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

[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 1673e18..62aa383 100644 (file)
--- a/webservices/compbio/ws/client/Jws2Client.java
+++ b/webservices/compbio/ws/client/Jws2Client.java
@@ -37,18 +37,19 @@ import java.io.OutputStream;
 import java.net.MalformedURLException;\r
 import java.net.URL;\r
 import java.util.Arrays;\r
+import java.util.HashSet;\r
 import java.util.List;\r
-import java.util.Set;\r
+import java.util.Map;\r
 import java.util.logging.Level;\r
 import java.util.logging.Logger;\r
 \r
 import javax.xml.ws.Service;\r
 import javax.xml.ws.WebServiceException;\r
 \r
-import compbio.data.msa.Annotation;\r
 import compbio.data.msa.JABAService;\r
 import compbio.data.msa.Metadata;\r
 import compbio.data.msa.MsaWS;\r
+import compbio.data.msa.SequenceAnnotation;\r
 import compbio.data.sequence.Alignment;\r
 import compbio.data.sequence.FastaSequence;\r
 import compbio.data.sequence.Score;\r
@@ -160,8 +161,8 @@ public class Jws2Client {
                                outStream = System.out;\r
                        }\r
                        if (service == Services.AAConWS) {\r
-                               Set<Score> result = analize(inputFile, ((Annotation<T>) msaws),\r
-                                               preset, customOptions);\r
+                               Map<String, HashSet<Score>> result = analize(inputFile,\r
+                                               ((SequenceAnnotation<T>) msaws), preset, customOptions);\r
                                IOHelper.writeOut(outStream, result);\r
                        } else {\r
                                alignment = align(inputFile, (MsaWS<T>) msaws, preset,\r
@@ -202,11 +203,12 @@ public class Jws2Client {
         * @return Set<Score> the conservation scores\r
         * @throws UnknownFileFormatException\r
         */\r
-       <T> Set<Score> analize(File file, Annotation<T> wsproxy, Preset<T> preset,\r
+       <T> Map<String, HashSet<Score>> analize(File file,\r
+                       SequenceAnnotation<T> wsproxy, Preset<T> preset,\r
                        List<Option<T>> customOptions) {\r
 \r
                List<FastaSequence> fastalist = null;\r
-               Set<Score> scores = null;\r
+               Map<String, HashSet<Score>> scores = null;\r
                try {\r
                        fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());\r
 \r