MS-SQL deadlock and hang the Java application

Hi.. We have a java application which connect to our MS-SQL DB during midnight using JDBC connector and extract information. But very often ,the java applicatian halted and because of the deadlock as shown below.

Caused by: java.sql.SQLException: [Microsoft][SQLServer 2000 Driver for JDBC][SQLServer]Transaction (Process ID 54) was deadlocked o n lock resources with another process and has been chosen as the deadlock victim.

now the java programmer is blaming me that the MS SQL DB is having deadlock and cause their Java application to hang.

Is there any way to clear the deadlock before the the Java applcation run or how to prove the Java application script itself is having problem and causing the deadlock ?