[Cdk-commits] SF.net SVN: cdk: [10535] cdk-taverna/trunk/src/main/java/org/openscience/ cdk/applications/taverna/io/WriteToMDLMolFile.java

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

Revision: 10535
          http://cdk.svn.sourceforge.net/cdk/?rev=10535&view=rev
Author:   thomaskuhn
Date:     2008-03-26 14:28:20 -0700 (Wed, 26 Mar 2008)

Log Message:
-----------
Some clean up and upgrade to Java 5 standards

Modified Paths:
--------------
    cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/io/WriteToMDLMolFile.java

Modified: cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/io/WriteToMDLMolFile.java
===================================================================
--- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/io/WriteToMDLMolFile.java	2008-03-26 19:43:54 UTC (rev 10534)
+++ cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/io/WriteToMDLMolFile.java	2008-03-26 21:28:20 UTC (rev 10535)
@@ -25,14 +25,12 @@
  */
 package org.openscience.cdk.applications.taverna.io;
 import java.io.BufferedWriter;
-import java.io.File;
 import java.io.FileWriter;
 import java.io.PrintWriter;
 import java.io.StringWriter;
 import java.io.Writer;
 import java.util.ArrayList;
 import java.util.HashMap;
-import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
@@ -40,9 +38,9 @@
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.applications.taverna.CMLChemFile;
 import org.openscience.cdk.applications.taverna.LocalWorkerCDK;
+import org.openscience.cdk.applications.taverna.basicutilities.CMLChemFileWrapper;
 import org.openscience.cdk.applications.taverna.basicutilities.FileNameGenerator;
 import org.openscience.cdk.interfaces.IMolecule;
-import org.openscience.cdk.interfaces.IMoleculeSet;
 import org.openscience.cdk.io.MDLWriter;
 import org.openscience.cdk.math.RandomNumbersTool;
 
@@ -52,7 +50,7 @@
 	private String[] inputNames  = new String[] { "inputStructures"};
 	private String[] outputNames = new String[] { "Comment" };
 
-	//	 Region: input and outpout definition
+	//	 Region: input and output definition
 
 	public String[] inputNames() {
 		return inputNames;
@@ -71,30 +69,29 @@
 	// End of region
 
 	//  Region: local worker execution
-	public Map execute(Map inputs) throws TaskExecutionException {
-		List inputList = null;
-		List matchedList = new ArrayList();
+	public Map<String, DataThing> execute(Map<String, DataThing> inputs) throws TaskExecutionException {
+		List<CMLChemFile> inputList = null;
+		List<String> commentList = new ArrayList<String>();
 		FileNameGenerator fileNameGenerator = new FileNameGenerator();
 		int counter = 0;
 		String comment = "false";  
-		if(inputs.get("inputStructures") != null) {
-			inputList = (List)((DataThing)(inputs.get("inputStructures"))).getDataObject();
+		Map<String, DataThing> outputs = new HashMap<String, DataThing>();
+		if(inputs.get(inputNames[0]) != null) {
+			inputList = CMLChemFileWrapper.getListOfCMLChemfileFromDataThing(inputs.get(inputNames[0]));
 			if (inputList.isEmpty()){
-				matchedList.add("no entry in list");
-				Map outputs = new HashMap();
-				outputs.put(outputNames[0], new DataThing(matchedList));
+				commentList.add("no entry in list");
+				
+				outputs.put(outputNames[0], new DataThing(commentList));
 				return outputs;
 			}
 		} else {
-			matchedList.add("no entry in map");
-			Map outputs = new HashMap();
-			outputs.put(outputNames[0], new DataThing(matchedList));
+			commentList.add("no entry in map");
+			outputs.put(outputNames[0], new DataThing(commentList));
 			return outputs;
 		}
 		try {
 			String[] mdlContent = new String[1];
-			for (Iterator iter = inputList.iterator(); iter.hasNext(); ) {
-				CMLChemFile file = (CMLChemFile)iter.next();
+			for (CMLChemFile file : inputList) {
 				StringWriter writer = new StringWriter();
 				MDLWriter molWriter = new MDLWriter(writer);
 				for (int i = 0; i < file.getChemSequenceCount(); i++) {
@@ -117,7 +114,7 @@
 								counter++;
 							}   	
 							comment = "true " + count;
-							matchedList.add((String)comment);
+							commentList.add((String)comment);
 						}
 					}
 				}
@@ -125,8 +122,7 @@
 		} catch (Exception exception) {
 			throw new TaskExecutionException(exception);
 		}
-		Map outputs = new HashMap();
-		outputs.put(outputNames[0], new DataThing(matchedList));
+		outputs.put(outputNames[0], new DataThing(commentList));
 		return outputs;
 	}
 //	End of region
@@ -155,21 +151,4 @@
 			}
 		}
 	}
-	/**
-	 * Method which checks if the path exists and if not if it is possible to
-	 * build. If it is possible to build the path it will be done.
-	 * 
-	 * @param path
-	 *            Path which will be check
-	 * @throws Exception
-	 */
-	private void checkPath(String path) throws Exception {
-		File file = new File(path);
-		if (!file.exists()) {
-			if (!file.mkdirs()) {
-				throw new Exception("Could not create the directory: "
-						+ file.getPath());
-			}
-		}
-	}
 }


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