package compbio.runner.structure;\r
\r
-\r
import java.io.FileNotFoundException;\r
import java.io.IOException;\r
-import java.util.Arrays;\r
-import java.util.List;\r
-\r
-\r
-\r
-\r
\r
import org.apache.log4j.Logger;\r
\r
-import compbio.data.sequence.ScoreManager;\r
import compbio.data.sequence.RNAStructScoreManager;\r
-import compbio.data.sequence.UnknownFileFormatException;\r
import compbio.engine.client.PipedExecutable;\r
import compbio.engine.client.SkeletalExecutable;\r
import compbio.metadata.ResultNotAvailableException;\r
-import compbio.runner.Util;\r
-\r
-\r
-import compbio.engine.client.CommandBuilder;\r
+import compbio.runner.RunnerUtil;\r
\r
public class RNAalifold extends SkeletalExecutable<RNAalifold> \r
implements PipedExecutable<RNAalifold> {\r
- \r
- \r
+\r
private static Logger log = Logger.getLogger(RNAalifold.class);\r
\r
// May not be necessary as defult is "<space>" but still dont know\r
public RNAStructScoreManager getResults(String workDirectory)\r
throws ResultNotAvailableException {\r
try {\r
- return Util.readRNAStruct(workDirectory, getOutput());\r
- \r
+ return RunnerUtil.readRNAStruct(workDirectory, getOutput());\r
} catch (FileNotFoundException e) {\r
log.error(e.getMessage(), e.getCause());\r
throw new ResultNotAvailableException(e);\r