=head1 MySAXHandler

MySAXHandler is a little package to describe what to do with the events generated by the SAX parser.
All events are treated by methods described here. MySAXHandler is instanciated in the parser declaration.

Variable %entryArgs keeps data until end_element = 'entry' event and then it writes data. It's keys are :

=over 3
  =item 'Accession' which is a hash structure also as there can be more than one accession number for each entry. Accession number is hold in the key, and value is empty.
  =item 'Organism' which stores the organism name
  =item
  =item
  =item 

=back

Other variables used in this package

=over 3
  
  =item $currentElement : Stores the Name of the current element
  =item $currentAttributes : Store a hash reference towards the current element's attributes
  =item $entryCounter : counts <entry> tags seen
  =item $entryDone : counts </entry> tags seen
  =item $dbReferenceOn : Set to 1 if we are in a <dbReference> ... </dbReference> block
  =item $comment : as above for <comment> ... </comment>
  
=back

=head1 Methods

=cut

package MySAXHandler;
use base qw(XML::SAX::Base);

$|=1;

my (%entryArgs);
my (
	$currentElement, $currentAttributes, $entryCounter,
	$entryDone,      $accessionNumber,   $currentAttrs
);
my ( $dbReferenceOn, $commentOn, $organismOn ) = ( 0, 0, 0 );

=head2 start_document

For us this method does nothing for now.

=cut

sub start_document {
	my ( $self, $doc ) = @_;

	#What to do with the document start
	print "Here we go ..............\n\n";
}

=head2 start_element

Event 'start_element' calls this function.
Depending on the tag Name, it does various things.
Tag name is stored into $currentElement. It's attributes into $currentAttributes.

=cut

sub start_element {
	my ( $self, $el ) = @_;

	#clear %entryArgs when start_element = <entry>
	if ( $el->{Name} eq 'entry' ) {
		undef(%entryArgs);
		$entryCounter++;
	}

	#Set the current element name and attributes
	$currentElement = $el->{Name};

	#print $el->{Name}."\n";

	$currentAttributes = $el->{Attributes};

#	foreach my $key (keys %{$currentAttributes}) {
#			print "===============$key => ".%{$currentAttributes}->{$key}->{Value}."================\n";
#		}

	#Set some flag to 1 for interesting blocks
	$dbReferenceOn = 1                  if ( $el->{Name} eq 'dbReference' );
	$commentOn     = 1                  if ( $el->{Name} eq 'comment' );
	$organismOn    = 1                  if ( $el->{Name} eq 'organism' );
	$organismAttrs = $currentAttributes if ( $el->{Name} eq 'name' );
}

=head2 end_element

Store data into the dB, and prints out if tag name = entry.

Set flags back to 0.

=cut

sub end_element {
	my ( $self, $el ) = @_;

	#What to do now ... print out or store in dB
	if ( $el->{Name} eq 'entry' ) {
		print "Accession number(s) :\n";
		foreach my $key ( sort keys %{ $entryArgs{'Accession'} } ) {
			print "\t=>$key\n";
		}

		print "\n\tOrganism Name = " . $entryArgs{'Organism'} . "\n";
	}

	#foreach my $key (sort keys %entryArgs) {

	#Store Accession Number
	$entryArgs{'Accession'}{$accessionNumber}++
	  if ( $el->{Name} eq 'accession' );
	undef($accessionNumber) if ( $el->{Name} eq 'accession' );

	#Set the flags back
	$dbReferenceOn = 0 if ( $el->{Name} eq 'dbReference' );
	$commentOn     = 0 if ( $el->{Name} eq 'comment' );
	$organismOn    = 0 if ( $el->{Name} eq 'organism' );
}

=head2 characters

Store data into the entryArgs hash.

=cut

sub characters {
	my ( $self, $char ) = @_;
	my $text = $char->{Data};

	#Store accesion number
	if ( $currentElement eq 'accession' ) {
		$accessionNumber .= $text;

		$accessionNumber =~ s/[\s\r\n]//g;
	}

	#Store organism name
	if ( $organismOn == 1 and $currentElement eq 'name' ) {
		if ( $organismAttrs->{'{}type'}->{Value} eq 'scientific' ) {
			$entryArgs{'Organism'} .= $text;
		}
	}

}

sub end_document {
	my ( $self, $doc ) = @_;

	print "\n\n ...................... et voilą ;-)\n";
}