package ClustalW;
use Sets;


sub new {
    my ($self)  = {};
    $self->{FILE} = undef;
    $self->{TEXT} = undef;
    #my %tmp = ();
    $self->{SEQS} = undef; #\%tmp;
    $self->{STARS} = "";
    $self->{NAMES} = undef;
    $self->{SEQ_ARRAY} = [];

    $self->{SEQ_UA}    = [];
    $self->{NAM_UA}    = [];

    bless($self);
    return $self;
}

sub setSequences {
  my ($self, $a_ref_n, $a_ref_s) = @_;

  $self->{NAMES}     = $a_ref_n;
  $self->{SEQ_ARRAY} = $a_ref_s;
}


sub setSequencesToAlign {
  my ($self, $a_ref_n, $a_ref_s) = @_;

  $self->{NAM_UA}  = $a_ref_n;
  $self->{SEQ_UA} = $a_ref_s;
}




sub getClustalWformat {
  
  my ($self) = @_;

  my $l   = length($self->{SEQ_ARRAY}->[0]);
  my $n   = scalar(@{ $self->{NAMES} });
  my $txt = "CLUSTAL W(1.4) multiple sequence alignment\n";
  $txt   .= "\n\n";

  my $nb_blocks = int($l / 50) + 1;

  for (my $i=0; $i<$nb_blocks; $i++) {
    
    for (my $j=0; $j<$n; $j++) {
      
      $txt .= $self->{NAMES}->[$j];
      $txt .=  substr("                                   ", 0, 16 - length($self->{NAMES}->[$j]));
      
      for (my $k=0; $k<5; $k++) {
	$txt .= substr($self->{SEQ_ARRAY}->[$j], $i*50 + $k*10, 10); 
	#  $txt .= " " if ($k != 4);
      }

      $txt .= "\n";
      

    }
    $txt .= "\n\n";
  }
  
  return $txt;
  
}

sub setFile {
    my ($self, $s) = @_;
    $self->{FILE} = $s;
    $self->{HANDLE} = Sets::getRandomString("HANDLE");
    open  $self->{HANDLE}, $self->{FILE} or die "Cannot open $self->{FILE} ..\n";

    #system("cat $self->{FILE}\n");

    my %tmp = ();
    $self->{SEQS} = \%tmp;
   
    $self->{NAMES} = [];
    $self->{STARS} = "";
    $self->{TEXT} = undef;

    $self->_process;   

    close $self->{HANDLE};
}

sub setText {
    my ($self, $s) = @_;
    $self->{TEXT} = $s;
    
    

    my @a = split /[\r\n]/, $s;
    $self->{TEXT_ARRAY} = \@a;
    $self->{CNT} = 0;
    
    $self->_process;   
    
    
}

sub _readline {
    my ($self) = @_;
    
    if ($self->{FILE}) {
	my $tmp = $self->{HANDLE};
	return <$tmp>;
    } else {
	return $self->{TEXT_ARRAY}->[ $self->{CNT} ++];
    }
    
}


sub run {
  my ($self) = @_;
  
  if (defined($self->{SEQ_UA})) {
    
    # create a temp file
    my $tmpfile = Sets::getTempFile("/tmp/toto");
    $tmpfile .= ".seq";

    open OUTCL, ">$tmpfile";
    my $i = 0;
    foreach my $s (@{ $self->{SEQ_UA} }) {
      my $n = $self->{NAM_UA}->[$i];
      print OUTCL ">$n\n$s\n\n";
      $i++;
    }
    close OUTCL;

    my $todo = "clustalw $tmpfile -OUTORDER=INPUT > /dev/null";
    system($todo);
    
    my $outfile = $tmpfile;
    $outfile =~ s/\.seq$/\.aln/;
    
    $self->setFile($outfile);
    
  } else {
    die "no sequences to align\n";
  }
  
}

sub _process {
    my ($self) = @_;
    
    
    
    $self->{STARS} = "";
    my $cnt = 0;
    while (defined(my $l = $self->_readline)) {
	chomp $l;
	next if ($l =~ /CLUSTAL/);
	next if ($l eq "");

	#print "L=$l\n";
	
	my ($n, $s) = $l =~ /^(.{16})(.+)$/;
	       	
	$n =~ s/\s//g;
	$s =~ s/\s//g;

	if ($n eq "") {
	    $self->{STARS} .= $s;
	} else {
	    if (!defined($self->{SEQS}->{$n})) {
		$self->{NAMES}->[ $cnt ] = $n;
		$cnt ++;
	    }

	    #print "adding \"$s\"\n";
	    $self->{SEQS}->{$n} .= $s;

	    
	}
	
	
    }

    #
    #  check
    #
    

}

sub lc {
    my ($self) = @_;
    
    foreach my $k (keys(%{ $self->{SEQS} })) {
	$self->{SEQS}->{$k} = lc ($self->{SEQS}->{$k});
    }
	
    
}

sub getHTMLAlignment {
    my ($self) = @_;

    my $i_linewidth = 90;
    my $i = 0;
    my $s_output = "";

    my @a = keys(%{ $self->{SEQS} });


    my $l = length($self->{SEQS}->{$a[0]});
    

    $s_output .= "<table>\n";
    while ($i < $l) {

        my $i_toend = $l - $i;


        foreach my $k (keys(%{ $self->{SEQS} })) {
            $s_output .= "<tr>\n";
            $s_output .= "<td width=\"50\"><tt>\n";
            $s_output .= $k;
            $s_output .= "</tt></td>\n";
            $s_output .= "<td><tt><table  border=0 cellspacing=0 cellpadding=0><tr><td>";
	    
	    my $subseq = substr($self->{SEQS}->{$k}, $i, ($i_linewidth<$i_toend?$i_linewidth:$i_toend));
	    
	    if ($self->{REDIFY} == 1) {
		$subseq =~ s/([ATGC]{1,})/\<\/td\>\<td bgcolor\=\"red\"\>\<font color=\"white\"\>$1\<\/font\>\<\/td\>\<td\>/g;	
	    }

            $s_output .= $subseq;
            $s_output .= "</td></tr></table></tt></td>\n";
            $s_output .= "\n";
            $s_output .= "</tr>\n";
        }

        $s_output .= "<tr><td width=\"50\">&nbsp;</td><td><tt>";
        my $s_colorized = substr($self->{STARS}, $i, ($i_linewidth<$i_toend?$i_linewidth:$i_toend));
	$s_colorized =~ s/\ /\&nbsp\;/g;
        $s_output .= $s_colorized;
        $s_output .= "</tt></td></tr>\n";

        $s_output .= "\n";

        $s_output .= "\n";

        $i += $i_linewidth;

    }
   
     $s_output .= "</table>\n";
    
    
    return $s_output;
    
}

sub kmerize {
    my ($self, $a_ref_kmers) = @_;

    foreach my $k (keys(%{ $self->{SEQS} })) {
	
	foreach my $r (@$a_ref_kmers) {
	    my $se              =  $r->[0];
	    my $suc             =  uc($se);
	    $self->{SEQS}->{$k} =~ s/$suc/$se/ig;
	    my $se              =  Sets::getComplement($se);
	    my $suc             =  uc($se);
	    $self->{SEQS}->{$k} =~ s/$suc/$se/ig;
	} 

    }
}

sub redify {
    my ($self) = @_;

    $self->{REDIFY} = 1;

}
   
    


sub getSeqArray {
    my ($self) = @_;
    
    my @a = ();
    foreach my $k (keys(%{$self->{SEQS}})) {
	push @a, $self->{SEQS}->{$k};
    }

    return \@a; #$self->{SEQS};
}


sub getInputOrderedSeqArray {
    my ($self) = @_;
        
    my @a = ();
    foreach my $k (@{ $self->{NAMES} }) {
	push @a, $self->{SEQS}->{$k};
    }
    
    return \@a; 
}

sub getSeqs {
    my ($self) = @_;
    
    return $self->{SEQS};
    
}


sub getStars {
    my ($self) = @_;
    
    return $self->{STARS};
}



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