#!/usr/bin/perl
# Description: Calculate SIDD of input sequence (fasta)
# Author: Peter Fischer Hallin
# Email: pfh@cbs.dtu.dk
# Version: 1.0a ws0
# Date: 2009-05-04

use strict;
use Data::Dumper;
require "xml-compile.pl";
require "fasta.inc.pl";

my $proxy = WSDLclient ( 'http://www.cbs.dtu.dk/ws/SIDDbase/SIDDbase_1_0a_ws0.wsdl' );

# read fasta from stdin
my @fasta = read_fasta();

my $ENERGETICS = "c";
my $GEOMETRY = "c";
my $SIGMA = "-0.045";
my $WEIGHT = '10';

for ( my $i = 0 ; $i < scalar ( @fasta ) ; $i++ ) {
	runSIDD (
	 $proxy,
	 $fasta[$i]->{id},
	 $fasta[$i]->{comment},
	 $fasta[$i]->{seq},
	 $ENERGETICS,
	 $GEOMETRY,
	 $SIGMA,
	 $WEIGHT
	);
}

sub runSIDD {
	my ($proxy,$id,$comment,$seq,$energetics,$geometry,$sigma,$weight,$format) = @_;
	my $response = $proxy->{runService}->(
	  parameters => {
	   parameters => {
	    sequencedata => { 
	     sequence => [ {
	      id => $id , 
	      comment => $comment , 
	      seq => $seq ,
	     } ]
	    } ,
	    energetics => $energetics ,
	    geometry => $geometry ,
	    sigma => $sigma ,
	    weight => $weight ,
	    format => 'element' ,
	   }
	  }
	 );
	my ($jobid,$status,$expires);
	die "error obtaining jobid\n" unless defined ( $response->{parameters}->{queueentry});
	$jobid = $response->{parameters}->{queueentry}->{jobid};
	wait_job($proxy->{pollQueue},$jobid);
	$response = $proxy->{fetchResult}->( job => { jobid => $jobid   }) ;

	printf STDERR "version: %s\n"  , $response->{parameters}->{output}->{version};
	printf STDERR "organism_name: %s\n"  , $response->{parameters}->{output}->{organism_name};
	printf STDERR "segment: %s\n"  , $response->{parameters}->{output}->{segment};
	printf STDERR "entrez_pid: %s\n"  , $response->{parameters}->{output}->{entrez_pid};
	printf STDERR "method: %s\n"  , $response->{parameters}->{output}->{method};
	printf STDERR "digest: %s\n"  , $response->{parameters}->{output}->{digest};
	printf STDERR "geometry: %s\n"  , $response->{parameters}->{output}->{geometry};
	print STDERR  "pos base probability energy\n";
	print ">$id $comment\n";
	foreach my $sidd (@{$response->{parameters}->{output}->{element}->{pos}}) {
		printf ("%s\t%s\t%0.2e\t%0.2f\n",$sidd->{x},$sidd->{nt},$sidd->{P},$sidd->{G});
	}
}