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 c5f3f6d..fd8fb9b 100644 (file)
--- a/testsrc/compbio/ws/client/TestRNAalifoldWS.java
+++ b/testsrc/compbio/ws/client/TestRNAalifoldWS.java
@@ -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;
@@ -87,7 +88,11 @@ public class TestRNAalifoldWS {
                        String jobId = foldws.customAnalize(fsl, options);
                        System.out.println("J: " + jobId);
                        ScoreManager result = foldws.getAnnotation(jobId);
-                       System.out.println("fold results: \n" + result.asRNAStruct().toString());
+                       System.out.println("fold results: \n" + result.toString());
+                       
+                       Writer writer = new OutputStreamWriter(System.out);
+                       result.writeOut(writer);
+                       
                        assertNotNull(result);
                        
                } catch (UnsupportedRuntimeException e) {