X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fclient%2FIOHelper.java;h=3e4b72696a69bef9362e0ee19f6f05cadcf101eb;hb=4c022b67a736b6f79dbe212d73016607cf298422;hp=88b695a2ffb44f09b6705c3d09d0ffd61e2c2ff0;hpb=99ab39d360a99ec101152070146b63773a1d6453;p=jabaws.git

diff --git a/webservices/compbio/ws/client/IOHelper.java b/webservices/compbio/ws/client/IOHelper.java
index 88b695a..3e4b726 100644
--- a/webservices/compbio/ws/client/IOHelper.java
+++ b/webservices/compbio/ws/client/IOHelper.java
@@ -1,3 +1,20 @@
+/* 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;
@@ -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());
@@ -112,6 +129,9 @@ public class IOHelper {
 	 *            the AACon scores to output
 	 */
 	static void writeOut(Writer writer, ScoreManager results) {
+		if (results == null) {
+			return;
+		}
 		try {
 			results.writeOut(writer);
 		} catch (IOException e) {