From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Thu, 19 Aug 2010 10:25:41 +0000 (+0000)
Subject: Fixed version of Preset class from JABA_r1 branch (see bug JWS-19)
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=589af47c756cfdfb8651f71ba1071c8b240129ff;p=jabaws.git

Fixed version of Preset class from JABA_r1 branch (see bug JWS-19)

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@2907 e3abac25-378b-4346-85de-24260fe3988d
---

diff --git a/datamodel/compbio/metadata/Preset.java b/datamodel/compbio/metadata/Preset.java
index 9fd17a0..be9b8f1 100644
--- a/datamodel/compbio/metadata/Preset.java
+++ b/datamodel/compbio/metadata/Preset.java
@@ -111,7 +111,11 @@ public class Preset<T> {
 	    if (option != null) {
 		// Set default value to the preset value
 		if (containValue(optionName)) {
+		    // extract and set value to the parameter 
 		    option.setDefaultValue(getValue(optionName));
+		} else {
+		    // set value to the option as default, as this could be a multi-option value
+		    option.setDefaultValue(oname);
 		}
 		options.add(option);
 	    }
diff --git a/testsrc/compbio/metadata/PresetTester.java b/testsrc/compbio/metadata/PresetTester.java
index 1665e23..0b5a0a3 100644
--- a/testsrc/compbio/metadata/PresetTester.java
+++ b/testsrc/compbio/metadata/PresetTester.java
@@ -47,114 +47,148 @@ import compbio.runner.msa.Mafft;
 
 public class PresetTester {
 
-	public static final String input =  AllTestSuit.TEST_DATA_PATH
-			+ "MafftPresets.xml";
-	public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE
-			+ "MafftParameters.xml";
-
-	PresetManager<Mafft> presets = null;
-	RunnerConfig<Mafft> rconfParams = null;
-
-	@BeforeTest(enabled = true)
-	public void loadPresets() {
-		try {
-			// Load Preset definitions
-			RunnerConfigMarshaller<Mafft> rconfigPresets = new RunnerConfigMarshaller<Mafft>(
-					PresetManager.class);
-			File infile = new File(input);
-			assertTrue(infile.exists());
-			presets = rconfigPresets.read(new FileInputStream(infile),
-					PresetManager.class);
-			assertNotNull(presets);
-			assertFalse(presets.preset.isEmpty());
-
-			// Load Parameters definitions
-			File input = new File(this.test_input);
-			assertTrue(input.exists());
-			JAXBContext ctx = JAXBContext.newInstance(RunnerConfig.class);
-			Unmarshaller um = ctx.createUnmarshaller();
-			JAXBElement<RunnerConfig> rconfigParams = um.unmarshal(
-					new StreamSource(input), RunnerConfig.class);
-			rconfParams = rconfigParams.getValue();
-			assertNotNull(rconfParams);
-
-		} catch (JAXBException e) {
-			e.printStackTrace();
-			fail(e.getMessage());
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-			fail(e.getMessage());
-		}
+    public static final String input = AllTestSuit.TEST_DATA_PATH
+	    + "MafftPresets.xml";
+    public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE
+	    + "MafftParameters.xml";
+
+    PresetManager<Mafft> presets = null;
+    RunnerConfig<Mafft> rconfParams = null;
+
+    @BeforeTest(enabled = true)
+    public void loadPresets() {
+	try {
+	    // Load Preset definitions
+	    RunnerConfigMarshaller<Mafft> rconfigPresets = new RunnerConfigMarshaller<Mafft>(
+		    PresetManager.class);
+	    File infile = new File(input);
+	    assertTrue(infile.exists());
+	    presets = rconfigPresets.read(new FileInputStream(infile),
+		    PresetManager.class);
+	    assertNotNull(presets);
+	    assertFalse(presets.preset.isEmpty());
+
+	    // Load Parameters definitions
+	    File input = new File(this.test_input);
+	    assertTrue(input.exists());
+	    JAXBContext ctx = JAXBContext.newInstance(RunnerConfig.class);
+	    Unmarshaller um = ctx.createUnmarshaller();
+	    JAXBElement<RunnerConfig> rconfigParams = um.unmarshal(
+		    new StreamSource(input), RunnerConfig.class);
+	    rconfParams = rconfigParams.getValue();
+	    assertNotNull(rconfParams);
+
+	} catch (JAXBException e) {
+	    e.printStackTrace();
+	    fail(e.getMessage());
+	} catch (FileNotFoundException e) {
+	    e.printStackTrace();
+	    fail(e.getMessage());
 	}
-
-	@Test
-	public void marshallPreset() {
-		try {
-			RunnerConfigMarshaller<Mafft> rconfig = new RunnerConfigMarshaller<Mafft>(
-					PresetManager.class);
-			PresetManager<Mafft> pman = getPresets();
-			assertNotNull(pman);
-			rconfig.readAndValidate(new FileInputStream(new File(input)),
-					PresetManager.class);
-		} catch (JAXBException e) {
-			e.printStackTrace();
-			fail(e.getMessage());
-		} catch (IOException e) {
-			e.printStackTrace();
-			fail(e.getMessage());
-		} catch (SAXException e) {
-			e.printStackTrace();
-			fail(e.getMessage());
-		}
+    }
+
+    @Test
+    public void marshallPreset() {
+	try {
+	    RunnerConfigMarshaller<Mafft> rconfig = new RunnerConfigMarshaller<Mafft>(
+		    PresetManager.class);
+	    PresetManager<Mafft> pman = getPresets();
+	    assertNotNull(pman);
+	    rconfig.readAndValidate(new FileInputStream(new File(input)),
+		    PresetManager.class);
+	} catch (JAXBException e) {
+	    e.printStackTrace();
+	    fail(e.getMessage());
+	} catch (IOException e) {
+	    e.printStackTrace();
+	    fail(e.getMessage());
+	} catch (SAXException e) {
+	    e.printStackTrace();
+	    fail(e.getMessage());
 	}
-
-	@Test
-	public void validatePresets() {
-		assertNotNull(presets);
-		assertEquals(presets.getPresets().size(), 6);
-		try {
-			for (Preset<Mafft> pr : presets.getPresets()) {
-				List<Option<Mafft>> options;
-				options = pr.getArguments(rconfParams);
-				assertFalse(options.isEmpty());
-				if (pr.name.equals("L-INS-i (Accuracy-oriented)")) {
-					assertEquals(options.size(), 2);
-					Option<Mafft> o = options.get(0);
-					if (o.name.equals("Pairwise alignment computation method")) {
-						List<String> onames = o.getOptionNames();
-						boolean match = false;
-						for (String oname : onames) {
-							if (oname.equals("--localpair")) {
-								match = true;
-								break;
-							}
-						}
-						assertTrue(match);
-					}
-				}
-				if (pr.name.equals("NW-NS-PartTree-1 (Speed oriented)")) {
-					assertEquals(options.size(), 4);
-				}
+    }
+
+    @Test
+    public void validatePresets() {
+	assertNotNull(presets);
+	assertEquals(presets.getPresets().size(), 6);
+	try {
+	    for (Preset<Mafft> pr : presets.getPresets()) {
+		List<Option<Mafft>> options;
+		options = pr.getArguments(rconfParams);
+		assertFalse(options.isEmpty());
+		if (pr.name.equals("L-INS-i (Accuracy-oriented)")) {
+		    assertEquals(options.size(), 2);
+		    Option<Mafft> o = options.get(0);
+		    if (o.name.equals("Pairwise alignment computation method")) {
+			List<String> onames = o.getOptionNames();
+			boolean match = false;
+			for (String oname : onames) {
+			    if (oname.equals("--localpair")) {
+				match = true;
+				break;
+			    }
 			}
-		} catch (WrongParameterException e) {
-			e.printStackTrace();
-			fail(e.getMessage());
+			assertTrue(match);
+		    }
+		}
+		if (pr.name.equals("NW-NS-PartTree-1 (Speed oriented)")) {
+		    assertEquals(options.size(), 4);
 		}
+	    }
+	} catch (WrongParameterException e) {
+	    e.printStackTrace();
+	    fail(e.getMessage());
 	}
-
-	private static PresetManager<Mafft> getPresets() {
-		Preset<Mafft> preset1 = new Preset<Mafft>();
-		preset1.name = "L-INS-i (Accuracy-oriented)";
-		preset1.description = "dsfjkg fdjksghkjsgdfh jksdfg sdfgkjhsdfgk kjsdfg ";
-
-		List<String> optionNames = new ArrayList<String>();
-		optionNames.add("--localpair");
-		optionNames.add("--maxiterate 1000");
-		preset1.option = optionNames;
-		PresetManager<Mafft> prman = new PresetManager<Mafft>();
-		prman.preset = Collections.singletonList(preset1);
-		prman.runnerClassName = Mafft.class.getCanonicalName();
-
-		return prman;
+    }
+
+    @Test
+    public void testPresetWithMuptiOptions() {
+	assertNotNull(presets);
+	assertEquals(presets.getPresets().size(), 6);
+	try {
+	    for (Preset<Mafft> pr : presets.getPresets()) {
+		List<Option<Mafft>> options;
+		options = pr.getArguments(rconfParams);
+		assertFalse(options.isEmpty());
+		if (pr.name.equals("E-INS-i (Accuracy-oriented)")) {
+		    assertEquals(options.size(), 3);
+		    Option<Mafft> o = options.get(0);
+		    if (o.name.equals("Pairwise alignment computation method")) {
+			List<String> onames = o.getOptionNames();
+			boolean match = false;
+			for (String oname : onames) {
+			    if (oname.equals("--genafpair")) {
+				match = true;
+				break;
+			    }
+			}
+			assertTrue(match);
+		    }
+		}
+		if (pr.name.equals("NW-NS-PartTree-1 (Speed oriented)")) {
+		    assertEquals(options.size(), 4);
+		}
+	    }
+	} catch (WrongParameterException e) {
+	    e.printStackTrace();
+	    fail(e.getMessage());
 	}
+    }
+
+    private static PresetManager<Mafft> getPresets() {
+	Preset<Mafft> preset1 = new Preset<Mafft>();
+	preset1.name = "L-INS-i (Accuracy-oriented)";
+	preset1.description = "dsfjkg fdjksghkjsgdfh jksdfg sdfgkjhsdfgk kjsdfg ";
+
+	List<String> optionNames = new ArrayList<String>();
+	optionNames.add("--localpair");
+	optionNames.add("--maxiterate 1000");
+	preset1.option = optionNames;
+	PresetManager<Mafft> prman = new PresetManager<Mafft>();
+	prman.preset = Collections.singletonList(preset1);
+	prman.runnerClassName = Mafft.class.getCanonicalName();
+
+	return prman;
+    }
 }