Clean up logging system

[jabaws.git] / runner / compbio / runner / msa / ClustalO.java

diff --git a/runner/compbio/runner/msa/ClustalO.java b/runner/compbio/runner/msa/ClustalO.java
index e5c93b3..da35cee 100644 (file)
--- a/runner/compbio/runner/msa/ClustalO.java
+++ b/runner/compbio/runner/msa/ClustalO.java
@@ -36,12 +36,12 @@ import compbio.runner.Util;
 public class ClustalO extends SkeletalExecutable<ClustalO> {\r
 \r
        private static Logger log = Logger.getLogger(ClustalO.class);\r
+\r
        private static final String EXEC_STAT_FILE = "stat.log";\r
-       \r
 \r
        public static final String KEY_VALUE_SEPARATOR = "=";\r
        \r
-       /*\r
+       /**\r
         * Number of cores parameter name\r
         */\r
        private final static String ncorePrm = "--threads";\r
@@ -52,7 +52,6 @@ public class ClustalO extends SkeletalExecutable<ClustalO> {
         */\r
        private int ncoreNumber = 0;\r
 \r
-       \r
        /**\r
         * --threads=<n> Number of processors to use\r
         * \r
@@ -60,8 +59,7 @@ public class ClustalO extends SkeletalExecutable<ClustalO> {
         */\r
        public ClustalO() {\r
                super(KEY_VALUE_SEPARATOR);\r
-               addParameters(Arrays.asList("--outfmt=clustal", "-v", "--log="\r
-                               + EXEC_STAT_FILE));\r
+               addParameters(Arrays.asList("--outfmt=clustal", "-v", "--log=" + EXEC_STAT_FILE));\r
                // set default in, outs and err files\r
                this.setInput(super.inputFile);\r
                this.setOutput(super.outputFile);\r
@@ -130,8 +128,7 @@ public class ClustalO extends SkeletalExecutable<ClustalO> {
        \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
@@ -141,5 +138,4 @@ public class ClustalO extends SkeletalExecutable<ClustalO> {
                return ncoreNumber;\r
        }\r
 \r
-\r
 }\r