X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=testsrc%2Fcompbio%2Fws%2Fclient%2FTestRNAalifoldWS.java;h=fd8fb9be8112df03d0cb9c23878de967b11b75d8;hb=d182b2d2b6ede7c952c6ca5a24b1576c6a194eed;hp=2d392f74f5e5cc4b8e48fb7b84266b7c1c2bf585;hpb=fa61eaad52ffe5ee0db449c3dd9ec5fa67aec43f;p=jabaws.git

diff --git a/testsrc/compbio/ws/client/TestRNAalifoldWS.java b/testsrc/compbio/ws/client/TestRNAalifoldWS.java
index 2d392f7..fd8fb9b 100644
--- a/testsrc/compbio/ws/client/TestRNAalifoldWS.java
+++ b/testsrc/compbio/ws/client/TestRNAalifoldWS.java
@@ -1,5 +1,6 @@
-package compbio.ws.client;
+	package compbio.ws.client;
 
+import compbio.metadata.AllTestSuit;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertNotNull;
 import static org.testng.Assert.fail;
@@ -8,6 +9,8 @@ import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.io.Writer;
+import java.io.OutputStreamWriter;
 import java.net.ConnectException;
 import java.util.ArrayList;
 import java.util.List;
@@ -17,11 +20,10 @@ import javax.xml.ws.WebServiceException;
 import org.testng.annotations.BeforeTest;
 import org.testng.annotations.Test;
 
+import compbio.data.msa.FoldWS;
 import compbio.data.msa.JABAService;
 import compbio.data.msa.SequenceAnnotation;
 import compbio.data.sequence.Alignment;
-import compbio.data.structure.FoldWS;
-import compbio.data.sequence.RNAstruct;
 import compbio.data.sequence.ClustalAlignmentUtil;
 import compbio.data.sequence.ConservationMethod;
 import compbio.data.sequence.FastaSequence;
@@ -37,47 +39,60 @@ import compbio.metadata.ResultNotAvailableException;
 import compbio.metadata.RunnerConfig;
 import compbio.metadata.UnsupportedRuntimeException;
 import compbio.metadata.WrongParameterException;
-
 import compbio.runner.conservation.AACon;
 import compbio.util.SysPrefs;
 import compbio.ws.server.RNAalifoldWS;
 
+
 public class TestRNAalifoldWS {
 	
-	FoldWS<RNAalifoldWS> foldws;
+	SequenceAnnotation<RNAalifoldWS> foldws;
 	
-//	@BeforeTest(groups = {AllTestSuit.test_group_webservices})
-//	void initConnection() {
-//		
-//		try {
-//			JABAService client = Jws2Client.connect(
-//					"http://localhost:8080/jabaws", Services.RNAalifoldWS);
-//			foldws = (FoldWS<RNAalifoldWS>) client;
-//		} catch (ConnectException e) {
-//			e.printStackTrace();
-//			fail(e.getMessage());
-//		} catch (WebServiceException e) {
-//			e.printStackTrace();
-//			fail(e.getMessage());
-//		}
-//	}
+	@BeforeTest(groups = {AllTestSuit.test_group_webservices})
+	void initConnection() {
+		
+		try {
+			JABAService client = Jws2Client.connect(
+					"http://localhost:8080/jabaws", Services.RNAalifoldWS);
+			foldws = (SequenceAnnotation<RNAalifoldWS>) client;
+		} catch (ConnectException e) {
+			e.printStackTrace();
+			fail(e.getMessage());
+		} catch (WebServiceException e) {
+			e.printStackTrace();
+			fail(e.getMessage());
+		}
+	}
 
 	
 	@Test(groups = {AllTestSuit.test_group_webservices})
 	public void testFold() throws FileNotFoundException, IOException,
 			UnknownFileFormatException {
 		
-		String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
-				+ File.separator;
+//		String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
+//				+ File.separator;
 		
 		Alignment aln = ClustalAlignmentUtil.readClustalFile(new FileInputStream(
-				CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
-					+ File.separator + "unfolded_RF00031.aln"));
+				AllTestSuit.test_input_aln));
+		
+		List<FastaSequence> fsl = aln.getSequences();
 		
 		try {
-			String jobId = foldws.fold(aln);
+			List<Option<RNAalifoldWS>> options  = new ArrayList<Option<RNAalifoldWS>>();
+			options.add(foldws.getRunnerOptions().getArgumentByOptionName("--mis"));
+			options.add(foldws.getRunnerOptions().getArgumentByOptionName("-p"));
+			options.add(foldws.getRunnerOptions().getArgumentByOptionName("--MEA"));
+			
+			System.out.println("TestRNAalifoldWS: print options: " + options.toString());
+			
+			String jobId = foldws.customAnalize(fsl, options);
 			System.out.println("J: " + jobId);
-			RNAstruct result = foldws.getResult(jobId);
+			ScoreManager result = foldws.getAnnotation(jobId);
+			System.out.println("fold results: \n" + result.toString());
+			
+			Writer writer = new OutputStreamWriter(System.out);
+			result.writeOut(writer);
+			
 			assertNotNull(result);
 			
 		} catch (UnsupportedRuntimeException e) {
@@ -92,7 +107,10 @@ public class TestRNAalifoldWS {
 		} catch (ResultNotAvailableException e) {
 			e.printStackTrace();
 			fail(e.getMessage());
-		} 
+		} catch (WrongParameterException e) {
+			e.printStackTrace();
+			fail(e.getMessage());
+		}
 	}
 }