--- a
+++ b/src/net/timbusproject/dpes/alternative/AlternativesBuilder/ToolAlternativesBuilder.java
@@ -0,0 +1,179 @@
+/**
+ * Copyright (c) 2013/2014 Verein zur Foerderung der IT-Sicherheit in Oesterreich (SBA).
+ * The work has been developed in the TIMBUS Project and the above-mentioned are Members of the TIMBUS Consortium.
+ * TIMBUS is supported by the European Union under the 7th Framework Programme for research and technological
+ * development and demonstration activities (FP7/2007-2013) under grant agreement no. 269940.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with
+ * the License. You may obtain a copy of the License at: http://www.apache.org/licenses/LICENSE-2.0
+ * Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on
+ * an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including without
+ * limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTIBITLY, or FITNESS FOR A PARTICULAR
+ * PURPOSE. In no event and under no legal theory, whether in tort (including negligence), contract, or otherwise,
+ * unless required by applicable law or agreed to in writing, shall any Contributor be liable for damages, including
+ * any direct, indirect, special, incidental, or consequential damages of any character arising as a result of this
+ * License or out of the use or inability to use the Work.
+ * See the License for the specific language governing permissions and limitation under the License.
+ */
+
+package net.timbusproject.dpes.alternative.AlternativesBuilder;
+
+import ch.lambdaj.function.convert.Converter;
+import com.hp.hpl.jena.query.QuerySolution;
+import net.timbusproject.dpes.alternative.PreservationAlternative;
+import net.timbusproject.dpes.alternative.PreservationIdentifierException;
+import net.timbusproject.dpes.alternative.Risk;
+import org.apache.commons.lang3.tuple.ImmutablePair;
+import org.apache.commons.lang3.tuple.Pair;
+import org.sba_research.timbus.kb.ToolKnowledgeBase;
+import org.sbaresearch.owl.AlternativesBuilder;
+import org.sbaresearch.owl.JenaQueryFacade;
+import org.sbaresearch.owl.OwlApiFacade;
+import org.sbaresearch.owl.OwlElementNotFoundException;
+import org.semanticweb.owlapi.model.*;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import static ch.lambdaj.Lambda.convert;
+
+/**
+ * Creates alternative ontologies where tools at risk are replaced.
+ */
+public class ToolAlternativesBuilder implements PreservationAlternativesBuilder {
+
+    private final ToolKnowledgeBase knowledgeBase;
+    private final String baseURL;
+    private final OwlApiFacade originalModelFacade;
+    private final String identifier;
+
+    public ToolAlternativesBuilder(ToolKnowledgeBase knowledgeBase, String baseURL, OwlApiFacade originalModelFacade, String identifier) {
+        this.knowledgeBase = knowledgeBase;
+        this.baseURL = baseURL;
+        this.originalModelFacade = originalModelFacade;
+        this.identifier = identifier;
+    }
+
+    @Override
+    public List<PreservationAlternative> createAlternatives(Risk identifiedRisk, IRI individualAtRisk) throws OWLOntologyStorageException, OWLOntologyCreationException, IOException, OwlElementNotFoundException {
+        List<PreservationAlternative> alternatives = new ArrayList<>();
+        String affectedResourceName = identifiedRisk.getAffectedResource();
+        List<String> alternativeTools = getAlternativeTools(originalModelFacade, affectedResourceName);
+        ChangesOntologyBuilder changesOntologyBuilder = new ChangesOntologyBuilder(
+                originalModelFacade.getOntology(), originalModelFacade.getIndividual(individualAtRisk.toString()), "SoftwareReplacement");
+        if (alternativeTools.size() < 1) {
+            System.out.println("No alternatives found for risk: " + identifiedRisk.getRiskIdentifier());
+            System.out.println("Using fake alternatives for test purposes...");
+            for (int i = 0; i < 3; ++i) {
+                System.out.println("Replacing identified software " + affectedResourceName);
+                String replacingIndividual = affectedResourceName + "-replacement_" + i;
+
+                String alternativeOntologyIri = createIriFragment(baseURL, identifier, identifiedRisk, i);//, originalModel.getOntologyID().getOntologyIRI());
+                String iriSuffix = identifier + "/" + i;
+                alternatives.add(createAlternativeOntology(originalModelFacade.getOntology(), identifiedRisk,
+                        individualAtRisk, replacingIndividual, alternativeOntologyIri, changesOntologyBuilder, iriSuffix));
+            }
+        } else {
+            for (int i = 0; i < alternativeTools.size(); ++i) {
+                System.out.println("Replacing identified software " + affectedResourceName);
+                String alternativeOntologyIri = createIriFragment(baseURL, identifier, identifiedRisk, i);//, originalModel.getOntologyID().getOntologyIRI());
+                String iriSuffix = identifier + "/" + i;
+                alternatives.add(createAlternativeOntology(originalModelFacade.getOntology(), identifiedRisk,
+                        individualAtRisk, alternativeTools.get(i), alternativeOntologyIri, changesOntologyBuilder, iriSuffix));
+            }
+        }
+        return alternatives;
+    }
+
+    private List<String> getAlternativeTools(OwlApiFacade originalModelFacade, String affectedResourceName) throws OWLOntologyStorageException, OWLOntologyCreationException, IOException {
+        // get alternatives based on the tool
+        List<String> alternativeTools = knowledgeBase.getAlternativeTools(affectedResourceName);
+        // get alternatives based on the formats
+        JenaQueryFacade originalModelQueryFacade = new JenaQueryFacade(originalModelFacade.getJenaModel(false));
+        List<Pair<String, String>> formatPairs = convertToIDs(originalModelQueryFacade.query(QueryHelper.getQueryFormatPairs(affectedResourceName)), originalModelQueryFacade);
+        for (Pair<String, String> formatPair : formatPairs) {
+            alternativeTools.addAll(JenaQueryFacade.removeNamespace(knowledgeBase.getSupportingTools(formatPair)));
+        }
+        return alternativeTools;
+    }
+
+
+    private PreservationAlternative createAlternativeOntology(OWLOntology originalModel,
+                                                              Risk identifiedRisk, IRI individualAtRisk,
+                                                              String replacingIndividual, String alternativeOntologyIriPrefix, ChangesOntologyBuilder changesOntologyBuilder, String iriSuffix) throws OWLOntologyCreationException, OwlElementNotFoundException, OWLOntologyStorageException {
+
+        AlternativesBuilder alternativesBuilder = new AlternativesBuilder(new OwlApiFacade(originalModel));
+        OWLOntology modifiedModel = alternativesBuilder.copyOntology(IRI.create(alternativeOntologyIriPrefix, originalModel.getOntologyID().getOntologyIRI().getFragment()));
+        OWLOntologyManager modifiedModelOntologyManager = modifiedModel.getOWLOntologyManager();
+
+
+        IRI individualInModifiedModelModifiedIRI = null;
+        if (originalModel.containsIndividualInSignature(individualAtRisk)) {
+            individualInModifiedModelModifiedIRI = renameIndividual(individualAtRisk, replacingIndividual, modifiedModel);
+        }
+        List<String> changedOntologies = new ArrayList<>();
+
+        for (OWLOntology ontology : originalModel.getDirectImports()) {
+            if (!ontology.containsIndividualInSignature(individualAtRisk)) continue;
+
+            AlternativesBuilder alternativesBuilderImportedOntology = new AlternativesBuilder(new OwlApiFacade(ontology));
+            OWLOntology modifiedOntology = alternativesBuilderImportedOntology.copyOntology(
+                    IRI.create(alternativeOntologyIriPrefix, ontology.getOntologyID().getOntologyIRI().getFragment()),
+                    modifiedModel.getOWLOntologyManager()
+            );
+            individualInModifiedModelModifiedIRI = renameIndividual(individualAtRisk, replacingIndividual, modifiedOntology);
+
+            modifiedModelOntologyManager.applyChange(new RemoveImport(modifiedModel,
+                    modifiedModelOntologyManager.getOWLDataFactory().getOWLImportsDeclaration(ontology.getOntologyID().getOntologyIRI())));
+            modifiedModelOntologyManager.applyChange(new AddImport(modifiedModel,
+                    modifiedModelOntologyManager.getOWLDataFactory().getOWLImportsDeclaration(modifiedOntology.getOntologyID().getOntologyIRI())));
+            changedOntologies.add(OwlApiFacade.toOwlXml(modifiedOntology));
+        }
+
+        OWLNamedIndividual modifiedIndividual = modifiedModelOntologyManager.getOWLDataFactory().getOWLNamedIndividual(individualInModifiedModelModifiedIRI);
+
+        OWLOntology eventsOntology = changesOntologyBuilder.createChangesOntology(iriSuffix, modifiedModel, modifiedIndividual);
+        return new PreservationAlternative(
+                OwlApiFacade.toOwlXml(originalModel), OwlApiFacade.toOwlXml(modifiedModel),
+                OwlApiFacade.toOwlXml(eventsOntology), identifiedRisk.getRiskIdentifier(), changedOntologies);
+    }
+
+    private String createIriFragment(String baseURL, String identifier, Risk identifiedRisk, int count) {
+        return baseURL + "/" + identifier + "/" + identifiedRisk.getRiskIdentifier() + "/" + count + "/";
+    }
+
+    private IRI renameIndividual(IRI individualAtRisk, String replacingIndividual, OWLOntology modifiedModel) throws OwlElementNotFoundException {
+        OwlApiFacade model = new OwlApiFacade(modifiedModel);
+        IRI sourceIRI = model.createIri(OwlApiFacade.getFragment(individualAtRisk));
+        if (!model.containsIndividual(sourceIRI.toString())) {
+            throw new PreservationIdentifierException("Original individual not found in modified model: " + sourceIRI);
+        }
+
+        AlternativesBuilder alternativesBuilder = new AlternativesBuilder(model);
+        alternativesBuilder.renameIndividualByIRI(model.createIri(OwlApiFacade.getFragment(individualAtRisk)), replacingIndividual); // TODO: not sure why fragment only does not work... bug!
+
+        IRI targetIRI = model.createIri(replacingIndividual);
+        if (!model.containsIndividual(targetIRI.toString())) {
+            throw new PreservationIdentifierException("Modified individual not found in modified model: " + targetIRI);
+        }
+        System.out.println("\tReplaced " + sourceIRI + " with " + targetIRI);
+
+        return targetIRI;
+    }
+
+    private List<Pair<String, String>> convertToIDs(List<QuerySolution> query, final JenaQueryFacade queryFacade) {
+        return convert(query, new Converter<QuerySolution, Pair<String, String>>() {
+            public Pair<String, String> convert(QuerySolution solution) {
+                return new ImmutablePair<>(getID(solution, "readFormat", queryFacade), getID(solution, "writeFormat", queryFacade));
+            }
+        });
+    }
+
+    private String getID(QuerySolution solution, String formatIndex, JenaQueryFacade queryFacade) {
+        String format = solution.contains(formatIndex) ? solution.get(formatIndex).toString() : null;
+        if (format == null) return null;
+        List<String> pronomIDs = JenaQueryFacade.extractColumn(queryFacade.query(QueryHelper.getQueryGetFormatID(format)), "pronom_id");
+        return (pronomIDs.size() > 0 ? pronomIDs.get(0) : format);
+    }
+}