import sublocapi.*;

// example code to illustrate how to write a SOAP client for SubLoc in java
public class Client
{
	public static void main(String[] args)
	{
		// initiate
		SOAPServiceLocator locator = new SOAPServiceLocator();
		try
		{
			API_PortType serv = locator.getAPI();
			Struct[] results = new Struct[999];
			/////////////////////////////////////////////////////////////////////////
			//name_search
			results = serv.name_search("actin");
			//get the contents of all entries
			// show the number of matched entries
			System.out.println(results.length);
			for (int i=0; i<results.length; i++)
			{
				System.out.println(results[i].getID());
				System.out.println(results[i].getCX());
				System.out.println(results[i].getDE());
				System.out.println(results[i].getLC());
				System.out.println(results[i].getOS());
				System.out.println(results[i].getSQ());
			}

			/////////////////////////////////////////////////////////////////////////
			// id_search
			// by SWISSPROT ID	
			results = serv.id_search("SWISSPROT", "O03978");
			// or you can search by DBSubLoc ID 
			results = serv.id_search("DBSubLoc", "10021133");
			// or you can search by GO ID
			//Caution! Search By GO ID may return MANY MANY entries, making it quite slow. Please be Patient.
			//Struct[] results = serv.id_search("GO", "0005739");
			
			// show the number of matched entries
			System.out.println(results.length);
			//get the contents of all entries
			for (int i=0; i<results.length; i++)
			{
				System.out.println(results[i].getID());
				System.out.println(results[i].getCX());
				System.out.println(results[i].getDE());
				System.out.println(results[i].getLC());
				System.out.println(results[i].getOS());
				System.out.println(results[i].getSQ());
			}

			//declare a sequence for test, you could read sequences from your files.
			String seq = "TKRFFNKNNRLNKGYAKTFSINEPDNNFYRKKFEHILPPVDLISEYESIYPGTLQELMHMAQKEQAHKHAIDLKNLKIQERIAKLTRICLLIFGIGLVVLIFLKLLK";

			/////////////////////////////////////////////////////////////////////////
			//blast_search
			// we provide two kinds of output formats: original BLAST output and parsed results by BioPerl's BPlite, users could choose one they like.
			BlastResult result = serv.blast_search("all","full",seq,"1");
			//get the original output of BLAST program, you could use BioJava to parse it quite easily. There are many example scripts on the Internet.
			System.out.println(result.getParsed());
			// or you can get the parsed result (using BioPerl's BPlite)
			// the parsed output's fields, every field is separated by a TAB. 
			// HIT_NUM    SCORE   BITS    PERCENT EXPECT  SUBJECT_NAME    IDENTITIES  MATCH_LENGTH    QUERY_START QUERY_END   SUBJECT_START   SUBJECT_END
			System.out.println(result.getPlain());

			/////////////////////////////////////////////////////////////////////////
			// SubLoc prediction by SVM
			// for more details about the method, please see:
			// Hua, S. and Sun, Z. (2001). Support vector machine approach for protein subcellular localization prediction. Bioinformatics 17, 721-8.
			// for prokaryotic organisms 
			PredictStruct pro_result = serv.pro_predict(seq);
			System.out.println(pro_result.getPrediction());
			System.out.println(pro_result.getRI());
			System.out.println(pro_result.getExpectAcc());
			// for eukaryotic organisms
			PredictStruct eu_result = serv.eu_predict(seq);
			System.out.println(eu_result.getPrediction());
			System.out.println(eu_result.getRI());
			System.out.println(eu_result.getExpectAcc());

			///////////////////////////////////////////////////////////////////////////
			// SubLoc prediction by PSORT
			//for more details about PSORT, please refer:
			//Nakai, K. and Horton, P. (1999). PSORT: a program for detecting sorting signals in proteins and
			//predicting their subcellular localization. Trends Biochem Sci 24, 34-6.
			PsortStruct psort_result = serv.psort_predict(seq);
			System.out.println(psort_result.getPrediction());
			System.out.println(psort_result.getDetail());
		    	
			String feed_result =serv.feed_entry("p53","cancer inhibitor","human","nuclear","....","SequenceHereAAAXXXXX");		
			System.out.println(feed_result);
			
		}
		catch (Exception e)
		{}
	}
}