import compbio.engine.client.Executable;\r
import compbio.engine.client.SkeletalExecutable;\r
import compbio.metadata.ResultNotAvailableException;\r
-import compbio.runner.Util;\r
+import compbio.engine.client.EngineUtil;\r
\r
/**\r
* Command line\r
\r
private static Logger log = Logger.getLogger(Jronn.class);\r
\r
- /**\r
- * Number of cores to use, defaults to 1 for local execution or the value of\r
- * "jronn.cluster.cpunum" property for cluster execution\r
- */\r
+/*\r
+ * Number of cores to use, defaults to 1 for local execution or the value of\r
+ * "jronn.cluster.cpunum" property for cluster execution\r
+ */\r
private int ncoreNumber = 0;\r
\r
private final String ncorePrm = "-n=";\r
\r
- public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
public static final String STAT_FILE = "stat.txt";\r
\r
public Jronn() {\r
- addParameters(Arrays.asList("-jar", getLibPath(), "-s=" + STAT_FILE,\r
- "-f=H"));\r
+ addParameters(Arrays.asList("-jar", getLibPath(), "-s=" + STAT_FILE, "-f=H"));\r
}\r
\r
@SuppressWarnings("unchecked")\r
throws ResultNotAvailableException {\r
ScoreManager sequences = null;\r
try {\r
- InputStream inStream = new FileInputStream(new File(workDirectory,\r
- getOutput()));\r
- sequences = ScoreManager.newInstanceSingleScore(SequenceUtil\r
- .readJRonn(inStream));\r
+ InputStream inStream = new FileInputStream(new File(workDirectory, getOutput()));\r
+ sequences = ScoreManager.newInstanceSingleScore(SequenceUtil.readJRonn(inStream));\r
inStream.close();\r
} catch (FileNotFoundException e) {\r
log.error(e.getMessage(), e.getCause());\r
String settings = ph.getProperty("jronn.jar.file");\r
if (compbio.util.Util.isEmpty(settings)) {\r
throw new NullPointerException(\r
- "Please define jronn.jar.file property in Executable.properties file"\r
- + "and initialize it with the location of jronn jar file");\r
+ "Please define jronn.jar.file property in Executable.properties file and initialize it with the location of jronn jar file");\r
}\r
if (new File(settings).isAbsolute()) {\r
// Jronn jar can be found so no actions necessary\r
// no further actions is necessary\r
return settings;\r
}\r
- return compbio.engine.client.Util.convertToAbsolute(settings);\r
+ return EngineUtil.convertToAbsolute(settings);\r
}\r
\r
@Override\r
\r
@Override\r
public CommandBuilder<Jronn> getParameters(ExecProvider provider) {\r
- // If number of cores is provided, set it for the cluster execution\r
- // only!\r
+ // If number of cores is provided, set it for the cluster execution only!\r
if (provider == Executable.ExecProvider.Cluster) {\r
int cpunum = SkeletalExecutable.getClusterCpuNum(getType());\r
cpunum = (cpunum == 0) ? 1 : cpunum;\r