[Biojava-l] MultiAlignClustalW tutorial example

[Bornman, Daniel M]

All,

I am currently trying to work through the MultiAlignClustalW example on
the wiki but I am having some problems getting output.
After changing the necessary variable to work on my Linux machine and
choosing to use the ClustalWAlign(BufferedReader,String) construtor from
my test class, I cannot get any output from this external process.

I am using the latest version of ClustalW and I have noticed that when
running it from the command line directly, I am prompted for many
inputs.  Does the java example take these into account?

It seems like it attempts to in this section of code:

String [] strComando =  
	
{clustalwPath+"ClustalW.EXE",
	
"/infile="  + clustalwPath + fileName + ".input",
	
"/outfile=" + clustalwPath + fileName + ".output",
	
"/output=" + fileFormat,
	
"/align"};

...but I don't quite understand what all elements of this array are
intending to do or how if fits into the series of prompts when running
clustalw from the command line?


Thank You for any insight,  

Daniel Bornman
Researcher
Battelle Memorial Institute
505 King Ave
Columbus, OH 43201
614.424.3229