Reverted some testing changes in TestRNAalifoldWS so that it will run

[jabaws.git] / testsrc / compbio / ws / client / TestRNAalifoldWS.java

diff --git a/testsrc/compbio/ws/client/TestRNAalifoldWS.java b/testsrc/compbio/ws/client/TestRNAalifoldWS.java
index b061fcc..fd8fb9b 100644 (file)
--- a/testsrc/compbio/ws/client/TestRNAalifoldWS.java
+++ b/testsrc/compbio/ws/client/TestRNAalifoldWS.java
@@ -1,4 +1,4 @@
-package compbio.ws.client;
+       package compbio.ws.client;
 
 import compbio.metadata.AllTestSuit;
 import static org.testng.Assert.assertEquals;
@@ -9,6 +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;
@@ -22,7 +24,6 @@ import compbio.data.msa.FoldWS;
 import compbio.data.msa.JABAService;
 import compbio.data.msa.SequenceAnnotation;
 import compbio.data.sequence.Alignment;
-import compbio.data.sequence.RNAstruct;
 import compbio.data.sequence.ClustalAlignmentUtil;
 import compbio.data.sequence.ConservationMethod;
 import compbio.data.sequence.FastaSequence;
@@ -45,7 +46,7 @@ import compbio.ws.server.RNAalifoldWS;
 
 public class TestRNAalifoldWS {
        
-       FoldWS<RNAalifoldWS> foldws;
+       SequenceAnnotation<RNAalifoldWS> foldws;
        
        @BeforeTest(groups = {AllTestSuit.test_group_webservices})
        void initConnection() {
@@ -53,7 +54,7 @@ public class TestRNAalifoldWS {
                try {
                        JABAService client = Jws2Client.connect(
                                        "http://localhost:8080/jabaws", Services.RNAalifoldWS);
-                       foldws = (FoldWS<RNAalifoldWS>) client;
+                       foldws = (SequenceAnnotation<RNAalifoldWS>) client;
                } catch (ConnectException e) {
                        e.printStackTrace();
                        fail(e.getMessage());
@@ -74,14 +75,24 @@ public class TestRNAalifoldWS {
                Alignment aln = ClustalAlignmentUtil.readClustalFile(new FileInputStream(
                                AllTestSuit.test_input_aln));
                
+               List<FastaSequence> fsl = aln.getSequences();
+               
                try {
                        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.customFold(aln, options);
+                       
+                       String jobId = foldws.customAnalize(fsl, options);
                        System.out.println("J: " + jobId);
-                       String result = foldws.getResult(jobId);
-                       System.out.println("fold results: \n" + result);
+                       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) {