Fix problem with the JpredWS service. Now Jws2Client is able to test the service

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

diff --git a/webservices/compbio/ws/client/AAConClient.java b/webservices/compbio/ws/client/AAConClient.java
index 57cf59f..f7f2603 100644 (file)
--- a/webservices/compbio/ws/client/AAConClient.java
+++ b/webservices/compbio/ws/client/AAConClient.java
@@ -1,6 +1,6 @@
-/* Copyright (c) 2010 Peter Troshin\r
+/* Copyright (c) 2011 Peter Troshin\r
  *  \r
- *  Amino Acid Conservation Web Service client @version: 1.0     \r
+ *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \r
  * \r
  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
  *  Apache License version 2 as published by the Apache Software Foundation\r
@@ -30,13 +30,11 @@ import static compbio.ws.client.Constraints.pseparator;
 import java.io.Closeable;\r
 import java.io.File;\r
 import java.io.IOException;\r
-import java.io.OutputStream;\r
+import java.io.PrintWriter;\r
+import java.io.Writer;\r
 import java.net.MalformedURLException;\r
 import java.net.URL;\r
-import java.util.HashSet;\r
 import java.util.List;\r
-import java.util.Map;\r
-import java.util.Set;\r
 import java.util.logging.Level;\r
 import java.util.logging.Logger;\r
 \r
@@ -46,7 +44,7 @@ import javax.xml.ws.WebServiceException;
 \r
 import compbio.data.msa.SequenceAnnotation;\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
@@ -115,17 +113,17 @@ public class AAConClient {
                        customOptions = MetadataHelper.processParameters(prms,\r
                                        msaws.getRunnerOptions());\r
                }\r
-               Map<String, HashSet<Score>> result = null;\r
+               ScoreManager result = null;\r
                if (inputFile != null) {\r
                        System.out.println("Calculating conservation...");\r
                        result = analize(inputFile, msaws, preset, customOptions);\r
-                       OutputStream outStream = null;\r
+                       Writer outStream = null;\r
                        if (outFile != null) {\r
-                               outStream = IOHelper.getOutStream(outFile);\r
+                               outStream = IOHelper.getWriter(outFile);\r
                        } else {\r
                                // this stream is going to be closed later which is fine as\r
                                // std.out will not be\r
-                               outStream = System.out;\r
+                               outStream = new PrintWriter(System.out, true);\r
                        }\r
                        writeOut(outStream, result);\r
                        // stream is closed in the method no need to close it here\r
@@ -155,22 +153,17 @@ public class AAConClient {
         * @param result\r
         *            the AACon scores to output\r
         */\r
-       static void writeOut(OutputStream outStream,\r
-                       Map<String, HashSet<Score>> result) {\r
+       static void writeOut(Writer writer, ScoreManager result) {\r
                try {\r
-                       for (Map.Entry<String, ? extends Set<Score>> entry : result\r
-                                       .entrySet()) {\r
-                               System.out.println(">" + entry.getKey());\r
-                               Score.write(entry.getValue(), outStream);\r
-                       }\r
+                       result.writeOut(writer);\r
                } catch (IOException e) {\r
                        System.err\r
                                        .println("Problems writing output file! Stack trace is below: ");\r
                        e.printStackTrace();\r
                } finally {\r
-                       if (outStream != null) {\r
+                       if (writer != null) {\r
                                try {\r
-                                       outStream.close();\r
+                                       writer.close();\r
                                } catch (IOException ignored) {\r
                                        // e.printStackTrace();\r
                                }\r
@@ -222,12 +215,11 @@ public class AAConClient {
         * @return Set<Score> the conservation scores\r
         * @throws UnknownFileFormatException\r
         */\r
-       static Map<String, HashSet<Score>> analize(File file,\r
-                       SequenceAnnotation<AAConWS> wsproxy, Preset<AAConWS> preset,\r
-                       List<Option<AAConWS>> customOptions) {\r
+       static ScoreManager analize(File file, SequenceAnnotation<AAConWS> wsproxy,\r
+                       Preset<AAConWS> preset, List<Option<AAConWS>> customOptions) {\r
 \r
                List<FastaSequence> fastalist = null;\r
-               Map<String, HashSet<Score>> scores = null;\r
+               ScoreManager scores = null;\r
                try {\r
                        fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());\r
 \r