Fix wrong error message

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