System.out.println("Pres: " + msaws.getPresets().getPresets());\r
String jobId = msaws.analize(fsl);\r
System.out.println("J: " + jobId);\r
- HashSet<Score> result = msaws.getConservation(jobId);\r
+ HashSet<Score> result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
assertEquals(result.size(), 1);\r
assertEquals(result.iterator().next().getMethod(), Method.SHENKIN);\r
PresetManager<AACon> presets = msaws.getPresets();\r
jobId = msaws.presetAnalize(fsl,\r
presets.getPresetByName("Quick conservation"));\r
- result = msaws.getConservation(jobId);\r
+ result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
assertEquals(result.size(), 13);\r
\r
jobId = msaws.presetAnalize(fsl,\r
presets.getPresetByName("Slow conservation"));\r
- result = msaws.getConservation(jobId);\r
+ result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
assertEquals(result.size(), 5);\r
\r
jobId = msaws.presetAnalize(fsl,\r
presets.getPresetByName("Complete conservation"));\r
- result = msaws.getConservation(jobId);\r
+ result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
assertEquals(result.size(), 18);\r
\r
PresetManager<AACon> presets = msaws.getPresets();\r
String jobId = msaws.presetAnalize(fsl,\r
presets.getPresetByName("Quick conservation"));\r
- HashSet<Score> result = msaws.getConservation(jobId);\r
+ HashSet<Score> result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
assertEquals(result.size(), 13);\r
\r
jobId = msaws.presetAnalize(fsl,\r
presets.getPresetByName("Slow conservation"));\r
- result = msaws.getConservation(jobId);\r
+ result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
assertEquals(result.size(), 5);\r
\r
jobId = msaws.presetAnalize(fsl,\r
presets.getPresetByName("Complete conservation"));\r
- result = msaws.getConservation(jobId);\r
+ result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
assertEquals(result.size(), 18);\r
\r
try {\r
options.getArgument("Calculation method").setDefaultValue("SMERFS");\r
String jobId = msaws.customAnalize(fsl, options.getArguments());\r
- HashSet<Score> result = msaws.getConservation(jobId);\r
+ HashSet<Score> result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
assertEquals(result.size(), 1);\r
assertEquals(\r
options.removeArgument("Normalize");\r
System.out.println(options);\r
jobId = msaws.customAnalize(fsl, options.getArguments());\r
- result = msaws.getConservation(jobId);\r
+ result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
assertEquals(result.size(), 1);\r
assertEquals(\r