Import RNAalifold removed from RNAStructReader. @XmlSeeAlso line added

[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 fd8fb9b..5452c4e 100644 (file)
--- a/testsrc/compbio/ws/client/TestRNAalifoldWS.java
+++ b/testsrc/compbio/ws/client/TestRNAalifoldWS.java
@@ -27,6 +27,7 @@ import compbio.data.sequence.Alignment;
 import compbio.data.sequence.ClustalAlignmentUtil;
 import compbio.data.sequence.ConservationMethod;
 import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.RNAStructScoreManager;
 import compbio.data.sequence.ScoreManager;
 import compbio.data.sequence.SequenceUtil;
 import compbio.data.sequence.UnknownFileFormatException;
@@ -40,6 +41,7 @@ import compbio.metadata.RunnerConfig;
 import compbio.metadata.UnsupportedRuntimeException;
 import compbio.metadata.WrongParameterException;
 import compbio.runner.conservation.AACon;
+import compbio.runner.structure.RNAalifold;
 import compbio.util.SysPrefs;
 import compbio.ws.server.RNAalifoldWS;
 
@@ -47,6 +49,7 @@ import compbio.ws.server.RNAalifoldWS;
 public class TestRNAalifoldWS {
        
        SequenceAnnotation<RNAalifoldWS> foldws;
+//     RNAalifoldWS foldws;
        
        @BeforeTest(groups = {AllTestSuit.test_group_webservices})
        void initConnection() {
@@ -54,6 +57,7 @@ public class TestRNAalifoldWS {
                try {
                        JABAService client = Jws2Client.connect(
                                        "http://localhost:8080/jabaws", Services.RNAalifoldWS);
+//                     foldws = (RNAalifoldWS) client;
                        foldws = (SequenceAnnotation<RNAalifoldWS>) client;
                } catch (ConnectException e) {
                        e.printStackTrace();
@@ -69,6 +73,7 @@ public class TestRNAalifoldWS {
        public void testFold() throws FileNotFoundException, IOException,
                        UnknownFileFormatException {
                
+               
 //             String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
 //                             + File.separator;
                
@@ -87,7 +92,10 @@ public class TestRNAalifoldWS {
                        
                        String jobId = foldws.customAnalize(fsl, options);
                        System.out.println("J: " + jobId);
-                       ScoreManager result = foldws.getAnnotation(jobId);
+                       RNAStructScoreManager result = (RNAStructScoreManager)foldws.getAnnotation(jobId);
+
+                       
+                       // standard and RNAStruct specific ways of formatting scoremanager
                        System.out.println("fold results: \n" + result.toString());
                        
                        Writer writer = new OutputStreamWriter(System.out);