You normally build connections indirectly using a connection factory. A JNDI namespace can store a configured factory, therefore insulating the JMS application from provider-specific information. See the section Using JNDI, below, for details on how to store and retrieve objects using JNDI.
QueueConnectionFactory factory; factory = new com.ibm.mqe.jms.MQeJNDIQueueConnectionFactory(); ((com.ibm.mqe.jms.MQeJNDIQueueConnectionFactory)factory). setIniFileName(<initialisation file>)