In addition to answer of @Rahul, you can import certificate (.cer) file using following command on command prompt for windows OS :
(Assuming you have set required Java paths)
keytool -importcert -file <path of certificate>\<YourCertificateName>.cer -keystore D:\java\jdk1.7.0_40\jre\lib\security\cacerts -alias <certificateAliasName> -storepass <Password>
usually default <password> is 'changeit'. 
In case webservice is used for third party client then you can use HttpClient to interact. I am not sure what kind of operation you are performing with that webservice. I assume you want to send some xml to that URL. You can refer following code :
            HttpPost httppost = new HttpPost(url);
            CredentialsProvider credentialsProvider = new BasicCredentialsProvider();
            credentialsProvider.setCredentials(AuthScope.ANY,
                    new UsernamePasswordCredentials(username, password));
            CloseableHttpClient client = HttpClientBuilder.create().setDefaultCredentialsProvider(credentialsProvider).build();
            StringEntity entity = null;
            try {
                entity = new StringEntity(xmlToSend);
            } catch (UnsupportedEncodingException e) {
                LOG.error("Unsupported Encoding ", e);
            }
            entity.setContentType("text/xml");
            httppost.setEntity(entity);
            try{
                CloseableHttpResponse response = client.execute(httppost);
                returnCode = response.getStatusLine().getStatusCode();
                EntityUtils.consume(entity);
                LOG.debug("HttpResponse :" + EntityUtils.toString(response.getEntity()));
            }catch(IOException e){
                LOG.error("Error occured while sending the xml");
            }