- 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.net.ConnectException;
-import java.util.ArrayList;
-import java.util.List;
-
-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.RNAStruct;
-import compbio.data.sequence.ClustalAlignmentUtil;
-import compbio.data.sequence.ConservationMethod;
-import compbio.data.sequence.FastaSequence;
-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.util.SysPrefs;
-import compbio.ws.server.RNAalifoldWS;
-
-
-public class TestRNAalifoldWS {
-
- SequenceAnnotation<RNAalifoldWS> foldws;
-
- @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;
-
- 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.customAnalize(fsl, options);
- System.out.println("J: " + jobId);
- ScoreManager result = foldws.getAnnotation(jobId);
- System.out.println("fold results: \n" + result.asRNAStruct().toString());
- assertNotNull(result);
-
- } catch (UnsupportedRuntimeException e) {
- e.printStackTrace();
- fail(e.getMessage());
- } catch (LimitExceededException e) {
- e.printStackTrace();
- fail(e.getMessage());
- } catch (JobSubmissionException e) {
- e.printStackTrace();
- fail(e.getMessage());
- } catch (ResultNotAvailableException e) {
- e.printStackTrace();
- fail(e.getMessage());
- } catch (WrongParameterException e) {
- e.printStackTrace();
- fail(e.getMessage());
- }
- }
-}
-
-
-
+ package compbio.ws.client;\r
+\r
+import static org.testng.Assert.assertNotNull;\r
+import static org.testng.Assert.fail;\r
+\r
+import java.io.FileInputStream;\r
+import java.io.FileNotFoundException;\r
+import java.io.IOException;\r
+import java.io.OutputStreamWriter;\r
+import java.io.Writer;\r
+import java.net.ConnectException;\r
+import java.util.ArrayList;\r
+import java.util.List;\r
+\r
+import javax.xml.ws.WebServiceException;\r
+\r
+import org.testng.annotations.BeforeTest;\r
+import org.testng.annotations.Test;\r
+\r
+import compbio.data.msa.JABAService;\r
+import compbio.data.msa.SequenceAnnotation;\r
+import compbio.data.sequence.Alignment;\r
+import compbio.data.sequence.ClustalAlignmentUtil;\r
+import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.RNAStructScoreManager;\r
+import compbio.data.sequence.ScoreManager;\r
+import compbio.data.sequence.UnknownFileFormatException;\r
+import compbio.metadata.AllTestSuit;\r
+import compbio.metadata.JobSubmissionException;\r
+import compbio.metadata.LimitExceededException;\r
+import compbio.metadata.Option;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.metadata.UnsupportedRuntimeException;\r
+import compbio.metadata.WrongParameterException;\r
+import compbio.runner.structure.RNAalifold;\r
+import compbio.ws.server.RNAalifoldWS;\r
+\r
+\r
+public class TestRNAalifoldWS {\r
+ \r
+// SequenceAnnotation<RNAalifoldWS> foldws;\r
+ RNAalifoldWS foldws;\r
+ \r
+ @BeforeTest(groups = {AllTestSuit.test_group_webservices})\r
+ void initConnection() {\r
+ \r
+ try {\r
+ JABAService client = Jws2Client.connect(\r
+ "http://localhost:8080/jabaws", Services.RNAalifoldWS);\r
+ foldws = (RNAalifoldWS) client;\r
+ } catch (ConnectException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (WebServiceException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
+\r
+ \r
+ @Test(groups = {AllTestSuit.test_group_webservices})\r
+ public void testFold() throws FileNotFoundException, IOException,\r
+ UnknownFileFormatException {\r
+ \r
+// String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()\r
+// + File.separator;\r
+ \r
+ Alignment aln = ClustalAlignmentUtil.readClustalFile(new FileInputStream(\r
+ AllTestSuit.test_input_aln));\r
+ \r
+ List<FastaSequence> fsl = aln.getSequences();\r
+ \r
+ try {\r
+ List<Option<RNAalifold>> options = new ArrayList<Option<RNAalifold>>();\r
+ options.add(foldws.getRunnerOptions().getArgumentByOptionName("--mis"));\r
+ options.add(foldws.getRunnerOptions().getArgumentByOptionName("-p"));\r
+ options.add(foldws.getRunnerOptions().getArgumentByOptionName("--MEA"));\r
+ \r
+// System.out.println("TestRNAalifoldWS: print options: " + options.toString());\r
+ \r
+ String jobId = foldws.customAnalize(fsl, options);\r
+ System.out.println("J: " + jobId);\r
+ \r
+ Writer stdout = new OutputStreamWriter(System.out);\r
+ \r
+ System.out.println("results class: " + foldws.getAnnotation(jobId).getClass().getName());\r
+ RNAStructScoreManager result = (RNAStructScoreManager)foldws.getAnnotation(jobId);\r
+ \r
+ \r
+ result.writeOut(stdout);\r
+ System.out.println("fold results: \n" + result.toString());\r
+ assertNotNull(result);\r
+ \r
+ } catch (UnsupportedRuntimeException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (LimitExceededException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (WrongParameterException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
+}\r
+ \r
+\r
+\r
git://source.jalview.org / jabaws.git / blobdiff