// A sample client for the EMBL BioSequence retrieval service
// from the EMBL-EBI (http://www.ebi.ac.uk/). This service
// will return the EMBL entry of a
// given accession number (or identifier) as used by the international
// DDBJ/GenBank/EMBL nucleotide sequence databases, e.g. HSERPG, in 
// either BSML or AGAVE (SCIOBJ) format.

// Dependencies:

// This class uses the GLUE toolkit from "The Mind Electric"
// http://www.themindelectric.com/ Follow the instructions on
// installation (add GLUE.jar, servlet.jar and jnet.jar to your
// CLASSPATH and update your PATH).

// This client uses helper classes generated by the GLUE wsdl2java
// tool located in $GLUE_HOME/bin directory. Before compiling and
// executing the client, issue the following command (note that you
// don't even need to download the WSDL file!):

// > wsdl2java http://www.ebi.ac.uk/xembl/XEMBL.wsdl

// This will generate new classes: XEMBL.java
// & IXEMBL.java. Compile everything, and then run
// the client.

// Usage: java Client_GLUE <format> <identifiers>;
//   E.g. java Client_GLUE BSML HSERPG HSAPX35

// The WSDL file for this service is located at:
//   http://www.ebi.ac.uk/xembl/XEMBL.wsdl

// Contact: Alan Robinson <alan@ebi.ac.uk>


public class Client_GLUE {

    public static void main( String[] args )
	throws Exception
    {
	
	// The accession number or identifier to be looked up in the
	// EMBL nucleotide sequence database.
	String format = null;
	StringBuffer identifiers = null;
	
	// Check if sufficient command line arguements have been specified:
	if (args.length < 2) {
	    System.err.println("Usage: java Client_GLUE <format> <identifiers>");
	    System.err.println("  format = BSML or SCIOBJ");
	    System.err.println("  E.g. java Client_GLUE BSML HSERPG HSAPX35");
	    System.exit(0);
	}
	
	format = args[0];

	if ( !format.equalsIgnoreCase("BSML") && !format.equalsIgnoreCase("sciobj") ) {
	    System.err.println("Usage: java Client_GLUE <format> <identifiers>");
	    System.err.println("  format = BSML or SCIOBJ");
	    System.err.println("  E.g. java Client_GLUE SCIOBJ HSERPG HSAPX35");
	    System.exit(0);
	}

	// The identifiers need to be in a single comma-delimited string.
	identifiers = new StringBuffer( args[1] );
        for (int i=2; i<args.length; i++) {
	    identifiers.append(" "+args[i]);
	}

	// Bind to the SOAP server via the helper classes created by
	// GLUE's wsdl2java tool and return a reference to a Java
	// proxy object implementing the interfaces defined in the
	// WSDL file.
	IXEMBL bioSeqService = XEMBL.bind();
	
	// Call the 'getNucSeq' method on the SOAP proxy.
	String embl = bioSeqService.getNucSeq(format, identifiers.toString() );
	
	// Print out the sequence.
	System.out.println( embl );
    }
}