import java.io.FileNotFoundException;\r
import java.io.IOException;\r
import java.io.InputStream;\r
-import java.util.HashMap;\r
-import java.util.HashSet;\r
\r
import org.apache.log4j.Logger;\r
\r
-import compbio.data.sequence.Score;\r
+import compbio.data.sequence.ScoreManager;\r
import compbio.data.sequence.SequenceUtil;\r
import compbio.data.sequence.UnknownFileFormatException;\r
import compbio.engine.client.Executable;\r
\r
@SuppressWarnings("unchecked")\r
@Override\r
- public HashMap<String, HashSet<Score>> getResults(String workDirectory)\r
+ public ScoreManager getResults(String workDirectory)\r
throws ResultNotAvailableException {\r
\r
InputStream inStream = null;\r
- HashMap<String, HashSet<Score>> results = null;\r
+ ScoreManager results = null;\r
\r
try {\r
inStream = new FileInputStream(new File(workDirectory, getOutput()));\r
- results = SequenceUtil.removeSequences(SequenceUtil\r
+ results = ScoreManager.newInstance(SequenceUtil\r
.readDisembl(inStream));\r
inStream.close();\r
} catch (FileNotFoundException e) {\r
log.trace("DRESULTS: " + results);\r
return results;\r
}\r
-\r
@Override\r
public Disembl setInput(String inFile) {\r
super.setInput(inFile);\r