import compbio.engine.client.PipedExecutable;\r
import compbio.engine.client.SkeletalExecutable;\r
import compbio.metadata.ResultNotAvailableException;\r
-import compbio.runner.Util;\r
+import compbio.runner.RunnerUtil;\r
\r
public class Probcons extends SkeletalExecutable<Probcons>\r
implements\r
\r
private final static String ANNOTATION = "annotation.txt";\r
\r
- public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
+ public static final String KEY_VALUE_SEPARATOR = " ";\r
\r
/**\r
- * \r
- * @param workDirectory\r
*/\r
public Probcons() {\r
addParameters(Arrays.asList("-v", "-clustalw", "-annot", ANNOTATION));\r
public Alignment getResults(String workDirectory)\r
throws ResultNotAvailableException {\r
try {\r
- return Util.readClustalFile(workDirectory, getOutput());\r
+ return RunnerUtil.readClustalFile(workDirectory, getOutput());\r
} catch (FileNotFoundException e) {\r
log.error(e.getMessage(), e.getCause());\r
throw new ResultNotAvailableException(e);\r