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The Apache WSS4J project provides a Java implementation of the primary security standards for Web Services, namely the OASIS Web Services Security (WS-Security) specifications from the OASIS Web Services Security TC.
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/**
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements. See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership. The ASF licenses this file
 * to you under the Apache License, Version 2.0 (the
 * "License"); you may not use this file except in compliance
 * with the License. You may obtain a copy of the License at
 *
 * http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing,
 * software distributed under the License is distributed on an
 * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
 * KIND, either express or implied. See the License for the
 * specific language governing permissions and limitations
 * under the License.
 */

package org.apache.ws.security.action;

import javax.security.auth.callback.CallbackHandler;

import org.apache.ws.security.WSPasswordCallback;
import org.apache.ws.security.WSSecurityException;
import org.apache.ws.security.components.crypto.Crypto;
import org.apache.ws.security.handler.RequestData;
import org.apache.ws.security.handler.WSHandler;
import org.apache.ws.security.handler.WSHandlerConstants;
import org.apache.ws.security.saml.SAMLIssuer;
import org.apache.ws.security.saml.SAMLIssuerFactory;
import org.apache.ws.security.saml.WSSecSignatureSAML;
import org.apache.ws.security.saml.ext.AssertionWrapper;

import org.w3c.dom.Document;

public class SAMLTokenSignedAction implements Action {
    
    private static org.apache.commons.logging.Log log = 
        org.apache.commons.logging.LogFactory.getLog(SAMLTokenSignedAction.class);

    public void execute(WSHandler handler, int actionToDo, Document doc, RequestData reqData)
            throws WSSecurityException {
        Crypto crypto = null;
        /*
        * it is possible and legal that we do not have a signature
        * crypto here - thus ignore the exception. This is usually
        * the case for the SAML option "sender vouches". In this case
        * no user crypto is required.
        */
        try {
            crypto = handler.loadSignatureCrypto(reqData);
        } catch (Exception ex) {
            if (log.isDebugEnabled()) {
                log.debug(ex.getMessage(), ex);
            }
        }

        SAMLIssuer saml = loadSamlIssuer(handler, reqData);

        AssertionWrapper assertion = saml.newAssertion();
        if (assertion == null) {
            throw new WSSecurityException("WSHandler: Signed SAML: no SAML token received");
        }

        WSSecSignatureSAML wsSign = new WSSecSignatureSAML(reqData.getWssConfig());

        CallbackHandler callbackHandler = 
            handler.getPasswordCallbackHandler(reqData);
        WSPasswordCallback passwordCallback = 
            handler.getPasswordCB(reqData.getUsername(), actionToDo, callbackHandler, reqData);
        wsSign.setUserInfo(reqData.getUsername(), passwordCallback.getPassword());
        
        if (reqData.getSigKeyId() != 0) {
            wsSign.setKeyIdentifierType(reqData.getSigKeyId());
        }
        if (reqData.getSigAlgorithm() != null) {
            wsSign.setSignatureAlgorithm(reqData.getSigAlgorithm());
        }
        if (reqData.getSigDigestAlgorithm() != null) {
            wsSign.setDigestAlgo(reqData.getSigDigestAlgorithm());
        }

         /*
         * required to add support for the 
         * signatureParts parameter.
         * If not set WSSecSignatureSAML
         * defaults to only sign the body.
         */
        if (reqData.getSignatureParts().size() > 0) {
            wsSign.setParts(reqData.getSignatureParts());
        }

        try {
            wsSign.build(
                    doc,
                    crypto,
                    assertion,
                    saml.getIssuerCrypto(),
                    saml.getIssuerKeyName(),
                    saml.getIssuerKeyPassword(),
                    reqData.getSecHeader());
            reqData.getSignatureValues().add(wsSign.getSignatureValue());
        } catch (WSSecurityException e) {
            throw new WSSecurityException("Error when signing the SAML token: ", e);
        }
    }

    protected SAMLIssuer loadSamlIssuer(
        WSHandler handler, 
        RequestData reqData
    ) throws WSSecurityException {
        String samlPropFile = 
            handler.getString(WSHandlerConstants.SAML_PROP_FILE, reqData.getMsgContext());
        SAMLIssuer samlIssuer = SAMLIssuerFactory.getInstance(samlPropFile);
        CallbackHandler callbackHandler = 
            handler.getCallbackHandler(
                WSHandlerConstants.SAML_CALLBACK_CLASS,
                WSHandlerConstants.SAML_CALLBACK_REF, 
                reqData
            );
        if (callbackHandler != null) {
            samlIssuer.setCallbackHandler(callbackHandler);
        }
        return samlIssuer;
    }

}