getSTs

Description: Returns list of STs that contain all the alleles specified. Any number of loci can be included in a query - include all loci for an exact match.

Arguments

• database (string)
• n x [alleleNumber]
  where alleleNumber is defined as {locus,id}

Sample Perl code

#!/usr/bin/perl
#Written by Keith Jolley

use SOAP::Lite;
use strict;
use warnings;

#####Sample arguments#########
my $database = 'neisseria';
my @profile = (2,3,4,3,8,4,6);
##############################

my $soap = SOAP::Lite
    -> uri('http://pubmlst.org/MLST')
    -> proxy('http://pubmlst.org/cgi-bin/mlstdbnet/mlstFetch.pl');

#Get list of loci
my $soapResponse = $soap->getLocusList($database);
my @loci;
for my $locus ($soapResponse->valueof('//locus')) {
    push @loci,$locus;
}
my @profileElements;
my $i=0;
foreach my $locus (@loci){
    push @profileElements,SOAP::Data->name('alleleNumber' => \SOAP::Data->value(
	SOAP::Data->name('locus' => $locus),
	SOAP::Data->name('id' => $profile[$i])));
    $i++;
}
$soapResponse = $soap->getSTs($database,@profileElements);
unless ($soapResponse->fault){
    print "Matching STs:\n";
    for my $t ($soapResponse->valueof('//ST')) {
	print "$t\n";
    }
} else {
    print join ', ',$soapResponse->faultcode,$soapResponse->faultstring;
}

Sample Java code

package org.pubmlst.mlstSOAP;

import org.apache.axis.client.Call;
import org.apache.axis.client.Service;
import javax.xml.namespace.QName;

import java.util.ArrayList;
import java.util.Vector;
import java.util.HashMap;

public class GetSTs {

    public static void main(String[] args) {
	//Sample arguments////////////////
	String database = "neisseria";
	Integer[] profile = {2,3,4,3,8,4,6};
	//////////////////////////////////
	try {
	    String endpoint = "http://pubmlst.org/cgi-bin/mlstdbnet/mlstFetch.pl";
	    Service service = new Service();
	    Call call = (Call) service.createCall();
	    call.setTargetEndpointAddress(new java.net.URL(endpoint));
	    // Get list of loci
	    call.setOperationName(new QName("http://pubmlst.org/MLST/",
					    "getLocusList"));
	    @SuppressWarnings("unchecked")
	    ArrayList<String> loci = (ArrayList) call.invoke(new Object[] { database });

	    call.setOperationName(new QName("http://pubmlst.org/MLST/",
					    "getSTs"));
	    Vector<Object> callArgs = new Vector<Object>();
	    callArgs.add(database);
	    for (int i=0; i<loci.size(); i++){
		HashMap<String,Object> alleleNumber = new HashMap<String,Object>();
		alleleNumber.put("locus", loci.get(i));
		alleleNumber.put("id", profile[i]);
		callArgs.addElement(alleleNumber);
	    }
	    Object stList = call.invoke(callArgs.toArray());
	    if (stList instanceof ArrayList){
		for (int i=0; i<((ArrayList)stList).size(); i++){
		    System.out.println(((ArrayList)stList).get(i));
		}
	    } else if (stList instanceof Integer) {
		System.out.println(stList);
	    }
	} catch (Exception e) {
	    System.err.println(e.toString());
	}
    }
}

Output

Matching STs:
11