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

	$self->SUPER::_initialize(@args);
	$self->sequence_factory(new Bio::Seq::SeqFactory(
			-type => 'Bio::Seq::RichSeq')
	);

	# Parse the document
	$self->_process();

	my ($self) = @_;
	
	# Check for any more sequences
	return if !defined($self->{_sequences}) or scalar(@{$self->{_sequences}}) < 1;

	# get the next sequence
	my $seq = shift(@{ $self->{_sequences} } );

	# Get the 5' and 3' ends
	my ($source) = grep { $_->primary_tag() eq 'source' } $seq->get_SeqFeatures();
	my ($end5) = $source->get_tag_values('end5');
	my ($end3) = $source->get_tag_values('end3');

	# Sort the 5' and 3':
	my ($start, $end) = ( $end5 < $end3  ? ( $end5, $end3 ) : ( $end3, $end5 ) );

	# make the start a perl index
	$start -= 1;

	# Figure out the length
	my $length = $end - $start;

	# check to make sure $start >= 0 and $end <= length(assembly_seq)
    if($start < 0) {
        throw Bio::Root::OutOfRange("the sequence start is $start < 0");
    } elsif($end > length($self->{_assembly}->{seq})) {
        throw Bio::Root::OutOfRange("the sequence end is $end < " . length($self->{_assembly}->{seq}));
    } elsif($start >= $end) {
        throw Bio::Root::OutOfRange("the sequence start is after end $start >= $end");
    }

	# Get and set the real sequence
	$seq->seq(substr($self->{_assembly}->{seq}, $start, $length));

	if( $end5 > $end3 ) {
		# Reverse complement the sequence
		$seq->seq( $seq->primary_seq()->revcom()->seq() );
	}

	# add the translation to each CDS
	foreach my $feat ($seq->get_SeqFeatures()) {
		next if $feat->primary_tag() ne "CDS";

		# Check for an invalid protein
		try {
			# Get the subsq
			my $cds = new Bio::PrimarySeq(
				-strand => 1,
				-id  => $seq->accession_number(),
				-seq => $seq->subseq($feat->location())
			);

			# Translate it
			my $trans = $cds->translate(undef, undef, undef, undef, 1, 1)->seq();

			# Add the tag
			$feat->add_tag_value(translation => $trans);
		} catch Bio::Root::Exception with {
			print STDERR 'TIGR strikes again, the CDS is not a valid protein: ', $seq->accession_number(), "\n"
				if $self->verbose() > 0;
		};
	}

	# Set the display id to the accession number if there
	# is no display id
	$seq->display_id( $seq->accession_number() ) unless $seq->display_id();
	
	return $seq;

	my($self) = @_;
	my $line;
	my $tu = undef;

	$line = $self->_readline();
	do {
		if($line =~ /<\?xml\s+version\s+=\s+"\d+\.\d+"\?>/o) {
			# do nothing
		} elsif ($line =~ /<!DOCTYPE (\w+) SYSTEM "[\w\.]+">/o) {
			$self->throw("DOCTYPE of $1, not TIGR!")
				if $1 ne "TIGR" ;
		} elsif ($line =~ /<TIGR>/o) {
			$self->_pushback($line);
			$self->_process_tigr();
		} elsif ($line =~ /<ASSEMBLY.*?>/o) {
			$self->_pushback($line);
			$self->_process_assembly();
		} elsif ($line =~ /<\/TIGR>/o) {
			$self->{'eof'}     = 1;
			return;
		} else {
			$self->throw("Unknown or Invalid process directive:",
				join('', ($line =~ /^\s*(<[^>]+>)/o)));
		}
		$line = $self->_readline();
	} while( defined( $line ) );

	my($self) = @_;
	my $line;

	$line = $self->_readline();
	if($line !~ /<TIGR>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_tigr called but no ",
		             "<TIGR> found in stream");
	}

	$line = $self->_readline();
	if($line =~ /<PSEUDOCHROMOSOME>/o) {
		$self->_pushback($line);
		$self->_process_pseudochromosome();
	} elsif ($line =~ /<ASSEMBLY.*?>/o) {
		$self->_pushback($line);
		$self->_process_assembly();
	}

	my($self) = @_;
	my $line;

	$line = $self->_readline();
	return if $line !~ /<PSEUDOCHROMOSOME>/o;

	$line = $self->_readline();

	if($line =~ /<SCAFFOLD>/o) {
		$self->_pushback($line);
		$self->_process_scaffold();
		$line = $self->_readline();
	} else {
		$self->warn( "No Scaffold found in <PSUEDOCHROMOSOME> this " .
		             "is a violation of the TIGR dtd, but we ignore " .
		             "it so we are ignoring the error\n"
		);
	}

	if($line =~ /<ASSEMBLY.*>/o) {
		$self->_pushback($line);
		$self->_process_assembly();
		$line = $self->_readline();
	} else {
		$self->throw("Missing required ASSEMBLY in <PSEUDOCHROMOSOME>");
	}

	if($line =~ /<\/PSEUDOCHROMOSOME>/) {
		return;
	}

	$self->throw("Reached end of _process_psuedochromosome");

	my($self) = @_;
	my $line;

	$line = $self->_readline();
	if($line !~ /<ASSEMBLY([^>]*)>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_assembly called ",
		             "but no <ASSEMBLY> found in stream");
	}

	my %attribs = ($1 =~ /(\w+)\s*=\s+"(.*?)"/og);
	$self->{_assembly}->{date}       = $attribs{CURRENT_DATE};
	$self->{_assembly}->{db}         = $attribs{DATABASE};
	$self->{_assembly}->{chromosome} = $attribs{CHROMOSOME};

	$line = $self->_readline();
	my($attr, $val); 
	if(($attr, $val) = ($line =~ /<ASMBL_ID([^>]*)>([^<]*)<\/ASMBL_ID>/o)) {
		%attribs = ($attr =~ /(\w+)\s*=\s+"(.*?)"/og);
		$self->{_assembly}->{clone_name} = $attribs{CLONE_NAME};
		$self->{_assembly}->{clone} = $val;
		$line = $self->_readtag();
	} else {
		$self->throw("Required <ASMBL_ID> missing");
	}

	if($line =~ /<COORDSET>/o) {
		$self->_pushback($line);
		my $cs = $self->_process_coordset();

		$self->{_assembly}->{end5} = $cs->{end5};
		$self->{_assembly}->{end3} = $cs->{end3};

		$line = $self->_readline();
	} else {
		$self->throw("Required <COORDSET> missing");
	}

	if($line =~ /<HEADER>/o) {
		$self->_pushback($line);
		$self->_process_header();
		$line = $self->_readline();
	} else {
		$self->throw("Required <HEADER> missing");
	}

	if($line =~ /<TILING_PATH>/o) {
		$self->_pushback($line);
		$self->_process_tiling_path();
		$line = $self->_readline();
	}

	if($line =~ /<GENE_LIST>/o) {
		$self->_pushback($line);
		$self->_process_gene_list();
		$line = $self->_readline();
	} else {
		$self->throw("Required <GENE_LIST> missing");
	}

	if($line =~ /<MISC_INFO>/o) {
		$self->_pushback($line);
		$self->_process_misc_info();
		$line = $self->_readline();
	}

	if($line =~ /<REPEAT_LIST>/o) {
		$self->_pushback($line);
		$self->_process_repeat_list();
		$line = $self->_readline();
	}

	if($line =~ /<ASSEMBLY_SEQUENCE>/o) {
		$self->_pushback($line);
		$self->_process_assembly_seq();
		$line = $self->_readline();
	} else {
		$self->throw("Required <ASSEMBLY_SEQUENCE> missing");
	}

	if($line =~ /<\/ASSEMBLY>/o) {
		return;
	}
	$self->throw("Reached the end of <ASSEMBLY>");

	my ($self) = @_;
	my $line;
	
	$line = $self->_readline();
	if($line !~ /<ASSEMBLY_SEQUENCE>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_assembly_seq called ".
			     "with no <ASSEMBLY_SEQUENCE> in the stream");
	}

	# Protect agains lots of smaller lines
	my @chunks;

	do {
		$line = $self->_readline();
		last unless $line;

		my $seq;
		if (($seq) = ($line =~ /^\s*(\w+)\s*$/o)) {
			push(@chunks, $seq);
		} elsif( ($seq) = ( $line =~ /^\s*(\w+)<\/ASSEMBLY_SEQUENCE>\s*$/o) ) {
			push(@chunks, $seq);
			$self->{_assembly}->{seq} = join('', @chunks);
			return;
		}
	} while( $line );

	$self->throw("Reached end of _proces_assembly");

	my ($self) = @_;
	my $line;
	my $h;

	$line = $self->_readline();
	if($line =~ /<COORDSET>/o) {
		$self->_pushback($line);
		$line = $self->_readtag();
		($h->{end5}, $h->{end3}) = ($line =~ /<COORDSET>\s*<END5>\s*(\d+)\s*<\/END5>\s*<END3>\s*(\d+)\s*<\/END3>/os);
		if(!defined($h->{end5}) or !defined($h->{end3})) {
			$self->throw("Invalid <COORDSET>: $line");
		}
		return $h;
	} else {
		$self->throw("Bio::SeqIO::tigr::_process_coordset() called ",
		             "but no <COORDSET> found in stream");
	}

	my ($self) = @_;
	my $line = $self->_readline();

	if($line !~ /<HEADER>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_header called ",
		             "but no <HEADER> found in stream");
	}

	$line = $self->_readtag();
	if($line =~ /<CLONE_NAME>([^>]+)<\/CLONE_NAME>/o) {
		$self->{_assembly}->{clone_name} = $1;
		$line = $self->_readtag();
	} else {
		$self->throw("Required <CLONE_NAME> missing");
	}

	if($line =~ /<SEQ_LAST_TOUCHED>/o) {
		# Ignored for now
		$line = $self->_readtag();
	} else {
		$self->throw("Reqired <SEQ_LAST_TOUCHED> missing");
	}

	if($line =~ /<GB_ACCESSION>([^<]*)<\/GB_ACCESSION>/o) {
		$self->{_assembly}->{gb} = $1;
		$line = $self->_readtag();
	} else {
		$self->throw("Required <GB_ACCESSION> missing");
	}

	if($line =~ /<ORGANISM>\s*(.+)\s*<\/ORGANISM>/o) {
		my( $genus, $species, @ss ) = split(/\s+/o, $1);
		$self->{_assembly}->{species} = new Bio::Species();
		$self->{_assembly}->{species}->genus($genus);
		$self->{_assembly}->{species}->species($species);
		$self->{_assembly}->{species}->sub_species(join(' ', @ss)) if scalar(@ss) > 0;

		$line = $self->_readtag();
	} else {
		$self->throw("Required <ORGANISM> missing");
	}

	if($line =~ /<LINEAGE>([^<]*)<\/LINEAGE>/o) {
		$self->{_assembly}->{species}->classification(
			$self->{_assembly}->{species}->species(),
			reverse(split(/\s*;\s*/o, $1))
		);
		$line = $self->_readtag();
	} else {
		$self->throw("Required <LINEAGE> missing");
	}

	if($line =~ /<SEQ_GROUP>([^<]*)<\/SEQ_GROUP>/o) {
		# ingnored
		$line = $self->_readtag();
	} else {
		$self->throw("Required <SEQ_GROUP> missing");
	}

	while($line =~ /<KEYWORDS>[^<]*<\/KEYWORDS>/o) {
		push(@{$self->{_assembly}->{keywords}}, $1);
		$line = $self->_readtag();
	}

	while($line =~ /<GB_DESCRIPTION>([^<]+)<\/GB_DESCRIPTION>/o) {
		push(@{$self->{_assembly}->{gb_desc}},$1);
		$line = $self->_readtag();
	}

	while($line =~ /<GB_COMMENT>([^<]+)<\/GB_COMMENT>/o) {
		push(@{$self->{_assembly}->{gb_comment}}, $1);
		$line = $self->_readtag();
	}

	if(my %h = ($line =~ /<AUTHOR_LIST(?:\s*(\w+)\s*=\s*"([^"]+)"\s*)*>/o)) {
		#$header->{'AUTHOR_LIST'}=$h{'CONTACT'};
		# Ignored
		while($line !~ /<\/AUTHOR_LIST>/o) {
			$self->_readtag();
		}
		$line = $self->_readline();
	} else {
		$self->throw("Required <AUTHOR_LIST> missing");
	}

	if($line =~ /<\/HEADER>/o) {
		return;
	}

	$self->throw("Reached end of header\n");

	my($self) = @_;
	my $line;

	$line = $self->_readline();
	if($line !~ /<GENE_LIST>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_gene_list called ",
		             "but no <GENE_LIST> in the stream");
	}

	$line = $self->_readline();
	if($line =~ /<PROTEIN_CODING>/o) {
		$self->_pushback($line);
		$self->_process_protein_coding();
		$line = $self->_readline();
	} else {
		$self->throw("Required <PROTEIN_CODING> missing");
	}

	if($line =~ /<RNA_GENES>/o) {
		$self->_pushback($line);
		$self->_process_rna_genes();
		$line = $self->_readline();
	} else {
		$self->throw("Required <RNA_GENES> missing");
	}

	if($line =~ /<\/GENE_LIST>/o) {
		return;
	}

	$self->throw("Reached end of _process_gene_list");

	my ($self) = @_;
	my $line = $self->_readline();

	if($line !~ /<PROTEIN_CODING>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_protein_coding called"
		             . "but no <GENE_LIST> in the stream");
	}

	$line = $self->_readline();
	while($line and $line =~ /<TU>/o) {
		$self->_pushback($line);
		$self->_process_tu();
		$line = $self->_readline();
	}

	# Sort the sequences
	@{$self->{_sequences}} = sort {
		my($one, $two) = ( $a, $b );
		($one) = grep { $_->primary_tag() eq 'source' } $one->get_SeqFeatures();
		($two) = grep { $_->primary_tag() eq 'source' } $two->get_SeqFeatures();
		return 0 unless defined $one and defined $two;
		($one) = sort { $a <=> $b } $one->get_tagset_values(qw/end5 end3/);
		($two) = sort { $a <=> $b } $two->get_tagset_values(qw/end5 end3/);
		return $one <=> $two;
	} @{$self->{_sequences}};

	if($line =~ /<\/PROTEIN_CODING>/o) {
		return;
	}

	$self->throw("Reached end of _process_protein_coding");

	my ($self) = @_;
	my $line = $self->_readline();

	if($line =~ /<RNA_GENES>/o) {
		while($line !~ /<\/RNA_GENES>/o) {
			$line = $self->_readline();
		}
	} else {
		$self->throw("Bio::SeqIO::tigr::_process_rna_genes called ",
		             "but no <RNA_GENES> in the stream");
	}

	my ($self) = @_;
	my $line = $self->_readline();

	if($line =~ /<MISC_INFO>/o) {
		while($line !~ /<\/MISC_INFO>/o) {
			$line = $self->_readline();
		}
	} else {
		$self->throw("Bio::SeqIO::tigr::_process_misc_info called ",
		             "but no <MISC_INFO> in the stream");
	}

	my ($self) = @_;
	my $line = $self->_readline();

	if($line =~ /<REPEAT_LIST>/o) {
		while($line !~ /<\/REPEAT_LIST>/o) {
			$line = $self->_readline();
		}
	} else {
		$self->throw("Bio::SeqIO::tigr::_process_repeat_list called ",
		             "but no <MISC_INFO> in the stream");
	}

	my($self) = @_;
	my $line = $self->_readline();


	if($line =~ /<TILING_PATH>/o) {
		while($line !~ /<\/TILING_PATH>/o) {
			$line = $self->_readline();
		}
	} else {
		$self->throw("Bio::SeqIO::tigr::_process_repeat_list called ",
		             "but no <MISC_INFO> in the stream");
	}

	my ($self) = @_;
	my $line;

	# for now we just skip them
	$line = $self->_readline();
	return if $line !~ /<SCAFFOLD>/o;
	do {
		$line = $self->_readline();
	} while(defined($line) && $line !~ /<\/SCAFFOLD>/o);

	my($self) = @_;
	my $line = $self->_readline();

	try {
		my $tu = new Bio::Seq::RichSeq(-strand => 1);
		$tu->species( $self->{_assembly}->{species} );

		# Add the source tag, so we can add the GO annotations to it
		$tu->add_SeqFeature(new Bio::SeqFeature::Generic(-source_tag => 'TIGR', -primary_tag => 'source'));
		
		if($line !~ /<TU>/o) {
			$self->throw("Process_tu called when no <TU> tag");
		}

		$line = $self->_readtag();
		if ($line =~ /<FEAT_NAME>([\w\.]+)<\/FEAT_NAME>/o) {
			$tu->accession_number($1);
			$tu->add_secondary_accession($1);
			$line = $self->_readtag();
		} else {
			$self->throw("Invalid Feat_Name");
		}

		while($line =~ /<GENE_SYNONYM>/o) {
			# ignore
			$line = $self->_readtag();
		}
	
		while($line =~ /<CHROMO_LINK>\s*([\w\.]+)\s*<\/CHROMO_LINK>/o) {
			$tu->add_secondary_accession($1);
			$line = $self->_readtag();
		}

		if ($line =~ /<DATE>([^>]*)<\/DATE>/o) {
			$tu->add_date($1) if $1 and $1 !~ /^\s*$/o;
			$line = $self->_readline();
		} else {
			#$self->throw("Invalid Date: $line");
		}

		if ($line =~ /<GENE_INFO>/o) {
			$self->_pushback($line);
			$self->_process_gene_info($tu);
			$line = $self->_readline();
		} else {
			$self->throw("Invalid Gene_Info");
		}

		my $source;
		my $end5;
		my $end3;
		if($line =~ /<COORDSET>/o) {
			$self->_pushback($line);
			my $cs = $self->_process_coordset();
	
			$end5 = $cs->{end5};
			$end3 = $cs->{end3};

			my $length = $end3 - $end5;
			my $strand = $length <=> 0;
			$length = $length * $strand;
			$length++; # Correct for starting at 1, not 0

			# Add X filler sequence
			$tu->seq('X' x $length);

			# Get the source tag:
			my($source) = grep { $_->primary_tag() eq 'source' } $tu->get_SeqFeatures();

			# Set the start and end values
			$source->start(1);
			$source->end($length);
			$source->strand(1);

			# Add a bunch of tags to it
			$source->add_tag_value(clone      => $self->{_assembly}->{clone});
			$source->add_tag_value(clone_name => $self->{_assembly}->{clone_name});
			$source->add_tag_value(end5       => $end5);
			$source->add_tag_value(end3       => $end3);
			$source->add_tag_value(chromosome => $self->{_assembly}->{chromosome});
			$source->add_tag_value(strand     => ( $strand == 1 ? 'positive' : 'negative' ));

			$line = $self->_readline();
		} else {
			$self->throw("Invalid Coordset");
		}

		if($line =~ /<MODEL[^>]*>/o) {
			do {
				$self->_pushback($line);
				$self->_process_model($tu, $end5, $end3);
				$line = $self->_readline();
			} while($line =~ /<MODEL[^>]*>/o);
			$self->_pushback($line);
			$line = $self->_readtag();
		} else {
			$self->throw("Expected <MODEL> not found");
		}
		
		if($line =~ /<TRANSCRIPT_SEQUENCE>/o) {
			my @chunks;
			$line = $self->_readline();
			while ($line =~ /^\s*([ACGT]+)\s*$/o) {
				push( @chunks, $1 );
				$line = $self->_readline();
			}
			#	$line = $self->_readline();
		}
		
		if($line =~ /<GENE_EVIDENCE>/o) {
			$line = $self->_readtag();
		}
		
		while($line =~ /<URL[^>]*>[^<]*<\/URL>/o) {
			$line = $self->_readtag();
		}
		
		if($line =~ /<\/TU>/o) {
			push(@{$self->{_sequences}}, $tu);
			return;
		} else {
			$self->throw("Expected </TU> not found: $line");
		}
	} catch Bio::Root::OutOfRange with {
		my $E = shift;
		$self->warn(sprintf("One sub location of a sequence is invalid near line $.\: %s", $E->text()));
		$line = $self->_readline() until $line =~ /<\/TU>/o;
		return;
	};

	my($self, $tu) = @_;
	my $line = $self->_readline();

	$self->throw("Invalid Gene Info: $line") if $line !~ /<GENE_INFO>/o;
	$line = $self->_readline();

	if($line =~ /<LOCUS>\s*([\w\.]+)\s*<\/LOCUS>/o) {
		$tu->accession_number($1);
		$tu->add_secondary_accession($1);
		$line = $self->_readline();
	} elsif( $line =~ /<LOCUS>.*<\/LOCUS>/o) {
		# We should throw an error, but TIGR doesn't alwasy play
		# nice with adhering to their dtd
		$line = $self->_readtag();
	} else {
		#$self->throw("Invalid Locus: $line");
	}

	if($line =~ /<ALT_LOCUS>\s*([\w\.]+)\s*<\/ALT_LOCUS>/o) {
		$tu->accession_number($1);
		$tu->add_secondary_accession($1);
		$line = $self->_readline();
	}

	if($line =~ /<PUB_LOCUS>\s*([\w\.]+)\s*<\/PUB_LOCUS>/o) {
		$tu->accession_number($1);
		$tu->add_secondary_accession($1);
		$line = $self->_readtag();
	} elsif( $line =~ /<PUB_LOCUS>.*<\/PUB_LOCUS>/o) {
		$line = $self->_readtag();
#		$self->throw("Invalid Pub_Locus");
	}

	if($line =~ /<GENE_NAME.*>.*<\/GENE_NAME>/o) {
		# Skip the GENE_NAME
		$line = $self->_readtag();
	}

	if(my($attr, $value) = ($line =~ /<COM_NAME([^>]*)>([^>]+)<\/COM_NAME>/o)) {
		#%attribs = ($attr =~ /(\w+)\s*=\s+"(.*?)"/og);
		#$geneinfo->{'CURATED'} = $attribs{CURATED};
		#$geneinfo->{IS_PRIMARY} = $attribs{IS_PRIMARY}
		# TODO: add a tag on sources for curated
		$tu->desc($value);
		$line = $self->_readtag();
	} else {
		$self->throw("invalid com_name: $line");
	}

	while($line =~ /<COMMENT>([^<]+)<\/COMMENT>/o) {
		my $comment = new Bio::Annotation::Comment(
			-text => $1
		);
		$tu->annotation()->add_Annotation('comment', $comment);
		$line = $self->_readtag();
	}

	while($line =~ /<PUB_COMMENT>([^<]+)<\/PUB_COMMENT>/o) {
		my $comment = new Bio::Annotation::Comment(
			-text => $1
		);
		$tu->annotation()->add_Annotation('comment', $comment);
		$line = $self->_readtag();
	}

	if($line =~ /<EC_NUM>([\w\-\\\.]+)<\/EC_NUM>/o) {
		#$geneinfo->{'EC_NUM'} = $1;
		$line = $self->_readtag();
	}

	if($line =~ /<GENE_SYM>\s*([^<]+)\s*<\/GENE_SYM>/o) {
		#$tu->add_secondary_accession($1);
		$line = $self->_readtag();
	}

	if($line =~ /<IS_PSEUDOGENE>([^>]+)<\/IS_PSEUDOGENE>/o) {
		#$geneinfo->{'IS_PSEUDOGENE'} = $1;
		$line = $self->_readtag();
	} else {
		$self->throw("invalid is_pseudogene: $line");
	}

	if($line =~ /<FUNCT_ANNOT_EVIDENCE/o) {
		$line = $self->_readtag();
	}

	if($line =~ /<DATE>([^>]+)<\/DATE>/o) {
		#$geneinfo->{'DATE'} = $1;
		$line = $self->_readtag();
	}

	while($line =~ /<GENE_ONTOLOGY>/o) {
		# Get the source tag
		my($source) = grep { $_->primary_tag() eq 'source' } $tu->get_SeqFeatures();

		my @ids = ( $line =~ /(<GO_ID.*?<\/GO_ID>)/gso);
		foreach my $go (@ids) {
			my($assignment) = ($go =~ /<GO_ID\s+ASSIGNMENT\s+=\s+"GO:(\d+)">/os);
			my($term)       = ($go =~ /<GO_TERM>([^<]+)<\/GO_TERM>/os);
			my($type)       = ($go =~ /<GO_TYPE>([^<]+)<\/GO_TYPE>/os);
			# TODO: Add GO annotation
			if(defined $type and defined $assignment and defined $term) {
				# Add the GO Annotation
				$source->add_tag_value(
				GO => "ID: $assignment; Type: $type; $term"
				);
			}
		}
		$line = $self->_readtag();
	}
	
	if($line =~ /<\/GENE_INFO/o) {
		return;
	}

	$self->throw("unexpected end of gene_info");

	my($self, $end5, $end3, $length, $cs) = @_;
	
	# Find the start and end of the location
	# relative to the sequence.
	my $start = abs( $end5 - $cs->{end5} ) + 1;
	my $end   = abs( $end5 - $cs->{end3} ) + 1;

	# Do some bounds checking:
	if( $start < 1 ) {
		throw Bio::Root::OutOfRange(
			-text => "locations' start( $start) must be >= 1"
		);
	} elsif( $end > $length ) {
		throw Bio::Root::OutOfRange(
			-text => "locations' end( $end ) must be <= length( $length )"
		);
	} elsif( $start > $end ) {
		throw Bio::Root::OutOfRange(
			-text => "locations' start ( $start ) must be < end ( $end ) $end5, $end3, $cs->{end5}, $cs->{end3}"
		);
	}

	return new Bio::Location::Simple( -start => $start, -end => $end, -strand => 1 );

	my($self, $tu, $end5, $end3) = @_;
	my $line;
	my( $source ) = grep { $_->primary_tag() eq 'source' } $tu->get_SeqFeatures();
	my $model = new Bio::SeqFeature::Generic(
		-source_tag  => 'TIGR',
		-primary_tag => 'MODEL',
	);

	$line = $self->_readline();
	if($line !~ /<MODEL ([^>]+)>/o) {
		$self->throw("Invalid Model: $line")
	}
	my %attribs = ($1 =~ /(\w+)\s*=\s*"([^"]*)"/og);
	#$model->{'CURATED'} = $attribs{'CURATED'};
	# TODO: Add tag to model
	$line = $self->_readline();

	if($line =~ /<FEAT_NAME>\s*([\w\.]+)\s*<\/FEAT_NAME>/o) {
		$model->add_tag_value( feat_name => $1 );
		$tu->add_secondary_accession($1);
		$line = $self->_readline();
	} else {
		$self->throw("Invalid Feature Name: $line");
	}

	if($line =~ /<PUB_LOCUS>\s*([\w\.]+)\s*<\/PUB_LOCUS>/o) {
		$model->add_tag_value( pub_locus => $1 );
		$tu->add_secondary_accession($1);
		$line = $self->_readline();
	} else {
#		$self->throw("Invalid Pub_Locus: $line");
	}

	if($line =~ /<CDNA_SUPPORT>/o) {
		$self->_pushback($line);
		$self->_process_cdna_support( $model );
		$line = $self->_readline();
	}

	while($line =~ /<CHROMO_LINK>([^>]+)<\/CHROMO_LINK>/o) {
		$model->add_tag_value( chromo_link => $1 );
		$line = $self->_readline();
	} 

	if($line =~ /<DATE>([^>]+)<\/DATE>/o) {
		$line = $self->_readline();
	} else {
		$self->throw("Invalid Date: $line");
	}

	if($line =~ /<COORDSET>/o) {
		$self->_pushback($line);
		my $cs = $self->_process_coordset();
		my $loc = $self->_build_location($end5, $end3, $tu->length(), $cs);
		
		$model->start( $loc->start() );
		$model->end(   $loc->end()   );
		$line = $self->_readline();
	} else {
		$self->throw("Invalid Coordset: $line");
	}

	my $exon = new Bio::SeqFeature::Generic(
		-source_tag  => 'TIGR',
		-primary_tag => 'EXON',
		-location => new Bio::Location::Split(),
		-tags => [ locus => $tu->accession_number() ],
	);
	$exon->add_tag_value( model => $model->get_tag_values('feat_name') );

	my $cds  = new Bio::SeqFeature::Generic(
		-source_tag  => 'TIGR',
		-primary_tag => 'CDS',
		-location => new Bio::Location::Split(),
		-tags => [ locus => $tu->accession_number() ],
	);
	$cds->add_tag_value( model => $model->get_tag_values('feat_name') );
	my $utr = [];

	if($line =~ /<EXON>/o) {
		do {
			$self->_pushback($line);
			$self->_process_exon( $tu, $exon, $cds, $utr, $end5, $end3 );
			$line = $self->_readline();
		} while($line =~ /<EXON>/o);
	} else {
		$self->throw("Required <EXON> missing");
	}
	
	until($line =~ /<\/MODEL>/o) {
		$line = $self->_readline();
	}


	$_->add_tag_value( model => $model->get_tag_values('feat_name') )
		foreach @$utr;

	# Add the model, EXONs, CDS, and UTRs
	$tu->add_SeqFeature($model) if $model and $model->start() >= 1;
	$tu->add_SeqFeature($exon)  if $exon  and scalar($exon->location()->each_Location()) >= 1;
	$tu->add_SeqFeature($cds)   if $cds   and scalar($cds->location()->each_Location()) >= 1;
	$tu->add_SeqFeature(@$utr);

	return;

	my($self, $model) = @_;
	my $line = $self->_readline();

	if($line !~ /<CDNA_SUPPORT>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_cdna_support called ",
		             "but no <CDNA_SUPPORT> in the stream");
	}

	$line = $self->_readline();

	while( $line =~ /<ACCESSION([^>]+)>(.*)<\/ACCESSION>/o) {
		# Save the text
		my $desc = $2;
		
		# Get the element's attributes
		my %attribs = ($1 =~ /(\w+)\s*=\s*"([^"]*)"/og);

		# Add the tag to the model
		$model->add_tag_value(
			cdna_support => "DBXRef: $attribs{DBXREF}; $desc"
		);

		$line = $self->_readline();
	}

	if( $line =~ /<\/CDNA_SUPPORT>/o) {
		return;
	}
	$self->throw("reached end of _process_cdna_support");

	my($self, $tu, $exon, $cds, $utr, $end5, $end3 ) = @_;
	my $line = $self->_readline();

	if($line !~ /<EXON>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_exon called ",
		             "but no <EXON> in the stream");
	}

	$line = $self->_readtag();
	if($line =~ /<FEAT_NAME>([^<]+)<\/FEAT_NAME>/o) {
		# Ignore
		$line = $self->_readtag();
	} else {
		$self->throw("Required <FEAT_NAME> missing");
	}

	if($line =~ /<DATE>([^<]+)<\/DATE>/o) {
		# Ignore
		$line = $self->_readtag();
	} else {
		$self->throw("Required <DATE> missing");
	}

	if($line =~ /<COORDSET>/o) {
		$self->_pushback($line);
		my $cs = $self->_process_coordset();
		my $loc = $self->_build_location($end5, $end3, $tu->length(), $cs);
		$exon->location()->add_sub_Location($loc);
		$line = $self->_readline();
	} else {
		$self->throw("Required <COORDSET> missing");
	}

	if($line =~ /<CDS>/o) {
		$self->_pushback($line);
		$self->_process_cds($tu, $end5, $end3, $cds);
		$line = $self->_readline();
	}

	if($line =~ /<UTRS>/o) {
		$self->_pushback($line);
		$self->_process_utrs($tu, $end5, $end3, $utr);
		$line = $self->_readline();
	}

	if($line =~ /<\/EXON>/o) {
		return;
	}

	$self->throw("Reached End of Bio::SeqIO::tigr::_process_exon");

	my($self, $tu, $end5, $end3, $cds) = @_;
	my $line = $self->_readline();

	if($line !~ /<CDS>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_cda_support called ",
		             "but no <CDS> in the stream");
	}
	
	$line = $self->_readtag();
	if($line =~ /<FEAT_NAME>([^<]+)<\/FEAT_NAME>/o) {
		#$cds->{'FEAT_NAME'} = $1;
		$line = $self->_readtag();
	} else {
		$self->throw("Required <FEAT_NAME> missing");
	}

	if($line =~ /<DATE>([^<]+)<\/DATE>/o) {
		#$cds->{'DATE'} = $1;
		$line = $self->_readtag();
	} else {
		$self->throw("Required <DATE> missing");
	}

	if($line =~ /<COORDSET>/o) {
		$self->_pushback($line);
		my $cs = $self->_process_coordset();
		my $loc = $self->_build_location($end5, $end3, $tu->length(), $cs);
		$cds->location()->add_sub_Location($loc);
		$line = $self->_readline();
	} else {
		$self->throw("Required <COORDSET> missing");
	}

	if($line =~ /<\/CDS>/o) {
		return;
	}

	$self->throw("Reached onf of Bio::SeqIO::tigr::_process_cds");

	my($self, $tu, $end5, $end3, $utrs) = @_;
	my $line = $self->_readline();

	if($line !~ /<UTRS/o) {
		$self->throw("Bio::SeqIO::tigr::_process_utrs called but no ",
		             "<UTRS> found in stream");
	}

	$line = $self->_readline();
	while($line !~ /<\/UTRS>/o) {
		$self->_pushback($line);
		if($line =~ /<LEFT_UTR>/o) {
			$self->_process_left_utr($tu, $end5, $end3, $utrs);
		} elsif ($line =~ /<RIGHT_UTR>/o) {
			$self->_process_right_utr($tu, $end5, $end3, $utrs);
		} elsif ($line =~ /<EXTENDED_UTR>/o) {
			$self->_process_ext_utr($tu, $end5, $end3, $utrs);
		} else {
			$self->throw("Unexpected tag");
		}
	
		$line = $self->_readline();
	}

	if($line =~ /<\/UTRS>/o) {
		return $utrs;
	}
	$self->throw("Reached end of Bio::SeqIO::tigr::_process_utrs");

	my($self, $tu, $end5, $end3, $utrs) = @_;
	my $line = $self->_readline();
	my $coordset;

	if($line !~ /<LEFT_UTR>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_left_utr called but ",
		             "no <LEFT_UTR> found in stream");
	}

	$line = $self->_readtag();
	if($line =~ /<COORDSET>/o) {
		$self->_pushback($line);
		my $cs = $self->_process_coordset();
		my $loc = $self->_build_location($end5, $end3, $tu->length(), $cs);

		push(@$utrs, new Bio::SeqFeature::Generic(
		        -source_tag  => 'TIGR',
				-primary_tag => 'LEFT_UTR',
				-strand => 1,
				-start => $loc->start(),
				-end   => $loc->end()
		));

		$line = $self->_readline();
	} else {
		$self->throw("Required <COORDSET> missing");
	}

	if($line =~ /<\/LEFT_UTR>/o) {
		return;
	}
	$self->throw("Reached end of Bio::SeqIO::tigr::_process_left_utr");

	my($self, $tu, $end5, $end3, $utrs) = @_;
	my $line = $self->_readline();
	my $coordset;

	if($line !~ /<RIGHT_UTR>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_right_utr called but ",
		             "no <RIGHT_UTR> found in stream");
	}

	$line = $self->_readtag();
	if($line =~ /<COORDSET>/o) {
		$self->_pushback($line);
		$coordset = $self->_process_coordset();
		$self->_pushback($line);
		my $cs = $self->_process_coordset();
		my $loc = $self->_build_location($end5, $end3, $tu->length(), $cs);

		push(@$utrs, new Bio::SeqFeature::Generic(
		        -source_tag  => 'TIGR',
				-primary_tag => 'RIGHT_UTR',
				-strand => 1,
				-start => $loc->start(),
				-end   => $loc->end()
		));

		$line = $self->_readline();
	} else {
		$self->throw("Required <COORDSET> missing");
	}

	if($line =~ /<\/RIGHT_UTR>/o) {
		return $coordset;
	}
	$self->throw("Reached end of Bio::SeqIO::tigr::_process_right_utr");

	my($self, $tu, $end5, $end3, $utrs) = @_;
	my $line = $self->_readline();
	my $coordset;

	if($line !~ /<EXTENDED_UTR>/o) {
		$self->throw("Bio::SeqIO::tigr::_process_ext_utr called but ",
		             "no <EXTENDED_UTR> found in stream");
	}

	$line = $self->_readtag();
	if($line =~ /<COORDSET>/o) {
		$self->_pushback($line);
		my $cs = $self->_process_coordset();
		my $loc = $self->_build_location($end5, $end3, $tu->length(), $cs);

		push(@$utrs, new Bio::SeqFeature::Generic(
		        -source_tag  => 'TIGR',
				-primary_tag => 'EXTENDED_UTR',
				-strand => 1,
				-start => $loc->start(),
				-end   => $loc->end()
		));

		$line = $self->_readline();
	} else {
		$self->throw("Required <COORDSET> missing");
	}

	if($line =~ /<\/EXTENDED_UTR>/o) {
		return $coordset;
	}
	$self->throw("Reached end of Bio::SeqIO::tigr::_process_ext_utr");

	my($self) = @_;
	my $line = $self->_readline();
	chomp($line);

	my $tag;
	if(($tag) = ($line =~ /^[^<]*<\/(\w+)/o)) {
		$self->_pushback($1) if $line =~ /<\/$tag>(.+)$/;
		return "</$tag>";
	}
 
	until(($tag) = ($line =~ /<(\w+)[^>]*>/o)) {
		$line = $self->_readline();
		chomp $line;
	}

	until($line =~ /<\/$tag>/) {
		$line .= $self->_readline();
	}

	if(my ($val) = ($line =~ /(<$tag.*>.*?<\/$tag>)/s)) {
		if($line =~ /<\/$tag>\s*(\w+[\s\w]*?)\s*$/s) {
			$self->_pushback($1)
		}
		return $val;
	}
	$self->throw("summerror");

	my($self) = @_;
	my $line;
	do {
		$line = $self->SUPER::_readline();
	} while(defined($line) and $line =~ /^\s*$/o);

	return $line;

	my($self, @s) = @_;
	my $string = "[$.]" . join('', @s);
	$self->SUPER::throw($string);

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

  http://bugzilla.bioperl.org

 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream
 Returns : Bio::Seq object
 Args    : NONE