Impove coding style

[jabaws.git] / engine / compbio / engine / client / SkeletalExecutable.java

diff --git a/engine/compbio/engine/client/SkeletalExecutable.java b/engine/compbio/engine/client/SkeletalExecutable.java
index 369f8e7..b991440 100644 (file)
--- a/engine/compbio/engine/client/SkeletalExecutable.java
+++ b/engine/compbio/engine/client/SkeletalExecutable.java
@@ -34,8 +34,7 @@ import compbio.util.Util;
 \r
 public abstract class SkeletalExecutable<T> implements Executable<T> {\r
 \r
-       protected static final PropertyHelper ph = PropertyHelperManager\r
-                       .getPropertyHelper();\r
+       protected static final PropertyHelper ph = PropertyHelperManager.getPropertyHelper();\r
 \r
        private static Logger log = Logger.getLogger(SkeletalExecutable.class);\r
 \r
@@ -79,11 +78,8 @@ public abstract class SkeletalExecutable<T> implements Executable<T> {
        }\r
 \r
        public SkeletalExecutable<T> setOutput(String outFile) {\r
-               if (compbio.util.Util.isEmpty(outFile)\r
-                               || PathValidator.isAbsolutePath(outFile)) {\r
-                       throw new IllegalArgumentException(\r
-                                       "Output file must not be NULL and Absolute path could not be used! Please provide the filename only. Value provided: "\r
-                                                       + outFile);\r
+               if (compbio.util.Util.isEmpty(outFile) || PathValidator.isAbsolutePath(outFile)) {\r
+                       throw new IllegalArgumentException("Output file must not be NULL and Absolute path could not be used! Please provide the filename only. Value provided: " + outFile);\r
                }\r
                this.outputFile = outFile;\r
                this.isOutputSet = true;\r
@@ -91,11 +87,8 @@ public abstract class SkeletalExecutable<T> implements Executable<T> {
        }\r
 \r
        public SkeletalExecutable<T> setError(String errFile) {\r
-               if (compbio.util.Util.isEmpty(errFile)\r
-                               || PathValidator.isAbsolutePath(errFile)) {\r
-                       throw new IllegalArgumentException(\r
-                                       "Error file must not be NULL and Absolute path could not be used! Please provide the filename only. Value provided: "\r
-                                                       + errFile);\r
+               if (compbio.util.Util.isEmpty(errFile) || PathValidator.isAbsolutePath(errFile)) {\r
+                       throw new IllegalArgumentException("Error file must not be NULL and Absolute path could not be used! Please provide the filename only. Value provided: " + errFile);\r
                }\r
                this.errorFile = errFile;\r
                this.isErrorSet = true;\r
@@ -152,8 +145,7 @@ public abstract class SkeletalExecutable<T> implements Executable<T> {
                                // necessary\r
                                continue;\r
                        }\r
-                       String absMatrixPath = compbio.engine.client.Util\r
-                                       .convertToAbsolute(propertyPath);\r
+                       String absMatrixPath = compbio.engine.client.Util.convertToAbsolute(propertyPath);\r
                        command.value = absMatrixPath + File.separator + command.value;\r
                        cbuilder.setParam(command);\r
                }\r
@@ -263,20 +255,16 @@ public abstract class SkeletalExecutable<T> implements Executable<T> {
 \r
        @Override\r
        public String getClusterJobSettings() {\r
-               String settings = ph.getProperty(getType().getSimpleName()\r
-                               .toLowerCase() + ".cluster.settings");\r
+               String settings = ph.getProperty(getType().getSimpleName().toLowerCase() + ".cluster.settings");\r
                return settings == null ? "" : settings;\r
        }\r
 \r
        /**\r
-        * \r
-        * @return number of cpus to use on the cluster or 0 if the value is\r
-        *         undefined\r
+        * @return number of cpus to use on the cluster or 0 if the value is undefined\r
         */\r
        public static int getClusterCpuNum(Class<? extends Executable<?>> type) {\r
                int cpus = 0;\r
-               String cpuNum = ph.getProperty(type.getSimpleName().toLowerCase()\r
-                               + ".cluster.cpunum");\r
+               String cpuNum = ph.getProperty(type.getSimpleName().toLowerCase() + ".cluster.cpunum");\r
                if (compbio.util.Util.isEmpty(cpuNum)) {\r
                        return 0;\r
                }\r
@@ -284,15 +272,12 @@ public abstract class SkeletalExecutable<T> implements Executable<T> {
                        cpus = Integer.parseInt(cpuNum);\r
                } catch (NumberFormatException e) {\r
                        // safe to ignore\r
-                       log.debug("Number of cpus to use for cluster execution is defined but could not be parsed as integer! Given value is: "\r
-                                       + cpuNum);\r
+                       log.debug("Number of cpus to use for cluster execution is defined but could not be parsed as integer! Given value is: " + cpuNum);\r
                        return 0;\r
                }\r
                if (cpus < 1 || cpus > 100) {\r
-                       throw new InvalidParameterException(\r
-                                       "Number of cpu for cluster execution must be within 1 and 100! "\r
-                                                       + "Look at the value of 'tcoffee.cluster.cpunum' property. Given value is "\r
-                                                       + cpus);\r
+                       throw new InvalidParameterException("Number of cpu for cluster execution must be within 1 and 100! "\r
+                                                       + "Look at the value of 'tcoffee.cluster.cpunum' property. Given value is " + cpus);\r
                }\r
                return cpus;\r
        }\r
@@ -335,9 +320,7 @@ public abstract class SkeletalExecutable<T> implements Executable<T> {
        }\r
 \r
        /**\r
-        * \r
         * @return subclasses must return their type\r
         */\r
        public abstract Class<T> getType();\r
-\r
 }\r