+ // Using presets\r
+ PresetManager<AACon> presets = msaws.getPresets();\r
+ jobId = msaws.presetAnalize(fsl,\r
+ presets.getPresetByName("Quick conservation"));\r
+ result = msaws.getAnnotation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.getFirstSequenceScores().getNumberOfScores(),\r
+ 13);\r
+\r
+ jobId = msaws.presetAnalize(fsl,\r
+ presets.getPresetByName("Slow conservation"));\r
+ result = msaws.getAnnotation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.getFirstSequenceScores().getNumberOfScores(), 5);\r
+\r
+ jobId = msaws.presetAnalize(fsl,\r
+ presets.getPresetByName("Complete conservation"));\r
+ result = msaws.getAnnotation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.getFirstSequenceScores().getNumberOfScores(),\r
+ 18);\r
+\r
+ } catch (UnsupportedRuntimeException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (LimitExceededException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (WrongParameterException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+\r
+ }\r
+ @Test\r
+ public void testPresetAnalize() throws FileNotFoundException, IOException {\r
+\r
+ String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()\r
+ + File.separator;\r
+\r
+ List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
+ CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"\r
+ + File.separator + "TO1381.fasta.aln"));\r
+\r
+ try {\r
+ System.out.println("Pres: " + msaws.getPresets().getPresets());\r
+\r
+ // Using presets\r
+ PresetManager<AACon> presets = msaws.getPresets();\r
+ String jobId = msaws.presetAnalize(fsl,\r
+ presets.getPresetByName("Quick conservation"));\r
+ ScoreManager result = msaws.getAnnotation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.getFirstSequenceScores().getNumberOfScores(),\r
+ 13);\r
+\r
+ jobId = msaws.presetAnalize(fsl,\r
+ presets.getPresetByName("Slow conservation"));\r
+ result = msaws.getAnnotation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.getFirstSequenceScores().getNumberOfScores(), 5);\r
+\r
+ jobId = msaws.presetAnalize(fsl,\r
+ presets.getPresetByName("Complete conservation"));\r
+ result = msaws.getAnnotation(jobId);\r
+ assertNotNull(result);\r
+ assertEquals(result.getFirstSequenceScores().getNumberOfScores(),\r
+ 18);\r
+\r