq->start - 1,
                                "fmax"          => $seq->end,
                                "strand"        => $strand,
                                "phase"         => $phase,
                                );

                $datahash{'featureloc'} = \%fl;
 
        }


    #if $srcfeature is not given, use the Bio::Seq object itself as the srcfeature for featureloc's
    if (!defined $srcfeature) {
        $srcfeature = $uniquename;
        $srcfeattype = $ftype;
    }

    #default data source is 'GenBank'
    if (!defined $datasource) {
        $datasource = 'GenBank';
    }

    if ($datasource =~ /GenBank/i) {
        #sequence topology as feature_cvterm
        if ($seq->can('is_circular') && $seq->is_circular) {
            %sthash = (
                "cvterm_id" => {'name' => 'circular',
                            'cv_id' => {
                            'name' => 'sequence topology',
                            },
                        },
                   "pub_id" => {'uniquename' => 'nullpub',
                            'type_id' => {
                            'name' => 'null pub',
                            'cv_id' => {
                                'name'=> 'pub type',
                            },
                            },
                        },
                );
        } else {
            %sthash = (
                "cvterm_id" => { 'name' => 'linear',
                             'cv_id' => {
                             'name' => 'sequence topology',
                             }
                         },
                "pub_id"    => {'uniquename' => 'nullpub',
                            'type_id' => {
                            'name' => 'null pub',
                            'cv_id' => {
                                'name'=> 'pub type',
                            },
                            },
                        },
                   );
        }
        push(@feature_cvterms, \%sthash);

        #division as feature_cvterm
            if ($seq->can('division') && defined $seq->division()) {
                $div = $seq->division();
            %dvhash = (
                "cvterm_id" => {'name' => $div,
                            'cv_id' => {
                            'name' => 'GenBank division'}},
                "pub_id"    => {'uniquename' => 'nullpub',
                            'type_id' => {
                            'name' => 'null pub',
                            'cv_id' => {
                                'name'=> 'pub type'},
                                }},
                );
            push(@feature_cvterms, \%dvhash);
        }

        $datahash{'feature_cvterm'} = \@feature_cvterms;
    } # closes if GenBank

    #featureprop's
    #DEFINITION
    if ($seq->can('desc') && defined $seq->desc()) {
        $temp = $seq->desc();

        my %prophash = (
            "type_id"   => {'name' => 'description',
                        'cv_id' => {
                        'name' => 
                                                 $cv_name{'feature_property'} 
                                                       },
                                           },
            "value"     => $temp,
            );

        push(@top_featureprops, \%prophash);
        }

    #KEYWORDS
    if ($seq->can('keywords')) {
        $temp = $seq->keywords();

        if (defined $temp && $temp ne '.' && $temp ne '') {
        my %prophash = (
                "type_id"   => {'name' => 'keywords',
                            'cv_id' => {
                                                  'name' => 
                                                   $cv_name{'feature_property'}
                                                           }
                        },
                "value"     => $temp,
                            );

        push(@top_featureprops, \%prophash);
        }
        }

    #COMMENT
    if ($seq->can('annotation')) { 
        $ann = $seq->annotation();
        foreach my $comment ($ann->get_Annotations('comment')) {
            $temp = $comment->as_text();
            #print "fcomment: $temp\n";
            my %prophash = (
                "type_id"   => {'name' => 'comment',
                            'cv_id' => {
                                                  'name' => 
                                                   $cv_name{'feature_property'}
                                                           }
                                               },
                "value"     => $temp,
                );

            push(@top_featureprops, \%prophash);
        }
    }

        my @top_dbxrefs = ();
        #feature object from Bio::DB::SeqFeature::Store
        if ($seq->can('attributes')) {
                my %attributes = $seq->attributes;
                for my $key (keys %attributes) {
                    next if ($key eq 'parent_id');
                    next if ($key eq 'load_id');

                    if ($key eq 'Alias') {
                        @featuresyns = $self->handle_Alias_tag($seq,@featuresyns);
                    }

                    ###FIXME deal with Dbxref, Ontology_term,source, 
                    elsif ($key eq 'Ontology_term') {
                        @top_featurecvterms = $self->handle_Ontology_tag($seq,@top_featurecvterms);
                    }

                    elsif ($key eq 'dbxref' or $key eq 'Dbxref') {
                        @top_dbxrefs = $self->handle_dbxref($seq, $key, @top_dbxrefs);
                    }

                    elsif ($key =~ /^[a-z]/) {
                        @top_featureprops 
                             = $self->handle_unreserved_tags($seq,$key,@top_featureprops);
                    }
                }
        }
        $datahash{'feature_synonym'} = \@featuresyns;

        if ($seq->can('source')) {
                @top_dbxrefs = $self->handle_source($seq,@top_dbxrefs);
        }

    #accession and version as feature_dbxref
    if ($seq->can('accession_number') && defined $seq->accession_number && $seq->accession_number ne 'unknown') {
        my $db = $self->_guess_acc_db($seq, $seq->accession_number);
        my %acchash = (
               "db_id"  => {'name' => $db},
               "accession"  => $seq->accession_number,
               "version"    => $seq->seq_version,
               );
        my %fdbx = ('dbxref_id' => \%acchash);
        push(@top_dbxrefs, \%fdbx);
    }

    if( $seq->isa('Bio::Seq::RichSeqI') && defined $seq->get_secondary_accessions() ) {
        my @secacc = $seq->get_secondary_accessions();
        my $acc;
        foreach $acc (@secacc) {
            my %acchash = (
                "db_id"         => {'name' => 'GB'},
                "accession" => $acc,
                );
            my %fdbx = ('dbxref_id' => \%acchash);
            push(@top_dbxrefs, \%fdbx);
        }
    }

    #GI number
    if( $seq->isa('Bio::Seq::RichSeqI') && defined ($seq->pid)) {
        my $id = $seq->pid;
        #print "reftype: ", ref($id), "\n";

        #if (ref($id) eq 'HASH') {
        my %acchash = (
            "db_id"     => {'name' => 'GI'},
            "accession" => $id,
            );
        my %fdbx = ('dbxref_id' => \%acchash);
        push (@top_dbxrefs, \%fdbx);
    }

    #REFERENCES as feature_pub
    if (defined $ann) {
        #get the references
        @references = $ann->get_Annotations('reference');
        foreach $ref (@references) {
        undef(my %pubhash);
        $refhash = $ref->hash_tree();
        $location = $ref->location || $refhash->{'location'};
        #print "location: $location\n";

        #get FBrf#, special for FlyBase SEAN loading
        if (index($location, ' ==') >= 0) {
            $location =~ /\s==/;
                #print "match: $MATCH\n";
                #print "prematch: $PREMATCH\n";
                #print "postmatch: $POSTMATCH\n";
            $fbrf = $PREMATCH;
            $location = $POSTMATCH;
            $location =~ s/^\s//;
        }

        #print "location: $location\n";
        #unpublished reference
        if ($location =~ /Unpublished/) {
            $pubtype = 'unpublished';
            %pubhash = (
                "title"     => $ref->title || $refhash->{'title'},
                #"miniref"  => substr($location, 0, 255),
                #"uniquename"   => $fbrf,
                "type_id"   => {'name' => $pubtype, 'cv_id' => {'name' =>'pub type'}}
                );
        }
        #submitted
        elsif ($location =~ /Submitted/) {
            $pubtype = 'submitted';

            %pubhash = (
                "title"     => $ref->title || $refhash->{'title'},
                #"miniref"  => substr($location, 0, 255),
                #"uniquename"   => $fbrf,
                "type_id"   => {'name' => $pubtype, 'cv_id' => {'name' =>'pub type'}}
                );

            undef(my $pyear);
            $pyear = $self->_getSubmitYear($location);
            if (defined $pyear) {
            $pubhash{'pyear'} = $pyear;
            }
        }

        #published journal paper
        elsif ($location =~ /\D+\s\d+\s\((\d+|\d+-\d+)\),\s(\d+-\d+|\d+--\d+)\s\(\d\d\d\d\)$/) {
            $pubtype = 'paper';

                #parse location to get journal, volume, issue, pages & year
            $location =~ /\(\d\d\d\d\)$/;

            $year = $MATCH;
            my $stuff = $PREMATCH;
            $year =~ s/\(//; #remove the leading parenthesis
            $year =~ s/\)//; #remove the trailing parenthesis

            $stuff =~ /,\s(\d+-\d+|\d+--\d+)\s$/;

            $pages = $MATCH;
            $stuff = $PREMATCH;
            $pages =~ s/^, //; #remove the leading comma and space
            $pages =~ s/ $//; #remove the last space

            $stuff =~ /\s\d+\s\((\d+|\d+-\d+)\)$/;

            $volumeissue = $MATCH;
            $journal = $PREMATCH;
            $volumeissue =~ s/^ //; #remove the leading space
            $volumeissue =~ /\((\d+|\d+-\d+)\)$/;
            $issue = $MATCH;
            $volume = $PREMATCH;
            $issue =~ s/^\(//; #remove the leading parentheses
            $issue =~ s/\)$//; #remove the last parentheses
            $volume =~ s/^\s//; #remove the leading space
            $volume =~ s/\s$//; #remove the last space

            %pubhash = (
                "title"     => $ref->title || $refhash->{'title'},
                "volume"    => $volume,
                "issue"     => $issue,
                "pyear"     => $year,
                "pages"     => $pages,
                #"miniref"  => substr($location, 0, 255),
                #"miniref"  => ' ',
                #"uniquename"   => $fbrf,
                "type_id"   => {'name' => $pubtype, 'cv_id' => {'name' =>'pub type'}},
                "pub_relationship" => {
                    'obj_pub_id' => {
                    'uniquename' => $journal,
                    'title' => $journal,
                    #'miniref' => substr($journal, 0, 255),
                    'type_id' =>{'name' => 'journal',
                             'cv_id' =>
                             {'name' => 'pub type'
                              },
                         },
                             #'pubprop' =>{'value'=> $journal,
                             #       'type_id'=>{'name' => 'abbreviation', 'cv_id' => {'name' => 'pubprop type'}},
                             #      },
                         },
                       'type_id' => {
                           'name' => 'published_in',
                           'cv_id' => {
                           'name' => 'pub relationship type'},
                       },
                },
                );
        }

        #other references
        else {
            $pubtype = 'other';
            %pubhash = (
                "title"     => $ref->title || $refhash->{'title'},
                #"miniref"  => $fbrf,
                "type_id"   => {
                    'name' => $pubtype,
                    'cv_id' => {'name' =>'pub type'}
                }
                );
        }

        #pub_author
        my $autref = $self->_getRefAuthors($ref);
        if (defined $autref) {
            $pubhash{'pub_author'} = $autref;
        }
        # if no author and is type 'submitted' and has submitter address, use the first 100 characters of submitter address as the author lastname.
        else {
            if ($pubtype eq 'submitted') {
            my $autref = $self->_getSubmitAddr($ref);
            if (defined $autref) {
                $pubhash{'pub_author'} = $autref;
            }
            }
        }

        #$ref->comment as pubprop
        #print "ref comment: ", $ref->comment, "\n";
        #print "ref comment: ", $refhash->{'comment'}, "\n";
        if (defined $ref->comment || defined $refhash->{'comment'}) {
            my $comnt = $ref->comment || $refhash->{'comment'};
                #print "remark: ", $comnt, "\n";
            $pubhash{'pubprop'} = {
            "type_id"       => {'name' => 'comment', 'cv_id' => {'name' => 'pubprop type'}},
            "value"     => $comnt,
            };
        }

        #pub_dbxref
        undef(my @pub_dbxrefs);
        if (defined $fbrf) {
            push(@pub_dbxrefs, {dbxref_id => {accession => $fbrf, db_id => {'name' => 'FlyBase'}}});
        }
        if (defined ($temp = $ref->medline)) {
            push(@pub_dbxrefs, {dbxref_id => {accession => $temp, db_id => {'name' => 'MEDLINE'}}});
                #use medline # as the pub's uniquename
            $pubhash{'uniquename'} = $temp;
        }
        if (defined ($temp = $ref->pubmed)) {
            push(@pub_dbxrefs, {dbxref_id => {accession => $temp, db_id => {'name' => 'PUBMED'}}});
        }
        $pubhash{'pub_dbxref'} = \@pub_dbxrefs;

        #if the pub uniquename is not defined or blank, put its FBrf# as its uniquename
        #this is unique to FlyBase
        #USERS OF THIS MODULE: PLEASE MODIFY HERE TO IMPLEMENT YOUR POLICY
        # ON PUB UNIQUENAME!!!
        if (!defined $pubhash{'uniquename'} || $pubhash{'uniquename'} eq '') {
            if (defined $fbrf) {
            $pubhash{'uniquename'} = $fbrf;
            }
                #else {
                #   $pubhash{'uniquename'} = $self->_CreatePubUname($ref);
                #}
        }

        #add to collection of references
        #if the pub covers the entire sequence of the top-level feature, add it to feature_pubs
        if (($ref->start == 1 && $ref->end == $len) || (!defined $ref->start && !defined $ref->end)) {
            push(@feature_pubs, {"pub_id" => \%pubhash});
        }
        #the pub is about a sub-sequence of the top-level feature
        #create a feature for the sub-sequence and add pub as its feature_pub
        #featureloc of this sub-sequence is against the top-level feature, in interbase coordinates.
        else {
            my %parf = (
                'uniquename'    => $uniquename . ':' . $ref->start . "\.\." . $ref->end,
                'organism_id'   =>\%organism,
                'type_id'   =>{'name' =>'region', 'cv_id' => {'name' => $cv_name{'sequence'} }},
                );
            my %parfsrcf = (
                    'uniquename'    => $uniquename,
                    'organism_id'   =>\%organism,
                    );
            my %parfloc = (
                   'srcfeature_id'  => \%parfsrcf,
                   'fmin'       => $ref->start - 1,
                   'fmax'       => $ref->end,
                   );
            $parf{'featureloc'} = \%parfloc;
            $parf{'feature_pub'} = {'pub_id' => \%pubhash};
            my %ffr = (
                   'subject_id' => \%parf,
                   'type_id'        => { 'name' => 'partof', 'cv_id' => { 'name' => $cv_name{'relationship'}}},
                   );
            push(@top_featrels, \%ffr);
        }
        }
        $datahash{'feature_pub'} = \@feature_pubs;
    }

    ##construct srcfeature hash for use in featureloc
    if (defined $srcfeature) {
                %srcfhash = $self->_srcf_hash($srcfeature, 
                                              $srcfeattype, 
                                              \%organism);
    #   my %fr = (
    #       "object_id" => \%srcfhash,
    #       "type_id"   => { 'name' => 'partof', 'cv_id' => { 'name' => 'relationship type'}},
    #       );

    #   push (@top_featrels, \%fr);
    }

    #unflatten the seq features in $seq if $seq is a gene or a DNA sequence
    if (($gb_type eq 'gene' || $gb_type eq 'DNA') &&
        !$nounflatten) {
        my $u = Bio::SeqFeature::Tools::Unflattener->new;
        $u->unflatten_seq(-seq=>$seq, -use_magic=>1);
    }

    my @top_sfs = $seq->get_SeqFeatures;
    #print $#top_sfs, "\n";

    #SUBFEATURES

    if ($datasource =~ /GenBank/i) {
        $tag_cv = 'GenBank feature qualifier';
    } elsif ($datasource =~ /GFF/i) {
        $tag_cv = 'feature_property';
    } else {
        $tag_cv = $cv_name{'feature_property'};
    }

    my $si = 0;
    foreach $feat (@top_sfs) {
        #$feat = $top_sfs[$si];
        #print "si: $si\n";
        my $prim_tag = $feat->primary_tag;
        #print $prim_tag, "\n";

        # get all qualifiers of the 'source' feature, load these as top_featureprops of the top level feature
        if ($prim_tag eq 'source') {
            foreach $tag ($feat->all_tags()) {
                #db_xref
                if ($tag eq 'db_xref' 
                                 or $tag eq 'Dbxref'
                                 or $tag eq 'dbxref')   {
                    my @t1 = $feat->each_tag_value($tag);
                    foreach $temp (@t1) {
                       $temp =~ /([^:]*?):(.*)/;
                                           my $db = $1; 
                                           my $xref = $2;
                                           #PRE/POST very inefficent
                       #my $db = $PREMATCH;
                       #my $xref = $POSTMATCH;
                       my %acchash = (
                        "db_id"     => {'name' => $db},
                        "accession" => $xref,
                        );
                       my %fdbx = ('dbxref_id' => \%acchash);
                       push (@top_dbxrefs, \%fdbx);
                    }
                                #Ontology_term
                                } elsif ($tag eq 'Ontology_term') {
                                        my @t1 = $feat->each_tag_value($tag);
                                        foreach $temp (@t1) {
                                            ###FIXME
                                        }
                #other tags as featureprop
                } elsif ($tag ne 'gene') {
                    my %prophash = undef;
                    %prophash = (
                                    "type_id"       => {'name' => $tag, 'cv_id' => {'name' => $tag_cv}},
                        "value"     => join(' ',$feat->each_tag_value($tag)),
                        );
                    push(@top_featureprops, \%prophash);
                }
            }

                        if ($feat->can('source')) {
                            my $source = $feat->source();
                            @top_dbxrefs = $self->handle_source($feat, @top_dbxrefs);
                        }

            #featureloc for the top-level feature
            my $fmin = undef;
            my $fmax = undef;
            my $strand = undef;
                        my $phase = undef;
            my %fl = undef;

            $fmin = $feat->start - 1;
            $fmax = $feat->end;
            $strand = $feat->strand;

                        if ($feat->can('phase')) {
                            $phase = $feat->phase;
                        }

            %fl = (
                "srcfeature_id" => \%srcfhash,
                "fmin"      => $fmin,
                "fmax"      => $fmax,
                "strand"    => $strand,
                                "phase"         => $phase,
                );

            $datahash{'featureloc'} = \%fl;

            #delete 'source' feature from @top_sfs
            splice(@top_sfs, $si, 1);
        }
        $si ++;
    #close loop over top_sfs
    }

    #the top-level features other than 'source'
    foreach $feat (@top_sfs) {
        #print $feat->primary_tag, "\n";

        my $r = $self->_subfeat2featrelhash($name, $ftype, $feat, \%srcfhash, $tag_cv, $isanalysis);

        if (!($ftype eq 'mRNA' && $feat->primary_tag eq 'gene')) {
            my %fr = %$r;
            push(@top_featrels, \%fr);
        } else {
            %finaldatahash = %$r;
        }
    }

    if (@top_dbxrefs) {
        $datahash{'feature_dbxref'} = \@top_dbxrefs;
    }

    if (@top_featureprops) {
        $datahash{'featureprop'} = \@top_featureprops;
    }

    if (@top_featrels) {
        $datahash{'feature_relationship'} = \@top_featrels;
    }

        if (@top_featurecvterms) {
                $datahash{'feature_cvterm'} = \@top_featurecvterms;
        }

    if ($ftype eq 'mRNA' && %finaldatahash) {
        $finaldatahash{'feature_relationship'} = {
                        'subject_id'    => \%datahash,
                        'type_id'   => { 'name' => 'partof', 'cv_id' => { 'name' => $cv_name{'relationship'} }},
                             };
    } else {
        %finaldatahash = %datahash;
    }

    my $mainTag = 'feature';
    $self->_hash2xml(undef, $mainTag, \%finaldatahash);

    return 1;
}

sub _hash2xml {
    my $self = shift;
    my $isMatch = undef;
    $isMatch = shift;
    my $ult = shift;
    my $ref = shift;
    my %mh = %$ref;
    my $key;
    my $v;
    my $sh;
    my $xx;
    my $yy;
    my $nt;
    my $ntref;
    my $output;
    my $root = shift if (@_);
    #print "ult: $ult\n";
    if (!defined $self->{'writer'}) {
    $root = 1;
        $self->_create_writer();
    }
    my $temp;
    my %subh = undef;

    #start opeing tag
    #if pub record of type 'journal', form the 'ref' attribute for special pub lookup
    #requires that the journal name itself is also stored as a pubprop record for the journal with value equal
    #to the journal name and type of 'abbreviation'.
    if ($ult eq 'pub' && $mh{'type_id'}->{'name'} eq 'journal') {
    $self->{'writer'}->startTag($ult, 'ref' => $mh{'title'} . ':journal:abbreviation');
    }

    #special pub match if pub uniquename not known
    elsif ($ult eq 'pub' && !defined $mh{'uniquename'}) {
    $self->{'writer'}->startTag($ult, 'op' => 'match');
    #set the match flag, all the sub tags should also have "op"="match"
    $isMatch = 1;
    }

    #if cvterm or cv, lookup only
    elsif (($ult eq 'cvterm') || ($ult eq 'cv')) {
    $self->{'writer'}->startTag($ult, 'op' => 'lookup');
    }

    #if nested tables of match table, match too
    elsif ($isMatch) {
    $self->{'writer'}->startTag($ult, 'op' => 'match');
    }

    else {
    $self->{'writer'}->startTag($ult);
    }

    #first loop to produce xml for all the table columns
    foreach $key (keys %mh)
    {
    #print "key: $key\n";
    $xx = ' ' . $key;
    $yy = $key . ' ';
    if (index($chadotables, $xx) < 0 && index($chadotables, $yy) < 0)
    {
        if ($isMatch) {
        $self->{'writer'}->startTag($key, 'op' => 'match');
        } else {
        $self->{'writer'}->startTag($key);
        }

        my $x = $ult . '.' . $key;
        #the column is a foreign key
        if (defined $fkey{$x})
        {
        $nt = $fkey{$x};
        $sh = $mh{$key};
        $self->_hash2xml($isMatch, $nt, $sh, 0);
        } else
        {
        #print "$key: $mh{$key}\n";
        $self->{'writer'}->characters($mh{$key});
        }
        $self->{'writer'}->endTag($key);
    }
    }

    #second loop to produce xml for all the nested tables
    foreach $key (keys %mh)
    {
    #print "key: $key\n";
    $xx = ' ' . $key;
    $yy = $key . ' ';
    #a nested table
    if (index($chadotables, $xx) > 0 || index($chadotables, $yy) > 0)
    {
        #$writer->startTag($key);
        $ntref = $mh{$key};
        #print "$key: ", ref($ntref), "\n";
        if (ref($ntref) =~ 'HASH') {
        $self->_hash2xml($isMatch, $key, $ntref, 0);
        } elsif (ref($ntref) =~ 'ARRAY') {
        #print "array dim: ", $#$ntref, "\n";
        foreach $ref (@$ntref) {
                #print "\n";
            $self->_hash2xml($isMatch, $key, $ref, 0);
        }
        }
        #$writer->endTag($key);
    }
    }

    #end tag
    $self->{'writer'}->endTag($ult);

    #if ($root == 1) {
#   $self->{'writer'}->endTag('chado');
#    }
}

sub _guess_acc_db {
    my $self = shift;
    my $seq = shift;
    my $acc = shift;
    #print "acc: $acc\n";

    if ($acc =~ /^NM_\d{6}/ || $acc =~ /^NP_\d{6}/ || $acc =~ /^NT_\d{6}/ || $acc =~ /^NC_\d{6}/) {
        return "RefSeq";
    } elsif ($acc =~ /^XM_\d{6}/ || $acc =~ /^XP_\d{6}/ || $acc =~ /^XR_\d{6}/) {
        return "RefSeq";
    } elsif ($acc =~ /^[a-zA-Z]{1,2}\d{5,6}/) {
        return "GB";
    } elsif ($seq->molecule() eq 'protein' && $acc =~ /^[a-zA-z]\d{5}/) {
        return "PIR";
    } elsif ($seq->molecule() eq 'protein' && $acc =~ /^\d{6,7}[a-zA-Z]/) {
        return "PRF";
    } elsif ($acc =~ /\d+/ && $acc !~ /[a-zA-Z]/) {
        return "LocusID";
    } elsif ($acc =~ /^CG\d+/ || $acc =~ /^FB[a-z][a-z]\d+/) {
        return "FlyBase";
    } else {
        return "unknown";
    }
}

sub _subfeat2featrelhash {
    my $self = shift;
    my $genename = shift;
    my $seqtype = shift;
    my $feat = shift;
    my $r = shift;
    my %srcf = %$r;     #srcfeature hash for featureloc.srcfeature_id
    my $tag_cv = shift;
    my $isanalysis = shift;

    my $prim_tag = $feat->primary_tag;

    my $sfunique = undef;       #subfeature uniquename
    my $sfname = undef;     #subfeature name
    my $sftype = undef;     #subfeature type

    if ($feat->has_tag('symbol')) {
        ($sfunique) = $feat->each_tag_value("symbol");
    } elsif ($feat->has_tag('label')) {
        ($sfunique) = $feat->each_tag_value("label");
    } else {
        #$self->throw("$prim_tag at " . $feat->start . "\.\." . $feat->end . " does not have symbol or label! To convert into chadoxml, a seq feature must have a /symbol or /label tag holding its unique name.");
        #generate feature unique name as <genename>-<feature-type>-<span>
        $sfunique = $self->_genFeatUniqueName($genename, $feat);
    }

    if ($feat->has_tag('Name')) {
        ($sfname) = $feat->each_tag_value("Name");
    }

    #feature type translation
    if (defined $feattype_args2so{$prim_tag}) {
        $sftype = $feattype_args2so{$prim_tag};
    } else {
        $sftype = $prim_tag;
    }

    if ($prim_tag eq 'mutation') {
        if ($feat->start == $feat->end) {
            $sftype = $feattype_args2so{'mutation1'};
        } else {
            $sftype = $feattype_args2so{'mutation2'};
        }
    }

    #set is_analysis flag for gene model features
    undef(my $isanal);
    if ($sftype eq 'gene' || $sftype eq 'mRNA' || $sftype eq 'exon' || $sftype eq 'protein' || $sftype eq 'polypeptide') {
        $isanal = $isanalysis;
    }

    my %sfhash = (
        "name"          => $sfname,
        "uniquename"        => $sfunique,
        "organism_id"       => \%organism,
        "type_id"       => { 'name' => $sftype, 'cv_id' => { 'name' => $cv_name{'sequence'} }},
        "is_analysis"           => $isanal || 'false',
        );

    #make a copy of %sfhash for passing to this method when recursively called
    #my %srcfeat = (
        #        "name"                  => $sfname,
        #        "uniquename"            => $sfunique,
        #        "organism_id"           => \%organism,
        #        "type_id"               => { 'name' => $sftype, 'cv_id' => { 'name' => 'SO'}},
        #        );

    #featureloc for subfeatures
    undef(my $sfmin);
    undef(my $sfmax);
    undef(my $is_sfmin_partial);
    undef(my $is_sfmax_partial);
    undef(my $sfstrand);
        undef(my $sfphase);
    $sfmin = $feat->start - 1;
    $sfmax = $feat->end;
    $sfstrand = $feat->strand();

        if ($feat->can('phase')) {
            $sfphase = $feat->phase;
        }

    #if the gene feature in an mRNA record, cannot use its coordinates, omit featureloc
    if ($seqtype eq 'mRNA' && $sftype eq 'gene') {
    } else {
        if ($feat->location->isa('Bio::Location::FuzzyLocationI')) {
            if ($feat->location->start_pos_type() ne 'EXACT') {
                $is_sfmin_partial = 'true';
            }
            if ($feat->location->end_pos_type() ne 'EXACT') {
                $is_sfmax_partial = 'true';
            }
        }

        my %sfl = (
            "srcfeature_id" => \%srcf,
            "fmin"      => $sfmin,
            "is_fmin_partial" => $is_sfmin_partial || 'false',
            "fmax"      => $sfmax,
            "is_fmax_partial" => $is_sfmax_partial || 'false',
            "strand"    => $sfstrand,
                        "phase"         => $sfphase,
            );

        $sfhash{'featureloc'} = \%sfl;
    }


    #subfeature tags
    undef(my @sfdbxrefs);       #subfeature dbxrefs
    undef(my @sub_featureprops);    #subfeature props
        undef(my @sub_featuresyns);     #subfeature synonyms
        undef(my @sub_featurecvterms);  #subfeature cvterms
    foreach my $tag ($feat->all_tags()) {
        #feature_dbxref for features
        if ($tag eq 'db_xref' or $tag eq 'dbxref' or $tag eq 'Dbxref')   {
            my @t1 = $feat->each_tag_value($tag);
            #print "# of dbxref: @t1\n";
            for my $temp (@t1) {
               $temp =~ /:/;
               my $db = $PREMATCH;
               my $xref = $POSTMATCH;
               #print "db: $db; xref: $xref\n";
               my %acchash = (
                "db_id"     => {'name' => $db},
                "accession" => $xref,
                );
               my %sfdbx = ('dbxref_id' => \%acchash);
               push (@sfdbxrefs, \%sfdbx);
            }
                #Alias tags
                } elsif ($tag eq 'Alias') {
                        @sub_featuresyns = $self->handle_Alias_tag($feat, @sub_featuresyns);
                } elsif ($tag eq 'Ontology_term') {
                        @sub_featurecvterms = $self->handle_Ontology_tag($feat, @sub_featurecvterms);
        #featureprop for features, excluding GFF Name & Parent tags
        } elsif ($tag ne 'gene' && $tag ne 'symbol' && $tag ne 'Name' && $tag ne 'Parent') {
                        next if ($tag eq 'parent_id');
                        next if ($tag eq 'load_id');
            foreach my $val ($feat->each_tag_value($tag)) {
                my %prophash = undef;
                %prophash = (
                                "type_id"       => {'name' => $tag, 'cv_id' => {'name' => $tag_cv}},
                    "value"     => $val,
                );
                push(@sub_featureprops, \%prophash);
            }
        }
    }

        if ($feat->can('source')) {
                @sfdbxrefs = $self->handle_source($feat,@sfdbxrefs);
        }

    if (@sub_featureprops) {
        $sfhash{'featureprop'} = \@sub_featureprops;
    }
    if (@sfdbxrefs) {
        $sfhash{'feature_dbxref'} = \@sfdbxrefs;
    }
        if (@sub_featuresyns) {
                $sfhash{'feature_synonym'} = \@sub_featuresyns;
        }
        if (@sub_featurecvterms) {
                $sfhash{'feature_cvterm'} = \@sub_featurecvterms;
        }

    undef(my @ssfeatrel);
    if ($feat->has_tag('locus_tag')) {
        ($genename)= $feat->each_tag_value('locus_tag');
    } elsif ($feat->has_tag('gene')) {
        ($genename)= $feat->each_tag_value('gene');
    }

    foreach my $sf ($feat->get_SeqFeatures()) {
        #print $sf->primary_tag, "\n";
        my $rref = $self->_subfeat2featrelhash($genename, $sftype, $sf, \%srcf, $tag_cv, $isanalysis);
        if (defined $rref) {
            push(@ssfeatrel, $rref);
        }
    }

    if (@ssfeatrel) {
        $sfhash{'feature_relationship'} = \@ssfeatrel;
    }

    #subj-obj relationship type
    undef(my $reltypename);
        $reltypename = return_reltypename($sftype);

    my %fr = (
        "subject_id"    => \%sfhash,
        "type_id"       => { 'name' => $reltypename, 
                                             'cv_id' => { 'name' => $cv_name{'relationship'} }},
        );

    if ($seqtype eq 'mRNA' && $sftype eq 'gene') {
        return \%sfhash;
    } else {
        return \%fr;
    }

}

#generate uniquename for feature as: <genename>-<feature-type>-<span> (foo-mRNA-10..1000)
sub _genFeatUniqueName {
    my $self = shift;
    my $genename = shift;
    my $feat = shift;
    undef(my $uniquename);
    my $ftype = $feat->primary_tag;
    my $start = $feat->start;
    my $end = $feat->end;

    if ($feat->has_tag('locus_tag')) {
        ($genename) = $feat->each_tag_value("locus_tag");
    } elsif ($feat->has_tag('gene')) {
        ($genename) = $feat->each_tag_value("gene");
    }

    $uniquename = $genename . '-' . $ftype . '-' . $start . "\.\." . $end;

    return $uniquename;
}

#create uniquename for pubs with no medline id and no FBrf#
#use "<authors>, <year>, <type>" as the uniquename (same as miniref)
#<authors> is <sole-author-surname>    if one author,
#  or <first-author-surname> and <second-author-surname>   if two,
#  or <first-author-surname> et al.   if more
#sub _CreatePubUname {
#   my $self = shift;
#   my $pub = shift;
#   undef(my $pubuname);
#
#   return $pubuname;
#}

#get authors of a reference
#returns ref to the array of author hashes
sub _getRefAuthors {
    my $self = shift;
    my $ref = shift;

    my $temp = $ref->authors;
    undef(my @authors);
    undef(my @aut);

    #there are authors
    if ($temp ne '.') {
        if (index($temp, ' and ') > 0) {
            $temp =~ / and /;
            my $lastauthor = $POSTMATCH;
            @authors = split(/\, /, $PREMATCH);
            push (@authors, $lastauthor);
        } else {
            @authors = split(/\, /, $temp);
        }

        my $a;
        my $i = 0;
        foreach $a (@authors) {
            $i ++;
            #parse the author lastname and givennames
            undef(my $last);
            undef(my $given);
            if (index($a, ',') > 0) {   #genbank format, last,f.m.
                ($last, $given) = split(/\,/, $a);
            } elsif (index($a, ' ') > 0) {  #embl format, last f.m.
                ($last, $given) = split(/ /, $a);
            }
            my %au = (
                'surname'   => $last,
                'givennames'    => $given,
                );
            push(@aut, {author_id => \%au, arank => $i});
        }

        return \@aut;
    }

    #no authors, Bio::SeqIO::genbank doesn't pick up 'CONSRTM' line.
    else {
        return;
    }

}

#extract submission year from the citation of the submitted reference
#genbank format for the submitted citation: JOURNAL   Submitted (DD-MON-YYYY) submitter address
sub _getSubmitYear {
    my $self = shift;
    my $citation = shift;

    if ($citation !~ /Submitted/) {
    $self->warn("not citation for a submitted reference. cannot extract submission year.");
    return;
    } else {
    $citation =~ /Submitted \(\d\d-[a-zA-Z]{3}-\d{4}\)/;
    my $a = $MATCH;
    $a =~ /\d{4}/;
    my $year = $MATCH;

    return $year;
    }
}

sub _getSubmitAddr {
    my $self = shift;
    my $ref = shift;
    undef(my %author);

    my $citation = $ref->location;
    if ($citation !~ /Submitted/) {
    $self->warn("not citation for a submitted reference. cannot extract submission year.");
    return;
    } else {
    $citation =~ /Submitted \(\d\d-[a-zA-Z]{3}-\d{4}\)/;
    my $a = $POSTMATCH;
    if (defined $a) {
        $a =~ s/^\s//;
        %author = (
               'author_id'  => {'surname'   => substr($a, 0, 100)},
               );
        return \%author;
    } else {
        return;
    }
    }
}

=head2 suppress_residues

 Title    : suppress_residues
 Usage    : $obj->suppress_residues()        #get existing value
            $obj->suppress_residues($newval) #set new value
 Function : Keep track of the flag to suppress printing of residues in the
            chadoxml file. The default it to allow all residues to go into the
            file.
 Returns  : value of suppress_residues (a scalar)
 Args     : new value of suppress_residues (to set)

=cut

sub suppress_residues {
    my $self = shift;
    my $suppress_residues = shift if defined(@_);
    return $self->{'suppress_residues'} = $suppress_residues if defined($suppress_residues);
    return $self->{'suppress_residues'};
}

=head2 allow_residues

 Title    : allow_residues
 Usage    : $obj->allow_residues()        #get existing value
            $obj->allow_residues($feature_type) #set new value
 Function : Track the allow_residues type.  This can be used in conjunction
            with the suppress_residues flag to only allow residues from a
            specific feature type to be printed in the xml file, for example,
            only printing chromosome residues. When suppress_residues is set to
            true, then only chromosome features would would go into the xml
            file. If suppress_residues is not set, this function has no effect
            (since the default is to put all residues in the xml file).
 Returns  : value of allow_residues (string that corresponds to a feature type)
 Args     : new value of allow_residues (to set)
 Status   :

=cut

sub allow_residues {
    my $self = shift;
    my $allow_residues = shift if defined(@_);
    return $self->{'allow_residues'} = $allow_residues if defined($allow_residues);
    return $self->{'allow_residues'};
}

=head2 return_ftype_hash

 Title    : return_ftype_hash
 Usage    : $obj->return_ftype_hash()
 Function : A simple hash where returning it has be factored out of the main
            code to allow subclasses to override it.
 Returns  : A hash that indicates what the name of the SO term is and what
            the name of the Sequence Ontology is in the cv table.
 Args     : The string that represents the SO term.
 Status   :

=cut

sub return_ftype_hash {
    my $self  = shift;
    my $ftype = shift;
    my %ftype_hash = ( "name" => $ftype,
                       "cv_id" => {"name" => $cv_name{'sequence'} });
    return %ftype_hash;
}

=head2 return_reltypename

 Title    : return_reltypename
 Usage    : $obj->return_reltypename
 Function : Return the appropriate relationship type name depending on the
            feature type (typically part_of, but derives_from for polypeptide).
 Returns  : A relationship type name.
 Args     : A SO type name.
 Status   :

=cut

sub return_reltypename {
    my $self   = shift;
    my $sftype = shift;

    my $reltypename;
    if ($sftype eq 'protein' || $sftype eq 'polypeptide') {
        $reltypename = 'derives_from';
    } else {
        $reltypename = 'part_of';
    }

    return $reltypename;
}

=head2 next_seq

 Title    : next_seq
 Usage    : $obj->next_seq
 Function : 
 Returns  : 
 Args     : 
 Status   : Not implemented (write only adaptor)

=cut

sub next_seq {
    my ($self, %argv) = @_;

    $self->throw('next_seq is not implemented; this is a write-only adapter.');

}

=head2 _create_writer

 Title    : _create_writer
 Usage    : $obj->_create_writer
 Function : Creates XML::Writer object and writes start tag
 Returns  : Nothing, though the writer persists as part of the chadoxml object
 Args     : None
 Status   :

=cut

sub _create_writer {
    my $self = shift;

    $self->{'writer'} = new XML::Writer(OUTPUT => $self->_fh,
                                        DATA_MODE => 1,
                                        DATA_INDENT => 3);

    #print header
    $self->{'writer'}->xmlDecl("UTF-8");
    $self->{'writer'}->comment("created by Peili Zhang, Flybase, Harvard University\n".
                               "and Scott Cain, GMOD, Cold Spring Harbor Laboratory");

    #start chadoxml
    $self->{'writer'}->startTag('chado');

    return;
}

=head2 close_chadoxml

 Title    : close_chadoxml
 Usage    : $obj->close_chadoxml
 Function : Writes the closing xml tag
 Returns  : None
 Args     : None
 Status   :

=cut

sub close_chadoxml {
    my $self = shift;

    $self->{'writer'}->endTag('chado');
    return;
}

=head2 handle_unreserved_tags

 Title    : handle_unreserved_tags
 Usage    : $obj->handle_unreserved_tags
 Function : Converts tag value pairs to xml-ready hashrefs
 Returns  : The array containing the hashrefs
 Args     : In order: the Seq or SeqFeature object, the key, and the hasharray
 Status   :

=cut

sub handle_unreserved_tags {
    my $self = shift;
    my $seq  = shift;
    my $key  = shift;
    my @arr  = @_;

    my @values = $seq->attributes($key);
    for my $value (@values) {
        my %prophash = (
           "type_id"     => {'name' => $key,
                             'cv_id' => { 'name' => $cv_name{'feature_property'} }
                            },
                            "value"       => $value,
                       );
        push(@arr, \%prophash);
    }

    return @arr;
}

=head2 handle_Alias_tag

 Title    : handle_Alias_tag
 Usage    : $obj->handle_Alias_tag
 Function : Convert Alias values to synonym hash refs
 Returns  : An array of synonym hash tags
 Args     : The seq or seqFeature object and the synonym hash array
 Status   :

=cut

sub handle_Alias_tag {
    my $self = shift;
    my $seq  = shift;
    my @arr  = @_;

    my @Aliases = $seq->attributes('Alias');
    for my $Alias (@Aliases) {
        my %synhash = (
                  "type_id"   => { 'name' => 'exact',
                                  'cv_id' => { 'name'  => 'synonym_type' } },
                                 "name"         => $Alias,
                                 "synonym_sgml" => $Alias,
                      );
        push(@arr, {'synonym_id' => \%synhash,
                    'pub_id'     => {'uniquename' => 'null',
                                     'type_id'    => { 'name' => 'null',
                                                       'cv_id' => {
                                                            'name' => 'null', 
                                                                  },
                                                     },
                                    },
                   });
    }

    return @arr;
}

=head2 handle_Ontology_tag

 Title    : handle_Ontology_tag
 Usage    : $obj->handle_Ontology_tag
 Function : Convert Ontology_term values to ontology term hash refs
 Returns  : An array of ontology term hash refs
 Args     : The seq or seqFeature object and the ontology term array
 Status   :

=cut

sub handle_Ontology_tag  {
    my $self = shift;
    my $seq  = shift;
    my @arr  = @_;

    my @terms = $seq->attributes('Ontology_term');
    for my $term (@terms) {
        my $hashref;
        if ($term =~ /(\S+):(\S+)/) {
            my $db  = $1;
            my $acc = $2;
            $hashref = {
                    'cvterm_id' => {
                        'dbxref_id' => {
                           'db_id' => { 'name' => $db },
                           'accession' => $acc
                                      },
                                   },
                       };
        }
        push(@arr, {cvterm_id => $hashref});
    }

    return @arr;
}

=head2 handle_dbxref

 Title    : handle_dbxref
 Usage    : $obj->handle_dbxref
 Function : Convert Dbxref values to dbxref hashref
 Returns  : An array of dbxref hashrefs
 Args     : A seq or seqFeature object and the dbxref array 
 Status   :

=cut

sub handle_dbxref {
    my $self = shift;
    my $seq  = shift;
    my $tag  = shift;
    my @arr  = @_;

    my @terms = $seq->attributes($tag);
    for my $term (@terms) {
        my $hashref;
        if ($term =~ /(\S+):(\S+)/) {
            my $db = $1;
            my $acc= $2;
            my $version = 1;
            if ($acc =~ /(\S+)\.(\S+)/) {
                $acc = $1;
                $version = $2;
            }
            $hashref = {
                         'dbxref_id' => {
                               'db_id' => { 'name' => $db },
                               'accession' => $acc,
                               'version'   => $version,
                                        },
                       };
        }
        else {
            $self->throw("I don't know how to handle a dbxref like $term");
        }
        push(@arr, {'dbxref_id' => $hashref});
    }
    return @arr;
}

=head2 handle_source

 Title    : handle_source
 Usage    : $obj->handle_source
 Function : 
 Returns  : 
 Args     : 
 Status   :

=cut

sub handle_source {
    my $self = shift;
    my $seq  = shift;
    my @arr  = @_;

    my $source = $seq->source();
    return @arr unless $source;

    my $hashref = {
               'dbxref_id' => {
                       'db_id' => {'name' => 'GFF_source'},
                       'accession' => $source,
                              }
                  };

    push(@arr, {'dbxref_id' => $hashref});
    return @arr;
}

=head2 _srcf_hash

 Title    : _srcf_hash
 Usage    : $obj->_srcf_hash
 Function : Creates the srcfeature hash for use in featureloc hashes
 Returns  : The srcfeature hash
 Args     : The srcfeature name, the srcfeature type and a reference to the
            organism hash.
 Status   :

=cut

sub _srcf_hash {
    my $self = shift;
    my $srcf = shift;
    my $stype= shift;
    my $orgref = shift;

    my %hash = ('uniquename'    => $srcf,
                'organism_id'   => $orgref,
                'type_id'       => {'name' => $stype, 
                                    'cv_id' =>
                                       {'name' => $cv_name{'sequence'} }},
               );

    return %hash;
}


1;