X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fclient%2FIOHelper.java;h=3e4b72696a69bef9362e0ee19f6f05cadcf101eb;hb=4c022b67a736b6f79dbe212d73016607cf298422;hp=af9a52cf4d94762196079cbf47f0bb5f216c0429;hpb=6e1c873d0879f462b1fb1a1efa444cf993a9e76a;p=jabaws.git

diff --git a/webservices/compbio/ws/client/IOHelper.java b/webservices/compbio/ws/client/IOHelper.java
index af9a52c..3e4b726 100644
--- a/webservices/compbio/ws/client/IOHelper.java
+++ b/webservices/compbio/ws/client/IOHelper.java
@@ -1,19 +1,36 @@
+/* Copyright (c) 2011 Peter Troshin
+ *  
+ *  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
+ * 
+ *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
+ *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache 
+ *  License for more details.
+ * 
+ *  A copy of the license is in apache_license.txt. It is also available here:
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
+ * 
+ * Any republication or derived work distributed in source code form
+ * must include this copyright and license notice.
+ */
 package compbio.ws.client;
 
 import static compbio.ws.client.Constraints.pseparator;
 
 import java.io.BufferedReader;
 import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
 import java.io.FileReader;
+import java.io.FileWriter;
 import java.io.IOException;
-import java.io.OutputStream;
+import java.io.Writer;
 import java.util.ArrayList;
 import java.util.List;
 
 import compbio.data.sequence.Alignment;
 import compbio.data.sequence.ClustalAlignmentUtil;
+import compbio.data.sequence.ScoreManager;
 
 public class IOHelper {
 
@@ -29,8 +46,8 @@ public class IOHelper {
 	static File getFile(String[] cmd, String key, boolean mustExist)
 			throws IOException {
 		assert key != null && key.trim().length() != 0;
-		for (int i = 0; i < cmd.length; i++) {
-			String filename = cmd[i];
+		for (String c : cmd) {
+			String filename = c;
 			filename = filename.trim();
 			if (filename.toLowerCase().startsWith(key + pseparator)) {
 				filename = filename.substring((key + pseparator).length());
@@ -73,14 +90,9 @@ public class IOHelper {
 		return params;
 	}
 
-	static OutputStream getOutStream(File file) {
+	static Writer getWriter(File file) throws IOException {
 		assert file != null && file.exists();
-		try {
-			return new FileOutputStream(file);
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-		}
-		return null;
+		return new FileWriter(file);
 	}
 
 	/**
@@ -91,17 +103,45 @@ public class IOHelper {
 	 * @param align
 	 *            the alignment to output
 	 */
-	static void writeOut(OutputStream outStream, Alignment align) {
+	static void writeOut(Writer writer, Alignment align) {
+		try {
+			ClustalAlignmentUtil.writeClustalAlignment(writer, align);
+		} catch (IOException e) {
+			System.err
+					.println("Problems writing output file! Stack trace is below: ");
+			e.printStackTrace();
+		} finally {
+			if (writer != null) {
+				try {
+					writer.close();
+				} catch (IOException ignored) {
+					// e.printStackTrace();
+				}
+			}
+		}
+	}
+
+	/**
+	 * Outputs AAcon results into the file represented by the outStream
+	 * 
+	 * @param outStream
+	 * @param result
+	 *            the AACon scores to output
+	 */
+	static void writeOut(Writer writer, ScoreManager results) {
+		if (results == null) {
+			return;
+		}
 		try {
-			ClustalAlignmentUtil.writeClustalAlignment(outStream, align);
+			results.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();
 				}