From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Thu, 22 Jul 2010 12:59:22 +0000 (+0000)
Subject: Some refactoring
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c2c54b1cab5af0ac2604539a768174f5987fedf9;p=jabaws.git

Some refactoring

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@2651 e3abac25-378b-4346-85de-24260fe3988d
---

diff --git a/engine/compbio/engine/client/SkeletalExecutable.java b/engine/compbio/engine/client/SkeletalExecutable.java
index adc3e0b..dbdb4f5 100644
--- a/engine/compbio/engine/client/SkeletalExecutable.java
+++ b/engine/compbio/engine/client/SkeletalExecutable.java
@@ -19,6 +19,7 @@
 package compbio.engine.client;
 
 import java.io.File;
+import java.security.InvalidParameterException;
 import java.util.Arrays;
 import java.util.List;
 
@@ -258,6 +259,35 @@ public abstract class SkeletalExecutable<T> implements Executable<T> {
 	return settings == null ? "" : settings;
     }
 
+    /**
+	 * 
+	 * @return number of cpus to use on the cluster or 0 if the value is
+	 *         undefined
+	 */
+	public static int getClusterCpuNum(Class<? extends Executable<?>> type) {
+		int cpus = 0;
+		String cpuNum = ph.getProperty(type.getSimpleName().toLowerCase()+ ".cluster.cpunum");
+		if (compbio.util.Util.isEmpty(cpuNum)) {
+			return 0;
+		}
+		try {
+			cpus = Integer.parseInt(cpuNum);
+		} catch (NumberFormatException e) {
+			// safe to ignore
+			log
+			.debug("Number of cpus to use for cluster execution is defined but could not be parsed as integer! Given value is: "
+					+ cpuNum);
+			return 0;
+		}
+		if (cpus < 1 || cpus > 100) {
+			throw new InvalidParameterException(
+					"Number of cpu for cluster execution must be within 1 and 100! "
+					+ "Look at the value of 'tcoffee.cluster.cpunum' property. Given value is "
+					+ cpus);
+		}
+		return cpus;
+	}
+
     public abstract Class<? extends Executable<?>> getType();
 
 }
diff --git a/runner/compbio/runner/disorder/Jronn.java b/runner/compbio/runner/disorder/Jronn.java
index 1b9037e..0bf17e4 100644
--- a/runner/compbio/runner/disorder/Jronn.java
+++ b/runner/compbio/runner/disorder/Jronn.java
@@ -23,6 +23,7 @@ import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
+import java.security.InvalidParameterException;
 import java.util.Arrays;
 import java.util.List;
 
@@ -48,8 +49,18 @@ import compbio.runner.Util;
  */
 public class Jronn extends SkeletalExecutable<Jronn> {
 
+	
 	private static Logger log = Logger.getLogger(Jronn.class);
 
+	/**
+	 * Number of cores to use, defaults to 1 for local execution or the value of
+	 * "jronn.cluster.cpunum" property for cluster execution
+	 */
+	private int ncoreNumber = 0;
+
+	private String ncorePrm = "-n";
+
+	
 	// Cache for Limits information
 	private static LimitsManager<Jronn> limits;
 
@@ -57,7 +68,7 @@ public class Jronn extends SkeletalExecutable<Jronn> {
 	public static final String STAT_FILE = "stat.txt";
 
 	public Jronn() {
-		addParameters(Arrays.asList("-jar", getLibPath(), "-n=1", "-s="
+		addParameters(Arrays.asList("-jar", getLibPath(), "-s="
 				+ STAT_FILE, "-f=H"));
 	}
 
@@ -161,4 +172,19 @@ public class Jronn extends SkeletalExecutable<Jronn> {
 	public static String getStatFile() {
 		return STAT_FILE;
 	}
+	
+	public void setNCore(int ncoreNumber) {
+		if (ncoreNumber < 1 || ncoreNumber > 100) {
+			throw new IndexOutOfBoundsException(
+					"Number of cores must be within 1 and 100 ");
+		}
+		this.ncoreNumber = ncoreNumber;
+		cbuilder.setParam(ncorePrm, Integer.toString(getNCore()));
+	}
+
+	int getNCore() {
+		return ncoreNumber;
+	}
+	
+    
 }
diff --git a/runner/compbio/runner/msa/Tcoffee.java b/runner/compbio/runner/msa/Tcoffee.java
index 2fd2283..949c4f1 100644
--- a/runner/compbio/runner/msa/Tcoffee.java
+++ b/runner/compbio/runner/msa/Tcoffee.java
@@ -41,173 +41,145 @@ import compbio.runner.Util;
 import compbio.util.PropertyHelper;
 
 public class Tcoffee extends SkeletalExecutable<Tcoffee> implements
-	PipedExecutable<Tcoffee>, ClusterNativeSpecExecutable<Tcoffee> {
+PipedExecutable<Tcoffee>, ClusterNativeSpecExecutable<Tcoffee> {
 
-    private static Logger log = Logger.getLogger(Tcoffee.class);
+	private static Logger log = Logger.getLogger(Tcoffee.class);
 
-    private static PropertyHelper ph = PropertyHelperManager
-	    .getPropertyHelper();
+	private static PropertyHelper ph = PropertyHelperManager
+	.getPropertyHelper();
 
-    // Cache for Limits information
-    private static LimitsManager<Tcoffee> limits;
+	// Cache for Limits information
+	private static LimitsManager<Tcoffee> limits;
 
-    public static final String KEY_VALUE_SEPARATOR = "=";
+	public static final String KEY_VALUE_SEPARATOR = "=";
 
-    /**
-     * Number of cores to use, defaults to 1 for local execution or the value of
-     * "tcoffee.cluster.cpunum" property for cluster execution
-     */
-    private int ncoreNumber = 0;
-
-    /*
-     * Number of cores parameter name
-     */
-    private final static String ncorePrm = "-n_core";
+	/**
+	 * Number of cores to use, defaults to 1 for local execution or the value of
+	 * "tcoffee.cluster.cpunum" property for cluster execution
+	 */
+	private int ncoreNumber = 0;
 
-    /**
-     * 
-     * @param workDirectory
-     */
-    public Tcoffee() {
-	super(KEY_VALUE_SEPARATOR);
 	/*
-	 * Use "-quiet" to disable sdtout and progress to stderr inorder=input -
-	 * prevent t-coffee from sorting sequences
+	 * Number of cores parameter name
 	 */
-	addParameters(Arrays.asList("-output=clustalw"));
-	setInput(super.inputFile);
-    }
-
-    @Override
-    public Tcoffee setInput(String inFile) {
-	super.setInput(inFile);
-	cbuilder.setParam("-seq", inFile);
-	return this;
-    }
-
-    @SuppressWarnings("unchecked")
-    @Override
-    public Alignment getResults(String workDirectory)
-	    throws ResultNotAvailableException {
-	try {
-	    return Util.readClustalFile(workDirectory, getOutput());
-	} catch (FileNotFoundException e) {
-	    log.error(e.getMessage(), e.getCause());
-	    throw new ResultNotAvailableException(e);
-	} catch (IOException e) {
-	    log.error(e.getMessage(), e.getCause());
-	    throw new ResultNotAvailableException(e);
-	} catch (UnknownFileFormatException e) {
-	    log.error(e.getMessage(), e.getCause());
-	    throw new ResultNotAvailableException(e);
-	} catch (NullPointerException e) {
-	    log.error(e.getMessage(), e.getCause());
-	    throw new ResultNotAvailableException(e);
-	}
-    }
-
-    @Override
-    public List<String> getCreatedFiles() {
-	return Arrays.asList(getOutput());
-    }
+	private final static String ncorePrm = "-n_core";
 
-    public void setNCore(int ncoreNumber) {
-	if (ncoreNumber < 1 || ncoreNumber > 100) {
-	    throw new IndexOutOfBoundsException(
-		    "Number of cores must be within 1 and 100 ");
+	/**
+	 * 
+	 * @param workDirectory
+	 */
+	public Tcoffee() {
+		super(KEY_VALUE_SEPARATOR);
+		/*
+		 * Use "-quiet" to disable sdtout and progress to stderr inorder=input -
+		 * prevent t-coffee from sorting sequences
+		 */
+		addParameters(Arrays.asList("-output=clustalw"));
+		setInput(super.inputFile);
 	}
-	this.ncoreNumber = ncoreNumber;
-	cbuilder.setParam(ncorePrm, Integer.toString(getNCore()));
-    }
-
-    int getNCore() {
-	return ncoreNumber;
-    }
-
-    @Override
-    public CommandBuilder<Tcoffee> getParameters(ExecProvider provider) {
-	// Limit number of cores to 1 for ANY execution which does not set
-	// Ncores explicitly using setNCore method
-	if (ncoreNumber == 0) {
-	    setNCore(1);
+
+	@Override
+	public Tcoffee setInput(String inFile) {
+		super.setInput(inFile);
+		cbuilder.setParam("-seq", inFile);
+		return this;
 	}
-	if (provider == Executable.ExecProvider.Cluster) {
-	    int cpunum = getClusterCpuNum();
-	    if (cpunum != 0) {
-		setNCore(cpunum);
-	    }
+
+	@SuppressWarnings("unchecked")
+	@Override
+	public Alignment getResults(String workDirectory)
+	throws ResultNotAvailableException {
+		try {
+			return Util.readClustalFile(workDirectory, getOutput());
+		} catch (FileNotFoundException e) {
+			log.error(e.getMessage(), e.getCause());
+			throw new ResultNotAvailableException(e);
+		} catch (IOException e) {
+			log.error(e.getMessage(), e.getCause());
+			throw new ResultNotAvailableException(e);
+		} catch (UnknownFileFormatException e) {
+			log.error(e.getMessage(), e.getCause());
+			throw new ResultNotAvailableException(e);
+		} catch (NullPointerException e) {
+			log.error(e.getMessage(), e.getCause());
+			throw new ResultNotAvailableException(e);
+		}
 	}
-	return super.getParameters(provider);
-    }
 
-    @Override
-    public Limit<Tcoffee> getLimit(String presetName) {
-	if (limits == null) {
-	    limits = getLimits();
+	@Override
+	public List<String> getCreatedFiles() {
+		return Arrays.asList(getOutput());
 	}
 
-	Limit<Tcoffee> limit = null;
-	if (limits != null) {
-	    // this returns default limit if preset is undefined!
-	    limit = limits.getLimitByName(presetName);
+	public void setNCore(int ncoreNumber) {
+		if (ncoreNumber < 1 || ncoreNumber > 100) {
+			throw new IndexOutOfBoundsException(
+					"Number of cores must be within 1 and 100 ");
+		}
+		this.ncoreNumber = ncoreNumber;
+		cbuilder.setParam(ncorePrm, Integer.toString(getNCore()));
 	}
-	// If limit is not defined for a particular preset, then return default
-	// limit
-	if (limit == null) {
-	    log.debug("Limit for the preset " + presetName
-		    + " is not found. Using default");
-	    limit = limits.getDefaultLimit();
+
+	int getNCore() {
+		return ncoreNumber;
 	}
-	return limit;
-    }
-
-    @Override
-    public LimitsManager<Tcoffee> getLimits() {
-	// synchronise on static field
-	synchronized (log) {
-	    if (limits == null) {
-		limits = Util.getLimits(this.getClass());
-	    }
+
+	@Override
+	public CommandBuilder<Tcoffee> getParameters(ExecProvider provider) {
+		// Limit number of cores to 1 for ANY execution which does not set
+		// Ncores explicitly using setNCore method
+		if (ncoreNumber == 0) {
+			setNCore(1);
+		}
+		if (provider == Executable.ExecProvider.Cluster) {
+			int cpunum = SkeletalExecutable.getClusterCpuNum(getType());
+			if (cpunum != 0) {
+				setNCore(cpunum);
+			}
+		}
+		return super.getParameters(provider);
 	}
-	return limits;
-    }
-
-    @Override
-    public String getNativeSpecs() {
-	return getClusterSettings();
-    }
-
-    /**
-     * 
-     * @return number of cpus to use on the cluster or 0 if the value is
-     *         undefined
-     */
-    public static int getClusterCpuNum() {
-	int cpus = 0;
-	String cpuNum = ph.getProperty("tcoffee.cluster.cpunum");
-	if (compbio.util.Util.isEmpty(cpuNum)) {
-	    return 0;
+
+	@Override
+	public Limit<Tcoffee> getLimit(String presetName) {
+		if (limits == null) {
+			limits = getLimits();
+		}
+
+		Limit<Tcoffee> limit = null;
+		if (limits != null) {
+			// this returns default limit if preset is undefined!
+			limit = limits.getLimitByName(presetName);
+		}
+		// If limit is not defined for a particular preset, then return default
+		// limit
+		if (limit == null) {
+			log.debug("Limit for the preset " + presetName
+					+ " is not found. Using default");
+			limit = limits.getDefaultLimit();
+		}
+		return limit;
 	}
-	try {
-	    cpus = Integer.parseInt(cpuNum);
-	} catch (NumberFormatException e) {
-	    // safe to ignore
-	    log
-		    .debug("Number of cpus to use for cluster execution is defined but could not be parsed as integer! Given value is: "
-			    + cpuNum);
-	    return 0;
+
+	@Override
+	public LimitsManager<Tcoffee> getLimits() {
+		// synchronise on static field
+		synchronized (log) {
+			if (limits == null) {
+				limits = Util.getLimits(this.getClass());
+			}
+		}
+		return limits;
 	}
-	if (cpus < 1 || cpus > 100) {
-	    throw new InvalidParameterException(
-		    "Number of cpu for cluster execution must be within 1 and 100! "
-			    + "Look at the value of 'tcoffee.cluster.cpunum' property. Given value is "
-			    + cpus);
+
+	@Override
+	public String getNativeSpecs() {
+		return getClusterSettings();
 	}
-	return cpus;
-    }
 
-    @Override
-    public Class<? extends Executable<?>> getType() {
-	return this.getClass();
-    }
+
+	@Override
+	public Class<? extends Executable<?>> getType() {
+		return this.getClass();
+	}
 }
diff --git a/testsrc/compbio/runner/disorder/JronnTester.java b/testsrc/compbio/runner/disorder/JronnTester.java
index 0193781..9385eb6 100644
--- a/testsrc/compbio/runner/disorder/JronnTester.java
+++ b/testsrc/compbio/runner/disorder/JronnTester.java
@@ -66,291 +66,315 @@ import compbio.util.SysPrefs;
 
 public class JronnTester {
 
-    public static String test_outfile = "TO1381.jronn.out"; // "/homes/pvtroshin/TO1381.clustal.cluster.out
+	public static String test_outfile = "TO1381.jronn.out"; // "/homes/pvtroshin/TO1381.clustal.cluster.out
 
-    private Jronn jronn;
+	private Jronn jronn;
 
-    @BeforeMethod(alwaysRun = true)
-    void init() {
-	jronn = new Jronn();
-	jronn.setInput(AllTestSuit.test_input).setOutput(test_outfile);
-    }
+	@BeforeMethod(alwaysRun = true)
+	void init() {
+		jronn = new Jronn();
+		jronn.setInput(AllTestSuit.test_input).setOutput(test_outfile);
+	}
 
-    @Test(groups = { AllTestSuit.test_group_cluster,
-	    AllTestSuit.test_group_runner })
-    public void testRunOnCluster() {
-	assertFalse(SysPrefs.isWindows,
-		"Cluster execution can only be in unix environment");
-	try {
-	    ConfiguredExecutable<Jronn> confJronn = Configurator
-		    .configureExecutable(jronn, Executable.ExecProvider.Cluster);
-	    JobRunner runner = JobRunner.getInstance(confJronn);
-
-	    assertNotNull(runner, "Runner is NULL");
-	    runner.executeJob();
-	    // assertNotNull("JobId is null", jobId1);
-	    JobStatus status = runner.getJobStatus();
-	    assertTrue(status == JobStatus.PENDING
-		    || status == JobStatus.RUNNING,
-		    "Status of the process is wrong!");
-	    JobInfo info = runner.getJobInfo();
-	    assertNotNull(info, "JobInfo is null");
-	    StatisticManager sm = new StatisticManager(info);
-	    assertNotNull(sm, "Statictic manager is null");
-	    try {
-
-		String exits = sm.getExitStatus();
-		assertNotNull("Exit status is null", exits);
-		// cut 4 trailing zeros from the number
-		int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)
-			.intValue();
-		assertEquals(0, exitsInt);
-		System.out.println(sm.getAllStats());
-
-	    } catch (ParseException e) {
-		e.printStackTrace();
-		fail("Parse Exception: " + e.getMessage());
-	    }
-	    //assertFalse(runner.cleanup());
-	    assertTrue(sm.hasExited());
-	    assertFalse(sm.wasAborted());
-	    assertFalse(sm.hasDump());
-	    assertFalse(sm.hasSignaled());
-
-	} catch (JobSubmissionException e) {
-	    e.printStackTrace();
-	    fail("DrmaaException caught:" + e.getMessage());
-	} catch (JobExecutionException e) {
-	    e.printStackTrace();
-	    fail("DrmaaException caught:" + e.getMessage());
-	} catch (DrmaaException e) {
-	    e.printStackTrace();
-	    fail("DrmaaException caught:" + e.getMessage());
+	@Test(groups = { AllTestSuit.test_group_cluster,
+			AllTestSuit.test_group_runner })
+			public void testRunOnCluster() {
+		assertFalse(SysPrefs.isWindows,
+				"Cluster execution can only be in unix environment");
+		try {
+			ConfiguredExecutable<Jronn> confJronn = Configurator
+			.configureExecutable(jronn, Executable.ExecProvider.Cluster);
+			JobRunner runner = JobRunner.getInstance(confJronn);
+
+			assertNotNull(runner, "Runner is NULL");
+			runner.executeJob();
+			// assertNotNull("JobId is null", jobId1);
+			JobStatus status = runner.getJobStatus();
+			assertTrue(status == JobStatus.PENDING
+					|| status == JobStatus.RUNNING,
+					"Status of the process is wrong!");
+			JobInfo info = runner.getJobInfo();
+			assertNotNull(info, "JobInfo is null");
+			StatisticManager sm = new StatisticManager(info);
+			assertNotNull(sm, "Statictic manager is null");
+			try {
+
+				String exits = sm.getExitStatus();
+				assertNotNull("Exit status is null", exits);
+				// cut 4 trailing zeros from the number
+				int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)
+				.intValue();
+				assertEquals(0, exitsInt);
+				System.out.println(sm.getAllStats());
+
+			} catch (ParseException e) {
+				e.printStackTrace();
+				fail("Parse Exception: " + e.getMessage());
+			}
+			//assertFalse(runner.cleanup());
+			assertTrue(sm.hasExited());
+			assertFalse(sm.wasAborted());
+			assertFalse(sm.hasDump());
+			assertFalse(sm.hasSignaled());
+
+		} catch (JobSubmissionException e) {
+			e.printStackTrace();
+			fail("DrmaaException caught:" + e.getMessage());
+		} catch (JobExecutionException e) {
+			e.printStackTrace();
+			fail("DrmaaException caught:" + e.getMessage());
+		} catch (DrmaaException e) {
+			e.printStackTrace();
+			fail("DrmaaException caught:" + e.getMessage());
+		}
 	}
-    }
-
-    /**
-     * This tests fails from time to time depending on the cluster load or some
-     * other factors. Any client code has to adjust for this issue
-     */
-    @Test(groups = { AllTestSuit.test_group_cluster,
-	    AllTestSuit.test_group_runner })
-    public void testRunOnClusterAsync() {
-	assertFalse(SysPrefs.isWindows,
+
+	/**
+	 * This tests fails from time to time depending on the cluster load or some
+	 * other factors. Any client code has to adjust for this issue
+	 */
+	@Test(groups = { AllTestSuit.test_group_cluster,
+			AllTestSuit.test_group_runner })
+			public void testRunOnClusterAsync() {
+		assertFalse(SysPrefs.isWindows,
 		"Cluster execution can only be in unix environment");
-	try {
-	    ConfiguredExecutable<Jronn> confJronn = Configurator
-		    .configureExecutable(jronn, Executable.ExecProvider.Cluster);
-	    AsyncExecutor aengine = Configurator.getAsyncEngine(confJronn);
-	    String jobId = aengine.submitJob(confJronn);
-	    assertNotNull(jobId, "Runner is NULL");
-	    // let drmaa to start
-	    Thread.sleep(500);
-	    JobStatus status = aengine.getJobStatus(jobId);
-	    while (status != JobStatus.FINISHED) {
-		System.out.println("Job Status: " + status);
-		Thread.sleep(1000);
-		status = aengine.getJobStatus(jobId);
-		ConfiguredExecutable<Jronn> result = (ConfiguredExecutable<Jronn>) aengine
-			.getResults(jobId);
-		assertNotNull(result);
-		System.out.println("RES:" + result);
-		// Some times the job could be removed from the cluster accounting 
-		// before it has been reported to finish. Make sure 
-		// to stop waiting in such case
-		if (status == JobStatus.UNDEFINED) {
-		    break;
+		try {
+			ConfiguredExecutable<Jronn> confJronn = Configurator
+			.configureExecutable(jronn, Executable.ExecProvider.Cluster);
+			AsyncExecutor aengine = Configurator.getAsyncEngine(confJronn);
+			String jobId = aengine.submitJob(confJronn);
+			assertNotNull(jobId, "Runner is NULL");
+			// let drmaa to start
+			Thread.sleep(500);
+			JobStatus status = aengine.getJobStatus(jobId);
+			while (status != JobStatus.FINISHED) {
+				System.out.println("Job Status: " + status);
+				Thread.sleep(1000);
+				status = aengine.getJobStatus(jobId);
+				ConfiguredExecutable<Jronn> result = (ConfiguredExecutable<Jronn>) aengine
+				.getResults(jobId);
+				assertNotNull(result);
+				System.out.println("RES:" + result);
+				// Some times the job could be removed from the cluster accounting 
+				// before it has been reported to finish. Make sure 
+				// to stop waiting in such case
+				if (status == JobStatus.UNDEFINED) {
+					break;
+				}
+			}
+		} catch (JobSubmissionException e) {
+			e.printStackTrace();
+			fail("DrmaaException caught:" + e.getMessage());
+		} catch (InterruptedException e) {
+			e.printStackTrace();
+			fail(e.getMessage());
+		} catch (ResultNotAvailableException e) {
+			e.printStackTrace();
+			fail(e.getMessage());
 		}
-	    }
-	} catch (JobSubmissionException e) {
-	    e.printStackTrace();
-	    fail("DrmaaException caught:" + e.getMessage());
-	} catch (InterruptedException e) {
-	    e.printStackTrace();
-	    fail(e.getMessage());
-	} catch (ResultNotAvailableException e) {
-	    e.printStackTrace();
-	    fail(e.getMessage());
 	}
-    }
-
-    @Test(groups = { AllTestSuit.test_group_runner })
-    public void testRunLocally() {
-	try {
-	    ConfiguredExecutable<Jronn> confJronn = Configurator
-		    .configureExecutable(jronn, Executable.ExecProvider.Local);
-
-	    // For local execution use relative
-	    LocalRunner lr = new LocalRunner(confJronn);
-	    lr.executeJob();
-	    ConfiguredExecutable<?> al1 = lr.waitForResult();
-	    assertNotNull(al1.getResults());
-	    List<AnnotatedSequence> al2 = confJronn.getResults();
-	    assertNotNull(al2);
-	    assertEquals(al2.size(), 3);
-	    assertEquals(al1.getResults(), al2);
-	} catch (JobSubmissionException e) {
-	    e.printStackTrace();
-	    fail(e.getLocalizedMessage());
-	} catch (ResultNotAvailableException e) {
-	    e.printStackTrace();
-	    fail(e.getLocalizedMessage());
-	} catch (JobExecutionException e) {
-	    e.printStackTrace();
-	    fail(e.getLocalizedMessage());
+
+	@Test(groups = { AllTestSuit.test_group_runner })
+	public void testRunLocally() {
+		try {
+			ConfiguredExecutable<Jronn> confJronn = Configurator
+			.configureExecutable(jronn, Executable.ExecProvider.Local);
+
+			// For local execution use relative
+			LocalRunner lr = new LocalRunner(confJronn);
+			lr.executeJob();
+			ConfiguredExecutable<?> al1 = lr.waitForResult();
+			assertNotNull(al1.getResults());
+			List<AnnotatedSequence> al2 = confJronn.getResults();
+			assertNotNull(al2);
+			assertEquals(al2.size(), 3);
+			assertEquals(al1.getResults(), al2);
+		} catch (JobSubmissionException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		} catch (ResultNotAvailableException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		} catch (JobExecutionException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		}
 	}
-    }
-
-    @Test(groups = { AllTestSuit.test_group_runner })
-    public void readStatistics() {
-	try {
-	    ConfiguredExecutable<Jronn> confJronn = Configurator
-		    .configureExecutable(jronn, Executable.ExecProvider.Local);
-	    // For local execution use relavive
-
-	    AsyncExecutor sexec = Configurator.getAsyncEngine(confJronn);
-	    String jobId = sexec.submitJob(confJronn);
-	    FilePuller fw = FilePuller.newFilePuller(confJronn
-		    .getWorkDirectory()
-		    + File.separator + Jronn.getStatFile(),
-		    FileWatcher.MIN_CHUNK_SIZE_BYTES);
-	    int count = 0;
-	    long position = 0;
-	    fw.waitForFile(4);
-	    JobStatus status = sexec.getJobStatus(jobId);
-	    while (status != JobStatus.FINISHED) {
-		System.out.println((status != JobStatus.FINISHED) + " d: "
-			+ fw.hasMoreData());
-		if (fw.hasMoreData()) {
-		    ChunkHolder ch = fw.pull(position);
-		    System.out.println("p:" + position);
-		    String chunk = ch.getChunk();
-		    position = ch.getNextPosition();
-		    System.out.println("np " + position + " c: " + chunk);
+
+	@Test(groups = { AllTestSuit.test_group_runner })
+	public void testRunLocallyOnTwoCpu() {
+		try {
+			jronn.setNCore(2);
+			ConfiguredExecutable<Jronn> confJronn = Configurator
+			.configureExecutable(jronn, Executable.ExecProvider.Local);
+			
+			// For local execution use relative
+			LocalRunner lr = new LocalRunner(confJronn);
+			lr.executeJob();
+			ConfiguredExecutable<?> al1 = lr.waitForResult();
+			assertNotNull(al1.getResults());
+			List<AnnotatedSequence> al2 = confJronn.getResults();
+			assertNotNull(al2);
+			assertEquals(al2.size(), 3);
+			assertEquals(al1.getResults(), al2);
+		} catch (JobSubmissionException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		} catch (ResultNotAvailableException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		} catch (JobExecutionException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
 		}
-		count++;
-		// Make sure the loop is terminated if the job fails
-		if ((status == JobStatus.UNDEFINED || status == JobStatus.FAILED)) {
-		    break;
+	}
+
+	
+	@Test(groups = { AllTestSuit.test_group_runner })
+	public void readStatistics() {
+		try {
+			ConfiguredExecutable<Jronn> confJronn = Configurator
+			.configureExecutable(jronn, Executable.ExecProvider.Local);
+			// For local execution use relavive
+
+			AsyncExecutor sexec = Configurator.getAsyncEngine(confJronn);
+			String jobId = sexec.submitJob(confJronn);
+			FilePuller fw = FilePuller.newFilePuller(confJronn
+					.getWorkDirectory()
+					+ File.separator + Jronn.getStatFile(),
+					FileWatcher.MIN_CHUNK_SIZE_BYTES);
+			int count = 0;
+			long position = 0;
+			fw.waitForFile(4);
+			JobStatus status = sexec.getJobStatus(jobId);
+			while (status != JobStatus.FINISHED) {
+				if (fw.hasMoreData()) {
+					ChunkHolder ch = fw.pull(position);
+					String chunk = ch.getChunk();
+					position = ch.getNextPosition();
+				}
+				count++;
+				// Make sure the loop is terminated if the job fails
+				if ((status == JobStatus.UNDEFINED || status == JobStatus.FAILED)) {
+					break;
+				}
+				Thread.sleep(300);
+				status = sexec.getJobStatus(jobId);
+			}
+			assertTrue(count > 1);
+			ConfiguredExecutable<?> al = sexec.getResults(jobId);
+			assertNotNull(al.getResults());
+		} catch (JobSubmissionException e) {
+			e.printStackTrace();
+			fail(e.getMessage());
+		} catch (ResultNotAvailableException e) {
+			e.printStackTrace();
+			fail(e.getMessage());
+		} catch (IOException e) {
+			e.printStackTrace();
+			fail(e.getMessage());
+		} catch (InterruptedException e) {
+			e.printStackTrace();
+			fail(e.getMessage());
 		}
-		Thread.sleep(300);
-		status = sexec.getJobStatus(jobId);
-	    }
-	    System.out.println("\nOut of the LOOP!! ");
-	    assertTrue(count > 1);
-	    ConfiguredExecutable<?> al = sexec.getResults(jobId);
-	    assertNotNull(al.getResults());
-	} catch (JobSubmissionException e) {
-	    e.printStackTrace();
-	    fail(e.getMessage());
-	} catch (ResultNotAvailableException e) {
-	    e.printStackTrace();
-	    fail(e.getMessage());
-	} catch (IOException e) {
-	    e.printStackTrace();
-	    fail(e.getMessage());
-	} catch (InterruptedException e) {
-	    e.printStackTrace();
-	    fail(e.getMessage());
 	}
-    }
-
-    @Test(groups = { AllTestSuit.test_group_runner })
-    public void testPersistance() {
-	try {
-	    Jronn jronn = new Jronn();
-	    jronn.setError("errrr.txt").setInput(AllTestSuit.test_input)
-		    .setOutput("outtt.txt");
-	    assertEquals(jronn.getInput(), AllTestSuit.test_input);
-	    assertEquals(jronn.getError(), "errrr.txt");
-	    assertEquals(jronn.getOutput(), "outtt.txt");
-	    ConfiguredExecutable<Jronn> cJronn = Configurator
-		    .configureExecutable(jronn, Executable.ExecProvider.Local);
-
-	    SyncExecutor sexec = Configurator.getSyncEngine(cJronn);
-	    sexec.executeJob();
-	    ConfiguredExecutable<?> al = sexec.waitForResult();
-	    assertNotNull(al.getResults());
-	    // Save run configuration
-	    assertTrue(cJronn.saveRunConfiguration());
-
-	    // See if loaded configuration is the same as saved
-	    RunConfiguration loadedRun = RunConfiguration
-		    .load(new FileInputStream(new File(cJronn
-			    .getWorkDirectory(), RunConfiguration.rconfigFile)));
-	    assertEquals(
-		    ((ConfExecutable<Jronn>) cJronn).getRunConfiguration(),
-		    loadedRun);
-	    // Load run configuration as ConfExecutable
-	    ConfiguredExecutable<Jronn> resurrectedCMuscle = (ConfiguredExecutable<Jronn>) cJronn
-		    .loadRunConfiguration(new FileInputStream(new File(cJronn
-			    .getWorkDirectory(), RunConfiguration.rconfigFile)));
-	    assertNotNull(resurrectedCMuscle);
-	    assertEquals(resurrectedCMuscle.getExecutable().getInput(),
-		    AllTestSuit.test_input);
-	    assertEquals(resurrectedCMuscle.getExecutable().getError(),
-		    "errrr.txt");
-	    assertEquals(resurrectedCMuscle.getExecutable().getOutput(),
-		    "outtt.txt");
-	    // See in details whether executables are the same
-	    assertEquals(resurrectedCMuscle.getExecutable(), jronn);
-
-	    ConfiguredExecutable<Jronn> resJronn = Configurator
-		    .configureExecutable(resurrectedCMuscle.getExecutable(),
-			    Executable.ExecProvider.Local);
-
-	    sexec = Configurator.getSyncEngine(resJronn,
-		    Executable.ExecProvider.Local);
-	    sexec.executeJob();
-	    al = sexec.waitForResult();
-	    assertNotNull(al);
-
-	} catch (JobSubmissionException e) {
-	    e.printStackTrace();
-	    fail(e.getMessage());
-	} catch (JobExecutionException e) {
-	    e.printStackTrace();
-	    fail(e.getMessage());
-	} catch (FileNotFoundException e) {
-	    e.printStackTrace();
-	    fail(e.getMessage());
-	} catch (IOException e) {
-	    e.printStackTrace();
-	    fail(e.getMessage());
-	} catch (ResultNotAvailableException e) {
-	    e.printStackTrace();
-	    fail(e.getMessage());
+
+	@Test(groups = { AllTestSuit.test_group_runner })
+	public void testPersistance() {
+		try {
+			Jronn jronn = new Jronn();
+			jronn.setError("errrr.txt").setInput(AllTestSuit.test_input)
+			.setOutput("outtt.txt");
+			assertEquals(jronn.getInput(), AllTestSuit.test_input);
+			assertEquals(jronn.getError(), "errrr.txt");
+			assertEquals(jronn.getOutput(), "outtt.txt");
+			ConfiguredExecutable<Jronn> cJronn = Configurator
+			.configureExecutable(jronn, Executable.ExecProvider.Local);
+
+			SyncExecutor sexec = Configurator.getSyncEngine(cJronn);
+			sexec.executeJob();
+			ConfiguredExecutable<?> al = sexec.waitForResult();
+			assertNotNull(al.getResults());
+			// Save run configuration
+			assertTrue(cJronn.saveRunConfiguration());
+
+			// See if loaded configuration is the same as saved
+			RunConfiguration loadedRun = RunConfiguration
+			.load(new FileInputStream(new File(cJronn
+					.getWorkDirectory(), RunConfiguration.rconfigFile)));
+			assertEquals(
+					((ConfExecutable<Jronn>) cJronn).getRunConfiguration(),
+					loadedRun);
+			// Load run configuration as ConfExecutable
+			ConfiguredExecutable<Jronn> resurrectedCMuscle = (ConfiguredExecutable<Jronn>) cJronn
+			.loadRunConfiguration(new FileInputStream(new File(cJronn
+					.getWorkDirectory(), RunConfiguration.rconfigFile)));
+			assertNotNull(resurrectedCMuscle);
+			assertEquals(resurrectedCMuscle.getExecutable().getInput(),
+					AllTestSuit.test_input);
+			assertEquals(resurrectedCMuscle.getExecutable().getError(),
+					"errrr.txt");
+			assertEquals(resurrectedCMuscle.getExecutable().getOutput(),
+			"outtt.txt");
+			// See in details whether executables are the same
+			assertEquals(resurrectedCMuscle.getExecutable(), jronn);
+
+			ConfiguredExecutable<Jronn> resJronn = Configurator
+			.configureExecutable(resurrectedCMuscle.getExecutable(),
+					Executable.ExecProvider.Local);
+
+			sexec = Configurator.getSyncEngine(resJronn,
+					Executable.ExecProvider.Local);
+			sexec.executeJob();
+			al = sexec.waitForResult();
+			assertNotNull(al);
+
+		} catch (JobSubmissionException e) {
+			e.printStackTrace();
+			fail(e.getMessage());
+		} catch (JobExecutionException e) {
+			e.printStackTrace();
+			fail(e.getMessage());
+		} catch (FileNotFoundException e) {
+			e.printStackTrace();
+			fail(e.getMessage());
+		} catch (IOException e) {
+			e.printStackTrace();
+			fail(e.getMessage());
+		} catch (ResultNotAvailableException e) {
+			e.printStackTrace();
+			fail(e.getMessage());
+		}
 	}
-    }
-
-    @Test(groups = { AllTestSuit.test_group_runner })
-    public void testConfigurationLoading() {
-	try {
-	    RunnerConfig<Jronn> jronnConfig = ConfExecutable
-		    .getRunnerOptions(Jronn.class);
-	    assertNotNull(jronnConfig);
-	    assertTrue(jronnConfig.getArguments().size() > 0);
-
-	    PresetManager<Jronn> jronnPresets = ConfExecutable
-		    .getRunnerPresets(Jronn.class);
-	    assertNull(jronnPresets); // there is no presets
-
-	    LimitsManager<Jronn> jronnLimits = ConfExecutable
-		    .getRunnerLimits(Jronn.class);
-	    assertNotNull(jronnLimits);
-	    assertTrue(jronnLimits.getLimits().size() > 0);
-	    jronnLimits.validate(jronnPresets);
-
-	} catch (FileNotFoundException e) {
-	    e.printStackTrace();
-	    fail(e.getLocalizedMessage());
-	} catch (IOException e) {
-	    e.printStackTrace();
-	    fail(e.getLocalizedMessage());
-	} catch (ValidationException e) {
-	    e.printStackTrace();
-	    fail(e.getLocalizedMessage());
+
+	@Test(groups = { AllTestSuit.test_group_runner })
+	public void testConfigurationLoading() {
+		try {
+			RunnerConfig<Jronn> jronnConfig = ConfExecutable
+			.getRunnerOptions(Jronn.class);
+			assertNotNull(jronnConfig);
+			assertTrue(jronnConfig.getArguments().size() > 0);
+
+			PresetManager<Jronn> jronnPresets = ConfExecutable
+			.getRunnerPresets(Jronn.class);
+			assertNull(jronnPresets); // there is no presets
+
+			LimitsManager<Jronn> jronnLimits = ConfExecutable
+			.getRunnerLimits(Jronn.class);
+			assertNotNull(jronnLimits);
+			assertTrue(jronnLimits.getLimits().size() > 0);
+			jronnLimits.validate(jronnPresets);
+
+		} catch (FileNotFoundException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		} catch (IOException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		} catch (ValidationException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		}
 	}
-    }
 
 }
diff --git a/webservices/compbio/ws/server/TcoffeeWS.java b/webservices/compbio/ws/server/TcoffeeWS.java
index afe2cae..07a1f41 100644
--- a/webservices/compbio/ws/server/TcoffeeWS.java
+++ b/webservices/compbio/ws/server/TcoffeeWS.java
@@ -34,6 +34,7 @@ import compbio.engine.AsyncExecutor;
 import compbio.engine.Configurator;
 import compbio.engine.client.ConfiguredExecutable;
 import compbio.engine.client.Executable;
+import compbio.engine.client.SkeletalExecutable;
 import compbio.metadata.ChunkHolder;
 import compbio.metadata.JobStatus;
 import compbio.metadata.JobSubmissionException;
@@ -75,18 +76,18 @@ public class TcoffeeWS implements MsaWS<Tcoffee> {
     }
 
     ConfiguredExecutable<Tcoffee> init(List<FastaSequence> sequences)
-	    throws JobSubmissionException {
-	Tcoffee tcoffee = new Tcoffee();
-	tcoffee.setInput("fasta.in").setOutput("fasta.out");
-	ConfiguredExecutable<Tcoffee> confCoffee = Configurator
-		.configureExecutable(tcoffee, sequences);
-	if (confCoffee.getExecProvider() == Executable.ExecProvider.Cluster) {
-	    int clusterCpuNum = Tcoffee.getClusterCpuNum();
-	    if (clusterCpuNum != 0) {
-		tcoffee.setNCore(clusterCpuNum);
-	    }
-	}
-	return confCoffee;
+    throws JobSubmissionException {
+    	Tcoffee tcoffee = new Tcoffee();
+    	tcoffee.setInput("fasta.in").setOutput("fasta.out");
+    	ConfiguredExecutable<Tcoffee> confCoffee = Configurator
+    	.configureExecutable(tcoffee, sequences);
+    	if (confCoffee.getExecProvider() == Executable.ExecProvider.Cluster) {
+    		int clusterCpuNum = SkeletalExecutable.getClusterCpuNum(Tcoffee.class);
+    		if (clusterCpuNum != 0) {
+    			tcoffee.setNCore(clusterCpuNum);
+    		}
+    	}
+    	return confCoffee;
     }
 
     @Override