import java.io.FileNotFoundException;\r
import java.io.IOException;\r
import java.io.InputStream;\r
-import java.security.InvalidParameterException;\r
import java.util.Arrays;\r
import java.util.List;\r
\r
import compbio.data.sequence.AnnotatedSequence;\r
import compbio.data.sequence.SequenceUtil;\r
import compbio.data.sequence.UnknownFileFormatException;\r
+import compbio.engine.client.CommandBuilder;\r
import compbio.engine.client.Executable;\r
import compbio.engine.client.SkeletalExecutable;\r
import compbio.metadata.Limit;\r
*/\r
public class Jronn extends SkeletalExecutable<Jronn> {\r
\r
- \r
- private static Logger log = Logger.getLogger(Jronn.class);\r
-\r
- /**\r
- * Number of cores to use, defaults to 1 for local execution or the value of\r
- * "jronn.cluster.cpunum" property for cluster execution\r
- */\r
- private int ncoreNumber = 0;\r
-\r
- private String ncorePrm = "-n";\r
-\r
- \r
- // Cache for Limits information\r
- private static LimitsManager<Jronn> limits;\r
-\r
- public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
- public static final String STAT_FILE = "stat.txt";\r
-\r
- public Jronn() {\r
- addParameters(Arrays.asList("-jar", getLibPath(), "-s="\r
- + STAT_FILE, "-f=H"));\r
+ private static Logger log = Logger.getLogger(Jronn.class);\r
+\r
+ /**\r
+ * Number of cores to use, defaults to 1 for local execution or the value of\r
+ * "jronn.cluster.cpunum" property for cluster execution\r
+ */\r
+ private int ncoreNumber = 0;\r
+\r
+ private final String ncorePrm = "-n=";\r
+\r
+ // Cache for Limits information\r
+ private static LimitsManager<Jronn> limits;\r
+\r
+ public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
+ public static final String STAT_FILE = "stat.txt";\r
+\r
+ public Jronn() {\r
+ addParameters(Arrays.asList("-jar", getLibPath(), "-s=" + STAT_FILE,\r
+ "-f=H"));\r
+ }\r
+\r
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public List<AnnotatedSequence> getResults(String workDirectory)\r
+ throws ResultNotAvailableException {\r
+ List<AnnotatedSequence> sequences = null;\r
+ try {\r
+ InputStream inStream = new FileInputStream(new File(workDirectory,\r
+ getOutput()));\r
+ sequences = SequenceUtil.readJRonn(inStream);\r
+ inStream.close();\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
+ return sequences;\r
+ }\r
\r
- @SuppressWarnings("unchecked")\r
- @Override\r
- public List<AnnotatedSequence> getResults(String workDirectory)\r
- throws ResultNotAvailableException {\r
- List<AnnotatedSequence> sequences = null;\r
- try {\r
- InputStream inStream = new FileInputStream(new File(workDirectory,\r
- getOutput()));\r
- sequences = SequenceUtil.readJRonn(inStream);\r
- inStream.close();\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
- return sequences;\r
- }\r
+ private static String getLibPath() {\r
\r
- private static String getLibPath() {\r
-\r
- String settings = ph.getProperty("jronn.jar.file");\r
- if (compbio.util.Util.isEmpty(settings)) {\r
- throw new NullPointerException(\r
- "Please define jronn.jar.file property in Executable.properties file"\r
- + "and initialize it with the location of jronn jar file");\r
- }\r
- if (new File(settings).isAbsolute()) {\r
- // Jronn jar can be found so no actions necessary\r
- // no further actions is necessary\r
- return settings;\r
- }\r
- return compbio.engine.client.Util.convertToAbsolute(settings);\r
+ String settings = ph.getProperty("jronn.jar.file");\r
+ if (compbio.util.Util.isEmpty(settings)) {\r
+ throw new NullPointerException(\r
+ "Please define jronn.jar.file property in Executable.properties file"\r
+ + "and initialize it with the location of jronn jar file");\r
}\r
-\r
- @Override\r
- public List<String> getCreatedFiles() {\r
- return Arrays.asList(getOutput(), getError());\r
+ if (new File(settings).isAbsolute()) {\r
+ // Jronn jar can be found so no actions necessary\r
+ // no further actions is necessary\r
+ return settings;\r
}\r
-\r
- @Override\r
- public Jronn setInput(String inFile) {\r
- super.setInput(inFile);\r
- cbuilder.setParam("-i=" + inFile);\r
- return this;\r
+ return compbio.engine.client.Util.convertToAbsolute(settings);\r
+ }\r
+\r
+ @Override\r
+ public List<String> getCreatedFiles() {\r
+ return Arrays.asList(getOutput(), getError());\r
+ }\r
+\r
+ @Override\r
+ public Jronn setInput(String inFile) {\r
+ super.setInput(inFile);\r
+ cbuilder.setParam("-i=" + inFile);\r
+ return this;\r
+ }\r
+\r
+ @Override\r
+ public Jronn setOutput(String outFile) {\r
+ super.setOutput(outFile);\r
+ cbuilder.setParam("-o=" + outFile);\r
+ return this;\r
+ }\r
+\r
+ @Override\r
+ public Limit<Jronn> getLimit(String presetName) {\r
+ if (limits == null) {\r
+ limits = getLimits();\r
}\r
-\r
- @Override\r
- public Jronn setOutput(String outFile) {\r
- super.setOutput(outFile);\r
- cbuilder.setParam("-o=" + outFile);\r
- return this;\r
+ Limit<Jronn> limit = null;\r
+ if (limits != null) {\r
+ // this returns default limit if preset is undefined!\r
+ limit = limits.getLimitByName(presetName);\r
}\r
-\r
- @Override\r
- public Limit<Jronn> getLimit(String presetName) {\r
- if (limits == null) {\r
- limits = getLimits();\r
- }\r
- Limit<Jronn> 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
+ // 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
-\r
- @Override\r
- public LimitsManager<Jronn> 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
+ return limit;\r
+ }\r
+\r
+ @Override\r
+ public LimitsManager<Jronn> getLimits() {\r
+ // synchronise on static field\r
+ synchronized (log) {\r
+ if (limits == null) {\r
+ limits = Util.getLimits(this.getClass());\r
+ }\r
}\r
-\r
- @Override\r
- public Class<? extends Executable<?>> getType() {\r
- return this.getClass();\r
+ return limits;\r
+ }\r
+\r
+ @Override\r
+ public Class<? extends Executable<?>> getType() {\r
+ return this.getClass();\r
+ }\r
+\r
+ public static String getStatFile() {\r
+ return STAT_FILE;\r
+ }\r
+\r
+ public void setNCore(int ncoreNumber) {\r
+ if (ncoreNumber < 1 || ncoreNumber > 100) {\r
+ throw new IndexOutOfBoundsException(\r
+ "Number of cores must be within 1 and 100 ");\r
}\r
-\r
- public static String getStatFile() {\r
- return STAT_FILE;\r
+ this.ncoreNumber = ncoreNumber;\r
+ cbuilder.setParam(ncorePrm + Integer.toString(getNCore()));\r
+ }\r
+\r
+ int getNCore() {\r
+ return ncoreNumber;\r
+ }\r
+\r
+ @Override\r
+ public CommandBuilder<Jronn> getParameters(ExecProvider provider) {\r
+ // Limit number of cores to 1 for ANY execution which does not set\r
+ // Ncores explicitly using setNCore method\r
+ if (ncoreNumber == 0) {\r
+ setNCore(1);\r
}\r
- \r
- public void setNCore(int ncoreNumber) {\r
- if (ncoreNumber < 1 || ncoreNumber > 100) {\r
- throw new IndexOutOfBoundsException(\r
- "Number of cores must be within 1 and 100 ");\r
- }\r
- this.ncoreNumber = ncoreNumber;\r
- cbuilder.setParam(ncorePrm, Integer.toString(getNCore()));\r
+ // If number of cores is provided, set it for the cluster execution only!\r
+ if (provider == Executable.ExecProvider.Cluster) {\r
+ int cpunum = SkeletalExecutable.getClusterCpuNum(getType());\r
+ if (cpunum != 0) {\r
+ setNCore(cpunum);\r
+ }\r
}\r
+ return super.getParameters(provider);\r
+ }\r
\r
- int getNCore() {\r
- return ncoreNumber;\r
- }\r
- \r
- \r
}\r
git://source.jalview.org / jabaws.git / commitdiff