From 9162b52a4bed5155831e19605228c866e1832586 Mon Sep 17 00:00:00 2001
From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Fri, 2 Aug 2013 17:20:05 +0100
Subject: [PATCH] Add Java wrapper class for Jpred

---
 runner/compbio/runner/predictors/Jpred.java |  143 +++++++++++++++++++++++++++
 1 file changed, 143 insertions(+)
 create mode 100644 runner/compbio/runner/predictors/Jpred.java

diff --git a/runner/compbio/runner/predictors/Jpred.java b/runner/compbio/runner/predictors/Jpred.java
new file mode 100644
index 0000000..017dcfc
--- /dev/null
+++ b/runner/compbio/runner/predictors/Jpred.java
@@ -0,0 +1,143 @@
+/* Copyright (c) 2013 Alexander Sherstnev
+ *  
+ *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 3.0     
+ * 
+ *  This library is free software; you can redistribute it and/or modify it under the terms of the
+ *  Apache License version 2 as published by the Apache Software Foundation
+ * 
+ *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
+ *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache 
+ *  License for more details.
+ * 
+ *  A copy of the license is in apache_license.txt. It is also available here:
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
+ * 
+ * Any republication or derived work distributed in source code form
+ * must include this copyright and license notice.
+ */
+
+package compbio.runner.predictors;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.Arrays;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import compbio.data.sequence.ScoreManager;
+import compbio.data.sequence.SequenceUtil;
+import compbio.engine.client.CommandBuilder;
+import compbio.engine.client.Executable;
+import compbio.engine.client.SkeletalExecutable;
+import compbio.metadata.ResultNotAvailableException;
+
+/**
+ * Command line
+ * 
+ * jpred.pl -in d16vpa_.fas -out res_d16vpa_ -dbname ported_db -dbpath /data/UNIREFdb -ncpu 4
+ * 
+ * @author asherstnev
+ * 
+ */
+public class Jpred extends SkeletalExecutable<Jpred> {
+
+	private static Logger log = Logger.getLogger(Jpred.class);
+
+	/**
+	 * Number of cores to use, defaults to 1 for local execution or the value of
+	 * "jpred.cluster.cpunum" property for cluster execution
+	 */
+	private int ncoreNumber = 0;
+
+	public static final String KEY_VALUE_SEPARATOR = " ";
+	public static final String STAT_FILE = "stat.txt";
+
+	public Jpred() {
+//		addParameters(Arrays.asList());
+	}
+	// HashMap<Method, float[]>
+	@Override
+	public ScoreManager getResults(String workDirectory)
+			throws ResultNotAvailableException {
+		ScoreManager annotations = null;
+		try {
+			InputStream inStream = new FileInputStream(new File(workDirectory, getOutput()));
+			annotations = ScoreManager.newInstanceSingleSequence(SequenceUtil.readAAConResults(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 (NullPointerException e) {
+			log.error(e.getMessage(), e.getCause());
+			throw new ResultNotAvailableException(e);
+		}
+		return annotations;
+	}
+
+	@Override
+	public List<String> getCreatedFiles() {
+		return Arrays.asList(getOutput(), getError());
+	}
+
+	@Override
+	public Jpred setInput(String inFile) {
+		super.setInput(inFile);
+		cbuilder.setParam("-in " + inFile);
+		return this;
+	}
+
+	@Override
+	public Jpred setOutput(String outFile) {
+		super.setOutput(outFile);
+		cbuilder.setParam("-out " + outFile);
+		return this;
+	}
+
+	@SuppressWarnings("unchecked")
+	@Override
+	public Class<Jpred> getType() {
+		return (Class<Jpred>) this.getClass();
+	}
+
+	public static String getStatFile() {
+		return STAT_FILE;
+	}
+
+	public void setNCore(int ncoreNumber) {
+		if (0 < ncoreNumber && ncoreNumber < 9) {
+			this.ncoreNumber = ncoreNumber;
+			cbuilder.setParam("-ncpu " + Integer.toString(getNCore()));
+		} else {
+			throw new IndexOutOfBoundsException("Number of cores must be between 1 and 8 ");
+		}
+	}
+
+	int getNCore() {
+		return ncoreNumber;
+	}
+
+	@Override
+	public CommandBuilder<Jpred> getParameters(ExecProvider provider) {
+		// If number of cores is provided, set it for the cluster execution only!
+		if (provider == Executable.ExecProvider.Cluster) {
+			int cpunum = SkeletalExecutable.getClusterCpuNum(getType());
+			cpunum = (cpunum == 0) ? 1 : cpunum;
+			setNCore(cpunum);
+		} else {
+			// Limit number of cores to 1 for ANY execution which does not set
+			// Ncores explicitly using setNCore method or is run on local VM
+			if (ncoreNumber == 0) {
+				setNCore(1);
+			}
+		}
+		return super.getParameters(provider);
+	}
+
+}
-- 
1.7.10.2