RNAStruct replaced by RNAStructScoreManager. Why does webservice

[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 a06a6fa..ce4980d 100644 (file)
--- a/webservices/compbio/ws/client/Jws2Client.java
+++ b/webservices/compbio/ws/client/Jws2Client.java
@@ -50,7 +50,7 @@ import compbio.data.msa.RegistryWS;
 import compbio.data.msa.SequenceAnnotation;\r
 import compbio.data.sequence.Alignment;\r
 import compbio.data.sequence.FastaSequence;\r
-import compbio.data.sequence.RNAstruct;\r
+import compbio.data.sequence.RNAStruct;\r
 import compbio.data.sequence.ScoreManager;\r
 import compbio.data.sequence.ClustalAlignmentUtil;\r
 import compbio.data.sequence.SequenceUtil;\r
@@ -150,7 +150,6 @@ public class Jws2Client {
                String presetName = CmdHelper.getPresetName(cmd);\r
 \r
                Metadata<T> msaws = (Metadata<T>) connect(hostname, service);\r
-               Metadata<T> foldws = (Metadata<T>) connect(hostname, service);\r
                Preset<T> preset = null;\r
                if (presetName != null) {\r
                        preset = MetadataHelper.getPreset(msaws, presetName);\r
@@ -164,7 +163,6 @@ public class Jws2Client {
 //             System.out.println("The Options read from the command line: " + customOptions);\r
                \r
                Alignment alignment = null;\r
-               String rnastruct = null;\r
                if (inputFile != null) {\r
                        Writer writer = null;\r
                        if (outFile != null) {\r
@@ -178,17 +176,12 @@ public class Jws2Client {
                                ScoreManager result = analize(inputFile,\r
                                                ((SequenceAnnotation<T>) msaws), preset, customOptions);\r
 \r
+                               System.out.println(result\.asRNAStruct().toString());\r
                                IOHelper.writeOut(writer, result);\r
                        } else if (service.getServiceType() == MsaWS.class) {\r
                                alignment = align(inputFile, (MsaWS<T>) msaws, preset,\r
                                                customOptions);\r
                                IOHelper.writeOut(writer, alignment);\r
-                       } else if (service.getServiceType() == FoldWS.class) {\r
-                               rnastruct = fold(inputFile, (FoldWS<T>) foldws, preset, customOptions);\r
-                               // No IOHelper method for rnastruct/String yet\r
-                               if (writer != null) {\r
-                                       writer.write(rnastruct);\r
-                               }\r
                        }\r
                        writer.close();\r
                }\r