X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=engine%2Fcompbio%2Fengine%2Fclient%2FSkeletalExecutable.java;h=adc3e0b3fc72431fd69ba175489705e8f937c199;hb=48190e32e896a6f674284844a9ae75605aa40157;hp=b4f82fda3f61bba4d3fb81d023b451c7dfb418cc;hpb=3d0867bf4ce1e80d1b147a29b3cbc982ee84167c;p=jabaws.git

diff --git a/engine/compbio/engine/client/SkeletalExecutable.java b/engine/compbio/engine/client/SkeletalExecutable.java
index b4f82fd..adc3e0b 100644
--- a/engine/compbio/engine/client/SkeletalExecutable.java
+++ b/engine/compbio/engine/client/SkeletalExecutable.java
@@ -31,233 +31,233 @@ import compbio.util.Util;
 
 public abstract class SkeletalExecutable<T> implements Executable<T> {
 
-	private static final PropertyHelper ph = PropertyHelperManager
-			.getPropertyHelper();
+    protected static final PropertyHelper ph = PropertyHelperManager
+	    .getPropertyHelper();
 
-	private static Logger log = Logger.getLogger(SkeletalExecutable.class);
+    private static Logger log = Logger.getLogger(SkeletalExecutable.class);
 
-	protected String inputFile = "input.txt";
-	protected String outputFile = "output.txt";
-	protected String errorFile = "error.txt";
+    protected String inputFile = "input.txt";
+    protected String outputFile = "output.txt";
+    protected String errorFile = "error.txt";
 
-	private boolean isInputSet = false;
-	private boolean isOutputSet = false;
-	private boolean isErrorSet = false;
+    private boolean isInputSet = false;
+    private boolean isOutputSet = false;
+    private boolean isErrorSet = false;
 
-	/**
-	 * This has to allow duplicate parameters as different options may have the
-	 * same value e.g. Muscle -weight1 clustalw -weight2 clustalw
-	 */
-	protected CommandBuilder<T> cbuilder;
-
-	public SkeletalExecutable() {
-		cbuilder = new CommandBuilder<T>(" ");
-	}
+    /**
+     * This has to allow duplicate parameters as different options may have the
+     * same value e.g. Muscle -weight1 clustalw -weight2 clustalw
+     */
+    protected CommandBuilder<T> cbuilder;
 
-	public SkeletalExecutable(String parameterKeyValueDelimiter) {
-		assert parameterKeyValueDelimiter != null;
-		cbuilder = new CommandBuilder<T>(parameterKeyValueDelimiter);
-	}
+    public SkeletalExecutable() {
+	cbuilder = new CommandBuilder<T>(" ");
+    }
 
-	public SkeletalExecutable<T> setInput(String inFile) {
-		if (compbio.util.Util.isEmpty(inFile)) {
-			throw new IllegalArgumentException("Input file must not be NULL");
-		}
-		this.inputFile = inFile;
-		this.isInputSet = true;
-		return this;
-	}
+    public SkeletalExecutable(String parameterKeyValueDelimiter) {
+	assert parameterKeyValueDelimiter != null;
+	cbuilder = new CommandBuilder<T>(parameterKeyValueDelimiter);
+    }
 
-	public SkeletalExecutable<T> setOutput(String outFile) {
-		if (compbio.util.Util.isEmpty(outFile)
-				|| PathValidator.isAbsolutePath(outFile)) {
-			throw new IllegalArgumentException(
-					"Output file must not be NULL and Absolute path could not be used! Please provide the filename only. Value provided: "
-							+ outFile);
-		}
-		this.outputFile = outFile;
-		this.isOutputSet = true;
-		return this;
+    public SkeletalExecutable<T> setInput(String inFile) {
+	if (compbio.util.Util.isEmpty(inFile)) {
+	    throw new IllegalArgumentException("Input file must not be NULL");
 	}
-
-	public SkeletalExecutable<T> setError(String errFile) {
-		if (compbio.util.Util.isEmpty(errFile)
-				|| PathValidator.isAbsolutePath(errFile)) {
-			throw new IllegalArgumentException(
-					"Error file must not be NULL and Absolute path could not be used! Please provide the filename only. Value provided: "
-							+ errFile);
-		}
-		this.errorFile = errFile;
-		this.isErrorSet = true;
-		return this;
+	this.inputFile = inFile;
+	this.isInputSet = true;
+	return this;
+    }
+
+    public SkeletalExecutable<T> setOutput(String outFile) {
+	if (compbio.util.Util.isEmpty(outFile)
+		|| PathValidator.isAbsolutePath(outFile)) {
+	    throw new IllegalArgumentException(
+		    "Output file must not be NULL and Absolute path could not be used! Please provide the filename only. Value provided: "
+			    + outFile);
 	}
-
-	@Override
-	public CommandBuilder<T> getParameters(ExecProvider provider) {
-		/*
-		 * Prevent modification of the parameters unintentionally. This is
-		 * important to preserve executable parameters intact as engine could
-		 * add things into the array as it see fit. For instance
-		 * ExecutableWrapper (part of local engines) add command line as the
-		 * first element of an array.
-		 */
-		paramValueUpdater();
-		return cbuilder;
+	this.outputFile = outFile;
+	this.isOutputSet = true;
+	return this;
+    }
+
+    public SkeletalExecutable<T> setError(String errFile) {
+	if (compbio.util.Util.isEmpty(errFile)
+		|| PathValidator.isAbsolutePath(errFile)) {
+	    throw new IllegalArgumentException(
+		    "Error file must not be NULL and Absolute path could not be used! Please provide the filename only. Value provided: "
+			    + errFile);
 	}
-
-	@Override
-	public Executable<T> addParameters(List<String> parameters) {
-		cbuilder.addParams(parameters);
-		return this;
-	}
-
-	public Executable<T> setParameter(String parameter) {
-		cbuilder.setParam(parameter);
-		return this;
-	}
-
-	/**
-	 * This is a generic method of changing values of the parameters with
-	 * properties
-	 * 
-	 * This method iterates via commands for an executable finding matches from
-	 * the Executable.properties file and replacing values in CommandBuilder
-	 * with a combination of value from CommandBuilder to merge path from
-	 * properties
+	this.errorFile = errFile;
+	this.isErrorSet = true;
+	return this;
+    }
+
+    @Override
+    public CommandBuilder<T> getParameters(ExecProvider provider) {
+	/*
+	 * Prevent modification of the parameters unintentionally. This is
+	 * important to preserve executable parameters intact as engine could
+	 * add things into the array as it see fit. For instance
+	 * ExecutableWrapper (part of local engines) add command line as the
+	 * first element of an array.
 	 */
-	void paramValueUpdater() {
-		for (Parameter command : cbuilder.getCommandList()) {
-			if (command.value == null) {
-				continue;
-			}
-			String propertyPath = compbio.engine.client.Util.getExecProperty(
-					command.name + ".path", getType());
-			if (Util.isEmpty(propertyPath)) {
-				continue;
-			}
-			if (new File(command.value).isAbsolute()) {
-				// Matrix can be found so no actions necessary
-				// This method has been called already and the matrix name
-				// is modified to contain full path // no further actions is
-				// necessary
-				continue;
-			}
-			String absMatrixPath = compbio.engine.client.Util
-					.convertToAbsolute(propertyPath);
-			command.value = absMatrixPath + File.separator + command.value;
-			cbuilder.setParam(command);
-		}
+	paramValueUpdater();
+	return cbuilder;
+    }
+
+    @Override
+    public Executable<T> addParameters(List<String> parameters) {
+	cbuilder.addParams(parameters);
+	return this;
+    }
+
+    public Executable<T> setParameter(String parameter) {
+	cbuilder.setParam(parameter);
+	return this;
+    }
+
+    /**
+     * This is a generic method of changing values of the parameters with
+     * properties
+     * 
+     * This method iterates via commands for an executable finding matches from
+     * the Executable.properties file and replacing values in CommandBuilder
+     * with a combination of value from CommandBuilder to merge path from
+     * properties
+     */
+    void paramValueUpdater() {
+	for (Parameter command : cbuilder.getCommandList()) {
+	    if (command.value == null) {
+		continue;
+	    }
+	    String propertyPath = compbio.engine.client.Util.getExecProperty(
+		    command.name + ".path", getType());
+	    if (Util.isEmpty(propertyPath)) {
+		continue;
+	    }
+	    if (new File(command.value).isAbsolute()) {
+		// Matrix can be found so no actions necessary
+		// This method has been called already and the matrix name
+		// is modified to contain full path // no further actions is
+		// necessary
+		continue;
+	    }
+	    String absMatrixPath = compbio.engine.client.Util
+		    .convertToAbsolute(propertyPath);
+	    command.value = absMatrixPath + File.separator + command.value;
+	    cbuilder.setParam(command);
 	}
-
-	/**
-	 * This method cannot really tell whether the files has actually been
-	 * created or not. It must be overridden as required.
-	 * 
-	 * @see compbio.engine.client.Executable#getCreatedFiles()
-	 */
-	@Override
-	public List<String> getCreatedFiles() {
-		return Arrays.asList(getOutput(), getError());
+    }
+
+    /**
+     * This method cannot really tell whether the files has actually been
+     * created or not. It must be overridden as required.
+     * 
+     * @see compbio.engine.client.Executable#getCreatedFiles()
+     */
+    @Override
+    public List<String> getCreatedFiles() {
+	return Arrays.asList(getOutput(), getError());
+    }
+
+    @Override
+    public String getInput() {
+	return inputFile;
+    }
+
+    protected boolean isInputSet() {
+	return isInputSet;
+    }
+
+    protected boolean isOutputSet() {
+	return isOutputSet;
+    }
+
+    protected boolean isErrorSet() {
+	return isErrorSet;
+    }
+
+    @Override
+    public String getOutput() {
+	return outputFile;
+    }
+
+    @Override
+    public String getError() {
+	return errorFile;
+    }
+
+    @Override
+    public String toString() {
+	String value = "Input: " + this.getInput() + "\n";
+	value += "Output: " + this.getOutput() + "\n";
+	value += "Error: " + this.getError() + "\n";
+	value += "Class: " + this.getClass() + "\n";
+	value += "Params: " + cbuilder + "\n";
+	return value;
+    }
+
+    @Override
+    public Executable<?> loadRunConfiguration(RunConfiguration rconfig) {
+	if (!compbio.util.Util.isEmpty(rconfig.getOutput())) {
+	    setOutput(rconfig.getOutput());
 	}
-
-	@Override
-	public String getInput() {
-		return inputFile;
+	if (!compbio.util.Util.isEmpty(rconfig.getError())) {
+	    setError(rconfig.getError());
 	}
-
-	protected boolean isInputSet() {
-		return isInputSet;
-	}
-
-	protected boolean isOutputSet() {
-		return isOutputSet;
-	}
-
-	protected boolean isErrorSet() {
-		return isErrorSet;
-	}
-
-	@Override
-	public String getOutput() {
-		return outputFile;
+	if (!compbio.util.Util.isEmpty(rconfig.getInput())) {
+	    setInput(rconfig.getInput());
 	}
-
-	@Override
-	public String getError() {
-		return errorFile;
+	this.cbuilder = (CommandBuilder<T>) rconfig.getParameters();
+	return this;
+    }
+
+    @Override
+    public boolean equals(Object obj) {
+	if (obj == null) {
+	    return false;
 	}
-
-	@Override
-	public String toString() {
-		String value = "Input: " + this.getInput() + "\n";
-		value += "Output: " + this.getOutput() + "\n";
-		value += "Error: " + this.getError() + "\n";
-		value += "Class: " + this.getClass() + "\n";
-		value += "Params: " + cbuilder + "\n";
-		return value;
+	if (!(obj instanceof SkeletalExecutable<?>)) {
+	    return false;
 	}
-
-	@Override
-	public Executable<?> loadRunConfiguration(RunConfiguration rconfig) {
-		if (!compbio.util.Util.isEmpty(rconfig.getOutput())) {
-			setOutput(rconfig.getOutput());
-		}
-		if (!compbio.util.Util.isEmpty(rconfig.getError())) {
-			setError(rconfig.getError());
-		}
-		if (!compbio.util.Util.isEmpty(rconfig.getInput())) {
-			setInput(rconfig.getInput());
-		}
-		this.cbuilder = (CommandBuilder<T>) rconfig.getParameters();
-		return this;
+	SkeletalExecutable<?> exec = (SkeletalExecutable<?>) obj;
+	if (!Util.isEmpty(this.inputFile) && !Util.isEmpty(exec.inputFile)) {
+	    if (!this.inputFile.equals(exec.inputFile)) {
+		return false;
+	    }
 	}
-
-	@Override
-	public boolean equals(Object obj) {
-		if (obj == null) {
-			return false;
-		}
-		if (!(obj instanceof SkeletalExecutable<?>)) {
-			return false;
-		}
-		SkeletalExecutable<?> exec = (SkeletalExecutable<?>) obj;
-		if (!Util.isEmpty(this.inputFile) && !Util.isEmpty(exec.inputFile)) {
-			if (!this.inputFile.equals(exec.inputFile)) {
-				return false;
-			}
-		}
-		if (!Util.isEmpty(this.outputFile) && !Util.isEmpty(exec.outputFile)) {
-			if (!this.outputFile.equals(exec.outputFile)) {
-				return false;
-			}
-		}
-		if (!Util.isEmpty(this.errorFile) && !Util.isEmpty(exec.errorFile)) {
-			if (!this.errorFile.equals(exec.errorFile)) {
-				return false;
-			}
-		}
-		if (!this.cbuilder.equals(exec.cbuilder)) {
-			return false;
-		}
-		return true;
+	if (!Util.isEmpty(this.outputFile) && !Util.isEmpty(exec.outputFile)) {
+	    if (!this.outputFile.equals(exec.outputFile)) {
+		return false;
+	    }
 	}
-
-	@Override
-	public int hashCode() {
-		int code = inputFile.hashCode();
-		code += outputFile.hashCode();
-		code += errorFile.hashCode();
-		code *= this.cbuilder.hashCode();
-		return code;
+	if (!Util.isEmpty(this.errorFile) && !Util.isEmpty(exec.errorFile)) {
+	    if (!this.errorFile.equals(exec.errorFile)) {
+		return false;
+	    }
 	}
-
-	public String getClusterSettings() {
-		String settings = ph.getProperty(getType().getSimpleName()
-				.toLowerCase()
-				+ ".cluster.settings");
-		return settings == null ? "" : settings;
+	if (!this.cbuilder.equals(exec.cbuilder)) {
+	    return false;
 	}
-
-	public abstract Class<? extends Executable<?>> getType();
+	return true;
+    }
+
+    @Override
+    public int hashCode() {
+	int code = inputFile.hashCode();
+	code += outputFile.hashCode();
+	code += errorFile.hashCode();
+	code *= this.cbuilder.hashCode();
+	return code;
+    }
+
+    public String getClusterSettings() {
+	String settings = ph.getProperty(getType().getSimpleName()
+		.toLowerCase()
+		+ ".cluster.settings");
+	return settings == null ? "" : settings;
+    }
+
+    public abstract Class<? extends Executable<?>> getType();
 
 }