#!/usr/bin/perl
# Description: This is a template example script. It reads an alignment as fasta and produces formatted output from the web service
# Author: Edita Bartaseviciute
# Email: edita@cbs.dtu.dk
# Version: 1.1 ws0
# Date: 2010-04-07
# usage: perl maxalign.pl alignment.fsa

# include standard XML::Compile helper functions (used to initiate WSDL proxys)
use strict;
require "xml-compile.pl";

# create proxy to maxalign
my $maxalign = WSDLclient ( 'http://www.cbs.dtu.dk/ws/MaxAlign/MaxAlign_1_1_ws1.wsdl' );

#my $maxalign = WSDL2proxy ( 'http://www.cbs.dtu.dk/ws/MaxAlign/MaxAlign_1_1_ws1.wsdl' );

#use Data::Dumper;
#print Dumper($maxalign);
=pod
# append schema definitions
$maxalign = appendSchemas ( $maxalign , 
	"http://www.cbs.dtu.dk/ws/common/ws_common_1_0b.xsd" ,
	"http://www.cbs.dtu.dk/ws/MaxAlign/ws_maxalign_1_1_ws1.xsd",
	"http://bioxsd.org/BioXSD-0.4.xsd"
);
=cut
# Get alignment in fasta format from STDIN
my @fasta;
my $entry = -1;
while (<STDIN>) {
	chomp;
	if (/^>(.*)/) {
		my ($id , $comment) = split (" ",$1);
		$entry++;
		$fasta[$entry]->{id} = $id;
		$fasta[$entry]->{comment} = $comment if defined $comment;
	} else {
		$fasta[$entry]->{seq} .= $_;
	}
}
# Create request
my @sequence;

for ( my $i = 0 ; $i < scalar ( @fasta ) ; $i ++ ) {
	my @array_gaps;
	my @seq1;
	my $dashes = 0;
	my $letters = 0;
	my $sequence;
	my @gaps = ();
	my @lengths = ();
	my $string = $fasta[$i]->{seq};
	#going through the sequence and saving starting positions and length of the gaps into arrays
	for (my $i = 0; $i < length($string); $i++) {
		my $symbol = substr ($string, $i, 1);
		if ($symbol eq "-") {
			$dashes++;
			if ($i == (length($string) - 1)) {
				push (@gaps, $letters);
				push (@lengths, $dashes);
			}
		}
		else {
			$sequence .= $symbol;			
			if ($dashes != 0 and $letters != 0) {
				push (@gaps, $letters);
				push (@lengths, $dashes);
				$dashes = 0;
			}
			
			elsif ($dashes != 0 and $letters == 0) {
				my $start = 1 - $dashes;
				push (@gaps, $start);
				push (@lengths, $dashes);
				$dashes = 0;
			}
		
			$letters++;
		}
	}
	$sequence[$i] = {sequenceRecord=> {sequence => $sequence, formalReference => {accession => $fasta[$i]->{id} }}};
	
	for (my $m = 0; $m <= $#gaps; $m++) {
		$sequence[$i] ->  {gap} -> {'start'} = $gaps[$m];#, 'len' => [$lengths[$m]] };
		$sequence[$i] ->  {gap} -> {'len'} = $lengths[$m]
         
      	}

	 #,  {gap => {'start' => [21], 'len' => [2] }};
	
}

use Data::Dumper;
print Dumper(@sequence);

# Do the request
my $response = $maxalign->{maxalign}->(
	 parameters => {
	  parameters => {
	   originalAlignment => {alignedSequence => [@sequence]} } });


 use Data::Dumper;
 print Dumper($response);

=pod
# Print the response
print "# Original number of sequences: $response->{parameters}->{output}->{originalsequencenumber}\n";
print "# Original total number of columns: $response->{parameters}->{output}->{originalcolumnnumber}\n";
print "# Original ungapped columns: $response->{parameters}->{output}->{originalungapcolumnnumber}\n";
print "# Original alignment area: $response->{parameters}->{output}->{originalalignmentarea}\n\n";
if (exists $response->{parameters}->{output}->{resultsequencenumber} and $response->{parameters}->{output}->{resultungapcolumnnumber} and $response->{parameters}->{output}->{resultalignmentarea} ) {
	print "# Number of sequences in result: $response->{parameters}->{output}->{resultsequencenumber}\n";
	print "# Ungapped columns in result: $response->{parameters}->{output}->{resultungapcolumnnumber}\n";
	print "# Resulting alignment area: $response->{parameters}->{output}->{resultalignmentarea}\n\n";
	print "#New alignment in fasta format:\n\n";
	foreach my $seqref (@{$response->{parameters}->{output}->{resultalignment}->{sequence}}) {
   	print ">$seqref->{id}";
   	print exists $seqref->{comment} ? " $seqref->{comment}\n" : "\n";
   	for (my $i = 0; $i < length $seqref->{seq}; $i += 60) {
      	print substr($seqref->{seq}, $i, 60), "\n"; }
	}
}
else {
	print "This alignment can't be improved by removing sequences\n";
}