X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fclient%2FAAConClient.java;h=f7f26038eb03001fe9da7605d7fb9e4964b229df;hb=1e1c3681ba25ee1797a46f871b8c80f259afe2ca;hp=34fc751a2f915414bb68da74f09bc772d62774fa;hpb=e98ca8829b7c42c00f2f2588e1168d3f31eb248f;p=jabaws.git

diff --git a/webservices/compbio/ws/client/AAConClient.java b/webservices/compbio/ws/client/AAConClient.java
index 34fc751..f7f2603 100644
--- a/webservices/compbio/ws/client/AAConClient.java
+++ b/webservices/compbio/ws/client/AAConClient.java
@@ -1,6 +1,6 @@
-/* Copyright (c) 2010 Peter Troshin
+/* Copyright (c) 2011 Peter Troshin
  *  
- *  Amino Acid Conservation Web Service client @version: 1.0     
+ *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     
  * 
  *  This library is free software; you can redistribute it and/or modify it under the terms of the
  *  Apache License version 2 as published by the Apache Software Foundation
@@ -30,11 +30,11 @@ import static compbio.ws.client.Constraints.pseparator;
 import java.io.Closeable;
 import java.io.File;
 import java.io.IOException;
-import java.io.OutputStream;
+import java.io.PrintWriter;
+import java.io.Writer;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.List;
-import java.util.Set;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
@@ -42,9 +42,9 @@ import javax.xml.namespace.QName;
 import javax.xml.ws.Service;
 import javax.xml.ws.WebServiceException;
 
-import compbio.data.msa.Annotation;
+import compbio.data.msa.SequenceAnnotation;
 import compbio.data.sequence.FastaSequence;
-import compbio.data.sequence.Score;
+import compbio.data.sequence.ScoreManager;
 import compbio.data.sequence.SequenceUtil;
 import compbio.data.sequence.UnknownFileFormatException;
 import compbio.metadata.JobSubmissionException;
@@ -102,7 +102,7 @@ public class AAConClient {
 		File parametersFile = IOHelper.getFile(cmd, paramFile, true);
 		String presetName = CmdHelper.getPresetName(cmd);
 
-		Annotation<AAConWS> msaws = connect();
+		SequenceAnnotation<AAConWS> msaws = connect();
 		Preset<AAConWS> preset = null;
 		if (presetName != null) {
 			preset = MetadataHelper.getPreset(msaws, presetName);
@@ -113,17 +113,17 @@ public class AAConClient {
 			customOptions = MetadataHelper.processParameters(prms,
 					msaws.getRunnerOptions());
 		}
-		Set<Score> result = null;
+		ScoreManager result = null;
 		if (inputFile != null) {
 			System.out.println("Calculating conservation...");
 			result = analize(inputFile, msaws, preset, customOptions);
-			OutputStream outStream = null;
+			Writer outStream = null;
 			if (outFile != null) {
-				outStream = IOHelper.getOutStream(outFile);
+				outStream = IOHelper.getWriter(outFile);
 			} else {
 				// this stream is going to be closed later which is fine as
 				// std.out will not be
-				outStream = System.out;
+				outStream = new PrintWriter(System.out, true);
 			}
 			writeOut(outStream, result);
 			// stream is closed in the method no need to close it here
@@ -153,17 +153,17 @@ public class AAConClient {
 	 * @param result
 	 *            the AACon scores to output
 	 */
-	static void writeOut(OutputStream outStream, Set<Score> result) {
+	static void writeOut(Writer writer, ScoreManager result) {
 		try {
-			Score.write(result, outStream);
+			result.writeOut(writer);
 		} catch (IOException e) {
 			System.err
 					.println("Problems writing output file! Stack trace is below: ");
 			e.printStackTrace();
 		} finally {
-			if (outStream != null) {
+			if (writer != null) {
 				try {
-					outStream.close();
+					writer.close();
 				} catch (IOException ignored) {
 					// e.printStackTrace();
 				}
@@ -175,11 +175,12 @@ public class AAConClient {
 	 * Connects to a AACon web service by the host and the service name
 	 * 
 	 * 
-	 * @return {@link Annotation}
+	 * @return {@link AlignmentAnnotation}
 	 * @throws WebServiceException
 	 *             if cannot connect to a web service
 	 */
-	public static Annotation<AAConWS> connect() throws WebServiceException {
+	public static SequenceAnnotation<AAConWS> connect()
+			throws WebServiceException {
 		URL url = null;
 		log.log(Level.FINE, "Attempting to connect...");
 		try {
@@ -193,8 +194,8 @@ public class AAConClient {
 		QName portName = new QName(QUALIFIED_SERVICE_NAME, "AAConWS" + "Port");
 
 		@SuppressWarnings("unchecked")
-		Annotation<AAConWS> serviceIF = serv
-				.getPort(portName, Annotation.class);
+		SequenceAnnotation<AAConWS> serviceIF = serv.getPort(portName,
+				SequenceAnnotation.class);
 
 		log.log(Level.FINE, "Connected successfully!");
 		return serviceIF;
@@ -214,11 +215,11 @@ public class AAConClient {
 	 * @return Set<Score> the conservation scores
 	 * @throws UnknownFileFormatException
 	 */
-	static Set<Score> analize(File file, Annotation<AAConWS> wsproxy,
+	static ScoreManager analize(File file, SequenceAnnotation<AAConWS> wsproxy,
 			Preset<AAConWS> preset, List<Option<AAConWS>> customOptions) {
 
 		List<FastaSequence> fastalist = null;
-		Set<Score> scores = null;
+		ScoreManager scores = null;
 		try {
 			fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());