Examples with RbmModelContainer cbit.vcell.model.Model.RbmModelContainer used on opensource projects
Example 1 with RbmModelContainer
use of cbit.vcell.model.Model.RbmModelContainer in project vcell by virtualcell.
the class ClientRequestManager method openAfterChecking.
private void openAfterChecking(VCDocumentInfo documentInfo, final TopLevelWindowManager requester, final boolean inNewWindow) {
final String DOCUMENT_INFO = "documentInfo";
final String SEDML_TASK = "SedMLTask";
final String SEDML_MODEL = "SedMLModel";
final String BNG_UNIT_SYSTEM = "bngUnitSystem";
/* asynchronous and not blocking any window */
bOpening = true;
Hashtable<String, Object> hashTable = new Hashtable<String, Object>();
// may want to insert corrected VCDocumentInfo later if our import debugger corrects it (BNGL Debugger).
hashTable.put(DOCUMENT_INFO, documentInfo);
// start a thread that gets it and updates the GUI by creating a new document desktop
String taskName = null;
if (documentInfo instanceof ExternalDocInfo) {
taskName = "Importing document";
ExternalDocInfo externalDocInfo = (ExternalDocInfo) documentInfo;
File file = externalDocInfo.getFile();
if (file != null && !file.getName().isEmpty() && file.getName().endsWith("bngl")) {
BngUnitSystem bngUnitSystem = new BngUnitSystem(BngUnitOrigin.DEFAULT);
String fileText;
String originalFileText;
try {
fileText = BeanUtils.readBytesFromFile(file, null);
originalFileText = new String(fileText);
} catch (IOException e1) {
e1.printStackTrace();
DialogUtils.showErrorDialog(requester.getComponent(), "<html>Error reading file " + file.getPath() + "</html>");
return;
}
Reader reader = externalDocInfo.getReader();
boolean bException = true;
while (bException) {
try {
BioModel bioModel = createDefaultBioModelDocument(bngUnitSystem);
boolean bStochastic = true;
boolean bRuleBased = true;
SimulationContext ruleBasedSimContext = bioModel.addNewSimulationContext("temp NFSim app", SimulationContext.Application.RULE_BASED_STOCHASTIC);
List<SimulationContext> appList = new ArrayList<SimulationContext>();
appList.add(ruleBasedSimContext);
RbmModelContainer rbmModelContainer = bioModel.getModel().getRbmModelContainer();
RbmUtils.reactionRuleLabelIndex = 0;
RbmUtils.reactionRuleNames.clear();
ASTModel astModel = RbmUtils.importBnglFile(reader);
// for now, hasUnitSystem() always returns false
if (astModel.hasUnitSystem()) {
bngUnitSystem = astModel.getUnitSystem();
}
if (astModel.hasCompartments()) {
Structure struct = bioModel.getModel().getStructure(0);
if (struct != null) {
bioModel.getModel().removeStructure(struct);
}
}
BnglObjectConstructionVisitor constructionVisitor = null;
if (!astModel.hasMolecularDefinitions()) {
System.out.println("Molecular Definition Block missing.");
constructionVisitor = new BnglObjectConstructionVisitor(bioModel.getModel(), appList, bngUnitSystem, false);
} else {
constructionVisitor = new BnglObjectConstructionVisitor(bioModel.getModel(), appList, bngUnitSystem, true);
}
astModel.jjtAccept(constructionVisitor, rbmModelContainer);
bException = false;
} catch (final Exception e) {
e.printStackTrace(System.out);
BNGLDebuggerPanel panel = new BNGLDebuggerPanel(fileText, e);
int oKCancel = DialogUtils.showComponentOKCancelDialog(requester.getComponent(), panel, "Bngl Debugger: " + file.getName());
if (oKCancel == JOptionPane.CANCEL_OPTION || oKCancel == JOptionPane.DEFAULT_OPTION) {
throw new UserCancelException("Canceling Import");
}
// inserting <potentially> corrected DocumentInfo
fileText = panel.getText();
externalDocInfo = new ExternalDocInfo(panel.getText());
reader = externalDocInfo.getReader();
hashTable.put(DOCUMENT_INFO, externalDocInfo);
}
}
if (!originalFileText.equals(fileText)) {
// file has been modified
String message = "Importing <b>" + file.getName() + "</b> into vCell. <br>Overwrite the file on the disk?<br>";
message = "<html>" + message + "</html>";
Object[] options = { "Overwrite and Import", "Import Only", "Cancel" };
int returnCode = JOptionPane.showOptionDialog(requester.getComponent(), message, "Bngl Debugger", JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null, options, options[2]);
if (returnCode == JOptionPane.YES_OPTION) {
try {
FileWriter fw = new FileWriter(file);
fw.write(fileText);
fw.close();
} catch (IOException e) {
e.printStackTrace();
}
} else if (returnCode == JOptionPane.CANCEL_OPTION || returnCode == JOptionPane.CLOSED_OPTION) {
return;
}
}
if (!(bngUnitSystem.getOrigin() == BngUnitOrigin.PARSER)) {
BNGLUnitsPanel panel = new BNGLUnitsPanel(bngUnitSystem);
int oKCancel = DialogUtils.showComponentOKCancelDialog(requester.getComponent(), panel, " Bngl Units Selector", null, false);
if (oKCancel == JOptionPane.CANCEL_OPTION || oKCancel == JOptionPane.DEFAULT_OPTION) {
// TODO: or do nothing and continue with default values?
return;
} else {
bngUnitSystem = panel.getUnits();
}
}
hashTable.put(BNG_UNIT_SYSTEM, bngUnitSystem);
} else if (file != null && !file.getName().isEmpty() && file.getName().toLowerCase().endsWith(".sedml")) {
try {
XMLSource xmlSource = externalDocInfo.createXMLSource();
File sedmlFile = xmlSource.getXmlFile();
SedML sedml = Libsedml.readDocument(sedmlFile).getSedMLModel();
if (sedml == null || sedml.getModels().isEmpty()) {
return;
}
AbstractTask chosenTask = SEDMLChooserPanel.chooseTask(sedml, requester.getComponent(), file.getName());
hashTable.put(SEDML_MODEL, sedml);
hashTable.put(SEDML_TASK, chosenTask);
} catch (Exception e) {
e.printStackTrace();
throw new RuntimeException("failed to read document: " + e.getMessage(), e);
}
} else if (file != null && !file.getName().isEmpty() && (file.getName().toLowerCase().endsWith(".sedx") || file.getName().toLowerCase().endsWith(".omex"))) {
try {
ArchiveComponents ac = null;
ac = Libsedml.readSEDMLArchive(new FileInputStream(file));
SEDMLDocument doc = ac.getSedmlDocument();
SedML sedml = doc.getSedMLModel();
if (sedml == null) {
throw new RuntimeException("Failed importing " + file.getName());
}
if (sedml.getModels().isEmpty()) {
throw new RuntimeException("Unable to find any model in " + file.getName());
}
AbstractTask chosenTask = SEDMLChooserPanel.chooseTask(sedml, requester.getComponent(), file.getName());
hashTable.put(SEDML_MODEL, sedml);
hashTable.put(SEDML_TASK, chosenTask);
} catch (Exception e) {
e.printStackTrace();
throw new RuntimeException("failed to read archive: " + e.getMessage(), e);
}
}
} else {
taskName = "Loading document '" + documentInfo.getVersion().getName() + "' from database";
}
AsynchClientTask task0 = new AsynchClientTask(taskName, AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
public void run(Hashtable<String, Object> hashTable) throws Exception {
if (!inNewWindow) {
// request was to replace the document in an existing window
getMdiManager().blockWindow(requester.getManagerID());
}
}
};
AsynchClientTask task1 = new AsynchClientTask(taskName, AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
VCDocument doc = null;
VCDocumentInfo documentInfo = (VCDocumentInfo) hashTable.get(DOCUMENT_INFO);
if (documentInfo instanceof BioModelInfo) {
BioModelInfo bmi = (BioModelInfo) documentInfo;
doc = getDocumentManager().getBioModel(bmi);
} else if (documentInfo instanceof MathModelInfo) {
MathModelInfo mmi = (MathModelInfo) documentInfo;
doc = getDocumentManager().getMathModel(mmi);
} else if (documentInfo instanceof GeometryInfo) {
GeometryInfo gmi = (GeometryInfo) documentInfo;
doc = getDocumentManager().getGeometry(gmi);
} else if (documentInfo instanceof ExternalDocInfo) {
ExternalDocInfo externalDocInfo = (ExternalDocInfo) documentInfo;
File file = externalDocInfo.getFile();
if (file != null && !file.getName().isEmpty() && (file.getName().toLowerCase().endsWith(".sedx") || file.getName().toLowerCase().endsWith(".omex"))) {
TranslationLogger transLogger = new TranslationLogger(requester);
doc = XmlHelper.sedmlToBioModel(transLogger, externalDocInfo, (SedML) hashTable.get(SEDML_MODEL), (AbstractTask) hashTable.get(SEDML_TASK));
} else if (!externalDocInfo.isXML()) {
if (hashTable.containsKey(BNG_UNIT_SYSTEM)) {
// not XML, look for BNGL etc.
// we use the BngUnitSystem already created during the 1st pass
BngUnitSystem bngUnitSystem = (BngUnitSystem) hashTable.get(BNG_UNIT_SYSTEM);
BioModel bioModel = createDefaultBioModelDocument(bngUnitSystem);
SimulationContext ruleBasedSimContext = bioModel.addNewSimulationContext("NFSim app", SimulationContext.Application.RULE_BASED_STOCHASTIC);
SimulationContext odeSimContext = bioModel.addNewSimulationContext("BioNetGen app", SimulationContext.Application.NETWORK_DETERMINISTIC);
List<SimulationContext> appList = new ArrayList<SimulationContext>();
appList.add(ruleBasedSimContext);
appList.add(odeSimContext);
// set convention for initial conditions in generated application for seed species (concentration or count)
ruleBasedSimContext.setUsingConcentration(bngUnitSystem.isConcentration());
odeSimContext.setUsingConcentration(bngUnitSystem.isConcentration());
RbmModelContainer rbmModelContainer = bioModel.getModel().getRbmModelContainer();
RbmUtils.reactionRuleLabelIndex = 0;
RbmUtils.reactionRuleNames.clear();
Reader reader = externalDocInfo.getReader();
ASTModel astModel = RbmUtils.importBnglFile(reader);
if (bioModel.getModel() != null && bioModel.getModel().getVcMetaData() != null) {
VCMetaData vcMetaData = bioModel.getModel().getVcMetaData();
vcMetaData.setFreeTextAnnotation(bioModel, astModel.getProlog());
}
if (astModel.hasCompartments()) {
Structure struct = bioModel.getModel().getStructure(0);
if (struct != null) {
bioModel.getModel().removeStructure(struct);
}
}
BnglObjectConstructionVisitor constructionVisitor = null;
if (!astModel.hasMolecularDefinitions()) {
System.out.println("Molecular Definition Block missing. Extracting it from Species, Reactions, Obserbables.");
constructionVisitor = new BnglObjectConstructionVisitor(bioModel.getModel(), appList, bngUnitSystem, false);
} else {
constructionVisitor = new BnglObjectConstructionVisitor(bioModel.getModel(), appList, bngUnitSystem, true);
}
// we'll convert the kinetic parameters to BngUnitSystem inside the visit(ASTKineticsParameter...)
astModel.jjtAccept(constructionVisitor, rbmModelContainer);
// set the volume in the newly created application to BngUnitSystem.bnglModelVolume
// TODO: set the right values if we import compartments from the bngl file!
// if(!bngUnitSystem.isConcentration()) {
Expression sizeExpression = new Expression(bngUnitSystem.getVolume());
ruleBasedSimContext.getGeometryContext().getStructureMapping(0).getSizeParameter().setExpression(sizeExpression);
odeSimContext.getGeometryContext().getStructureMapping(0).getSizeParameter().setExpression(sizeExpression);
// }
// we remove the NFSim application if any seed species is clamped because NFSim doesn't know what to do with it
boolean bClamped = false;
for (SpeciesContextSpec scs : ruleBasedSimContext.getReactionContext().getSpeciesContextSpecs()) {
if (scs.isConstant()) {
bClamped = true;
break;
}
}
if (bClamped) {
bioModel.removeSimulationContext(ruleBasedSimContext);
}
// // TODO: DON'T delete this code
// // the code below is needed if we also want to create simulations, example for 1 rule based simulation
// // it is rule-based so it wont have to flatten, should be fast.
// MathMappingCallback callback = new MathMappingCallbackTaskAdapter(getClientTaskStatusSupport());
// NetworkGenerationRequirements networkGenerationRequirements = null; // network generation should not be executed.
// ruleBasedSimContext.refreshMathDescription(callback,networkGenerationRequirements);
// Simulation sim = ruleBasedSimContext.addNewSimulation(SimulationOwner.DEFAULT_SIM_NAME_PREFIX,callback,networkGenerationRequirements);
doc = bioModel;
}
} else {
// is XML
try (TranslationLogger transLogger = new TranslationLogger(requester)) {
XMLSource xmlSource = externalDocInfo.createXMLSource();
org.jdom.Element rootElement = xmlSource.getXmlDoc().getRootElement();
String xmlType = rootElement.getName();
String modelXmlType = null;
if (xmlType.equals(XMLTags.VcmlRootNodeTag)) {
// For now, assuming that <vcml> element has only one child (biomodel, mathmodel or geometry).
// Will deal with multiple children of <vcml> Element when we get to model composition.
@SuppressWarnings("unchecked") List<Element> childElementList = rootElement.getChildren();
// assuming first child is the biomodel, mathmodel or geometry.
Element modelElement = childElementList.get(0);
modelXmlType = modelElement.getName();
}
if (xmlType.equals(XMLTags.BioModelTag) || (xmlType.equals(XMLTags.VcmlRootNodeTag) && modelXmlType.equals(XMLTags.BioModelTag))) {
doc = XmlHelper.XMLToBioModel(xmlSource);
} else if (xmlType.equals(XMLTags.MathModelTag) || (xmlType.equals(XMLTags.VcmlRootNodeTag) && modelXmlType.equals(XMLTags.MathModelTag))) {
doc = XmlHelper.XMLToMathModel(xmlSource);
} else if (xmlType.equals(XMLTags.GeometryTag) || (xmlType.equals(XMLTags.VcmlRootNodeTag) && modelXmlType.equals(XMLTags.GeometryTag))) {
doc = XmlHelper.XMLToGeometry(xmlSource);
} else if (xmlType.equals(XMLTags.SbmlRootNodeTag)) {
Namespace namespace = rootElement.getNamespace(XMLTags.SBML_SPATIAL_NS_PREFIX);
boolean bIsSpatial = (namespace == null) ? false : true;
doc = XmlHelper.importSBML(transLogger, xmlSource, bIsSpatial);
} else if (xmlType.equals(XMLTags.CellmlRootNodeTag)) {
if (requester instanceof BioModelWindowManager) {
doc = XmlHelper.importBioCellML(transLogger, xmlSource);
} else {
doc = XmlHelper.importMathCellML(transLogger, xmlSource);
}
} else if (xmlType.equals(MicroscopyXMLTags.FRAPStudyTag)) {
doc = VFrapXmlHelper.VFRAPToBioModel(hashTable, xmlSource, getDocumentManager(), requester);
} else if (xmlType.equals(XMLTags.SedMLTypeTag)) {
doc = XmlHelper.sedmlToBioModel(transLogger, externalDocInfo, (SedML) hashTable.get(SEDML_MODEL), (AbstractTask) hashTable.get(SEDML_TASK));
} else {
// unknown XML format
throw new RuntimeException("unsupported XML format, first element tag is <" + rootElement.getName() + ">");
}
if (externalDocInfo.getDefaultName() != null) {
doc.setName(externalDocInfo.getDefaultName());
}
}
}
if (doc == null) {
File f = externalDocInfo.getFile();
if (f != null) {
throw new RuntimeException("Unable to determine type of file " + f.getCanonicalPath());
}
throw new ProgrammingException();
}
}
// create biopax objects using annotation
if (doc instanceof BioModel) {
BioModel bioModel = (BioModel) doc;
try {
bioModel.getVCMetaData().createBioPaxObjects(bioModel);
} catch (Exception e) {
e.printStackTrace();
}
}
requester.prepareDocumentToLoad(doc, inNewWindow);
hashTable.put("doc", doc);
}
};
AsynchClientTask task2 = new AsynchClientTask("Showing document", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false, false) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
try {
Throwable exc = (Throwable) hashTable.get(ClientTaskDispatcher.TASK_ABORTED_BY_ERROR);
if (exc == null) {
VCDocument doc = (VCDocument) hashTable.get("doc");
DocumentWindowManager windowManager = null;
if (inNewWindow) {
windowManager = createDocumentWindowManager(doc);
// request was to create a new top-level window with this doc
getMdiManager().createNewDocumentWindow(windowManager);
// if (windowManager instanceof BioModelWindowManager) {
// ((BioModelWindowManager)windowManager).preloadApps();
// }
} else {
// request was to replace the document in an existing window
windowManager = (DocumentWindowManager) requester;
getMdiManager().setCanonicalTitle(requester.getManagerID());
windowManager.resetDocument(doc);
}
hashTable.put(WIN_MGR_KEY, windowManager);
}
} finally {
if (!inNewWindow) {
getMdiManager().unBlockWindow(requester.getManagerID());
}
bOpening = false;
}
}
};
AsynchClientTask task3 = new AsynchClientTask("Special Layout", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false, false) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
// TODO Auto-generated method stub
if (documentInfo instanceof ExternalDocInfo) {
ExternalDocInfo externalDocInfo = (ExternalDocInfo) documentInfo;
if (externalDocInfo.isBioModelsNet()) {
DocumentWindowManager windowManager = (DocumentWindowManager) hashTable.get(WIN_MGR_KEY);
if (windowManager instanceof BioModelWindowManager) {
((BioModelWindowManager) windowManager).specialLayout();
}
}
}
}
};
AsynchClientTask task4 = new AsynchClientTaskFunction(ClientRequestManager::setWindowFocus, "Set window focus", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false, false);
ClientTaskDispatcher.dispatch(requester.getComponent(), hashTable, new AsynchClientTask[] { task0, task1, task2, task3, task4 }, false);
}
Also used :
ArrayList(java.util.ArrayList)
UserCancelException(org.vcell.util.UserCancelException)
SpeciesContextSpec(cbit.vcell.mapping.SpeciesContextSpec)
SedML(org.jlibsedml.SedML)
ExternalDocInfo(cbit.vcell.xml.ExternalDocInfo)
AsynchClientTaskFunction(cbit.vcell.client.task.AsynchClientTaskFunction)
VCMetaData(cbit.vcell.biomodel.meta.VCMetaData)
BnglObjectConstructionVisitor(org.vcell.model.rbm.RbmUtils.BnglObjectConstructionVisitor)
RbmModelContainer(cbit.vcell.model.Model.RbmModelContainer)
GeometryInfo(cbit.vcell.geometry.GeometryInfo)
VCDocument(org.vcell.util.document.VCDocument)
FileInputStream(java.io.FileInputStream)
Namespace(org.jdom.Namespace)
BngUnitSystem(org.vcell.model.bngl.BngUnitSystem)
BNGLDebuggerPanel(org.vcell.model.bngl.gui.BNGLDebuggerPanel)
SEDMLDocument(org.jlibsedml.SEDMLDocument)
CSGObject(cbit.vcell.geometry.CSGObject)
ChooseFile(cbit.vcell.client.task.ChooseFile)
File(java.io.File)
AsynchClientTask(cbit.vcell.client.task.AsynchClientTask)
AbstractTask(org.jlibsedml.AbstractTask)
FileWriter(java.io.FileWriter)
Element(org.jdom.Element)
StlReader(cbit.vcell.geometry.surface.StlReader)
FileReader(java.io.FileReader)
ImageDatasetReader(org.vcell.vcellij.ImageDatasetReader)
Reader(java.io.Reader)
BufferedReader(java.io.BufferedReader)
ArchiveComponents(org.jlibsedml.ArchiveComponents)
ProgrammingException(org.vcell.util.ProgrammingException)
Structure(cbit.vcell.model.Structure)
Hashtable(java.util.Hashtable)
BNGLUnitsPanel(org.vcell.model.bngl.gui.BNGLUnitsPanel)
BioModelInfo(org.vcell.util.document.BioModelInfo)
IOException(java.io.IOException)
MathModelInfo(org.vcell.util.document.MathModelInfo)
SimulationContext(cbit.vcell.mapping.SimulationContext)
ProgrammingException(org.vcell.util.ProgrammingException)
GeometryException(cbit.vcell.geometry.GeometryException)
IOException(java.io.IOException)
DataAccessException(org.vcell.util.DataAccessException)
PropertyVetoException(java.beans.PropertyVetoException)
ImageException(cbit.image.ImageException)
UtilCancelException(org.vcell.util.UtilCancelException)
DataFormatException(java.util.zip.DataFormatException)
UserCancelException(org.vcell.util.UserCancelException)
VCDocumentInfo(org.vcell.util.document.VCDocumentInfo)
Expression(cbit.vcell.parser.Expression)
BioModel(cbit.vcell.biomodel.BioModel)
XMLSource(cbit.vcell.xml.XMLSource)
Element(org.jdom.Element)
ASTModel(org.vcell.model.bngl.ASTModel)
Example 2 with RbmModelContainer
use of cbit.vcell.model.Model.RbmModelContainer in project vcell by virtualcell.
the class XmlReader method getRbmMolecularTypePattern.
private MolecularTypePattern getRbmMolecularTypePattern(Element e, Model newModel) {
RbmModelContainer mc = newModel.getRbmModelContainer();
Element e1 = e.getChild(XMLTags.RbmMolecularTypeTag, vcNamespace);
String molecularTypeName = e1.getAttributeValue(XMLTags.NameAttrTag);
MolecularType mt = mc.getMolecularType(molecularTypeName);
if (mt == null) {
System.out.println("XMLReader: getRbmMolecularTypePattern: encountered reference to non-existing MolecularType.");
return null;
}
// we insert the component patterns below
MolecularTypePattern tp = new MolecularTypePattern(mt, false);
String index = e.getAttributeValue(XMLTags.RbmIndexAttrTag);
if (index != null && !index.isEmpty()) {
tp.setIndex(Integer.parseInt(index));
}
String match = e.getAttributeValue(XMLTags.RbmParticipantPatternMatchTag);
if (match != null && !match.isEmpty()) {
tp.setParticipantMatchLabel(match);
}
List<MolecularComponentPattern> cpl = new ArrayList<MolecularComponentPattern>();
List<Element> children = e.getChildren(XMLTags.RbmMolecularComponentPatternTag, vcNamespace);
for (Element e2 : children) {
MolecularComponentPattern cp = getRbmMolecularComponentPattern(e2, tp, mt, newModel);
if (cp != null) {
cpl.add(cp);
}
}
tp.setComponentPatterns(cpl);
return tp;
}
Also used :
ParticleMolecularType(cbit.vcell.math.ParticleMolecularType)
MolecularType(org.vcell.model.rbm.MolecularType)
RbmModelContainer(cbit.vcell.model.Model.RbmModelContainer)
ParticleMolecularComponentPattern(cbit.vcell.math.ParticleMolecularComponentPattern)
MolecularComponentPattern(org.vcell.model.rbm.MolecularComponentPattern)
Element(org.jdom.Element)
ArrayList(java.util.ArrayList)
ParticleMolecularTypePattern(cbit.vcell.math.ParticleMolecularTypePattern)
MolecularTypePattern(org.vcell.model.rbm.MolecularTypePattern)
Example 3 with RbmModelContainer
use of cbit.vcell.model.Model.RbmModelContainer in project vcell by virtualcell.
the class RbmNetworkGenerator method writeBngl.
/*
* Used for exporting to file with extension .bngl
*/
public static void writeBngl(SimulationContext simulationContext, PrintWriter writer, // if true, we cheat and transform all functions into constant parameters (always false)
boolean ignoreFunctions, boolean applyApplicationFilters) {
// if true, we only export those functions enabled in the Application / Specifications / Reaction tab
Model model = simulationContext.getModel();
RbmModelContainer rbmModelContainer = model.getRbmModelContainer();
checkConsistency(model);
writer.println(BEGIN_MODEL);
writer.println();
RbmNetworkGenerator.writeCompartments(writer, model, simulationContext);
RbmNetworkGenerator.writeParameters(writer, rbmModelContainer, ignoreFunctions);
RbmNetworkGenerator.writeMolecularTypes(writer, model, CompartmentMode.show);
RbmNetworkGenerator.writeSpecies(writer, model, simulationContext, CompartmentMode.show);
RbmNetworkGenerator.writeObservables(writer, rbmModelContainer, CompartmentMode.show);
RbmNetworkGenerator.writeFunctions(writer, rbmModelContainer, ignoreFunctions);
RbmNetworkGenerator.writeReactions(writer, rbmModelContainer, null, applyApplicationFilters, CompartmentMode.show);
writer.println(END_MODEL);
writer.println();
RbmNetworkGenerator.writeNetworkConstraints(writer, rbmModelContainer, simulationContext, NetworkGenerationRequirements.ComputeFullStandardTimeout);
writer.println();
}
Also used :
RbmModelContainer(cbit.vcell.model.Model.RbmModelContainer)
BioModel(cbit.vcell.biomodel.BioModel)
Model(cbit.vcell.model.Model)
Example 4 with RbmModelContainer
use of cbit.vcell.model.Model.RbmModelContainer in project vcell by virtualcell.
the class RbmNetworkGenerator method writeMolecularTypes.
public static void writeMolecularTypes(PrintWriter writer, Model model, CompartmentMode compartmentMode) {
boolean hasAnchors = false;
writer.println(BEGIN_MOLECULE_TYPES);
RbmModelContainer rbmModelContainer = model.getRbmModelContainer();
List<MolecularType> molList = rbmModelContainer.getMolecularTypeList();
for (MolecularType mt : molList) {
if (!mt.isAnchorAll()) {
hasAnchors = true;
}
writer.println(RbmUtils.toBnglString(mt, model, compartmentMode));
}
writer.println(END_MOLECULE_TYPES);
writer.println();
// don't write the anchors if the compartments are not properly represented
if (hasAnchors && compartmentMode == CompartmentMode.show) {
writer.println(BEGIN_ANCHORS);
for (MolecularType mt : molList) {
if (!mt.isAnchorAll()) {
writer.println(RbmUtils.anchorToBnglString(mt));
}
}
writer.println(END_ANCHORS);
writer.println();
}
}
Also used :
RbmModelContainer(cbit.vcell.model.Model.RbmModelContainer)
Example 5 with RbmModelContainer
use of cbit.vcell.model.Model.RbmModelContainer in project vcell by virtualcell.
the class XmlReader method getRbmMolecularComponentPattern.
private MolecularComponentPattern getRbmMolecularComponentPattern(Element e, MolecularTypePattern mtp, MolecularType mt, Model newModel) {
RbmModelContainer mc = newModel.getRbmModelContainer();
String s = e.getAttributeValue(XMLTags.RbmMolecularComponentTag);
if (s == null || s.isEmpty()) {
System.out.println("XMLReader: getRbmMolecularComponentPattern: MolecularComponent name is missing.");
return null;
}
MolecularComponent c = mt.getMolecularComponent(s);
if (c == null) {
System.out.println("XMLReader: getRbmMolecularComponentPattern: encountered reference " + s + " to non-existing MolecularComponent.");
return null;
}
ComponentStatePattern csp = new ComponentStatePattern();
MolecularComponentPattern mcp = new MolecularComponentPattern(c);
s = e.getAttributeValue(XMLTags.RbmMolecularComponentStatePatternTag);
if (s != null && !s.isEmpty()) {
// state may be missing, we set it only if is present
ComponentStateDefinition cs = c.getComponentStateDefinition(s);
if (cs == null) {
System.out.println("XMLReader: getRbmMolecularComponentPattern: encountered reference " + s + " to non-existing MolecularComponentState.");
return null;
}
csp = new ComponentStatePattern(cs);
mcp.setComponentStatePattern(csp);
}
// s = e.getAttributeValue(XMLTags.RbmMolecularTypeAnyTag);
// if(s!=null && !s.isEmpty()) {
// boolean any = Boolean.parseBoolean(s);
// csp.setAny(any);
// }
s = e.getAttributeValue(XMLTags.RbmBondTypeAttrTag);
BondType bondType = BondType.fromSymbol(s);
if (bondType == BondType.Specified) {
int bondId = Integer.parseInt(s);
mcp.setBondId(bondId);
}
mcp.setBondType(bondType);
// sanity check, we only read the names here and make sure they make sense
Element bondElement = e.getChild(XMLTags.RbmBondTag, vcNamespace);
if (bondElement != null) {
// it's actually the name of the MolecularType inside this pattern
String molecularTypeName = bondElement.getAttributeValue(XMLTags.RbmMolecularTypePatternTag);
String molecularComponentName = bondElement.getAttributeValue(XMLTags.RbmMolecularComponentPatternTag);
if (molecularTypeName == null || molecularTypeName.isEmpty()) {
System.out.println("XMLReader: getRbmMolecularComponentPattern: Bond Attribute molecularTypeName missing.");
return mcp;
}
if (molecularComponentName == null || molecularComponentName.isEmpty()) {
System.out.println("XMLReader: getRbmMolecularComponentPattern: Bond Attribute molecularComponentName missing.");
return mcp;
}
// we'll have a bond here, it will be properly initialized during RbmObservable.resolveBonds() call !!!
Bond bond = new Bond();
mcp.setBond(bond);
}
return mcp;
}
Also used :
BondType(org.vcell.model.rbm.MolecularComponentPattern.BondType)
ParticleBondType(cbit.vcell.math.ParticleMolecularComponentPattern.ParticleBondType)
RbmModelContainer(cbit.vcell.model.Model.RbmModelContainer)
ParticleMolecularComponent(cbit.vcell.math.ParticleMolecularComponent)
MolecularComponent(org.vcell.model.rbm.MolecularComponent)
ParticleMolecularComponentPattern(cbit.vcell.math.ParticleMolecularComponentPattern)
MolecularComponentPattern(org.vcell.model.rbm.MolecularComponentPattern)
ParticleComponentStatePattern(cbit.vcell.math.ParticleComponentStatePattern)
ComponentStatePattern(org.vcell.model.rbm.ComponentStatePattern)
Element(org.jdom.Element)
Bond(org.vcell.model.rbm.SpeciesPattern.Bond)
ParticleComponentStateDefinition(cbit.vcell.math.ParticleComponentStateDefinition)
ComponentStateDefinition(org.vcell.model.rbm.ComponentStateDefinition)
Aggregations
RbmModelContainer (cbit.vcell.model.Model.RbmModelContainer)26
MolecularType (org.vcell.model.rbm.MolecularType)12
Element (org.jdom.Element)10
BioModel (cbit.vcell.biomodel.BioModel)9
ArrayList (java.util.ArrayList)9
Model (cbit.vcell.model.Model)8
ReactionRule (cbit.vcell.model.ReactionRule)7
SimulationContext (cbit.vcell.mapping.SimulationContext)5
RbmObservable (cbit.vcell.model.RbmObservable)5
ReactionStep (cbit.vcell.model.ReactionStep)5
Structure (cbit.vcell.model.Structure)5
SpeciesContextSpec (cbit.vcell.mapping.SpeciesContextSpec)4
ParticleMolecularType (cbit.vcell.math.ParticleMolecularType)4
SpeciesContext (cbit.vcell.model.SpeciesContext)4
MathModel (cbit.vcell.mathmodel.MathModel)3
Expression (cbit.vcell.parser.Expression)3
SpeciesPattern (org.vcell.model.rbm.SpeciesPattern)3
Geometry (cbit.vcell.geometry.Geometry)2
BioEvent (cbit.vcell.mapping.BioEvent)2
GeometryContext (cbit.vcell.mapping.GeometryContext)2
