Clean-up, refactoring, commenting. Parameters file containts only options since Jalvi...

[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 5452c4e..cafe9cb 100644 (file)
--- a/testsrc/compbio/ws/client/TestRNAalifoldWS.java
+++ b/testsrc/compbio/ws/client/TestRNAalifoldWS.java
@@ -1,16 +1,13 @@
        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;
 
-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.io.Writer;
 import java.net.ConnectException;
 import java.util.ArrayList;
 import java.util.List;
@@ -20,29 +17,20 @@ 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.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;
 import compbio.metadata.AllTestSuit;
 import compbio.metadata.JobSubmissionException;
 import compbio.metadata.LimitExceededException;
 import compbio.metadata.Option;
-import compbio.metadata.PresetManager;
 import compbio.metadata.ResultNotAvailableException;
-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;
 
 
@@ -73,10 +61,6 @@ public class TestRNAalifoldWS {
        public void testFold() throws FileNotFoundException, IOException,
                        UnknownFileFormatException {
                
-               
-//             String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
-//                             + File.separator;
-               
                Alignment aln = ClustalAlignmentUtil.readClustalFile(new FileInputStream(
                                AllTestSuit.test_input_aln));
                
@@ -94,10 +78,6 @@ public class TestRNAalifoldWS {
                        System.out.println("J: " + 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);
                        result.writeOut(writer);