[Cdk-commits] SF.net SVN: cdk:[14333] cdk-taverna/trunk/src/main/java/org/openscience/cdk /applications/taverna/tools/ExtractIntermedIDFromMolFile.java

[<tho...@us...>]

Revision: 14333
          http://cdk.svn.sourceforge.net/cdk/?rev=14333&view=rev
Author:   thomaskuhn
Date:     2009-03-02 20:48:39 +0000 (Mon, 02 Mar 2009)

Log Message:
-----------
Extracts the intermed id's from a mol file

Added Paths:
-----------
    cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/tools/ExtractIntermedIDFromMolFile.java

Added: cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/tools/ExtractIntermedIDFromMolFile.java
===================================================================
--- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/tools/ExtractIntermedIDFromMolFile.java	                        (rev 0)
+++ cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/tools/ExtractIntermedIDFromMolFile.java	2009-03-02 20:48:39 UTC (rev 14333)
@@ -0,0 +1,193 @@
+/* $RCSfile$
+ * $Author: egonw $
+ * $Date: 2008-05-05 12:58:11 +0200 (Mo, 05 Mai 2008) $
+ * $Revision: 10819 $
+ * 
+ * Copyright (C) 2008 by Thomas Kuhn <tho...@us...>
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ * All we ask is that proper credit is given for our work, which includes
+ * - but is not limited to - adding the above copyright notice to the beginning
+ * of your source code files, and to any copyright notice that you may distribute
+ * with programs based on this work.
+ * 
+ * This program 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
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ */
+package org.openscience.cdk.applications.taverna.tools;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.embl.ebi.escience.baclava.DataThing;
+import org.openscience.cdk.applications.taverna.scuflworkers.cdk.CDKLocalWorker;
+
+import uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException;
+
+/**
+ * Class which implements a local worker for the cdk-taverna project which
+ * provides the possibility to extract the orginial ID of the molecule.
+ * In this specific case will it be the EXNO. This is an unique id used within the Chapman and Hall database. 
+ * 
+ * 
+ * @author Thomas Kuhn
+ * 
+ */
+public class ExtractIntermedIDFromMolFile implements CDKLocalWorker {
+
+	// Region: class variables
+
+	/**
+	 * Names of the input ports
+	 */
+	private String[] inputNames = new String[] { "inputMOLFileList", "Origin" };
+	/**
+	 * Names of the output ports
+	 */
+	private String[] outputNames = new String[] { "outputMOLFileList", "IDList", "Origin" };
+
+	// Region: XML tags/attributes
+
+	// End of region
+
+	// End of region
+
+	// Region: get / set properties
+
+	// End of region
+
+	// Region: public methods
+
+	// Region: input and output definition
+
+	/**
+	 * Get the input port names
+	 */
+	public String[] inputNames() {
+		return inputNames;
+	}
+
+	/**
+	 * Get the input port types
+	 */
+	public String[] inputTypes() {
+		return new String[] { CDKLocalWorker.STRING_ARRAY, CDKLocalWorker.STRING_ARRAY };
+	}
+
+	/**
+	 * Get the output port names
+	 */
+	public String[] outputNames() {
+		return outputNames;
+	}
+
+	/**
+	 * Get the output port types
+	 */
+	public String[] outputTypes() {
+		return new String[] { CDKLocalWorker.STRING_ARRAY, CDKLocalWorker.STRING_ARRAY, CDKLocalWorker.STRING_ARRAY};
+	}
+
+	// End of region
+
+	// Region: local worker execution
+
+	/**
+	 * Executes this processor. This worker gets a list of strings. Each string
+	 * contains a MDL MOL file. Each MOL file contains the original ID of this molecule.
+	 * This ID in this specific case is it the EXNO is used as unique identifier within the Chapman and Hall Database
+	 * 
+	 * @param inputs
+	 *            The input map which contains the input data
+	 * @return The map which contains the result of this worker
+	 * @throws TaskExecutionException
+	 *             If the execution of this method failed.
+	 */
+	@SuppressWarnings("unchecked")
+	public Map<String, DataThing> execute(Map<String, DataThing> inputs)
+	throws TaskExecutionException {
+		List<String> inputList = null;
+		List<String> originList = null;
+		List<String> originResultList = null;
+		boolean addOrigin = false;
+		boolean onlyOneOrigin = false;
+
+		Map<String, DataThing> outputs = new HashMap<String, DataThing>();
+		if (inputs.get(inputNames[0]) != null) {
+			inputList = (List<String>)((DataThing)inputs.get(inputNames[0])).getDataObject();
+		} else {
+			return null;
+		}
+		if (inputs.get(inputNames[1]) != null) {
+			originList = (List<String>)((DataThing)inputs.get(inputNames[1])).getDataObject();
+			if (originList != null && originList.size() > 0) {
+				addOrigin = true;			
+			}
+			if (originList.size() == 1) {
+				onlyOneOrigin = true;
+			}
+		}
+		List<String> listOfIDNumbers = new ArrayList<String>(100);
+
+		try {
+			originResultList = new ArrayList<String>();
+//			Pattern pattern = Pattern.compile("\\n>\\s<IMD-No>\\s+\\(\\D+\\.?\\D?\\)\\n(\\D{3}\\d\\d-?\\D?)\\n\\n>\\s<");
+//			Pattern pattern = Pattern.compile("\\n>\\s<IMD-No>\\s+\\(\\D+\\.?\\D?\\)\\n(IMD-\\D{6})\\n\\n>\\s<");
+			Pattern pattern = Pattern.compile("\\n>\\s+<IMD-No>\\s+\\(\\d+\\.?\\d*\\)\\n(IMD-\\d{6})\\n\\n>");
+//			Pattern pattern = Pattern.compile("(IMD-\\d{6})");
+
+			Matcher matcher;
+
+			for (String molFile : inputList) {
+				matcher = pattern.matcher(molFile);
+				if (matcher.find()) {
+					listOfIDNumbers.add(matcher.group(1));
+					if (onlyOneOrigin) {
+						originResultList.add(originList.get(0));
+					}
+				}
+				else
+				{
+					listOfIDNumbers.add("ID_Not_Found");
+				}
+			}
+			if (addOrigin) {
+				if (!onlyOneOrigin) {
+					originResultList = originList;
+				}
+			}
+		} catch (Exception exception) {
+			throw new TaskExecutionException(exception);
+		}
+		outputs.put(outputNames[0], new DataThing(inputList));
+		outputs.put(outputNames[1], new DataThing(listOfIDNumbers));
+		outputs.put(outputNames[2], new DataThing(originResultList));
+		return outputs;
+	}
+
+	// End of region
+
+	// Region: XML processing methods
+
+	// End of region
+
+	// End of region
+
+	// Region: private methods
+
+	// End of region
+
+}


Property changes on: cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/tools/ExtractIntermedIDFromMolFile.java
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Added: svn:mime-type
   + text/plain


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