From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Thu, 3 Oct 2013 12:13:22 +0000 (+0100)
Subject: Fix wrong error message
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e6227b3fc0bb5abdf275bb24a87607b0555bce10;p=jabaws.git

Fix wrong error message
---

diff --git a/runner/compbio/runner/conservation/AACon.java b/runner/compbio/runner/conservation/AACon.java
index 9ff6549..c878265 100644
--- a/runner/compbio/runner/conservation/AACon.java
+++ b/runner/compbio/runner/conservation/AACon.java
@@ -60,19 +60,16 @@ public class AACon extends SkeletalExecutable<AACon> {
 	public static final String STAT_FILE = "stat.txt";
 
 	public AACon() {
-		addParameters(Arrays.asList("-jar", getLibPath(), "-d=" + STAT_FILE,
-				"-f=RESULT_NO_ALIGNMENT"));
+		addParameters(Arrays.asList("-jar", getLibPath(), "-d=" + STAT_FILE, "-f=RESULT_NO_ALIGNMENT"));
 	}
+
 	// HashMap<Method, float[]>
 	@Override
-	public ScoreManager getResults(String workDirectory)
-			throws ResultNotAvailableException {
+	public ScoreManager getResults(String workDirectory) throws ResultNotAvailableException {
 		ScoreManager annotations = null;
 		try {
-			InputStream inStream = new FileInputStream(new File(workDirectory,
-					getOutput()));
-			annotations = ScoreManager.newInstanceSingleSequence(SequenceUtil
-					.readAAConResults(inStream));
+			InputStream inStream = new FileInputStream(new File(workDirectory, getOutput()));
+			annotations = ScoreManager.newInstanceSingleSequence(SequenceUtil.readAAConResults(inStream));
 			inStream.close();
 		} catch (FileNotFoundException e) {
 			log.error(e.getMessage(), e.getCause());
@@ -91,9 +88,8 @@ public class AACon extends SkeletalExecutable<AACon> {
 
 		String settings = ph.getProperty("aacon.jar.file");
 		if (compbio.util.Util.isEmpty(settings)) {
-			throw new NullPointerException(
-					"Please define aacon.jar.file property in Executable.properties file"
-							+ "and initialize it with the location of jronn jar file");
+			throw new NullPointerException("Please define aacon.jar.file property in Executable.properties file "
+					+ "and initialize it with the location of aaconservation jar file");
 		}
 		if (new File(settings).isAbsolute()) {
 			// the jar can be found so no actions necessary
@@ -134,8 +130,7 @@ public class AACon extends SkeletalExecutable<AACon> {
 
 	public void setNCore(int ncoreNumber) {
 		if (ncoreNumber < 1 || ncoreNumber > 100) {
-			throw new IndexOutOfBoundsException(
-					"Number of cores must be within 1 and 100 ");
+			throw new IndexOutOfBoundsException("Number of cores must be within 1 and 100 ");
 		}
 		this.ncoreNumber = ncoreNumber;
 		cbuilder.setParam(ncorePrm + Integer.toString(getNCore()));