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
\r
-public class Probcons extends SkeletalExecutable<Probcons> implements\r
- PipedExecutable<Probcons> {\r
+public class Probcons extends SkeletalExecutable<Probcons>\r
+ implements\r
+ PipedExecutable<Probcons> {\r
\r
- private static Logger log = Logger.getLogger(Probcons.class);\r
+ private static Logger log = Logger.getLogger(Probcons.class);\r
\r
- // Cache for Limits information\r
- private static LimitsManager<Probcons> limits;\r
- private final static String ANNOTATION = "annotation.txt";\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 = Util.SPACE;\r
\r
- /**\r
- * \r
- * @param workDirectory\r
- */\r
- public Probcons() {\r
- addParameters(Arrays.asList("-v", "-clustalw", "-annot", ANNOTATION));\r
- /*\r
- * Could either have probabilities or the alignment, but not both "-t",\r
- * "probabilities"\r
+ /**\r
+ * \r
+ * @param workDirectory\r
*/\r
- }\r
-\r
- @SuppressWarnings("unchecked")\r
- @Override\r
- public Alignment getResults(String workDirectory)\r
- throws ResultNotAvailableException {\r
- try {\r
- return Util.readClustalFile(workDirectory, getOutput());\r
- } catch (FileNotFoundException e) {\r
- log.error(e.getMessage(), e.getCause());\r
- throw new ResultNotAvailableException(e);\r
- } catch (IOException e) {\r
- log.error(e.getMessage(), e.getCause());\r
- throw new ResultNotAvailableException(e);\r
- } catch (UnknownFileFormatException e) {\r
- log.error(e.getMessage(), e.getCause());\r
- throw new ResultNotAvailableException(e);\r
- } catch (NullPointerException e) {\r
- log.error(e.getMessage(), e.getCause());\r
- throw new ResultNotAvailableException(e);\r
+ public Probcons() {\r
+ addParameters(Arrays.asList("-v", "-clustalw", "-annot", ANNOTATION));\r
+ /*\r
+ * Could either have probabilities or the alignment, but not both "-t",\r
+ * "probabilities"\r
+ */\r
}\r
- }\r
-\r
- @Override\r
- public List<String> getCreatedFiles() {\r
- return Arrays.asList(getOutput(), ANNOTATION, getError());\r
- }\r
-\r
- @Override\r
- public Probcons setInput(String inFile) {\r
- String input = getInput();\r
- super.setInput(inFile);\r
- // TODO replace with setLast\r
- cbuilder.setParam(inFile);\r
- return this;\r
- }\r
\r
- @Override\r
- public Limit<Probcons> getLimit(String presetName) {\r
- if (limits == null) {\r
- limits = getLimits();\r
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public Alignment getResults(String workDirectory)\r
+ throws ResultNotAvailableException {\r
+ try {\r
+ return Util.readClustalFile(workDirectory, getOutput());\r
+ } catch (FileNotFoundException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ } catch (IOException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ } catch (UnknownFileFormatException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ } catch (NullPointerException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ }\r
}\r
- Limit<Probcons> 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
+ @Override\r
+ public List<String> getCreatedFiles() {\r
+ return Arrays.asList(getOutput(), ANNOTATION, getError());\r
}\r
- return limit;\r
- }\r
\r
- @Override\r
- public LimitsManager<Probcons> getLimits() {\r
- // synchronise on static field\r
- synchronized (log) {\r
- if (limits == null) {\r
- limits = Util.getLimits(this.getClass());\r
- }\r
+ @Override\r
+ public Probcons setInput(String inFile) {\r
+ String input = getInput();\r
+ super.setInput(inFile);\r
+ // TODO replace with setLast\r
+ cbuilder.setParam(inFile);\r
+ return this;\r
}\r
- return limits;\r
- }\r
\r
- @Override\r
- public Class<? extends Executable<?>> getType() {\r
- return this.getClass();\r
- }\r
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public Class<Executable<Probcons>> getType() {\r
+ return (Class<Executable<Probcons>>) this.getClass();\r
+ }\r
}\r