- @Test(enabled = false)\r
- public void testAddParameters() {\r
- ArrayList<FastaSequence> seqs = new ArrayList<FastaSequence>();\r
- FastaSequence fs = new FastaSequence("tests1",\r
- "aqtctcatcatctcatctgcccccgggttatgagtagtacgcatctacg");\r
- FastaSequence fs2 = new FastaSequence("tests2",\r
- "aqtctcatcatctcatctgcccccgggttatgagtagtacgcatctacg");\r
- FastaSequence fs3 = new FastaSequence("tests3",\r
- "aqtctcatcatctcatctgcccccgggttatgagtagtacgcatctacg");\r
- seqs.add(fs);\r
- seqs.add(fs2);\r
- seqs.add(fs3);\r
- ClustalW cl = new ClustalW();\r
- cl.setInput("input.txt").setOutput("output.txt");\r
- ConfiguredExecutable<ClustalW> confClustal;\r
- try {\r
- confClustal = Configurator.configureExecutable(cl);\r
- Util.writeInput(seqs, confClustal);\r
-\r
- LocalRunner lr = new LocalRunner(confClustal);\r
- lr.executeJob();\r
- confClustal = (ConfiguredExecutable<ClustalW>) lr.waitForResult();\r
- assertNotNull(confClustal.getResults());\r
-\r
- assertTrue(confClustal.saveRunConfiguration());\r
- ConfiguredExecutable<ClustalW> cexec = (ConfiguredExecutable<ClustalW>) confClustal\r
- .loadRunConfiguration(new FileInputStream(new File(\r
- confClustal.getWorkDirectory(),\r
- RunConfiguration.rconfigFile)));\r
- assertNotNull(cexec);\r
-\r
- lr = new LocalRunner(cexec);\r
- lr.executeJob();\r
- confClustal = (ConfiguredExecutable<ClustalW>) lr.waitForResult();\r
- assertNotNull(confClustal.getResults());\r
-\r
- System.out.println("CE:" + cexec);\r
- } catch (JobSubmissionException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (JobExecutionException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (ResultNotAvailableException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (IOException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- }\r
- }\r
-\r