Replace Map<String, HashSet<Score>> with ScoreManager and ScoreHolder classes to...

[jabaws.git] / testsrc / compbio / ws / client / TestAAConWS.java

diff --git a/testsrc/compbio/ws/client/TestAAConWS.java b/testsrc/compbio/ws/client/TestAAConWS.java
index 4fa90ac..6476311 100644 (file)
--- a/testsrc/compbio/ws/client/TestAAConWS.java
+++ b/testsrc/compbio/ws/client/TestAAConWS.java
@@ -8,10 +8,7 @@ import java.io.File;
 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
@@ -20,7 +17,7 @@ import compbio.data.msa.JABAService;
 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
@@ -78,13 +75,14 @@ public class TestAAConWS {
                        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
@@ -94,19 +92,21 @@ public class TestAAConWS {
                                        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
@@ -126,7 +126,6 @@ public class TestAAConWS {
                }\r
 \r
        }\r
-\r
        @Test\r
        public void testPresetAnalize() throws FileNotFoundException, IOException {\r
 \r
@@ -144,21 +143,23 @@ public class TestAAConWS {
                        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
@@ -199,12 +200,11 @@ public class TestAAConWS {
                        // .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
@@ -212,10 +212,9 @@ public class TestAAConWS {
                        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