\r
import compbio.data.sequence.Alignment;\r
import compbio.data.sequence.UnknownFileFormatException;\r
-import compbio.engine.client.Executable;\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 Muscle extends SkeletalExecutable<Muscle> {\r
\r
- /*\r
- * Tell JAXB to ignore this while marshalling\r
- */\r
- @XmlTransient\r
- private static Logger log = Logger.getLogger(Muscle.class);\r
-\r
- // Cache for Limits information\r
- private static LimitsManager<Muscle> limits;\r
+ /*\r
+ * Tell JAXB to ignore this while marshalling\r
+ */\r
+ @XmlTransient\r
+ private static Logger log = Logger.getLogger(Muscle.class);\r
\r
- private static final String EXEC_STAT_FILE = "stat.log";\r
+ private static final String EXEC_STAT_FILE = "stat.log";\r
\r
- public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
+ public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
\r
- /**\r
- * Default options are\r
- * \r
- * -clwstrict - write output in clustal format\r
- * \r
- * @param workDirectory\r
- */\r
- public Muscle() {\r
- /*\r
- * The –quiet command-line option disables writing progress messages to\r
- * standard error. If the –verbose command-line option is specified, a\r
- * progress message will be written to the log file when each iteration\r
- * completes. So –quiet and –verbose are not contradictory."-quiet",\r
- * "-verbose"\r
+ /**\r
+ * Default options are\r
+ * \r
+ * -clwstrict - write output in clustal format\r
+ * \r
+ * @param workDirectory\r
*/\r
- addParameters(Arrays.asList("-clwstrict", "-quiet", "-verbose"));\r
- cbuilder.setParam("-log", EXEC_STAT_FILE);\r
- }\r
-\r
- @Override\r
- public Muscle setOutput(String outFile) {\r
- super.setOutput(outFile);\r
- cbuilder.setParam("-out", outFile);\r
- return this;\r
- }\r
-\r
- @Override\r
- public Muscle setInput(String inFile) {\r
- super.setInput(inFile);\r
- cbuilder.setParam("-in", inFile);\r
- return this;\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 Muscle() {\r
+ /*\r
+ * The –quiet command-line option disables writing progress messages to\r
+ * standard error. If the –verbose command-line option is specified, a\r
+ * progress message will be written to the log file when each iteration\r
+ * completes. So –quiet and –verbose are not contradictory."-quiet",\r
+ * "-verbose"\r
+ */\r
+ addParameters(Arrays.asList("-clwstrict", "-quiet", "-verbose",\r
+ "-nocore"));\r
+ cbuilder.setParam("-log", EXEC_STAT_FILE);\r
}\r
- }\r
-\r
- @Override\r
- public List<String> getCreatedFiles() {\r
- return Arrays.asList(getOutput(), EXEC_STAT_FILE);\r
- }\r
\r
- public static String getStatFile() {\r
- return EXEC_STAT_FILE;\r
- }\r
-\r
- @Override\r
- public Limit<Muscle> getLimit(String presetName) {\r
+ @Override\r
+ public Muscle setOutput(String outFile) {\r
+ super.setOutput(outFile);\r
+ cbuilder.setParam("-out", outFile);\r
+ return this;\r
+ }\r
\r
- if (limits == null) {\r
- limits = getLimits();\r
+ @Override\r
+ public Muscle setInput(String inFile) {\r
+ super.setInput(inFile);\r
+ cbuilder.setParam("-in", inFile);\r
+ return this;\r
}\r
\r
- Limit<Muscle> limit = null;\r
- if (limits != null) {\r
- // this returns default limit if preset is undefined!\r
- limit = limits.getLimitByName(presetName);\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
- // 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(), EXEC_STAT_FILE);\r
}\r
- return limit;\r
- }\r
-\r
- @Override\r
- public LimitsManager<Muscle> getLimits() {\r
- // synchronise on static field\r
- synchronized (log) {\r
- if (limits == null) {\r
- limits = Util.getLimits(this.getClass());\r
- }\r
+\r
+ public static String getStatFile() {\r
+ return EXEC_STAT_FILE;\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<Muscle> getType() {\r
+ return (Class<Muscle>) this.getClass();\r
+ }\r
\r
}\r
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