- public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
- + "MafftParameters.xml";\r
- public static String test_schema_output = "RunnerConfigSchema.xml";\r
- public static String test_output = AllTestSuit.OUTPUT_DIR_ABSOLUTE\r
- + "MafftParameters.out.xml";\r
-\r
- public static String invalidDoc = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
- + "InvalidMafftParameters.xml";\r
-\r
- RunnerConfig<Mafft> rconfig = null;\r
- Parameter<Mafft> matrixParam = null;\r
- RunnerConfigMarshaller<Mafft> pmarshaller = null;\r
-\r
- @BeforeMethod\r
- public void setup() {\r
- // write some parameters programmatically\r
- try {\r
- rconfig = new RunnerConfig<Mafft>();\r
- rconfig.setRunnerClassName(Mafft.class.getName());\r
- List<Option<Mafft>> prms = new ArrayList<Option<Mafft>>();\r
-\r
- Parameter<Mafft> p1 = new Parameter<Mafft>("Type",\r
- "Type of the sequence (PROTEIN or DNA)");\r
- // TODO publish help on a compbio web site\r
-\r
- p1.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
- p1.addPossibleValues("PROTEIN", "DNA");\r
- p1.setOptionName("-TYPE");\r
- p1.setRequired(false);\r
-\r
- /*\r
- * -MATRIX= :Protein weight matrix=BLOSUM, PAM, GONNET, ID or\r
- * filename\r
- */\r
- Option<Mafft> p2 = new Option<Mafft>("MATRIX",\r
- "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
-\r
- p2.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
-\r
- p2.addOptionNames("-jtree"); // "-retree"\r
- p2.setRequired(false);\r
-\r
- Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1",\r
- "Protein weight matrix");\r
- // TODO publish help on a compbio web site\r
- p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
-\r
- p3.addPossibleValues("BLOSUM", "PAM", "GONNET", "ID");\r
- // This attribute is required by strict schema\r
- p3.setOptionName("--AAMATRIX");\r
- p3.setRequired(true);\r
- p3.setDefaultValue("pam");\r
- ValueConstrain vc = new ValueConstrain();\r
- vc.setType(ValueConstrain.Type.Float);\r
- vc.setMin("-10.12");\r
- vc.setMax("0");\r
- p3.setValidValue(vc);\r
-\r
- prms.add(p1);\r
- prms.add(p2);\r
- prms.add(p3);\r
- matrixParam = p3;\r
- rconfig.setOptions(prms);\r
-\r
- pmarshaller = new RunnerConfigMarshaller<Mafft>(RunnerConfig.class,\r
- Parameter.class, Option.class, ValueConstrain.class);\r
- } catch (MalformedURLException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (JAXBException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
- } catch (WrongParameterException e) {\r
- e.printStackTrace();\r
- fail(e.getLocalizedMessage());\r
+ public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "MafftParameters.xml";\r
+ public static String test_schema_output = "RunnerConfigSchema.xml";\r
+ public static String test_output = AllTestSuit.OUTPUT_DIR_ABSOLUTE + "MafftParameters.out.xml";\r
+\r
+ public static String invalidDoc = AllTestSuit.TEST_DATA_PATH_ABSOLUTE + "InvalidMafftParameters.xml";\r
+\r
+ RunnerConfig<Mafft> rconfig = null;\r
+ Parameter<Mafft> matrixParam = null;\r
+ RunnerConfigMarshaller<Mafft> pmarshaller = null;\r
+\r
+ @BeforeMethod\r
+ public void setup() {\r
+ // write some parameters programmatically\r
+ try {\r
+ rconfig = new RunnerConfig<Mafft>();\r
+ rconfig.setRunnerClassName(Mafft.class.getName());\r
+ List<Option<Mafft>> prms = new ArrayList<Option<Mafft>>();\r
+\r
+ Parameter<Mafft> p1 = new Parameter<Mafft>("Type", "Type of the sequence (PROTEIN or DNA)");\r
+ // TODO publish help on a compbio web site\r
+\r
+ p1.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
+ p1.addPossibleValues("PROTEIN", "DNA");\r
+ p1.setOptionName("-TYPE");\r
+ p1.setRequired(false);\r
+\r
+ /*\r
+ * -MATRIX= :Protein weight matrix=BLOSUM, PAM, GONNET, ID or\r
+ * filename\r
+ */\r
+ Option<Mafft> p2 = new Option<Mafft>("MATRIX", "Protein weight matrix");\r
+ // TODO publish help on a compbio web site\r
+\r
+ p2.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
+\r
+ p2.addOptionNames("-jtree"); // "-retree"\r
+ p2.setRequired(false);\r
+\r
+ Parameter<Mafft> p3 = new Parameter<Mafft>("Matrix1", "Protein weight matrix");\r
+ // TODO publish help on a compbio web site\r
+ p3.setFurtherDetails("http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html");\r
+\r
+ p3.addPossibleValues("BLOSUM", "PAM", "GONNET", "ID");\r
+ // This attribute is required by strict schema\r
+ p3.setOptionName("--AAMATRIX");\r
+ p3.setRequired(true);\r
+ p3.setDefaultValue("pam");\r
+ ValueConstrain vc = new ValueConstrain();\r
+ vc.setType(ValueConstrain.Type.Float);\r
+ vc.setMin("-10.12");\r
+ vc.setMax("0");\r
+ p3.setValidValue(vc);\r
+\r
+ prms.add(p1);\r
+ prms.add(p2);\r
+ prms.add(p3);\r
+ matrixParam = p3;\r
+ rconfig.setOptions(prms);\r
+\r
+ pmarshaller = new RunnerConfigMarshaller<Mafft>(RunnerConfig.class, Parameter.class, Option.class, ValueConstrain.class);\r
+ } catch (JAXBException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (WrongParameterException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+\r