X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=runner%2Fcompbio%2Frunner%2Fdisorder%2FJronn.java;fp=runner%2Fcompbio%2Frunner%2Fdisorder%2FJronn.java;h=1b9037e218c28e077644f6160dcea3c643eabf43;hb=88d713ca7e5f0612550fafe5a0a2e9dbb35d691b;hp=0c4245a7b40b5c62b0b184f5528a603a7765226a;hpb=481202ddde7f0abba2c78e8dfb28c464f6019962;p=jabaws.git

diff --git a/runner/compbio/runner/disorder/Jronn.java b/runner/compbio/runner/disorder/Jronn.java
index 0c4245a..1b9037e 100644
--- a/runner/compbio/runner/disorder/Jronn.java
+++ b/runner/compbio/runner/disorder/Jronn.java
@@ -48,117 +48,117 @@ import compbio.runner.Util;
  */
 public class Jronn extends SkeletalExecutable<Jronn> {
 
-    private static Logger log = Logger.getLogger(Jronn.class);
-
-    // Cache for Limits information
-    private static LimitsManager<Jronn> limits;
-
-    public static final String KEY_VALUE_SEPARATOR = Util.SPACE;
-    public static final String STAT_FILE = "stat.txt";
-
-    public Jronn() {
-	addParameters(Arrays.asList("-jar", getLibPath(), "-n=1", "-s="
-		+ STAT_FILE, "-f=H"));
-    }
-
-    @SuppressWarnings("unchecked")
-    @Override
-    public List<AnnotatedSequence> getResults(String workDirectory)
-	    throws ResultNotAvailableException {
-	List<AnnotatedSequence> sequences = null;
-	try {
-	    InputStream inStream = new FileInputStream(new File(workDirectory,
-		    getOutput()));
-	    sequences = SequenceUtil.readJRonn(inStream);
-	    inStream.close();
-	} 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);
+	private static Logger log = Logger.getLogger(Jronn.class);
+
+	// Cache for Limits information
+	private static LimitsManager<Jronn> limits;
+
+	public static final String KEY_VALUE_SEPARATOR = Util.SPACE;
+	public static final String STAT_FILE = "stat.txt";
+
+	public Jronn() {
+		addParameters(Arrays.asList("-jar", getLibPath(), "-n=1", "-s="
+				+ STAT_FILE, "-f=H"));
 	}
-	return sequences;
-    }
 
-    private static String getLibPath() {
+	@SuppressWarnings("unchecked")
+	@Override
+	public List<AnnotatedSequence> getResults(String workDirectory)
+	throws ResultNotAvailableException {
+		List<AnnotatedSequence> sequences = null;
+		try {
+			InputStream inStream = new FileInputStream(new File(workDirectory,
+					getOutput()));
+			sequences = SequenceUtil.readJRonn(inStream);
+			inStream.close();
+		} 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 sequences;
+	}
 
-	String settings = ph.getProperty("jronn.jar.file");
-	if (compbio.util.Util.isEmpty(settings)) {
-	    throw new NullPointerException(
-		    "Please define jronn.jar.file property in Executable.properties file"
-			    + "and initialize it with the location of jronn jar file");
+	private static String getLibPath() {
+
+		String settings = ph.getProperty("jronn.jar.file");
+		if (compbio.util.Util.isEmpty(settings)) {
+			throw new NullPointerException(
+					"Please define jronn.jar.file property in Executable.properties file"
+					+ "and initialize it with the location of jronn jar file");
+		}
+		if (new File(settings).isAbsolute()) {
+			// Jronn jar can be found so no actions necessary
+			// no further actions is necessary
+			return settings;
+		}
+		return compbio.engine.client.Util.convertToAbsolute(settings);
 	}
-	if (new File(settings).isAbsolute()) {
-	    // Jronn jar can be found so no actions necessary
-	    // no further actions is necessary
-	    return settings;
+
+	@Override
+	public List<String> getCreatedFiles() {
+		return Arrays.asList(getOutput(), getError());
 	}
-	return compbio.engine.client.Util.convertToAbsolute(settings);
-    }
-
-    @Override
-    public List<String> getCreatedFiles() {
-	return Arrays.asList(getOutput(), getError());
-    }
-
-    @Override
-    public Jronn setInput(String inFile) {
-	super.setInput(inFile);
-	cbuilder.setParam("-i=" + inFile);
-	return this;
-    }
-
-    @Override
-    public Jronn setOutput(String outFile) {
-	super.setOutput(outFile);
-	cbuilder.setParam("-o=" + outFile);
-	return this;
-    }
-
-    @Override
-    public Limit<Jronn> getLimit(String presetName) {
-	if (limits == null) {
-	    limits = getLimits();
+
+	@Override
+	public Jronn setInput(String inFile) {
+		super.setInput(inFile);
+		cbuilder.setParam("-i=" + inFile);
+		return this;
 	}
-	Limit<Jronn> limit = null;
-	if (limits != null) {
-	    // this returns default limit if preset is undefined!
-	    limit = limits.getLimitByName(presetName);
+
+	@Override
+	public Jronn setOutput(String outFile) {
+		super.setOutput(outFile);
+		cbuilder.setParam("-o=" + outFile);
+		return this;
 	}
-	// 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 Limit<Jronn> getLimit(String presetName) {
+		if (limits == null) {
+			limits = getLimits();
+		}
+		Limit<Jronn> 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;
 	}
-	return limit;
-    }
-
-    @Override
-    public LimitsManager<Jronn> getLimits() {
-	// synchronise on static field
-	synchronized (log) {
-	    if (limits == null) {
-		limits = Util.getLimits(this.getClass());
-	    }
+
+	@Override
+	public LimitsManager<Jronn> getLimits() {
+		// synchronise on static field
+		synchronized (log) {
+			if (limits == null) {
+				limits = Util.getLimits(this.getClass());
+			}
+		}
+		return limits;
 	}
-	return limits;
-    }
 
-    @Override
-    public Class<? extends Executable<?>> getType() {
-	return this.getClass();
-    }
+	@Override
+	public Class<? extends Executable<?>> getType() {
+		return this.getClass();
+	}
 
-    public static String getStatFile() {
-	return STAT_FILE;
-    }
+	public static String getStatFile() {
+		return STAT_FILE;
+	}
 }