Disembl and Jronn web services work. Modified to produce raw scores Globplot script...

[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 acaf57f..4fa90ac 100644 (file)
--- a/testsrc/compbio/ws/client/TestAAConWS.java
+++ b/testsrc/compbio/ws/client/TestAAConWS.java
@@ -11,12 +11,13 @@ import java.io.IOException;
 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
 \r
-import compbio.data.msa.Annotation;\r
 import compbio.data.msa.JABAService;\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
@@ -33,7 +34,7 @@ import compbio.util.SysPrefs;
 \r
 public class TestAAConWS {\r
 \r
-       Annotation<AACon> msaws;\r
+       SequenceAnnotation<AACon> msaws;\r
 \r
        @BeforeTest\r
        void initConnection() {\r
@@ -49,7 +50,7 @@ public class TestAAConWS {
                 */\r
                JABAService client = Jws2Client.connect("http://localhost:8080/jabaws",\r
                                Services.AAConWS);\r
-               msaws = (Annotation<AACon>) client;\r
+               msaws = (SequenceAnnotation<AACon>) client;\r
        }\r
 \r
        @Test\r
@@ -77,12 +78,13 @@ public class TestAAConWS {
                        System.out.println("Pres: " + msaws.getPresets().getPresets());\r
                        String jobId = msaws.analize(fsl);\r
                        System.out.println("J: " + jobId);\r
-                       HashSet<Score> result = msaws.getAnnotation(jobId);\r
+                       Map<String, HashSet<Score>> result = msaws.getAnnotation(jobId);\r
                        assertNotNull(result);\r
                        assertEquals(result.size(), 1);\r
-                       assertEquals(result.iterator().next().getMethod(),\r
-                                       ConservationMethod.SHENKIN);\r
-                       List<Float> scores = result.iterator().next().getScores();\r
+                       assertEquals(result.values().iterator().next().iterator().next()\r
+                                       .getMethod(), ConservationMethod.SHENKIN);\r
+                       List<Float> scores = result.values().iterator().next().iterator()\r
+                                       .next().getScores();\r
                        assertNotNull(scores);\r
                        assertEquals(scores.size(), 568);\r
 \r
@@ -142,7 +144,7 @@ public class TestAAConWS {
                        PresetManager<AACon> presets = msaws.getPresets();\r
                        String jobId = msaws.presetAnalize(fsl,\r
                                        presets.getPresetByName("Quick conservation"));\r
-                       HashSet<Score> result = msaws.getAnnotation(jobId);\r
+                       Map<String, HashSet<Score>> result = msaws.getAnnotation(jobId);\r
                        assertNotNull(result);\r
                        assertEquals(result.size(), 13);\r
 \r
@@ -197,12 +199,12 @@ public class TestAAConWS {
                        // .setDefaultValue("MAX_SCORE");\r
                        // options.getArgument("SMERFS Gap Threshhold").setDefaultValue("1");\r
                        String jobId = msaws.customAnalize(fsl, options.getArguments());\r
-                       HashSet<Score> result = msaws.getAnnotation(jobId);\r
+                       Map<String, HashSet<Score>> result = msaws.getAnnotation(jobId);\r
                        assertNotNull(result);\r
                        assertEquals(result.size(), 1);\r
                        assertEquals(\r
-                                       new ArrayList<Score>(result).get(0).getScores().get(0),\r
-                                       0.698f);\r
+                                       new ArrayList<Score>(result.values().iterator().next())\r
+                                                       .get(0).getScores().get(0), 0.698f);\r
 \r
                        options.getArgument("Calculation method").setDefaultValue("SMERFS");\r
                        options.removeArgument("Normalize");\r
@@ -212,8 +214,8 @@ public class TestAAConWS {
                        assertNotNull(result);\r
                        assertEquals(result.size(), 1);\r
                        assertEquals(\r
-                                       new ArrayList<Score>(result).get(0).getScores().get(0),\r
-                                       0.401f);\r
+                                       new ArrayList<Score>(result.values().iterator().next())\r
+                                                       .get(0).getScores().get(0), 0.401f);\r
 \r
                } catch (WrongParameterException e) {\r
                        e.printStackTrace();\r