#!/usr/opt/java
# Description: Client script in Java (apache) running the RNAmmer Web Service
# Author: Karunakar Bayyapu
# Email: karun@cbs.dtu.dk
# Version: 1.2 ws1
# Date: 2012-04-23

//### for installation and usage notes please see below

//### client code starts here

package javaapplication;
public class Client 
{
    public static void main(String[] args) 
       {
         try {  
            
            //runService --You need to change the sequences and ids as per your requirement. 
	    //organism and method are optional as per wsdl document  
	       
                WSRNAmmer12ws1_Service service = new WSRNAmmer12ws1_Service();
                ObjectFactory objectFactory = new ObjectFactory();
                
                RunService.Parameters parameters = objectFactory.createRunServiceParameters();
               
                Sequencedata sequencedata = objectFactory.createSequencedata();
            
                Sequence sequence1 = objectFactory.createSequence();
                sequence1.setId("IPI:IPI00000006.1");
                sequence1.setSeq("MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
				  QEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDL
				  AARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPG
				  CMSCKCVLS");
                sequencedata.getSequence().add(sequence1);
                
                Sequence sequence2 = objectFactory.createSequence();
                sequence2.setId("IPI:IPI00000005.1");
                sequence2.setSeq("MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
				  QEEYSAMRDQYMRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDL
				  PTRTVDTKQAHELAKSYGIPFIETSAKTRQGVEDAFYTLVREIRQYRMKKLNSSDDGTQG
				  CMGLPCVVM");
                sequencedata.getSequence().add(sequence2);
              
                parameters.setSequencedata(sequencedata);
                RunServiceResponse.Queueentry result = service.getWSRNAmmer12ws1().runService(parameters);
                System.out.println(result.toString());

         //pollQueue --jobid needs to be changed as which you got from runService
               
	        PollQueue.Job job = objectFactory.createPollQueueJob();
                job.setJobid("216E97C8-429F-11E1-ACA9-C966F6AC78EB");
                PollQueueResponse.Queueentry pr = service.getWSRNAmmer12ws1().pollQueue(job);
                System.out.println(pr.toString());
 
         //fetchResult --jobid needs to be changed as which you got from runService
               
	        FetchResult.Job job1 = objectFactory.createFetchResultJob();
                job1.setJobid("216E97C8-429F-11E1-ACA9-C966F6AC78EB");
                Anndata ann = service.getWSRNAmmer12ws1().fetchResult(job1);
                System.out.println(ann.toString());
         
            }
          catch(Exception ex) 
            {
                ex.printStackTrace();
            }
       }
}

//### client code ends here

//#########################################################################################
//#############################				    #############################
//#############################          DOCUMENTATION        #############################
//#############################          			    #############################
//#########################################################################################


//   Introduction:
//
//	We developed simple Java client to test SOAP Webservices. It uses following version 
//	softwares, Libraries and IDE's
// 	  * Install Java JDK(1.6.0)
// 	  * Install GlassFish v3 Domain
// 	  * Install NetBeans IDE (preferably 6.0 + ), Web and Java EE 
//  	  * Add Libraries: jaxb-impl.jar, jaxws-rt-2.0.jar, stax-impl.
//   	   jar,JAX-WS 2.1-activation.jar,etc depends on your run time requirements
     
//   Settings:

//	We can use a wizard to generate Java objects from the web service's WSDL file. 
//	To generate Java objects, open net beans IDE then fallow these steps:
//  	 * Choose File > New Project (Ctrl-Shift-N). Under Categories, choose Java Application.
//   	   Under Projects, choose Java Application. Click Next.
//	 * Name the project as Test and make sure that you specify an appropriate server 
//	     as your target server. Leave all other options at default and  click Finish.
//	 * In the Projects window, right-click the Test project node and choose New -> Other. 
//	   In the New File wizard choose Web Services-> Web Service Client. In the Web Service
//	   Client wizard, specify the URL to the web service: 
//	     http://www.cbs.dtu.dk/ws/RNAmmer/RNAmmer_1_2_ws1.wsdl

//	 * If you are behind a firewall, you might need to specify a proxy server-otherwise 
//     	   the WSDL file cannot be downloaded. To specify the proxy server, click Set Proxy 
//     	   in the wizard. The IDE's Options window opens, where you can set the proxy universally
//         for the IDE.
//   	 * Leave the package name blank. By default the client class package name is taken from 
//     	   the WSDL. In this case is WSRNAmmer_1_2_ws1.Select JAX version JAX-WS. Click Finish. 
//   	 * In the Projects window, within the Web Service References node, you see our service 
//     		reference files.
//   	 * Add appropriate libraries/jar files.
//   	 * Once the java objects created then we can start to use generated Java objects. 
//   	 * In the main java class page, copy above client code and paste it.
  
//    Access Web service:

//      Ths RNAmmer service code access to see one method results at once. If you would like to 
//	see runService method results then you would need to comment the rest of the methods code 
//	and for rest also same. In the runService you need to submit required fileds like one id 
//	and corresponding sequence or more ids and their corresponding sequences as a input(STDIN) 
//	data to convert FASTA format to get the results.
//	For input data/FASTA format see example: 
//	http://www.cbs.dtu.dk/ws/RNAmmer/examples/example)

//	After getting jobid from runService then you would need to submit jobid in the pollQueue 
//	to know the status of the job. After knowing the status of the job from pollQueue then 
//	you need to submit jobid in the fetchResult to see complete final results. 
//	It means you can only see final results in the fetchResult since RNAmmer is implemented 
//	in asynchronous way

//    Run: 

//	* After saving above code in the main class. Right click and (down on the menu) click on run
//	  as java application or in the menu bar->run->run File. 
//	* Now We can see SOAP envelope request/Response..