From 0d8eb4b63551b6f61dc30294409dacc7dee14095 Mon Sep 17 00:00:00 2001
From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Mon, 30 Sep 2013 14:29:33 +0100
Subject: [PATCH] Bug Fixg: testing RNAalifold jobs have been considered as
 real ones

---
 .../compbio/stat/collector/InputFilter.java        |   36 +++++++++++++++++++-
 webservices/compbio/ws/client/WSTester.java        |    6 ++++
 2 files changed, 41 insertions(+), 1 deletion(-)

diff --git a/webservices/compbio/stat/collector/InputFilter.java b/webservices/compbio/stat/collector/InputFilter.java
index 03466fe..3b2f45f 100644
--- a/webservices/compbio/stat/collector/InputFilter.java
+++ b/webservices/compbio/stat/collector/InputFilter.java
@@ -14,6 +14,7 @@ import compbio.ws.client.WSTester;
 public class InputFilter {
 
 	private static final Logger log = Logger.getLogger(InputFilter.class);
+
 	/**
 	 * Accepts input as valid unless it is a test input
 	 * 
@@ -28,12 +29,17 @@ public class InputFilter {
 		assert fastainput.length == 4;
 		String[] aligninput = WSTester.fastaAlignment.split("\n");
 		assert aligninput.length == 4;
+		String[] rnaaligninput = WSTester.clustalRNAAlignment.split("\n");
+		assert aligninput.length == 5;
 		// We do now know the type of the input here so must compare with both
 		// references
 		boolean isReference = compareLines(input, fastainput);
 		if (!isReference) {
 			isReference = compareLines(input, aligninput);
 		}
+		if (!isReference) {
+			isReference = compareClustalLines(input, rnaaligninput);
+		}
 		// only accept genuine input
 		return !isReference;
 	}
@@ -45,7 +51,7 @@ public class InputFilter {
 			reader = new BufferedReader(new FileReader(input));
 			// only compare first four lines of the file with reference
 			// because the reference length is only 4 lines
-			for (int i = 0; i < 4; i++) {
+			for (int i = 0; i < reference.length; i++) {
 				String line = reader.readLine();
 				if (Util.isEmpty(line)) {
 					status = false;
@@ -65,4 +71,32 @@ public class InputFilter {
 		}
 		return status;
 	}
+
+	private static boolean compareClustalLines(File input, String[] reference) {
+		BufferedReader reader = null;
+		boolean status = true;
+		try {
+			reader = new BufferedReader(new FileReader(input));
+			// only compare first four lines of the file with reference
+			// because the reference length is only 4 lines
+			int i = 0;
+			String line;
+			while (null != (line = reader.readLine())) {
+				if (!Util.isEmpty(line)) {
+					line = line.trim();
+					if (!line.equals(reference[i].trim())) {
+						status = false;
+						break;
+					}
+					++i;
+				}
+			}
+			reader.close();
+		} catch (IOException ioe) {
+			log.warn(ioe, ioe.getCause());
+		} finally {
+			FileUtil.closeSilently(reader);
+		}
+		return status;
+	}
 }
diff --git a/webservices/compbio/ws/client/WSTester.java b/webservices/compbio/ws/client/WSTester.java
index 928288c..5450a1d 100644
--- a/webservices/compbio/ws/client/WSTester.java
+++ b/webservices/compbio/ws/client/WSTester.java
@@ -80,6 +80,12 @@ public class WSTester {
 			">Foo\nC-UUGCGUUAAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G-GGUUUCUGUUGGAUGGUUG----GCAAC\n"
 		+   ">Bar\nG-UGGCGCUUAUGACGCAGUUGUCU-UAAA-CUCGAAC--UCGA-GCGGGCAAUUGCUGAU-UACGAUUAACCAC\n";
 
+	public static final String clustalRNAAlignment = 
+			"CLUSTAL\n" +
+			"Foo             C-UUGCGUUAAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G-GGUUUCUGUUGGA\n" +
+			"Bar             G-UGGCGCUUAUGACGCAGUUGUCU-UAAA-CUCGAAC--UCGA-GCGGGCAAUUGCUGA\n" +
+			"Foo             UGGUUG----GCAAC\n" +
+			"Bar             U-UACGAUUAACCAC";
 	/**
 	 * Status strings
 	 */
-- 
1.7.10.2