Fixes to test cases

[jabaws.git] / webservices / compbio / ws / client / Jws2Client.java

diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java
index ec3cf65..eda6533 100644 (file)
--- a/webservices/compbio/ws/client/Jws2Client.java
+++ b/webservices/compbio/ws/client/Jws2Client.java
@@ -37,10 +37,7 @@ import java.io.OutputStream;
 import java.net.MalformedURLException;\r
 import java.net.URL;\r
 import java.util.Arrays;\r
-import java.util.HashMap;\r
-import java.util.HashSet;\r
 import java.util.List;\r
-import java.util.Map;\r
 import java.util.logging.Level;\r
 import java.util.logging.Logger;\r
 \r
@@ -53,7 +50,7 @@ import compbio.data.msa.MsaWS;
 import compbio.data.msa.SequenceAnnotation;\r
 import compbio.data.sequence.Alignment;\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.data.sequence.UnknownFileFormatException;\r
 import compbio.metadata.JobSubmissionException;\r
@@ -162,9 +159,9 @@ public class Jws2Client {
                                outStream = System.out;\r
                        }\r
                        if (service.getServiceType() == SequenceAnnotation.class) {\r
-                               Map<String, HashSet<Score>> result = analize(inputFile,\r
+                               ScoreManager result = analize(inputFile,\r
                                                ((SequenceAnnotation<T>) msaws), preset, customOptions);\r
-                               assert !result.values().isEmpty() : "No Result reported!";\r
+\r
                                IOHelper.writeOut(outStream, result);\r
                        } else {\r
                                alignment = align(inputFile, (MsaWS<T>) msaws, preset,\r
@@ -204,12 +201,11 @@ public class Jws2Client {
         * @return Set<Score> the conservation scores\r
         * @throws UnknownFileFormatException\r
         */\r
-       <T> HashMap<String, HashSet<Score>> analize(File file,\r
-                       SequenceAnnotation<T> wsproxy, Preset<T> preset,\r
-                       List<Option<T>> customOptions) {\r
+       <T> ScoreManager analize(File file, SequenceAnnotation<T> wsproxy,\r
+                       Preset<T> preset, List<Option<T>> customOptions) {\r
 \r
                List<FastaSequence> fastalist = null;\r
-               HashMap<String, HashSet<Score>> scores = null;\r
+               ScoreManager scores = null;\r
                try {\r
                        fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());\r
                        assert !fastalist.isEmpty() : "Input is empty!";\r
@@ -230,8 +226,6 @@ public class Jws2Client {
                        Thread.sleep(2000);\r
 \r
                        scores = wsproxy.getAnnotation(jobId);\r
-                       assert scores != null && !scores.values().isEmpty() : "Scores are NULL for job: "\r
-                                       + jobId;\r
 \r
                } catch (IOException e) {\r
                        System.err\r