use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.
the class ObservablePropertiesPanel method initialize.
private void initialize() {
observableTree = new BioModelNodeEditableTree();
observableTreeModel = new ObservableTreeModel(observableTree);
observableTree.setModel(observableTreeModel);
setLayout(new GridBagLayout());
// --------------------------------------------------------------------------------------------------------
splitPaneHorizontal.setOneTouchExpandable(true);
splitPaneHorizontal.setDividerLocation(120);
splitPaneHorizontal.setResizeWeight(0.1);
Border border = BorderFactory.createLineBorder(Color.gray);
Border loweredEtchedBorder = BorderFactory.createEtchedBorder(EtchedBorder.LOWERED);
Border loweredBevelBorder = BorderFactory.createLoweredBevelBorder();
TitledBorder annotationBorder = BorderFactory.createTitledBorder(loweredEtchedBorder, " Annotation ");
annotationBorder.setTitleJustification(TitledBorder.LEFT);
annotationBorder.setTitlePosition(TitledBorder.TOP);
annotationBorder.setTitleFont(getFont().deriveFont(Font.BOLD));
shapePanel = new LargeShapePanel() {
@Override
public void paintComponent(Graphics g) {
super.paintComponent(g);
for (SpeciesPatternLargeShape sps : spsList) {
if (sps == null) {
continue;
}
sps.paintSelf(g);
}
}
@Override
public DisplayMode getDisplayMode() {
return DisplayMode.other;
}
@Override
public RuleAnalysisChanged hasStateChanged(String reactionRuleName, MolecularComponentPattern molecularComponentPattern) {
return RuleAnalysisChanged.UNCHANGED;
}
@Override
public RuleAnalysisChanged hasStateChanged(MolecularComponentPattern molecularComponentPattern) {
return RuleAnalysisChanged.UNCHANGED;
}
@Override
public RuleAnalysisChanged hasBondChanged(String reactionRuleName, MolecularComponentPattern molecularComponentPattern) {
return RuleAnalysisChanged.UNCHANGED;
}
@Override
public RuleAnalysisChanged hasBondChanged(MolecularComponentPattern molecularComponentPattern) {
return RuleAnalysisChanged.UNCHANGED;
}
@Override
public RuleAnalysisChanged hasNoMatch(String reactionRuleName, MolecularTypePattern mtp) {
return RuleAnalysisChanged.UNCHANGED;
}
@Override
public RuleAnalysisChanged hasNoMatch(MolecularTypePattern molecularTypePattern) {
return RuleAnalysisChanged.UNCHANGED;
}
@Override
public RuleParticipantSignature getSignature() {
return null;
}
@Override
public GroupingCriteria getCriteria() {
return null;
}
@Override
public boolean isViewSingleRow() {
return true;
}
};
shapePanel.setBorder(border);
shapePanel.setBackground(Color.white);
shapePanel.setLayout(null);
shapePanel.setZoomFactor(-1);
shapePanel.setEditable(true);
shapePanel.setShowMoleculeColor(true);
shapePanel.setShowNonTrivialOnly(true);
shapePanel.addMouseListener(new MouseAdapter() {
@Override
public void mouseClicked(MouseEvent e) {
super.mouseClicked(e);
if (e.getButton() == 1) {
// left click selects the object (we highlight it)
Point whereClicked = e.getPoint();
PointLocationInShapeContext locationContext = new PointLocationInShapeContext(whereClicked);
manageMouseActivity(locationContext);
} else if (e.getButton() == 3) {
// right click invokes popup menu (only if the object is highlighted)
Point whereClicked = e.getPoint();
PointLocationInShapeContext locationContext = new PointLocationInShapeContext(whereClicked);
manageMouseActivity(locationContext);
if (locationContext.getDeepestShape() != null && !locationContext.getDeepestShape().isHighlighted()) {
// TODO: (maybe) add code here to highlight the shape if it's not highlighted already but don't show the menu
// return;
}
showPopupMenu(e, locationContext);
}
}
private void manageMouseActivity(PointLocationInShapeContext locationContext) {
Graphics g = shapePanel.getGraphics();
for (SpeciesPatternLargeShape sps : spsList) {
sps.turnHighlightOffRecursive(g);
}
for (SpeciesPatternLargeShape sps : spsList) {
if (sps.contains(locationContext)) {
// check if mouse is inside shape
break;
}
}
locationContext.highlightDeepestShape();
locationContext.paintDeepestShape(g);
}
});
// shapePanel.addMouseListener(eventHandler); // alternately use this
shapePanel.addMouseMotionListener(new MouseMotionAdapter() {
public void mouseMoved(MouseEvent e) {
Point overWhat = e.getPoint();
PointLocationInShapeContext locationContext = new PointLocationInShapeContext(overWhat);
for (SpeciesPatternLargeShape sps : spsList) {
if (sps.contains(locationContext)) {
break;
}
}
HighlightableShapeInterface hsi = locationContext.getDeepestShape();
if (hsi == null) {
shapePanel.setToolTipText(null);
} else {
shapePanel.setToolTipText("Right click for " + hsi.getDisplayType() + " menus");
}
for (SpeciesPatternLargeShape sps : spsList) {
for (MolecularTypeLargeShape mtls : sps.getMolecularTypeLargeShapes()) {
Rectangle r = mtls.getAnchorHotspot();
if (r != null && r.contains(overWhat)) {
mtls.getMolecularType();
shapePanel.setToolTipText(mtls.getAnchorsHTML());
break;
}
}
}
}
});
JPanel optionsPanel = new JPanel();
// gray options panel
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.gridwidth = 3;
// top, left bottom, right
gbc.insets = new Insets(4, 4, 2, 4);
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.anchor = GridBagConstraints.NORTHWEST;
optionsPanel.add(getAddSpeciesButton(), gbc);
ButtonGroup bg = new ButtonGroup();
bg.add(getSequenceMultimolecularButton());
bg.add(getSequencePolimerEqualButton());
bg.add(getSequencePolimerGreaterButton());
gridy++;
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.gridwidth = 2;
gbc.insets = new Insets(8, 4, 2, 4);
gbc.fill = GridBagConstraints.HORIZONTAL;
optionsPanel.add(getSequenceMultimolecularButton(), gbc);
gridy++;
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.insets = new Insets(4, 10, 2, 4);
gbc.fill = GridBagConstraints.HORIZONTAL;
JLabel label = new JLabel("Polymer of");
label.setToolTipText("Compact notation available below for single-Molecule polymers");
optionsPanel.add(label, gbc);
gridy++;
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.insets = new Insets(2, 4, 1, 2);
gbc.fill = GridBagConstraints.HORIZONTAL;
optionsPanel.add(getSequencePolimerEqualButton(), gbc);
gbc = new GridBagConstraints();
gbc.gridx = 1;
gbc.gridy = gridy;
gbc.gridwidth = 2;
gbc.insets = new Insets(2, 4, 1, 4);
gbc.fill = GridBagConstraints.HORIZONTAL;
optionsPanel.add(getLengthEqualTextField(), gbc);
gridy++;
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.insets = new Insets(1, 4, 4, 2);
gbc.fill = GridBagConstraints.HORIZONTAL;
optionsPanel.add(getSequencePolimerGreaterButton(), gbc);
gbc = new GridBagConstraints();
gbc.gridx = 1;
gbc.gridy = gridy;
gbc.gridwidth = 2;
gbc.insets = new Insets(1, 4, 4, 4);
gbc.fill = GridBagConstraints.HORIZONTAL;
optionsPanel.add(getLengthGreaterTextField(), gbc);
// --- zoom buttons in their own panel, for alignment ---
JPanel buttonPanel = new JPanel();
buttonPanel.setLayout(new GridBagLayout());
GridBagConstraints gbc2 = new GridBagConstraints();
gbc2.gridx = 0;
gbc2.gridy = 0;
gbc2.insets = new Insets(1, 1, 1, 1);
gbc2.anchor = GridBagConstraints.WEST;
buttonPanel.add(getZoomLargerButton(), gbc2);
gbc2 = new GridBagConstraints();
gbc2.gridx = 1;
gbc2.gridy = 0;
gbc2.insets = new Insets(1, 1, 1, 1);
gbc2.anchor = GridBagConstraints.WEST;
buttonPanel.add(getZoomSmallerButton(), gbc2);
// ---------------------------------------------------
gridy++;
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.anchor = GridBagConstraints.WEST;
gbc.insets = new Insets(1, 4, 4, 2);
gbc.fill = GridBagConstraints.HORIZONTAL;
// zoom buttons panel
optionsPanel.add(buttonPanel, gbc);
gridy++;
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.gridwidth = 3;
gbc.weightx = 1;
// fake cell used for filling all the vertical empty space
gbc.weighty = 1;
gbc.anchor = GridBagConstraints.WEST;
gbc.insets = new Insets(2, 1, 2, 10);
optionsPanel.add(new JLabel(""), gbc);
// -----------------------------------------------------------------------------------------
// right bottom panel, contains just the annotation
JPanel generalPanel = new JPanel();
generalPanel.setBorder(annotationBorder);
generalPanel.setLayout(new GridBagLayout());
gridy = 0;
annotationTextArea = new javax.swing.JTextArea("", 1, 30);
annotationTextArea.setLineWrap(true);
annotationTextArea.setWrapStyleWord(true);
annotationTextArea.setFont(new Font("monospaced", Font.PLAIN, 11));
annotationTextArea.setEditable(false);
javax.swing.JScrollPane jsp = new javax.swing.JScrollPane(annotationTextArea);
gbc = new java.awt.GridBagConstraints();
gbc.weightx = 1.0;
gbc.weighty = 0.1;
gbc.gridx = 0;
gbc.gridy = gridy;
gbc.anchor = GridBagConstraints.LINE_START;
gbc.fill = java.awt.GridBagConstraints.BOTH;
gbc.insets = new Insets(4, 4, 4, 4);
generalPanel.add(jsp, gbc);
// where we display the shapes
scrollPane = new JScrollPane(shapePanel);
scrollPane.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
scrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED);
JPanel containerOfScrollPanel = new JPanel();
containerOfScrollPanel.setLayout(new BorderLayout());
containerOfScrollPanel.add(optionsPanel, BorderLayout.WEST);
containerOfScrollPanel.add(scrollPane, BorderLayout.CENTER);
splitPaneHorizontal.setTopComponent(containerOfScrollPanel);
splitPaneHorizontal.setBottomComponent(generalPanel);
splitPaneHorizontal.setResizeWeight(0.9d);
splitPaneHorizontal.setDividerLocation(0.8d);
setName("ObservablePropertiesPanel");
setLayout(new BorderLayout());
add(splitPaneHorizontal, BorderLayout.CENTER);
setBackground(Color.white);
annotationTextArea.addFocusListener(eventHandler);
annotationTextArea.addMouseListener(eventHandler);
}
use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.
the class ObservableTableModel method getComparator.
@Override
protected Comparator<RbmObservable> getComparator(final int columnIndex, final boolean ascending) {
return new Comparator<RbmObservable>() {
int scale = ascending ? 1 : -1;
Column col = Column.values()[columnIndex];
public int compare(RbmObservable o1, RbmObservable o2) {
switch(col) {
case name:
return scale * o1.getName().compareToIgnoreCase(o2.getName());
case structure:
return scale * o1.getStructure().getName().compareToIgnoreCase(o2.getStructure().getName());
case species_pattern:
return scale * RbmUtils.toBnglString(o1.getSpeciesPattern(0), null, CompartmentMode.hide, 0).compareToIgnoreCase(RbmUtils.toBnglString(o2.getSpeciesPattern(0), null, CompartmentMode.hide, 0));
case type:
return scale * o1.getType().name().compareToIgnoreCase(o2.getType().name());
case depiction:
// the sp list is always allocated even though it may be empty
Integer s1 = o1.getSpeciesPatternList().size();
Integer s2 = o2.getSpeciesPatternList().size();
if (s1 != s2) {
// different number of species patterns, sort by number of patterns
return scale * s1.compareTo(s2);
// this includes the case when one list is empty
}
if (s1 > 1 && s2 > 1) {
// same number of species patterns, more than one - we don't bother to sort
return 0;
// TODO: add functionality to sort by total number of molecules / sites
}
// one pattern each, sort by number of molecules, if that equal sort by total number of sites
if (s1 == 1 && s2 == 1) {
Integer i1 = o1.getSpeciesPattern(0).getMolecularTypePatterns().size();
Integer i2 = o2.getSpeciesPattern(0).getMolecularTypePatterns().size();
if (scale * i1.compareTo(i2) == 0) {
// if same number of molecule we try to sort by number of sites of the mt
i1 = 0;
i2 = 0;
for (MolecularTypePattern mtp : o1.getSpeciesPattern(0).getMolecularTypePatterns()) {
i1 += mtp.getMolecularType().getComponentList().size();
}
for (MolecularTypePattern mtp : o2.getSpeciesPattern(0).getMolecularTypePatterns()) {
i2 += mtp.getMolecularType().getComponentList().size();
}
return scale * i1.compareTo(i2);
} else {
return scale * i1.compareTo(i2);
}
}
return 0;
default:
return 0;
}
}
};
}
use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.
the class ObservableTreeModel method valueForPathChanged.
@Override
public void valueForPathChanged(TreePath path, Object newValue) {
Object obj = path.getLastPathComponent();
if (obj == null || !(obj instanceof BioModelNode)) {
return;
}
BioModelNode selectedNode = (BioModelNode) obj;
BioModelNode parentNode = (BioModelNode) selectedNode.getParent();
Object userObject = selectedNode.getUserObject();
try {
if (newValue instanceof String) {
String inputString = (String) newValue;
if (inputString == null || inputString.length() == 0) {
return;
}
String mangled = TokenMangler.fixTokenStrict(inputString);
if (!mangled.equals(inputString)) {
String errMsg = ((Displayable) userObject).getDisplayType() + " '" + inputString + "' not legal identifier, try '" + mangled + "'";
throw new RuntimeException(errMsg);
}
if (userObject instanceof RbmObservable) {
// TODO: untested!!!
((RbmObservable) userObject).setName(inputString);
}
} else if (newValue instanceof MolecularComponentPattern) {
MolecularComponentPattern newMcp = (MolecularComponentPattern) newValue;
Object parentObject = parentNode == null ? null : parentNode.getUserObject();
if (parentObject instanceof MolecularTypePattern) {
MolecularTypePattern mtp = (MolecularTypePattern) parentObject;
MolecularComponent mc = newMcp.getMolecularComponent();
MolecularComponentPattern mcp = mtp.getMolecularComponentPattern(mc);
mcp.setComponentStatePattern(newMcp.getComponentStatePattern());
BondType bp = mcp.getBondType();
BondType newbp = newMcp.getBondType();
mcp.setBondType(newbp);
// specified -> specified
if (bp == BondType.Specified && newbp == BondType.Specified) {
// bond didn't change
} else if (bp == BondType.Specified && newbp != BondType.Specified) {
// specified -> non specified
// change the partner to possible
mcp.getBond().molecularComponentPattern.setBondType(BondType.Possible);
mcp.setBond(null);
} else if (bp != BondType.Specified && newbp == BondType.Specified) {
// non specified -> specified
int newBondId = newMcp.getBondId();
mcp.setBondId(newBondId);
mcp.setBond(newMcp.getBond());
mcp.getBond().molecularComponentPattern.setBondId(newBondId);
for (SpeciesPattern sp : observable.getSpeciesPatternList()) {
sp.resolveBonds();
}
} else {
}
}
}
} catch (Exception ex) {
DialogUtils.showErrorDialog(ownerTree, ex.getMessage());
}
}
use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.
the class RulebasedMathMapping method addSpeciesPatterns.
private HashMap<SpeciesPattern, VolumeParticleSpeciesPattern> addSpeciesPatterns(Domain domain, List<ReactionRule> rrList) throws MathException {
// Particle Molecular Types
//
Model model = getSimulationContext().getModel();
List<RbmObservable> observableList = model.getRbmModelContainer().getObservableList();
List<MolecularType> molecularTypeList = model.getRbmModelContainer().getMolecularTypeList();
for (MolecularType molecularType : molecularTypeList) {
ParticleMolecularType particleMolecularType = new ParticleMolecularType(molecularType.getName());
for (MolecularComponent molecularComponent : molecularType.getComponentList()) {
String pmcName = molecularComponent.getName();
String pmcId = particleMolecularType.getName() + "_" + molecularComponent.getName();
ParticleMolecularComponent particleMolecularComponent = new ParticleMolecularComponent(pmcId, pmcName);
for (ComponentStateDefinition componentState : molecularComponent.getComponentStateDefinitions()) {
ParticleComponentStateDefinition pcsd = particleMolecularComponent.getComponentStateDefinition(componentState.getName());
if (pcsd == null) {
particleMolecularComponent.addComponentStateDefinition(new ParticleComponentStateDefinition(componentState.getName()));
}
}
particleMolecularType.addMolecularComponent(particleMolecularComponent);
}
if (!molecularType.isAnchorAll()) {
List<String> anchorList = new ArrayList<>();
for (Structure struct : molecularType.getAnchors()) {
anchorList.add(struct.getName());
}
particleMolecularType.setAnchorList(anchorList);
}
mathDesc.addParticleMolecularType(particleMolecularType);
}
//
// Assemble list of all Species Patterns (from observables, reaction rules, and seed species).
//
// linked hash set maintains insertion order
LinkedHashMap<SpeciesPattern, Structure> speciesPatternStructureMap = new LinkedHashMap<SpeciesPattern, Structure>();
for (RbmObservable observable : observableList) {
for (SpeciesPattern speciesPattern : observable.getSpeciesPatternList()) {
speciesPatternStructureMap.put(speciesPattern, observable.getStructure());
}
}
for (ReactionRule reactionRule : rrList) {
for (ReactantPattern rp : reactionRule.getReactantPatterns()) {
speciesPatternStructureMap.put(rp.getSpeciesPattern(), rp.getStructure());
}
for (ProductPattern pp : reactionRule.getProductPatterns()) {
speciesPatternStructureMap.put(pp.getSpeciesPattern(), pp.getStructure());
}
}
for (SpeciesContext sc : model.getSpeciesContexts()) {
if (!sc.hasSpeciesPattern()) {
continue;
}
speciesPatternStructureMap.put(sc.getSpeciesPattern(), sc.getStructure());
}
//
// add list of unique speciesPatterns
//
HashMap<String, VolumeParticleSpeciesPattern> speciesPatternVCMLMap = new HashMap<String, VolumeParticleSpeciesPattern>();
HashMap<SpeciesPattern, VolumeParticleSpeciesPattern> speciesPatternMap = new HashMap<SpeciesPattern, VolumeParticleSpeciesPattern>();
String speciesPatternName = "speciesPattern0";
for (SpeciesPattern speciesPattern : speciesPatternStructureMap.keySet()) {
VolumeParticleSpeciesPattern volumeParticleSpeciesPattern = new VolumeParticleSpeciesPattern(speciesPatternName, domain, speciesPatternStructureMap.get(speciesPattern).getName());
for (MolecularTypePattern molecularTypePattern : speciesPattern.getMolecularTypePatterns()) {
ParticleMolecularType particleMolecularType = mathDesc.getParticleMolecularType(molecularTypePattern.getMolecularType().getName());
ParticleMolecularTypePattern particleMolecularTypePattern = new ParticleMolecularTypePattern(particleMolecularType);
String participantMatchLabel = molecularTypePattern.getParticipantMatchLabel();
if (molecularTypePattern.getParticipantMatchLabel() != null) {
particleMolecularTypePattern.setMatchLabel(participantMatchLabel);
}
for (MolecularComponentPattern molecularComponentPattern : molecularTypePattern.getComponentPatternList()) {
MolecularComponent molecularComponent = molecularComponentPattern.getMolecularComponent();
ParticleMolecularComponent particleMolecularComponent = particleMolecularType.getMolecularComponent(molecularComponent.getName());
ParticleMolecularComponentPattern particleMolecularComponentPattern = new ParticleMolecularComponentPattern(particleMolecularComponent);
ComponentStatePattern componentState = molecularComponentPattern.getComponentStatePattern();
if (componentState != null) {
if (componentState.isAny()) {
ParticleComponentStatePattern pcsp = new ParticleComponentStatePattern();
particleMolecularComponentPattern.setComponentStatePattern(pcsp);
} else {
String name = componentState.getComponentStateDefinition().getName();
ParticleComponentStateDefinition pcsd = particleMolecularComponent.getComponentStateDefinition(name);
// ParticleComponentStateDefinition pcsd = new ParticleComponentStateDefinition(componentState.getComponentStateDefinition().getName());
// particleMolecularComponent.addComponentStateDefinition(pcsd);
ParticleComponentStatePattern pcsp = new ParticleComponentStatePattern(pcsd);
particleMolecularComponentPattern.setComponentStatePattern(pcsp);
}
} else {
ParticleComponentStatePattern pcsp = new ParticleComponentStatePattern();
particleMolecularComponentPattern.setComponentStatePattern(pcsp);
}
switch(molecularComponentPattern.getBondType()) {
case Specified:
{
particleMolecularComponentPattern.setBondType(ParticleBondType.Specified);
particleMolecularComponentPattern.setBondId(molecularComponentPattern.getBondId());
break;
}
case Exists:
{
particleMolecularComponentPattern.setBondType(ParticleBondType.Exists);
particleMolecularComponentPattern.setBondId(-1);
break;
}
case None:
{
particleMolecularComponentPattern.setBondType(ParticleBondType.None);
particleMolecularComponentPattern.setBondId(-1);
break;
}
case Possible:
{
particleMolecularComponentPattern.setBondType(ParticleBondType.Possible);
particleMolecularComponentPattern.setBondId(-1);
break;
}
}
particleMolecularTypePattern.addMolecularComponentPattern(particleMolecularComponentPattern);
}
volumeParticleSpeciesPattern.addMolecularTypePattern(particleMolecularTypePattern);
}
String speciesPatternVCML = volumeParticleSpeciesPattern.getVCML("tempName");
VolumeParticleSpeciesPattern uniqueVolumeParticleSpeciesPattern = speciesPatternVCMLMap.get(speciesPatternVCML);
if (uniqueVolumeParticleSpeciesPattern == null) {
speciesPatternVCMLMap.put(speciesPatternVCML, volumeParticleSpeciesPattern);
speciesPatternName = TokenMangler.getNextEnumeratedToken(speciesPatternName);
speciesPatternMap.put(speciesPattern, volumeParticleSpeciesPattern);
} else {
speciesPatternMap.put(speciesPattern, uniqueVolumeParticleSpeciesPattern);
}
}
return speciesPatternMap;
}
use of org.vcell.model.rbm.MolecularTypePattern in project vcell by virtualcell.
the class RulebasedTransformer method transform.
private void transform(SimulationContext originalSimContext, SimulationContext transformedSimulationContext, ArrayList<ModelEntityMapping> entityMappings, MathMappingCallback mathMappingCallback) throws PropertyVetoException {
Model newModel = transformedSimulationContext.getModel();
Model originalModel = originalSimContext.getModel();
ModelEntityMapping em = null;
// list of rules created from the reactions; we apply the symmetry factor computed by bionetgen only to these
Set<ReactionRule> fromReactions = new HashSet<>();
for (SpeciesContext newSpeciesContext : newModel.getSpeciesContexts()) {
final SpeciesContext originalSpeciesContext = originalModel.getSpeciesContext(newSpeciesContext.getName());
// map new and old species contexts
em = new ModelEntityMapping(originalSpeciesContext, newSpeciesContext);
entityMappings.add(em);
if (newSpeciesContext.hasSpeciesPattern()) {
// it's perfect already and can't be improved
continue;
}
try {
MolecularType newmt = newModel.getRbmModelContainer().createMolecularType();
newModel.getRbmModelContainer().addMolecularType(newmt, false);
MolecularTypePattern newmtp_sc = new MolecularTypePattern(newmt);
SpeciesPattern newsp_sc = new SpeciesPattern();
newsp_sc.addMolecularTypePattern(newmtp_sc);
newSpeciesContext.setSpeciesPattern(newsp_sc);
RbmObservable newo = new RbmObservable(newModel, "O0_" + newmt.getName() + "_tot", newSpeciesContext.getStructure(), RbmObservable.ObservableType.Molecules);
MolecularTypePattern newmtp_ob = new MolecularTypePattern(newmt);
SpeciesPattern newsp_ob = new SpeciesPattern();
newsp_ob.addMolecularTypePattern(newmtp_ob);
newo.addSpeciesPattern(newsp_ob);
newModel.getRbmModelContainer().addObservable(newo);
// map new observable to old species context
em = new ModelEntityMapping(originalSpeciesContext, newo);
entityMappings.add(em);
} catch (ModelException e) {
e.printStackTrace();
throw new RuntimeException("unable to transform species context: " + e.getMessage());
} catch (PropertyVetoException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
ReactionSpec[] reactionSpecs = transformedSimulationContext.getReactionContext().getReactionSpecs();
for (ReactionSpec reactionSpec : reactionSpecs) {
if (reactionSpec.isExcluded()) {
// we create rules only from those reactions which are not excluded
continue;
}
ReactionStep rs = reactionSpec.getReactionStep();
String name = rs.getName();
String mangled = TokenMangler.fixTokenStrict(name);
mangled = newModel.getReactionName(mangled);
Kinetics k = rs.getKinetics();
if (!(k instanceof MassActionKinetics)) {
throw new RuntimeException("Only Mass Action Kinetics supported at this time, reaction \"" + rs.getName() + "\" uses kinetic law type \"" + rs.getKinetics().getName() + "\"");
}
boolean bReversible = rs.isReversible();
ReactionRule rr = new ReactionRule(newModel, mangled, rs.getStructure(), bReversible);
fromReactions.add(rr);
MassActionKinetics massActionKinetics = (MassActionKinetics) k;
List<Reactant> rList = rs.getReactants();
List<Product> pList = rs.getProducts();
// counting the stoichiometry - 2A+B means 3 reactants
int numReactants = 0;
for (Reactant r : rList) {
numReactants += r.getStoichiometry();
if (numReactants > 2) {
String message = "NFSim doesn't support more than 2 reactants within a reaction: " + name;
throw new RuntimeException(message);
}
}
int numProducts = 0;
for (Product p : pList) {
numProducts += p.getStoichiometry();
if (bReversible && numProducts > 2) {
String message = "NFSim doesn't support more than 2 products within a reversible reaction: " + name;
throw new RuntimeException(message);
}
}
RateLawType rateLawType = RateLawType.MassAction;
RbmKineticLaw kineticLaw = new RbmKineticLaw(rr, rateLawType);
try {
String forwardRateName = massActionKinetics.getForwardRateParameter().getName();
Expression forwardRateExp = massActionKinetics.getForwardRateParameter().getExpression();
String reverseRateName = massActionKinetics.getReverseRateParameter().getName();
Expression reverseRateExp = massActionKinetics.getReverseRateParameter().getExpression();
LocalParameter fR = kineticLaw.getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate);
fR.setName(forwardRateName);
LocalParameter rR = kineticLaw.getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate);
rR.setName(reverseRateName);
if (rs.hasReactant()) {
kineticLaw.setParameterValue(fR, forwardRateExp, true);
}
if (rs.hasProduct()) {
kineticLaw.setParameterValue(rR, reverseRateExp, true);
}
//
for (KineticsParameter reaction_p : massActionKinetics.getKineticsParameters()) {
if (reaction_p.getRole() == Kinetics.ROLE_UserDefined) {
LocalParameter rule_p = kineticLaw.getLocalParameter(reaction_p.getName());
if (rule_p == null) {
//
// after lazy parameter creation we didn't find a user-defined rule parameter with this same name.
//
// there must be a global symbol with the same name, that the local reaction parameter has overridden.
//
ParameterContext.LocalProxyParameter rule_proxy_parameter = null;
for (ProxyParameter proxyParameter : kineticLaw.getProxyParameters()) {
if (proxyParameter.getName().equals(reaction_p.getName())) {
rule_proxy_parameter = (LocalProxyParameter) proxyParameter;
}
}
if (rule_proxy_parameter != null) {
// we want to convert to local
boolean bConvertToGlobal = false;
kineticLaw.convertParameterType(rule_proxy_parameter, bConvertToGlobal);
} else {
// could find neither local parameter nor proxy parameter
throw new RuntimeException("user defined parameter " + reaction_p.getName() + " from reaction " + rs.getName() + " didn't map to a reactionRule parameter");
}
} else if (rule_p.getRole() == RbmKineticLawParameterType.UserDefined) {
kineticLaw.setParameterValue(rule_p, reaction_p.getExpression(), true);
rule_p.setUnitDefinition(reaction_p.getUnitDefinition());
} else {
throw new RuntimeException("user defined parameter " + reaction_p.getName() + " from reaction " + rs.getName() + " mapped to a reactionRule parameter with unexpected role " + rule_p.getRole().getDescription());
}
}
}
} catch (ExpressionException e) {
e.printStackTrace();
throw new RuntimeException("Problem attempting to set RbmKineticLaw expression: " + e.getMessage());
}
rr.setKineticLaw(kineticLaw);
KineticsParameter[] kpList = k.getKineticsParameters();
ModelParameter[] mpList = rs.getModel().getModelParameters();
ModelParameter mp = rs.getModel().getModelParameter(kpList[0].getName());
ReactionParticipant[] rpList = rs.getReactionParticipants();
for (ReactionParticipant p : rpList) {
if (p instanceof Reactant) {
int stoichiometry = p.getStoichiometry();
for (int i = 0; i < stoichiometry; i++) {
SpeciesPattern speciesPattern = new SpeciesPattern(rs.getModel(), p.getSpeciesContext().getSpeciesPattern());
ReactantPattern reactantPattern = new ReactantPattern(speciesPattern, p.getStructure());
rr.addReactant(reactantPattern);
}
} else if (p instanceof Product) {
int stoichiometry = p.getStoichiometry();
for (int i = 0; i < stoichiometry; i++) {
SpeciesPattern speciesPattern = new SpeciesPattern(rs.getModel(), p.getSpeciesContext().getSpeciesPattern());
ProductPattern productPattern = new ProductPattern(speciesPattern, p.getStructure());
rr.addProduct(productPattern);
}
}
}
// commented code below is probably obsolete, we verify (above) in the reaction the number of participants,
// no need to do it again in the corresponding rule
// if(rr.getReactantPatterns().size() > 2) {
// String message = "NFSim doesn't support more than 2 reactants within a reaction: " + name;
// throw new RuntimeException(message);
// }
// if(rr.getProductPatterns().size() > 2) {
// String message = "NFSim doesn't support more than 2 products within a reaction: " + name;
// throw new RuntimeException(message);
// }
newModel.removeReactionStep(rs);
newModel.getRbmModelContainer().addReactionRule(rr);
}
for (ReactionRuleSpec rrs : transformedSimulationContext.getReactionContext().getReactionRuleSpecs()) {
if (rrs == null) {
continue;
}
ReactionRule rr = rrs.getReactionRule();
if (rrs.isExcluded()) {
// delete those rules which are disabled (excluded) in the Specifications / Reaction table
newModel.getRbmModelContainer().removeReactionRule(rr);
continue;
}
}
// now that we generated the rules we can delete the reaction steps they're coming from
for (ReactionStep rs : newModel.getReactionSteps()) {
newModel.removeReactionStep(rs);
}
try {
// we invoke bngl just for the purpose of generating the xml file, which we'll then use to extract the symmetry factor
generateNetwork(transformedSimulationContext, fromReactions, mathMappingCallback);
} catch (ClassNotFoundException | IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
System.out.println("Finished RuleBased Transformer.");
}
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