#!/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: Peter Wad Sackett
# Email: 
# Version: 1.1 ws0
# Date: 2008-09-15
# usage: perl maxalign_ws.pl <alignmentfile>

# 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_ws0.wsdl' );
#my $maxalign = WSDL2proxy ( 'http://www.cbs.dtu.dk/ws/MaxAlign/MaxAlign_1_1_ws0.wsdl' );

# Get alignment in fasta format from STDIN
my @fasta;
my $entry = -1;
while (<>) {
	chomp;
	if (/^>(.*)/) {
		my ($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 ++ ) {
	push @sequence , { id => $fasta[$i]->{id} , comment => $fasta[$i]->{comment} , seq => $fasta[$i]->{seq} };
}
# Do the request
my $response = $maxalign->{maxalign}->(
parameters => {
parameters => {
alignment => {sequence => [@sequence]} } });
# 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";
}