From e6227b3fc0bb5abdf275bb24a87607b0555bce10 Mon Sep 17 00:00:00 2001 From: Sasha Sherstnev Date: Thu, 3 Oct 2013 13:13:22 +0100 Subject: [PATCH] Fix wrong error message --- runner/compbio/runner/conservation/AACon.java | 21 ++++++++------------- 1 file changed, 8 insertions(+), 13 deletions(-) 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 { 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 @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 { 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 { 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())); -- 1.7.10.2