Examples with Pair org.vcell.util.Pair used on opensource projects

Example 11 with Pair

use of org.vcell.util.Pair in project vcell by virtualcell.

the class ReactionRuleParticipantSignaturePropertiesPanel method initialize.

private void initialize() {
    try {
        shapePanel = new ParticipantSignatureShapePanel() {

            @Override
            public void paintComponent(Graphics g) {
                super.paintComponent(g);
                for (Pair<ReactionRulePatternLargeShape, ReactionRulePatternLargeShape> p : ruleShapeList) {
                    ReactionRulePatternLargeShape rp = p.one;
                    rp.paintSelf(g);
                    ReactionRulePatternLargeShape pp = p.two;
                    pp.paintSelf(g);
                }
            }
        };
        shapePanel.setLayout(new GridBagLayout());
        shapePanel.setBackground(Color.white);
        shapePanel.zoomSmaller();
        shapePanel.zoomSmaller();
        shapePanel.zoomSmaller();
        getZoomSmallerButton().setEnabled(true);
        getZoomLargerButton().setEnabled(true);
        scrollPane = new JScrollPane(shapePanel);
        scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
        scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
        JPanel optionsPanel = new JPanel();
        optionsPanel.setPreferredSize(new Dimension(140, 200));
        optionsPanel.setLayout(new GridBagLayout());
        getZoomSmallerButton().setEnabled(true);
        getZoomLargerButton().setEnabled(true);
        int gridy = 0;
        GridBagConstraints gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.weightx = 0;
        gbc.insets = new Insets(8, 4, 4, 0);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanel.add(getZoomLargerButton(), gbc);
        gbc = new GridBagConstraints();
        gbc.gridx = 1;
        gbc.gridy = gridy;
        gbc.weightx = 0;
        gbc.insets = new Insets(8, 0, 4, 4);
        gbc.anchor = GridBagConstraints.WEST;
        optionsPanel.add(getZoomSmallerButton(), gbc);
        // apparently we don't need a fake 3rd cell to the right
        gridy++;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.gridwidth = 2;
        gbc.weightx = 1;
        // fake cell used for filling all the vertical empty space
        gbc.weighty = 1;
        gbc.anchor = GridBagConstraints.WEST;
        gbc.insets = new Insets(4, 4, 4, 10);
        optionsPanel.add(new JLabel(""), gbc);
        gridy++;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.gridwidth = 2;
        gbc.insets = new Insets(0, 4, 4, 4);
        gbc.fill = GridBagConstraints.HORIZONTAL;
        gbc.anchor = GridBagConstraints.SOUTHWEST;
        optionsPanel.add(getShowMoleculeColorButton(), gbc);
        gridy++;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.gridwidth = 2;
        gbc.insets = new Insets(0, 4, 4, 4);
        gbc.fill = GridBagConstraints.HORIZONTAL;
        gbc.anchor = GridBagConstraints.SOUTHWEST;
        optionsPanel.add(getShowNonTrivialButton(), gbc);
        gridy++;
        gbc = new GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.gridwidth = 2;
        gbc.insets = new Insets(0, 4, 4, 4);
        gbc.fill = GridBagConstraints.HORIZONTAL;
        gbc.anchor = GridBagConstraints.SOUTHWEST;
        optionsPanel.add(getShowDifferencesButton(), gbc);
        getShowMoleculeColorButton().setSelected(true);
        getShowNonTrivialButton().setSelected(true);
        getShowDifferencesButton().setSelected(false);
        shapePanel.setShowMoleculeColor(getShowMoleculeColorButton().isSelected());
        shapePanel.setShowNonTrivialOnly(getShowNonTrivialButton().isSelected());
        shapePanel.setShowDifferencesOnly(getShowDifferencesButton().isSelected());
        containerOfScrollPanel = new JPanel();
        containerOfScrollPanel.setLayout(new BorderLayout());
        containerOfScrollPanel.add(optionsPanel, BorderLayout.WEST);
        containerOfScrollPanel.add(scrollPane, BorderLayout.CENTER);
        setLayout(new BorderLayout());
        add(containerOfScrollPanel, BorderLayout.CENTER);
        setBackground(Color.white);
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}

Example 12 with Pair

use of org.vcell.util.Pair in project vcell by virtualcell.

the class ReactionRuleParticipantSignaturePropertiesPanel method updateShape.

private void updateShape() {
    int maxXOffset = 0;
    ruleShapeList.clear();
    // all the reactants go in one single ReactionRulePatternLargeShape, all the products the other
    int yOffset = yOffsetReactantInitial + GraphConstants.ReactionRuleParticipantDisplay_ReservedSpaceForNameOnYAxis;
    for (Map.Entry<String, ReactionRule> entry : reactionRuleMap.entrySet()) {
        ReactionRule rr = entry.getValue();
        ReactionRulePatternLargeShape reactantShape = new ReactionRulePatternLargeShape(xOffsetInitial, yOffset, -1, shapePanel, rr, true, issueManager);
        reactantShape.setWriteName(true);
        int xOffset = reactantShape.getRightEnd() + 70;
        ReactionRulePatternLargeShape productShape = new ReactionRulePatternLargeShape(xOffset, yOffset, -1, shapePanel, rr, false, issueManager);
        xOffset += productShape.getRightEnd();
        yOffset += SpeciesPatternLargeShape.defaultHeight + GraphConstants.ReactionRuleParticipantDisplay_ReservedSpaceForNameOnYAxis;
        maxXOffset = Math.max(maxXOffset, xOffset);
        Pair<ReactionRulePatternLargeShape, ReactionRulePatternLargeShape> p = new Pair<>(reactantShape, productShape);
        ruleShapeList.add(p);
    }
    int maxYOffset = Math.max(yOffsetReactantInitial + SpeciesPatternLargeShape.defaultHeight + GraphConstants.ReactionRuleParticipantDisplay_ReservedSpaceForNameOnYAxis, yOffsetReactantInitial + (SpeciesPatternLargeShape.defaultHeight + GraphConstants.ReactionRuleParticipantDisplay_ReservedSpaceForNameOnYAxis) * ruleShapeList.size());
    Dimension preferredSize = new Dimension(maxXOffset, maxYOffset);
    shapePanel.setPreferredSize(preferredSize);
    containerOfScrollPanel.repaint();
}

Example 13 with Pair

use of org.vcell.util.Pair in project vcell by virtualcell.

the class BioModelEditorModelPanel method deleteButtonPressed.

private void deleteButtonPressed() {
    try {
        ArrayList<Object> deleteList = new ArrayList<Object>();
        int selectedIndex = tabbedPane.getSelectedIndex();
        if (selectedIndex == ModelPanelTabID.reaction_diagram.ordinal()) {
            deleteList.addAll(Arrays.asList(reactionCartoonEditorPanel.getReactionCartoon().getSelectedObjects()));
        // } else if (selectedIndex == ModelPanelTabID.structure_diagram.ordinal()) {
        // deleteList.addAll(Arrays.asList(cartoonEditorPanel.getStructureCartoon().getSelectedObjects()));
        } else {
            computeCurrentSelectedTable();
            int[] rows = currentSelectedTable.getSelectedRows();
            if (rows == null || rows.length == 0) {
                return;
            }
            if (currentSelectedTable == speciesTable) {
                for (int r : rows) {
                    if (r < speciesTableModel.getRowCount()) {
                        SpeciesContext speciesContext = speciesTableModel.getValueAt(r);
                        if (speciesContext != null) {
                            deleteList.add(speciesContext);
                        }
                    }
                }
            } else if (currentSelectedTable == molecularTypeTable) {
                // TODO: delete stuff
                for (int r : rows) {
                    if (r < molecularTypeTableModel.getRowCount()) {
                        MolecularType mt = molecularTypeTableModel.getValueAt(r);
                        if (mt != null) {
                            deleteList.add(mt);
                        }
                    }
                }
            } else if (currentSelectedTable == observablesTable) {
                for (int r : rows) {
                    if (r < observableTableModel.getRowCount()) {
                        RbmObservable o = observableTableModel.getValueAt(r);
                        if (o != null) {
                            deleteList.add(o);
                        }
                    }
                }
            } else if (currentSelectedTable == structuresTable) {
                for (int r : rows) {
                    if (r < structureTableModel.getRowCount()) {
                        Structure rowValue = structureTableModel.getValueAt(r);
                        if (rowValue instanceof Feature || rowValue instanceof Membrane) {
                            deleteList.add(rowValue);
                        }
                    }
                }
            } else if (currentSelectedTable == reactionsTable) {
                for (int r : rows) {
                    if (r < reactionTableModel.getRowCount()) {
                        ModelProcess reaction = reactionTableModel.getValueAt(r);
                        if (reaction != null) {
                            deleteList.add(reaction);
                        }
                    }
                }
            }
        }
        if (deleteList.size() == 0) {
            return;
        }
        StringBuilder deleteListText = new StringBuilder();
        for (Object object : deleteList) {
            if (object instanceof SpeciesContext) {
                deleteListText.append("Species\t'" + ((SpeciesContext) object).getName() + "'\n");
            } else if (object instanceof MolecularType) {
                deleteListText.append(((MolecularType) object).getDisplayType() + "\t'" + ((MolecularType) object).getDisplayName() + "'\n");
            } else if (object instanceof RbmObservable) {
                deleteListText.append("Observable\t'" + ((RbmObservable) object).getName() + "'\n");
            } else if (object instanceof ReactionStep) {
                deleteListText.append("Reaction\t'" + ((ReactionStep) object).getName() + "'\n");
            } else if (object instanceof ReactionRule) {
                deleteListText.append("Reaction rule\t'" + ((ReactionRule) object).getName() + "'\n");
            } else if (object instanceof Structure) {
                deleteListText.append("Structure\t'" + ((Structure) object).getName() + "'\n");
            }
        }
        // TODO: once we display reaction rules in the carton editor panel we'll have to change the way we delete reaction rules
        if (deleteList.get(0) instanceof SpeciesContext || deleteList.get(0) instanceof ReactionStep) {
            try {
                ArrayList<SpeciesContext> speciesContextArrList = new ArrayList<SpeciesContext>();
                ArrayList<ReactionStep> reactionStepArrList = new ArrayList<ReactionStep>();
                for (Object obj : deleteList) {
                    if (obj instanceof SpeciesContext) {
                        speciesContextArrList.add((SpeciesContext) obj);
                    } else if (obj instanceof ReactionStep) {
                        reactionStepArrList.add((ReactionStep) obj);
                    } else {
                        throw new Exception("Unexpected delete object " + obj.getClass().getName());
                    }
                }
                ReactionCartoonTool.deleteReactionsAndSpecies(reactionCartoonEditorPanel, reactionStepArrList.toArray(new ReactionStep[0]), speciesContextArrList.toArray(new SpeciesContext[0]));
            } catch (UserCancelException uce) {
                return;
            }
            return;
        } else {
            String confirm = DialogUtils.showOKCancelWarningDialog(this, "Deleting", "You are going to delete the following:\n\n" + deleteListText + "\n Continue?");
            if (confirm.equals(UserMessage.OPTION_CANCEL)) {
                return;
            }
            for (Object object : deleteList) {
                if (object instanceof ReactionRule) {
                    ReactionRule rr = (ReactionRule) object;
                    bioModel.getModel().getRbmModelContainer().removeReactionRule(rr);
                } else if (object instanceof MolecularType) {
                    Map<String, Pair<Displayable, SpeciesPattern>> usedHere = new LinkedHashMap<String, Pair<Displayable, SpeciesPattern>>();
                    MolecularType mt = (MolecularType) object;
                    if (!bioModel.getModel().getRbmModelContainer().isDeleteAllowed(mt, usedHere)) {
                        String errMsg = mt.getDisplayType() + " <b>'" + mt + "'</b> cannot be deleted because it's already being used by:<br>";
                        final int MaxListSize = 7;
                        int count = 0;
                        for (String key : usedHere.keySet()) {
                            System.out.println(key);
                            if (count >= MaxListSize) {
                                errMsg += "<br> ... and more.";
                                break;
                            }
                            Pair<Displayable, SpeciesPattern> o = usedHere.get(key);
                            Displayable e = o.one;
                            SpeciesPattern sp = o.two;
                            errMsg += "<br> - " + e.getDisplayType().toLowerCase() + " <b>" + e.getDisplayName() + "</b>";
                            errMsg += ", " + sp.getDisplayType().toLowerCase() + " " + " <b>" + sp.getDisplayName() + "</b>";
                            count++;
                        }
                        errMsg = "<html>" + errMsg + "</html>";
                        throw new RuntimeException(errMsg);
                    }
                    bioModel.getModel().getRbmModelContainer().removeMolecularType(mt);
                } else if (object instanceof RbmObservable) {
                    RbmObservable o = (RbmObservable) object;
                    bioModel.getModel().getRbmModelContainer().removeObservable(o);
                } else {
                    bioModel.getModel().removeObject(object);
                }
            }
        }
    } catch (Exception ex) {
        ex.printStackTrace();
        DialogUtils.showErrorDialog(this, ex.getMessage());
    }
}

Example 14 with Pair

use of org.vcell.util.Pair in project vcell by virtualcell.

the class NetworkTransformer method generateNetwork.

private BNGOutputSpec generateNetwork(SimulationContext simContext, MathMappingCallback mathMappingCallback, NetworkGenerationRequirements networkGenerationRequirements) throws ClassNotFoundException, IOException {
    TaskCallbackMessage tcm;
    BNGOutputSpec outputSpec;
    speciesEquivalenceMap.clear();
    kineticsParameterMap.clear();
    String input = convertToBngl(simContext, true, mathMappingCallback, networkGenerationRequirements);
    for (Map.Entry<FakeSeedSpeciesInitialConditionsParameter, Pair<SpeciesContext, Expression>> entry : speciesEquivalenceMap.entrySet()) {
        FakeSeedSpeciesInitialConditionsParameter key = entry.getKey();
        Pair<SpeciesContext, Expression> value = entry.getValue();
        SpeciesContext sc = value.one;
        Expression initial = value.two;
        System.out.println("key: " + key.fakeParameterName + ",   species: " + sc.getName() + ", initial: " + initial.infix());
    }
    String md5hash = MD5.md5(input);
    if (isBngHashValid(input, md5hash, simContext)) {
        String s = "Previously saved outputSpec is up-to-date, no need to generate network.";
        System.out.println(s);
        // not an error, we just want to show it in red
        tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, s);
        simContext.appendToConsole(tcm);
        if (simContext.isInsufficientIterations()) {
            s = NetworkTransformer.getInsufficientIterationsMessage();
            System.out.println(s);
            tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, s);
            simContext.appendToConsole(tcm);
        }
        if (simContext.isInsufficientMaxMolecules()) {
            s = NetworkTransformer.getInsufficientMaxMoleculesMessage();
            System.out.println(s);
            tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, s);
            simContext.appendToConsole(tcm);
        }
        outputSpec = simContext.getMostRecentlyCreatedOutputSpec();
        return (BNGOutputSpec) BeanUtils.cloneSerializable(outputSpec);
    }
    BNGInput bngInput = new BNGInput(input);
    BNGOutput bngOutput = null;
    try {
        final BNGExecutorService bngService = BNGExecutorService.getInstance(bngInput, networkGenerationRequirements.timeoutDurationMS);
        bngService.registerBngUpdaterCallback(simContext);
        bngOutput = bngService.executeBNG();
    } catch (BNGException ex) {
        ex.printStackTrace(System.out);
        System.out.println("bionetgen exception");
        if (ex.getMessage().contains("was asked to write the network, but no reactions were found")) {
            RuntimeException rex = new RuntimeException("Specified species and reaction rules are not sufficient to define reaction network.");
            throw rex;
        } else {
            // rethrow without losing context
            throw ex;
        }
    } catch (RuntimeException ex) {
        ex.printStackTrace(System.out);
        System.out.println("runtime exception");
        throw ex;
    } catch (Exception ex) {
        ex.printStackTrace(System.out);
        System.out.println("other exception");
        throw new RuntimeException(ex.getMessage());
    }
    // simContext.setInsufficientIterations(false);
    // simContext.setInsufficientMaxMolecules(false);
    String bngConsoleString = bngOutput.getConsoleOutput();
    // TODO: this message we check if insufficient iterations / max molecules
    // DO IT OUTSIDE (in the bng service), we now can
    // tcm = new TaskCallbackMessage(TaskCallbackStatus.DetailBatch, bngConsoleString);
    // simContext.appendToConsole(tcm);
    tcm = new TaskCallbackMessage(TaskCallbackStatus.TaskEndNotificationOnly, "");
    simContext.setNewCallbackMessage(tcm);
    tcm = new TaskCallbackMessage(TaskCallbackStatus.TaskEndAdjustSimulationContextFlagsOnly, "");
    simContext.setNewCallbackMessage(tcm);
    String bngNetString = bngOutput.getNetFileContent();
    outputSpec = BNGOutputFileParser.createBngOutputSpec(bngNetString);
    // prints all output to console
    BNGOutputFileParser.printBNGNetOutput(outputSpec);
    if (mathMappingCallback.isInterrupted()) {
        String msg = "Canceled by user.";
        tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, msg);
        simContext.appendToConsole(tcm);
        // clean the cache if the user interrupts
        simContext.setMd5hash(null);
        throw new UserCancelException(msg);
    }
    if (outputSpec.getBNGSpecies().length > NetworkTransformer.speciesLimit) {
        String message = NetworkTransformer.getSpeciesLimitExceededMessage(outputSpec);
        tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, message);
        simContext.appendToConsole(tcm);
        simContext.setMd5hash(null);
        message = "Unable to generate Math for Application " + simContext.getName() + ".\n" + message;
        throw new RuntimeException(message);
    }
    if (outputSpec.getBNGReactions().length > NetworkTransformer.reactionsLimit) {
        String message = NetworkTransformer.getReactionsLimitExceededMessage(outputSpec);
        tcm = new TaskCallbackMessage(TaskCallbackStatus.Error, message);
        simContext.appendToConsole(tcm);
        simContext.setMd5hash(null);
        message = "Unable to generate Math for Application " + simContext.getName() + ".\n" + message;
        throw new RuntimeException(message);
    }
    // System.out.println("old hash: " + simContext.getMd5hash());
    if (md5hash != null && md5hash.length() != 0 && outputSpec != null) {
        System.out.println("saving hash and output spec");
        synchronized (this) {
            simContext.setMd5hash(md5hash);
            simContext.setMostRecentlyCreatedOutputSpec(outputSpec);
        }
    } else {
        System.out.println("something is wrong with the hash and/or output spec");
    }
    return (BNGOutputSpec) BeanUtils.cloneSerializable(outputSpec);
}

Example 15 with Pair

use of org.vcell.util.Pair in project vcell by virtualcell.

the class RbmNetworkGenerator method writeBngl_internal.

public static void writeBngl_internal(SimulationContext simulationContext, PrintWriter writer, Map<FakeReactionRuleRateParameter, LocalParameter> kineticsParameterMap, Map<FakeSeedSpeciesInitialConditionsParameter, Pair<SpeciesContext, Expression>> speciesEquivalenceMap, NetworkGenerationRequirements networkGenerationRequirements, CompartmentMode compartmentMode) {
    String callerClassName = new Exception().getStackTrace()[1].getClassName();
    String networkTransformerClassName = NetworkTransformer.class.getName();
    String rulebasedTransformerClassName = RulebasedTransformer.class.getName();
    if (!callerClassName.equals(networkTransformerClassName) && !callerClassName.equals(rulebasedTransformerClassName)) {
        throw new UnsupportedOperationException("This method may only be called from within a " + networkTransformerClassName + " or " + rulebasedTransformerClassName + " instance.");
    }
    Model model = simulationContext.getModel();
    RbmModelContainer rbmModelContainer = model.getRbmModelContainer();
    checkConsistency(model);
    // first we prepare the fake parameters we need to maintain the relationship between the species context and the seed species
    List<FakeSeedSpeciesInitialConditionsParameter> fakeParameterList = new ArrayList<FakeSeedSpeciesInitialConditionsParameter>();
    List<String> seedSpeciesList = new ArrayList<String>();
    SpeciesContext[] speciesContexts = model.getSpeciesContexts();
    for (int i = 0; i < speciesContexts.length; i++) {
        SpeciesContext sc = speciesContexts[i];
        if (!sc.hasSpeciesPattern()) {
            continue;
        }
        SpeciesContextSpec scs = simulationContext.getReactionContext().getSpeciesContextSpec(sc);
        Expression initialConcentration = scs.getParameter(SpeciesContextSpec.ROLE_InitialConcentration).getExpression();
        // fake initial values for the seed species, we need to present them to bngl as parameters
        FakeSeedSpeciesInitialConditionsParameter fakeSeedSpeciesParam = new FakeSeedSpeciesInitialConditionsParameter(sc.getName());
        Pair<SpeciesContext, Expression> p = new Pair<SpeciesContext, Expression>(sc, initialConcentration);
        speciesEquivalenceMap.put(fakeSeedSpeciesParam, p);
        String modified;
        if (compartmentMode == CompartmentMode.show) {
            modified = RbmUtils.toBnglString(sc.getSpeciesPattern(), null, CompartmentMode.hide, 0);
            modified = "@" + sc.getStructure().getName() + ":" + modified;
        } else if (compartmentMode == CompartmentMode.asSite) {
            modified = RbmUtils.toBnglString(sc.getSpeciesPattern(), sc.getStructure(), CompartmentMode.asSite, 0);
        } else {
            // CompartmentMode.hide
            modified = RbmUtils.toBnglString(sc.getSpeciesPattern(), null, CompartmentMode.hide, 0);
        }
        modified += " " + fakeSeedSpeciesParam.fakeParameterName;
        // we label the seed species with the index
        modified = (i + 1) + " " + modified;
        // we build the seed species list now, we write it later (in the BEGIN SPECIES block)
        seedSpeciesList.add(modified);
        fakeParameterList.add(fakeSeedSpeciesParam);
    }
    // second we produce the bngl file
    writer.println(BEGIN_MODEL);
    writer.println();
    for (ReactionRuleSpec rrs : simulationContext.getReactionContext().getReactionRuleSpecs()) {
        if (!rrs.isExcluded()) {
            ReactionRule reactionRule = rrs.getReactionRule();
            RbmKineticLaw kineticLaw = reactionRule.getKineticLaw();
            switch(kineticLaw.getRateLawType()) {
                case MassAction:
                    {
                        FakeReactionRuleRateParameter fakeRateParameterForward = new FakeReactionRuleRateParameter(reactionRule, RbmKineticLawParameterType.MassActionForwardRate);
                        LocalParameter origForwardRateParameter = kineticLaw.getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate);
                        kineticsParameterMap.put(fakeRateParameterForward, origForwardRateParameter);
                        if (reactionRule.isReversible()) {
                            FakeReactionRuleRateParameter fakeRateParameterReverse = new FakeReactionRuleRateParameter(reactionRule, RbmKineticLawParameterType.MassActionReverseRate);
                            LocalParameter origReverseRateParameter = kineticLaw.getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate);
                            kineticsParameterMap.put(fakeRateParameterReverse, origReverseRateParameter);
                        }
                        break;
                    }
                default:
                    {
                        throw new RuntimeException("kinetic law type " + kineticLaw.getRateLawType().name() + " not yet implemented");
                    }
            }
        }
    }
    if (compartmentMode == CompartmentMode.show) {
        RbmNetworkGenerator.writeCompartments(writer, model, simulationContext);
    }
    writer.println(BEGIN_PARAMETERS);
    // the fake parameters used for reaction rule kinetics
    for (FakeReactionRuleRateParameter p : kineticsParameterMap.keySet()) {
        writer.println(p.fakeParameterName + "\t\t1");
    }
    // the fake parameters used at initial values for the seed species
    for (FakeSeedSpeciesInitialConditionsParameter s : fakeParameterList) {
        writer.println(s.fakeParameterName + "\t\t1");
    }
    writer.println(END_PARAMETERS);
    writer.println();
    RbmNetworkGenerator.writeMolecularTypes(writer, model, compartmentMode);
    // write modified version of seed species while maintaining the connection between the species context and the real seed species
    writer.println(BEGIN_SPECIES);
    for (String s : seedSpeciesList) {
        writer.println(s);
    }
    writer.println(END_SPECIES);
    writer.println();
    RbmNetworkGenerator.writeObservables(writer, rbmModelContainer, compartmentMode);
    RbmNetworkGenerator.writeReactions_internal(writer, simulationContext, compartmentMode);
    writer.println(END_MODEL);
    writer.println();
    if (callerClassName.equals(networkTransformerClassName)) {
        RbmNetworkGenerator.writeNetworkConstraints(writer, rbmModelContainer, simulationContext, networkGenerationRequirements);
    } else if (callerClassName.equals(rulebasedTransformerClassName)) {
        writer.println();
        writer.println("writeXML()");
    }
    writer.println();
}