import java.io.FileInputStream;\r
import java.io.FileNotFoundException;\r
import java.io.IOException;\r
-import java.util.ArrayList;\r
-import java.util.HashSet;\r
import java.util.List;\r
-import java.util.Map;\r
\r
import org.testng.annotations.BeforeTest;\r
import org.testng.annotations.Test;\r
import compbio.data.msa.SequenceAnnotation;\r
import compbio.data.sequence.ConservationMethod;\r
import compbio.data.sequence.FastaSequence;\r
-import compbio.data.sequence.Score;\r
+import compbio.data.sequence.ScoreManager;\r
import compbio.data.sequence.SequenceUtil;\r
import compbio.metadata.JobSubmissionException;\r
import compbio.metadata.LimitExceededException;\r
System.out.println("Pres: " + msaws.getPresets().getPresets());\r
String jobId = msaws.analize(fsl);\r
System.out.println("J: " + jobId);\r
- Map<String, HashSet<Score>> result = msaws.getAnnotation(jobId);\r
+ ScoreManager result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
- assertEquals(result.size(), 1);\r
- assertEquals(result.values().iterator().next().iterator().next()\r
+ assertEquals(result.getFirstSequenceScores().getNumberOfScores(), 1);\r
+\r
+ assertEquals(result.getFirstSequenceScores().getFirstScore()\r
.getMethod(), ConservationMethod.SHENKIN);\r
- List<Float> scores = result.values().iterator().next().iterator()\r
- .next().getScores();\r
+ List<Float> scores = result.getFirstSequenceScores()\r
+ .getFirstScore().getScores();\r
assertNotNull(scores);\r
assertEquals(scores.size(), 568);\r
\r
presets.getPresetByName("Quick conservation"));\r
result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
- assertEquals(result.size(), 13);\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.size(), 5);\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.size(), 18);\r
+ assertEquals(result.getFirstSequenceScores().getNumberOfScores(),\r
+ 18);\r
\r
} catch (UnsupportedRuntimeException e) {\r
e.printStackTrace();\r
}\r
\r
}\r
-\r
@Test\r
public void testPresetAnalize() throws FileNotFoundException, IOException {\r
\r
PresetManager<AACon> presets = msaws.getPresets();\r
String jobId = msaws.presetAnalize(fsl,\r
presets.getPresetByName("Quick conservation"));\r
- Map<String, HashSet<Score>> result = msaws.getAnnotation(jobId);\r
+ ScoreManager result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
- assertEquals(result.size(), 13);\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.size(), 5);\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.size(), 18);\r
+ assertEquals(result.getFirstSequenceScores().getNumberOfScores(),\r
+ 18);\r
\r
} catch (UnsupportedRuntimeException e) {\r
e.printStackTrace();\r
// .setDefaultValue("MAX_SCORE");\r
// options.getArgument("SMERFS Gap Threshhold").setDefaultValue("1");\r
String jobId = msaws.customAnalize(fsl, options.getArguments());\r
- Map<String, HashSet<Score>> result = msaws.getAnnotation(jobId);\r
+ ScoreManager result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
- assertEquals(result.size(), 1);\r
- assertEquals(\r
- new ArrayList<Score>(result.values().iterator().next())\r
- .get(0).getScores().get(0), 0.698f);\r
+ assertEquals(result.getFirstSequenceScores().getNumberOfScores(), 1);\r
+ assertEquals(result.getFirstSequenceScores().getFirstScore()\r
+ .getScores().get(0), 0.698f);\r
\r
options.getArgument("Calculation method").setDefaultValue("SMERFS");\r
options.removeArgument("Normalize");\r
jobId = msaws.customAnalize(fsl, options.getArguments());\r
result = msaws.getAnnotation(jobId);\r
assertNotNull(result);\r
- assertEquals(result.size(), 1);\r
- assertEquals(\r
- new ArrayList<Score>(result.values().iterator().next())\r
- .get(0).getScores().get(0), 0.401f);\r
+ assertEquals(result.getFirstSequenceScores().getNumberOfScores(), 1);\r
+ assertEquals(result.getFirstSequenceScores().getFirstScore()\r
+ .getScores().get(0), 0.401f);\r
\r
} catch (WrongParameterException e) {\r
e.printStackTrace();\r