X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=testsrc%2Fcompbio%2Fmetadata%2FRunnerConfigTester.java;fp=testsrc%2Fcompbio%2Fmetadata%2FRunnerConfigTester.java;h=99549e1bf92d74487732fe90a911e28a0d0c914c;hb=b9f54dfc066b99717d901ab5239513f891a7ee43;hp=3bf2368577d54a4be3d61cef9c4ee31566b013fd;hpb=2a4439190b9b6cf0f881d5d07531c25b057117d6;p=jabaws.git

diff --git a/testsrc/compbio/metadata/RunnerConfigTester.java b/testsrc/compbio/metadata/RunnerConfigTester.java
index 3bf2368..99549e1 100644
--- a/testsrc/compbio/metadata/RunnerConfigTester.java
+++ b/testsrc/compbio/metadata/RunnerConfigTester.java
@@ -40,8 +40,7 @@ import compbio.runner.msa.Mafft;
 
 public class RunnerConfigTester {
 
-	public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE
-			+ "MafftParameters.xml";
+	public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "MafftParameters.xml";
 
 	RunnerConfig<Mafft> rconfig = null;
 
@@ -52,9 +51,8 @@ public class RunnerConfigTester {
 			rconfig.setRunnerClassName(Mafft.class.getName());
 			List<Option<Mafft>> prms = new ArrayList<Option<Mafft>>();
 
-			RunnerConfigMarshaller<Mafft> pmarshaller = new RunnerConfigMarshaller<Mafft>(
-					RunnerConfig.class, Parameter.class, Option.class,
-					ValueConstrain.class);
+			RunnerConfigMarshaller<Mafft> pmarshaller = new RunnerConfigMarshaller<Mafft>(RunnerConfig.class, Parameter.class,
+					Option.class, ValueConstrain.class);
 		} catch (JAXBException e) {
 			e.printStackTrace();
 			fail(e.getLocalizedMessage());
@@ -76,88 +74,69 @@ public class RunnerConfigTester {
 
 	@Test(expectedExceptions = WrongParameterException.class)
 	public void testCreateParameter() throws WrongParameterException {
-		try {
-			Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");
-			// TODO publish help on a compbio web site
-			p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");
+		Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");
+		// TODO publish help on a compbio web site
+		p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");
 
-			p3.addPossibleValues("BLOSUM", "PAM", "GONNET", "ID");
-			// This attribute is required by strict schema
-			p3.setOptionName("--AAMATRIX");
-			p3.setRequired(true);
-			// THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED
-			// IN WITHIN POSSIBLE VALUES
-			p3.setDefaultValue("pam22");
-			String com = p3.toCommand(" ");
-			System.out.println("AAAAAAAAAAAAAA!" + com);
-		} catch (MalformedURLException e) {
-			e.printStackTrace();
-			fail(e.getMessage());
-		}
+		p3.addPossibleValues("BLOSUM", "PAM", "GONNET", "ID");
+		// This attribute is required by strict schema
+		p3.setOptionName("--AAMATRIX");
+		p3.setRequired(true);
+		// THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED
+		// IN WITHIN POSSIBLE VALUES
+		p3.setDefaultValue("pam22");
+		String com = p3.toCommand(" ");
+		System.out.println("AAAAAAAAAAAAAA!" + com);
 	}
 
 	@Test()
 	public void testParameterToCommand() throws WrongParameterException {
-		try {
-			Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");
-			// TODO publish help on a compbio web site
-			p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");
+		Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");
+		// TODO publish help on a compbio web site
+		p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");
 
-			p3.addPossibleValues("BLOSUM", "PAM", "GONNET", "ID");
-			// This attribute is required by strict schema
-			p3.setOptionName("--AAMATRIX");
-			p3.setRequired(true);
-			// THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED
-			// IN WITHIN POSSIBLE VALUES
-			p3.setDefaultValue("PAM");
-			String com = p3.toCommand("=");
-			assertTrue(com.startsWith("--AAMATRIX"));
-			assertTrue(com.endsWith("PAM"));
-			assertTrue(com.contains("="));
-			p3.setDefaultValue("ID");
-			com = p3.toCommand("=");
-			assertFalse(com.endsWith("PAM"));
-			assertFalse(com.contains("PAM"));
-		} catch (MalformedURLException e) {
-			e.printStackTrace();
-			fail(e.getMessage());
-		}
+		p3.addPossibleValues("BLOSUM", "PAM", "GONNET", "ID");
+		// This attribute is required by strict schema
+		p3.setOptionName("--AAMATRIX");
+		p3.setRequired(true);
+		// THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED
+		// IN WITHIN POSSIBLE VALUES
+		p3.setDefaultValue("PAM");
+		String com = p3.toCommand("=");
+		assertTrue(com.startsWith("--AAMATRIX"));
+		assertTrue(com.endsWith("PAM"));
+		assertTrue(com.contains("="));
+		p3.setDefaultValue("ID");
+		com = p3.toCommand("=");
+		assertFalse(com.endsWith("PAM"));
+		assertFalse(com.contains("PAM"));
 	}
 
 	@Test(expectedExceptions = ValidationException.class)
 	public void testOptionNoDefaultValidate() throws ValidationException {
-		try {
-			Option<Mafft> p3 = new Option<Mafft>("Matrix1", "Protein weight matrix");
-			// TODO publish help on a compbio web site
-			p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");
+		Option<Mafft> p3 = new Option<Mafft>("Matrix1", "Protein weight matrix");
+		// TODO publish help on a compbio web site
+		p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");
 
-			p3.setOptionNames(new HashSet(Arrays.asList("--AAMATRIX", "--ABMAT", "--BBBB")));
-			p3.setRequired(true);
-			// THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED
-			// IN WITHIN POSSIBLE VALUES
-			p3.validate();
-		} catch (MalformedURLException e) {
-			e.printStackTrace();
-			fail(e.getMessage());
-		}
+		p3.setOptionNames(new HashSet(Arrays.asList("--AAMATRIX", "--ABMAT", "--BBBB")));
+		p3.setRequired(true);
+		// THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED
+		// IN WITHIN POSSIBLE VALUES
+		p3.validate();
 	}
 
 	@Test(expectedExceptions = WrongParameterException.class)
 	public void testOptionSetInvalidValue() throws WrongParameterException {
-		try {
-			Option<Mafft> p3 = new Option<Mafft>("Matrix1", "Protein weight matrix");
-			// TODO publish help on a compbio web site
-			p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");
 
-			p3.setOptionNames(new HashSet(Arrays.asList("--AAMATRIX", "--ABMAT", "--BBBB")));
-			p3.setRequired(true);
-			// THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED
-			// IN WITHIN POSSIBLE VALUES
-			p3.setDefaultValue("AAA");
-		} catch (MalformedURLException e) {
-			e.printStackTrace();
-			fail(e.getMessage());
-		}
+		Option<Mafft> p3 = new Option<Mafft>("Matrix1", "Protein weight matrix");
+		// TODO publish help on a compbio web site
+		p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");
+
+		p3.setOptionNames(new HashSet(Arrays.asList("--AAMATRIX", "--ABMAT", "--BBBB")));
+		p3.setRequired(true);
+		// THIS LINE IS CAUSING EXCEPTION AS DEFAULT VALUE MUST BE DEFINED
+		// IN WITHIN POSSIBLE VALUES
+		p3.setDefaultValue("AAA");
 	}
 
 	@Test()
@@ -178,9 +157,6 @@ public class RunnerConfigTester {
 			p3.setDefaultValue("--ABMAT");
 			com = p3.toCommand("=");
 			assertEquals("--ABMAT", com);
-		} catch (MalformedURLException e) {
-			e.printStackTrace();
-			fail(e.getMessage());
 		} catch (ValidationException e) {
 			e.printStackTrace();
 			fail(e.getMessage());
@@ -222,51 +198,39 @@ public class RunnerConfigTester {
 	}
 
 	@Test(expectedExceptions = WrongParameterException.class)
-	public void testValidateLowerBoundaryConstrainCheck()
-			throws WrongParameterException {
-		try {
-			Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");
-			// TODO publish help on a compbio web site
-			p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");
-			// This attribute is required by strict schema
-			p3.setOptionName("--AAMATRIX");
-			p3.setRequired(true);
+	public void testValidateLowerBoundaryConstrainCheck() throws WrongParameterException {
+		Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");
+		// TODO publish help on a compbio web site
+		p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");
+		// This attribute is required by strict schema
+		p3.setOptionName("--AAMATRIX");
+		p3.setRequired(true);
 
-			ValueConstrain vc = new ValueConstrain();
-			vc.setType(ValueConstrain.Type.Float);
-			vc.setMin("-10.12");
-			vc.setMax("0");
-			p3.setValidValue(vc);
-			// THIS IS CAUSING EXCEPTION
-			p3.setDefaultValue("-11.0");
-		} catch (MalformedURLException e) {
-			e.printStackTrace();
-			fail(e.getMessage());
-		}
+		ValueConstrain vc = new ValueConstrain();
+		vc.setType(ValueConstrain.Type.Float);
+		vc.setMin("-10.12");
+		vc.setMax("0");
+		p3.setValidValue(vc);
+		// THIS IS CAUSING EXCEPTION
+		p3.setDefaultValue("-11.0");
 	}
 
 	@Test(expectedExceptions = WrongParameterException.class)
-	public void testValidateUpperBoundaryConstrainCheck()
-			throws WrongParameterException {
-		try {
-			Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");
-			// TODO publish help on a compbio web site
-			p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");
-			// This attribute is required by strict schema
-			p3.setOptionName("--AAMATRIX");
-			p3.setRequired(true);
+	public void testValidateUpperBoundaryConstrainCheck() throws WrongParameterException {
+		Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");
+		// TODO publish help on a compbio web site
+		p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");
+		// This attribute is required by strict schema
+		p3.setOptionName("--AAMATRIX");
+		p3.setRequired(true);
 
-			ValueConstrain vc = new ValueConstrain();
-			vc.setType(ValueConstrain.Type.Float);
-			vc.setMin("-10.12");
-			vc.setMax("0");
-			p3.setValidValue(vc);
-			// THIS IS CAUSING EXCEPTION
-			p3.setDefaultValue("1");
-		} catch (MalformedURLException e) {
-			e.printStackTrace();
-			fail(e.getMessage());
-		}
+		ValueConstrain vc = new ValueConstrain();
+		vc.setType(ValueConstrain.Type.Float);
+		vc.setMin("-10.12");
+		vc.setMax("0");
+		p3.setValidValue(vc);
+		// THIS IS CAUSING EXCEPTION
+		p3.setDefaultValue("1");
 	}
 
 	@Test()
@@ -286,9 +250,6 @@ public class RunnerConfigTester {
 			// Max value boundary is not defined so 1 is valid
 			p3.setDefaultValue("1");
 			p3.validate();
-		} catch (MalformedURLException e) {
-			e.printStackTrace();
-			fail(e.getMessage());
 		} catch (WrongParameterException e) {
 			e.printStackTrace();
 			fail(e.getMessage());