sub filter_by_Species()
{

print("New Blast File Opened<BR>");

open( NEWALIGN, "<blast_files/$newBlastFile") || die "$!";
print("Filtering Data........Please wait<P>");

#PARSE BLAST RESULT HERE....
#read results file one line at a time
my @resultLine = <NEWALIGN>;    # used instead of BLASTFILE
my $alignment = {};	# reference to an empty hash
my @subjects = [];  # reference to empty array
my $current_subject = "front_matter";
$alignment->{$current_subject} = "";

#so I produce a hash with key = >gi line of report and value = all lines after until next >gi
for (my $i = 0 ; $i<scalar @resultLine; $i++)
{
	if ($resultLine[$i] =~ /^>/)
	{
		$current_subject = $resultLine[ $i ];
		chomp ($current_subject);
		push (@subjects, $current_subject);
		$alignment->{$current_subject} = "";	#$alignment->{$current_subject} means give value of $alignment when $current_subject is the key
	}
	$alignment->{$current_subject} = $alignment->{$current_subject}.$resultLine[ $i ];
}

my @elements;
my $boolean;

print("<TABLE BORDER=2>");
print("<th align=center><B>Status</B></th>");
print("<th align=center><B>Information on new hits</B></th>");

foreach my $z (@subjects)
{
	chomp $z;
	@elements = split('\|', $z);
	if($elements[4] =~ /^$species_filter/) ##### filtering part here
	{
    $boolean = 0;
		print ("<TR><TD>Match to $species_filter");
    show_Output($boolean, $z, @elements);
	}
}

print("</TABLE><BR><BR>");

#close files
close NEWALIGN;
}


################################################################################
# Display the blast results to user in easy to view format
sub show_Output()          # HTML code
{
    my ($boolean, $z, @elements_copy) = @_;

    $elements_copy[1] = '<a href="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val='.$elements_copy[1].">Link</a>";
    if($boolean == 0)
    {
      print("<TR><TD> $z </TD><TD>@elements_copy[1]</TD></TR>");
    }
    else
    {
      print("<TD> $z <BR>&nbsp - New value added to new reference list &nbsp</TD><TD>@elements_copy[1]</TD></TR>");
    }
}