import java.io.FileNotFoundException;\r
import java.io.IOException;\r
import java.io.InputStream;\r
-import java.util.Map;\r
-import java.util.Set;\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
import compbio.engine.client.PipedExecutable;\r
import compbio.engine.client.SkeletalExecutable;\r
-import compbio.metadata.Limit;\r
-import compbio.metadata.LimitsManager;\r
import compbio.metadata.ResultNotAvailableException;\r
-import compbio.runner.Util;\r
+import compbio.runner.RunnerUtil;\r
\r
/**\r
* DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops\r
* This is not a standard DisEMBL! The script has been modified!\r
* \r
*/\r
-public class Disembl extends SkeletalExecutable<Disembl>\r
- implements\r
- PipedExecutable<Disembl> {\r
+public class Disembl extends SkeletalExecutable<Disembl> implements PipedExecutable<Disembl> {\r
\r
private static Logger log = Logger.getLogger(Disembl.class);\r
\r
- // Cache for Limits information\r
- private static LimitsManager<Disembl> limits;\r
-\r
- public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
-\r
/**\r
* For the region to be considered disordered the values must exceed these\r
*/\r
}\r
\r
@SuppressWarnings("unchecked")\r
- public Map<String, Set<Score>> getResults(String workDirectory)\r
+ @Override\r
+ public ScoreManager getResults(String workDirectory)\r
throws ResultNotAvailableException {\r
\r
InputStream inStream = null;\r
- Map<String, Set<Score>> results = null;\r
- // How about getting ranges?\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.error(e.getMessage(), e.getCause());\r
throw new ResultNotAvailableException(e);\r
}\r
-\r
+ log.trace("DRESULTS: " + results);\r
return results;\r
}\r
\r
return this;\r
}\r
\r
+ @SuppressWarnings("unchecked")\r
@Override\r
- public Limit<Disembl> getLimit(String presetName) {\r
- if (limits == null) {\r
- limits = getLimits();\r
- }\r
-\r
- Limit<Disembl> limit = null;\r
- if (limits != null) {\r
- // this returns default limit if preset is undefined!\r
- limit = limits.getLimitByName(presetName);\r
- }\r
- // If limit is not defined for a particular preset, then return default\r
- // limit\r
- if (limit == null) {\r
- log.debug("Limit for the preset " + presetName\r
- + " is not found. Using default");\r
- limit = limits.getDefaultLimit();\r
- }\r
- return limit;\r
- }\r
-\r
- @Override\r
- public LimitsManager<Disembl> getLimits() {\r
- // synchronise on static field\r
- synchronized (log) {\r
- if (limits == null) {\r
- limits = Util.getLimits(this.getClass());\r
- }\r
- }\r
- return limits;\r
- }\r
-\r
- @Override\r
- public Class<? extends Executable<?>> getType() {\r
- return this.getClass();\r
+ public Class<Disembl> getType() {\r
+ return (Class<Disembl>) this.getClass();\r
}\r
\r
}\r