Launching ClustalX2 and a file in it from java

Question

I have successfully launch clustalx from java(using only /home/b/Desktop/clustalx-2.1-linux-i686-libcppstatic/clustalx) but cannot launch a file in it directly. Here are the code what i have tried:

 String[] command= {"/home/b/Desktop/clustalx-2.1-linux-i686-libcppstatic/clustalx", "/home/b/Desktop/clustalx-2.1-linux-i686-libcppstatic/"+ "infile=F1F2CXAT211-alignment.aln" +".input"};
 String outlist[] = runCommand(command);

It is Running successfully without displaying clustalx.