X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=runner%2Fcompbio%2Frunner%2Fmsa%2FMuscle.java;h=1d3b8277578302c0c0c8a7f80af02df35fec30e4;hb=a0f3e53415428d2c6c803ec9581e5d8975e72102;hp=d220d1605a23c4f335b394807ef47b4712e959f6;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git

diff --git a/runner/compbio/runner/msa/Muscle.java b/runner/compbio/runner/msa/Muscle.java
index d220d16..1d3b827 100644
--- a/runner/compbio/runner/msa/Muscle.java
+++ b/runner/compbio/runner/msa/Muscle.java
@@ -29,127 +29,90 @@ import org.apache.log4j.Logger;
 
 import compbio.data.sequence.Alignment;
 import compbio.data.sequence.UnknownFileFormatException;
-import compbio.engine.client.Executable;
 import compbio.engine.client.SkeletalExecutable;
-import compbio.metadata.Limit;
-import compbio.metadata.LimitsManager;
 import compbio.metadata.ResultNotAvailableException;
 import compbio.runner.Util;
 
 public class Muscle extends SkeletalExecutable<Muscle> {
 
-    /*
-     * Tell JAXB to ignore this while marshalling
-     */
-    @XmlTransient
-    private static Logger log = Logger.getLogger(Muscle.class);
-
-    // Cache for Limits information
-    private static LimitsManager<Muscle> limits;
+	/*
+	 * Tell JAXB to ignore this while marshalling
+	 */
+	@XmlTransient
+	private static Logger log = Logger.getLogger(Muscle.class);
 
-    private static final String EXEC_STAT_FILE = "stat.log";
+	private static final String EXEC_STAT_FILE = "stat.log";
 
-    public static final String KEY_VALUE_SEPARATOR = Util.SPACE;
+	public static final String KEY_VALUE_SEPARATOR = Util.SPACE;
 
-    /**
-     * Default options are
-     * 
-     * -clwstrict - write output in clustal format
-     * 
-     * @param workDirectory
-     */
-    public Muscle() {
-	/*
-	 * The –quiet command-line option disables writing progress messages to
-	 * standard error. If the –verbose command-line option is specified, a
-	 * progress message will be written to the log file when each iteration
-	 * completes. So –quiet and –verbose are not contradictory."-quiet",
-	 * "-verbose"
+	/**
+	 * Default options are
+	 * 
+	 * -clwstrict - write output in clustal format
+	 * 
+	 * @param workDirectory
 	 */
-	addParameters(Arrays.asList("-clwstrict", "-quiet", "-verbose"));
-	cbuilder.setParam("-log", EXEC_STAT_FILE);
-    }
-
-    @Override
-    public Muscle setOutput(String outFile) {
-	super.setOutput(outFile);
-	cbuilder.setParam("-out", outFile);
-	return this;
-    }
-
-    @Override
-    public Muscle setInput(String inFile) {
-	super.setInput(inFile);
-	cbuilder.setParam("-in", 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);
+	public Muscle() {
+		/*
+		 * The –quiet command-line option disables writing progress messages to
+		 * standard error. If the –verbose command-line option is specified, a
+		 * progress message will be written to the log file when each iteration
+		 * completes. So –quiet and –verbose are not contradictory."-quiet",
+		 * "-verbose"
+		 */
+		addParameters(Arrays.asList("-clwstrict", "-quiet", "-verbose",
+				"-nocore"));
+		cbuilder.setParam("-log", EXEC_STAT_FILE);
 	}
-    }
-
-    @Override
-    public List<String> getCreatedFiles() {
-	return Arrays.asList(getOutput(), EXEC_STAT_FILE);
-    }
 
-    public static String getStatFile() {
-	return EXEC_STAT_FILE;
-    }
-
-    @Override
-    public Limit<Muscle> getLimit(String presetName) {
+	@Override
+	public Muscle setOutput(String outFile) {
+		super.setOutput(outFile);
+		cbuilder.setParam("-out", outFile);
+		return this;
+	}
 
-	if (limits == null) {
-	    limits = getLimits();
+	@Override
+	public Muscle setInput(String inFile) {
+		super.setInput(inFile);
+		cbuilder.setParam("-in", inFile);
+		return this;
 	}
 
-	Limit<Muscle> limit = null;
-	if (limits != null) {
-	    // this returns default limit if preset is undefined!
-	    limit = limits.getLimitByName(presetName);
+	@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);
+		}
 	}
-	// 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();
+
+	@Override
+	public List<String> getCreatedFiles() {
+		return Arrays.asList(getOutput(), EXEC_STAT_FILE);
 	}
-	return limit;
-    }
-
-    @Override
-    public LimitsManager<Muscle> getLimits() {
-	// synchronise on static field
-	synchronized (log) {
-	    if (limits == null) {
-		limits = Util.getLimits(this.getClass());
-	    }
+
+	public static String getStatFile() {
+		return EXEC_STAT_FILE;
 	}
-	return limits;
-    }
 
-    @Override
-    public Class<? extends Executable<?>> getType() {
-	return this.getClass();
-    }
+	@SuppressWarnings("unchecked")
+	@Override
+	public Class<Muscle> getType() {
+		return (Class<Muscle>) this.getClass();
+	}
 
 }