changeset 16:6863887e1b70

organized imports

added new "createV" and "createW" methods so that we can specifically create Vector Tables V or W as described in the paper

removed unnecessary code

added try/catch blocks where necessary

--- a/src/org/qmul/eecs/c4dm/sia/SiaVectorTableElementFactory.java	Tue Jan 08 18:22:26 2013 +0000
+++ b/src/org/qmul/eecs/c4dm/sia/SiaVectorTableElementFactory.java	Tue Jan 08 18:30:14 2013 +0000
@@ -5,6 +5,7 @@
 import java.util.List;
 import java.util.Vector;
 
+import org.qmul.eecs.c4dm.sia.exceptions.DimensionException;
 import org.qmul.eecs.c4dm.sia.model.Datapoint;
 import org.qmul.eecs.c4dm.sia.model.DimensionValue;
 import org.qmul.eecs.c4dm.sia.model.DirectlyFollows;
@@ -13,13 +14,13 @@
 import org.qmul.eecs.c4dm.sia.model.OrderedIndex;
 import org.qmul.eecs.c4dm.sia.model.OrderedSet;
 import org.qmul.eecs.c4dm.sia.model.ToDatapoint;
+import org.qmul.eecs.c4dm.sia.model.VectorTable;
 import org.qmul.eecs.c4dm.sia.model.VectorTableElement;
 
 import com.hp.hpl.jena.ontology.Individual;
 import com.hp.hpl.jena.ontology.OntClass;
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.rdf.model.AnonId;
-import com.hp.hpl.jena.rdf.model.Literal;
 import com.hp.hpl.jena.rdf.model.Property;
 import com.hp.hpl.jena.rdf.model.RDFNode;
 import com.hp.hpl.jena.rdf.model.Resource;
@@ -30,42 +31,54 @@
 
 public class SiaVectorTableElementFactory {
 
-	public static List<VectorTableElement> create(OntModel ontModel, List<Datapoint> datapoints) {
+	/**
+	 * @param ontModel
+	 * @param datapoints
+	 * @return
+	 */
+	public static VectorTable createV(OntModel ontModel, List<Datapoint> datapoints) {
+		return create(ontModel, datapoints, false);
+	}
+	
+	/**
+	 * @param ontModel
+	 * @param datapoints
+	 * @return
+	 */
+	public static VectorTable createW(OntModel ontModel, List<Datapoint> datapoints) {
+		return create(ontModel, datapoints, true);
+	}
+
+	/**
+	 * @param ontModel
+	 * @param datapoints
+	 * @param returnWResults
+	 * @return
+	 */
+	public static VectorTable create(OntModel ontModel, List<Datapoint> datapoints, boolean returnWResults) {
 		
 		OntClass vteClass = ontModel.getOntClass(VectorTableElement.RESOURCE_URI);
 
 		Resource vteResource = ontModel.getOntResource(vteClass);
 		ExtendedIterator<Individual> vteIter = ontModel.listIndividuals(vteResource);
 		
-		Property dimValProperty = ontModel.getOntProperty(DimensionValue.PROPERTY_URI);
-		Property dimensionProperty = ontModel.getOntProperty(DimensionValue.DIMENSION_URI);
-		Property valueProperty = ontModel.getOntProperty(DimensionValue.VALUE_URI);
 		Property fromDatapointProperty = ontModel.getOntProperty(FromDatapoint.PROPERTY_URI);
 		Property toDatapointProperty = ontModel.getOntProperty(ToDatapoint.PROPERTY_URI);
 
 		List<VectorTableElement> vteList = new ArrayList<VectorTableElement>();
 		VectorTableElement vte;
-		DimensionValue dimVal;
-		
 		Individual vteIndividual;
-		StmtIterator dimValStmtIter;
 		StmtIterator fromDPStmtIter;
 		StmtIterator toDPStmtIter;
-		StmtIterator dimValDimensionStmtIter;
-		StmtIterator dimValValueStmtIter;
 		Statement fromDatapointStmt;
 		Statement toDatapointStmt;
-		Resource dimValResource;
-		Statement dimValDimensionStmt;
-		Statement dimValValueStmt;
-		Literal dimension;
-		Literal value;
-
+		
+		VectorTable vectorTable = new VectorTable();
+		
 		// Find all rdf VectorTableElements
 		while (vteIter.hasNext())
 		{
 			vteIndividual = vteIter.next();
-			System.out.println(vteIndividual.toString());
 			vte = new VectorTableElement();
 			vte.setResource(vteIndividual);
 
@@ -73,33 +86,51 @@
 			fromDPStmtIter = ontModel.listStatements(vteIndividual, fromDatapointProperty, (RDFNode)null);			
 			fromDatapointStmt = fromDPStmtIter.next();
 			Datapoint fromDatapoint = findDatapoint(ontModel, datapoints, fromDatapointStmt.getResource());
-			vte.setFromDatapoint(fromDatapoint);
+			try {
+				vte.setFromDatapoint(fromDatapoint);
+			} catch (DimensionException e) {
+				e.printStackTrace();
+				System.exit(1);
+			}
 
 			// Find the 'toDatapoint' for this VectorTableElement
 			toDPStmtIter = ontModel.listStatements(vteIndividual, toDatapointProperty, (RDFNode)null);			
 			toDatapointStmt = toDPStmtIter.next();
 			Datapoint toDatapoint = findDatapoint(ontModel, datapoints, toDatapointStmt.getResource());
-			vte.setToDatapoint(toDatapoint);
+			try {
+				vte.setToDatapoint(toDatapoint);
+			} catch (DimensionException e) {
+				e.printStackTrace();
+				System.exit(1);
+			}
 
-			// Find all dimensionValues for this VectorTableElement
-			Vector<DimensionValue> dimensionValues = SiaDimensionValueFactory.getDimensionValuesForResource(ontModel, vteIndividual);
-			vte.setDimensionValues(dimensionValues);
-			
-			vteList.add(vte);
-			
+			// Only add VectorTableElements whose 'from' ordered index is less than the 'to' ordered index
+			if (returnWResults || vte.getFromDatapoint().getOrderedIndex() < vte.getToDatapoint().getOrderedIndex())
+			{
+				// Find all dimensionValues for this VectorTableElement
+				Vector<DimensionValue> dimensionValues = SiaDimensionValueFactory.getDimensionValuesForResource(ontModel, vteIndividual);
+				vte.setDimensionValues(dimensionValues);
+				
+				vteList.add(vte);
+			}
 		}
-		return vteList;
+		
+		vectorTable.setVteList(vteList);
+		vectorTable.setNumDatapoints(datapoints.size());
+		return vectorTable;
 	}
 
 	public static Datapoint findDatapoint(OntModel ontModel, List<Datapoint> datapoints, Resource resource) {
 		Iterator<Datapoint> datapointsIter = datapoints.iterator();
 		Datapoint datapoint;
+		
 		while (datapointsIter.hasNext())
 		{
 			datapoint = datapointsIter.next();
 			if (datapoint.getResource().getLocalName().equals(resource.getLocalName()))
 				return datapoint;
 		}
+		
 		datapoint = new Datapoint();
 		datapoint.setResource(resource);
 		Vector<DimensionValue> dimensionValues = SiaDimensionValueFactory.getDimensionValuesForResource(ontModel, resource);