X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=testsrc%2Fcompbio%2Fws%2Fclient%2FTestAAConWS.java;h=647631126b9c7cf76dd5b6865dd4c8ebc35071ad;hb=9d860c3793c6812f643caa01fc80a0036fa3fe2b;hp=a8814c8a9de7188fead2f2c6b2861c8ce2f72260;hpb=16561770367cb0b1203eb195eef91a74b1229036;p=jabaws.git

diff --git a/testsrc/compbio/ws/client/TestAAConWS.java b/testsrc/compbio/ws/client/TestAAConWS.java
index a8814c8..6476311 100644
--- a/testsrc/compbio/ws/client/TestAAConWS.java
+++ b/testsrc/compbio/ws/client/TestAAConWS.java
@@ -8,36 +8,51 @@ import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.net.URL;
-import java.util.HashSet;
 import java.util.List;
 
-import javax.xml.namespace.QName;
-import javax.xml.ws.Service;
-
+import org.testng.annotations.BeforeTest;
 import org.testng.annotations.Test;
 
-import compbio.conservation.Method;
-import compbio.data.msa.Annotation;
+import compbio.data.msa.JABAService;
+import compbio.data.msa.SequenceAnnotation;
+import compbio.data.sequence.ConservationMethod;
 import compbio.data.sequence.FastaSequence;
-import compbio.data.sequence.Score;
+import compbio.data.sequence.ScoreManager;
 import compbio.data.sequence.SequenceUtil;
 import compbio.metadata.JobSubmissionException;
 import compbio.metadata.LimitExceededException;
+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.AAConWS;
 
 public class TestAAConWS {
 
+	SequenceAnnotation<AACon> msaws;
+
+	@BeforeTest
+	void initConnection() {
+		/*
+		 * URL url = null; try { url = new
+		 * URL("http://localhost:8080/jabaws/AAConWS?wsdl"); } catch
+		 * (MalformedURLException e) { e.printStackTrace();
+		 * fail(e.getLocalizedMessage()); } String namespace =
+		 * "http://msa.data.compbio/01/12/2010/"; QName qname = new
+		 * QName(namespace, "AAConWS"); Service serv = Service.create(url,
+		 * qname); msaws = serv.getPort(new QName(namespace, "AAConWSPort"),
+		 * Annotation.class);
+		 */
+		JABAService client = Jws2Client.connect("http://localhost:8080/jabaws",
+				Services.AAConWS);
+		msaws = (SequenceAnnotation<AACon>) client;
+	}
+
 	@Test
-	public void test() throws FileNotFoundException, IOException {
+	public void testAnalize() throws FileNotFoundException, IOException {
 
-		URL url = new URL("http://localhost:8080/jabaws/AAConWS?wsdl");
-		String namespace = "http://msa.data.compbio/01/12/2010/";
-		QName qname = new QName(namespace, "AAConWS");
-		Service serv = Service.create(url, qname);
 		/*
 		 * MsaWS msaws = serv.getPort(new QName(
 		 * "http://msa.data.compbio/01/01/2010/", "ClustalWSPort"),
@@ -46,9 +61,6 @@ public class TestAAConWS {
 		// Annotation<AACon> msaws = serv.getPort(new QName(namespace,
 		// "ClustalWSPort"), Annotation.class);
 
-		Annotation<AAConWS> msaws = serv.getPort(new QName(namespace,
-				"AAConWSPort"), Annotation.class);
-
 		// List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
 		// AAConTester.test_alignment_input));
 
@@ -60,18 +72,95 @@ public class TestAAConWS {
 						+ File.separator + "TO1381.fasta.aln"));
 
 		try {
-			System.out.println("Pres: "
-					+ msaws.getPresets().getPresets().get(0));
+			System.out.println("Pres: " + msaws.getPresets().getPresets());
 			String jobId = msaws.analize(fsl);
 			System.out.println("J: " + jobId);
-			HashSet<Score> result = msaws.getConservation(jobId);
+			ScoreManager result = msaws.getAnnotation(jobId);
 			assertNotNull(result);
-			assertEquals(result.size(), 1);
-			assertEquals(result.iterator().next().getMethod(), Method.SHENKIN);
-			List<Float> scores = result.iterator().next().getScores();
+			assertEquals(result.getFirstSequenceScores().getNumberOfScores(), 1);
+
+			assertEquals(result.getFirstSequenceScores().getFirstScore()
+					.getMethod(), ConservationMethod.SHENKIN);
+			List<Float> scores = result.getFirstSequenceScores()
+					.getFirstScore().getScores();
 			assertNotNull(scores);
 			assertEquals(scores.size(), 568);
 
+			// Using presets
+			PresetManager<AACon> presets = msaws.getPresets();
+			jobId = msaws.presetAnalize(fsl,
+					presets.getPresetByName("Quick conservation"));
+			result = msaws.getAnnotation(jobId);
+			assertNotNull(result);
+			assertEquals(result.getFirstSequenceScores().getNumberOfScores(),
+					13);
+
+			jobId = msaws.presetAnalize(fsl,
+					presets.getPresetByName("Slow conservation"));
+			result = msaws.getAnnotation(jobId);
+			assertNotNull(result);
+			assertEquals(result.getFirstSequenceScores().getNumberOfScores(), 5);
+
+			jobId = msaws.presetAnalize(fsl,
+					presets.getPresetByName("Complete conservation"));
+			result = msaws.getAnnotation(jobId);
+			assertNotNull(result);
+			assertEquals(result.getFirstSequenceScores().getNumberOfScores(),
+					18);
+
+		} 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());
+		}
+
+	}
+	@Test
+	public void testPresetAnalize() throws FileNotFoundException, IOException {
+
+		String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
+				+ File.separator;
+
+		List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
+				CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
+						+ File.separator + "TO1381.fasta.aln"));
+
+		try {
+			System.out.println("Pres: " + msaws.getPresets().getPresets());
+
+			// Using presets
+			PresetManager<AACon> presets = msaws.getPresets();
+			String jobId = msaws.presetAnalize(fsl,
+					presets.getPresetByName("Quick conservation"));
+			ScoreManager result = msaws.getAnnotation(jobId);
+			assertNotNull(result);
+			assertEquals(result.getFirstSequenceScores().getNumberOfScores(),
+					13);
+
+			jobId = msaws.presetAnalize(fsl,
+					presets.getPresetByName("Slow conservation"));
+			result = msaws.getAnnotation(jobId);
+			assertNotNull(result);
+			assertEquals(result.getFirstSequenceScores().getNumberOfScores(), 5);
+
+			jobId = msaws.presetAnalize(fsl,
+					presets.getPresetByName("Complete conservation"));
+			result = msaws.getAnnotation(jobId);
+			assertNotNull(result);
+			assertEquals(result.getFirstSequenceScores().getNumberOfScores(),
+					18);
+
 		} catch (UnsupportedRuntimeException e) {
 			e.printStackTrace();
 			fail(e.getMessage());
@@ -84,7 +173,64 @@ public class TestAAConWS {
 		} catch (ResultNotAvailableException e) {
 			e.printStackTrace();
 			fail(e.getMessage());
+		} catch (WrongParameterException e) {
+			e.printStackTrace();
+			fail(e.getMessage());
 		}
 
 	}
+
+	@Test
+	public void testCustomAnalize() throws FileNotFoundException, IOException {
+
+		String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
+				+ File.separator;
+
+		List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(
+				CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"
+						+ File.separator + "TO1381.fasta.aln"));
+
+		// Using options
+		RunnerConfig<AACon> options = msaws.getRunnerOptions();
+		// System.out.println(options.getArguments());
+
+		try {
+			options.getArgument("Calculation method").setDefaultValue("SMERFS");
+			// options.getArgument("SMERFS Column Scoring Method")
+			// .setDefaultValue("MAX_SCORE");
+			// options.getArgument("SMERFS Gap Threshhold").setDefaultValue("1");
+			String jobId = msaws.customAnalize(fsl, options.getArguments());
+			ScoreManager result = msaws.getAnnotation(jobId);
+			assertNotNull(result);
+			assertEquals(result.getFirstSequenceScores().getNumberOfScores(), 1);
+			assertEquals(result.getFirstSequenceScores().getFirstScore()
+					.getScores().get(0), 0.698f);
+
+			options.getArgument("Calculation method").setDefaultValue("SMERFS");
+			options.removeArgument("Normalize");
+			System.out.println(options);
+			jobId = msaws.customAnalize(fsl, options.getArguments());
+			result = msaws.getAnnotation(jobId);
+			assertNotNull(result);
+			assertEquals(result.getFirstSequenceScores().getNumberOfScores(), 1);
+			assertEquals(result.getFirstSequenceScores().getFirstScore()
+					.getScores().get(0), 0.401f);
+
+		} catch (WrongParameterException e) {
+			e.printStackTrace();
+			fail(e.getMessage());
+		} 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());
+		}
+	}
 }