getProfile

Description: Returns allelic profile defined for a ST. Clonal complex is also returned if it is defined.

Arguments

• database (string)
• ST (integer)

Sample Perl code

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

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

#####Sample arguments#########
my $database = 'neisseria';
my $ST = '11';
##############################

my $soap = SOAP::Lite
    -> uri('http://pubmlst.org/MLST')
    -> proxy('http://pubmlst.org/cgi-bin/mlstdbnet/mlstFetch.pl');
my $soapResponse = $soap->getProfile($database,$ST);
unless ($soapResponse->fault){
    for my $t ($soapResponse->valueof('//alleleNumber')) {
	print $t->{'locus'}. ': ' . $t->{'id'} . "\n";
    }
    print "clonal complex: " .$soapResponse->valueof('//complex').
	"\n" if ($soapResponse->valueof('//complex'));
} else {
    print join ', ',$soapResponse->faultcode,$soapResponse->faultstring;
}

Sample Java code

package org.pubmlst.mlstSOAP;

import org.apache.axis.client.Call;
import org.apache.axis.client.Service;
import org.apache.axis.description.*;
import org.apache.axis.encoding.ser.*;
import javax.xml.namespace.QName;
import java.util.Map;

public class GetProfile {

    public static void main(String[] args) {
	//Sample arguments////////////////
	String database = "neisseria";
	int st = 11;
	//////////////////////////////////
	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));
	    call.registerTypeMapping(AlleleNumber.class, new QName(
			"http://pubmlst.org/MLST", "alleleNumber"),
		BeanSerializerFactory.class, BeanDeserializerFactory.class,
		false);
	    OperationDesc oper = new OperationDesc();
	    oper.addParameter(new ParameterDesc(new QName("", "database"),
		ParameterDesc.IN, new QName(
			"http://www.w3.org/2001/XMLSchema", "string"),
		String.class, false, false));
	    oper.addParameter(new ParameterDesc(new QName("", "ST"),
	    ParameterDesc.IN, new QName(
		        "http://www.w3.org/2001/XMLSchema", "int"),
		int.class, false, false));
	    ParameterDesc param = new ParameterDesc(new QName("", "profile"),
	        ParameterDesc.OUT, new QName("http://pubmlst.org/MLST",
			"profile"),
		AlleleNumber[].class, false, false);
	    param.setItemQName(new QName("", "alleleNumber"));
	    oper.addParameter(param);
	    param = new ParameterDesc(new QName("", "complex"),
	    ParameterDesc.OUT, new QName(
		        "http://www.w3.org/2001/XMLSchema", "string"),
		String.class, false, false);
	    param.setOmittable(true);
	    oper.addParameter(param);
	    oper.setReturnType(org.apache.axis.encoding.XMLType.AXIS_VOID);
	    call.setOperation(oper);
	    call.setOperationName(new QName("http://pubmlst.org/MLST",
		        "getProfile"));
	    call.invoke(new Object[] { database, st });
	    Map output = call.getOutputParams();
	    AlleleNumber[] alleles = (AlleleNumber[]) output.get(new QName("",
			"profile"));
	    for (int i = 0; i < alleles.length; i++) {
		System.out.println(alleles[i].getLocus() + ": "
				   + alleles[i].getId());
	    }
	    String complex = ((String) output.get(new QName("", "complex")));
	    if (complex != null) {
		System.out.println("clonal complex: " + complex);
	    }
	} catch (Exception e) {
	    System.err.println(e.toString());
	}
    }

    protected static class AlleleNumber {
	private String locus;
	private int id;

	public AlleleNumber(String locus, int id) {
	    this.locus = locus;
	    this.id = id;
	}

	public java.lang.String getLocus() {return locus;}
	public void setLocus(String locus) {this.locus = locus;}
	public int getId() {return id;}
	public void setId(int id) {this.id = id;}
    }
}

Output

abcZ: 2
adk_: 3
aroE: 4
fumC: 3
gdh_: 8
pdhC: 4
pgm_: 6
clonal complex: ST-11 complex/ET-37 complex