Example 11 with Structure
use of cbit.vcell.model.Structure 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 12 with Structure
use of cbit.vcell.model.Structure in project vcell by virtualcell.
the class XmlReader method getRbmReactionRule.
private ReactionRule getRbmReactionRule(Element reactionRuleElement, Model newModel) throws XmlParseException {
String n = reactionRuleElement.getAttributeValue(XMLTags.NameAttrTag);
if (n == null || n.isEmpty()) {
System.out.println("XMLReader: getRbmReactionRule: name is missing.");
return null;
}
try {
boolean reversible = Boolean.valueOf(reactionRuleElement.getAttributeValue(XMLTags.RbmReactionRuleReversibleTag));
// get 1st structure if attribute missing
String structureName = reactionRuleElement.getAttributeValue(XMLTags.StructureAttrTag, newModel.getStructures()[0].getName());
Structure structure = newModel.getStructure(structureName);
ReactionRule reactionRule = new ReactionRule(newModel, n, structure, reversible);
// we ignore this, name and label are the same thing for now
String reactionRuleLabel = reactionRuleElement.getAttributeValue(XMLTags.RbmReactionRuleLabelTag);
//
// old style kinetics placed parameter values as attributes
// look for attributes named ("MassActionKf","MassActionKr","MichaelisMentenKcat","MichaelisMentenKm","SaturableKs","SaturableVmax")
String[] oldKineticsAttributes = new String[] { XMLTags.RbmMassActionKfAttrTag_DEPRECATED, XMLTags.RbmMassActionKrAttrTag_DEPRECATED, XMLTags.RbmMichaelisMentenKcatAttrTag_DEPRECATED, XMLTags.RbmMichaelisMentenKmAttrTag_DEPRECATED, XMLTags.RbmSaturableKsAttrTag_DEPRECATED, XMLTags.RbmSaturableVmaxAttrTag_DEPRECATED };
boolean bOldKineticsFound = false;
for (String oldKineticsAttribute : oldKineticsAttributes) {
if (reactionRuleElement.getAttribute(oldKineticsAttribute) != null) {
bOldKineticsFound = true;
}
}
if (bOldKineticsFound) {
readOldRbmKineticsAttributes(reactionRuleElement, reactionRule);
} else {
Element kineticsElement = reactionRuleElement.getChild(XMLTags.KineticsTag, vcNamespace);
if (kineticsElement != null) {
String kineticLawTypeString = kineticsElement.getAttributeValue(XMLTags.KineticsTypeAttrTag);
RbmKineticLaw.RateLawType rateLawType = null;
if (XMLTags.RbmKineticTypeMassAction.equals(kineticLawTypeString)) {
rateLawType = RateLawType.MassAction;
} else if (XMLTags.RbmKineticTypeMichaelisMenten.equals(kineticLawTypeString)) {
rateLawType = RateLawType.MichaelisMenten;
} else if (XMLTags.RbmKineticTypeSaturable.equals(kineticLawTypeString)) {
rateLawType = RateLawType.Saturable;
} else {
throw new RuntimeException("unexpected rate law type " + kineticLawTypeString);
}
reactionRule.setKineticLaw(new RbmKineticLaw(reactionRule, rateLawType));
List<Element> parameterElements = kineticsElement.getChildren(XMLTags.ParameterTag, vcNamespace);
HashMap<String, ParameterRoleEnum> roleHash = new HashMap<String, ParameterContext.ParameterRoleEnum>();
roleHash.put(XMLTags.RbmMassActionKfRole, RbmKineticLawParameterType.MassActionForwardRate);
roleHash.put(XMLTags.RbmMassActionKrRole, RbmKineticLawParameterType.MassActionReverseRate);
roleHash.put(XMLTags.RbmMichaelisMentenKcatRole, RbmKineticLawParameterType.MichaelisMentenKcat);
roleHash.put(XMLTags.RbmMichaelisMentenKmRole, RbmKineticLawParameterType.MichaelisMentenKm);
roleHash.put(XMLTags.RbmSaturableVmaxRole, RbmKineticLawParameterType.SaturableVmax);
roleHash.put(XMLTags.RbmSaturableKsRole, RbmKineticLawParameterType.SaturableKs);
roleHash.put(XMLTags.RbmUserDefinedRole, RbmKineticLawParameterType.UserDefined);
HashSet<String> xmlRolesToIgnore = new HashSet<String>();
xmlRolesToIgnore.add(XMLTags.RbmRuleRateRole);
ParameterContext parameterContext = reactionRule.getKineticLaw().getParameterContext();
readParameters(parameterElements, parameterContext, roleHash, RbmKineticLawParameterType.UserDefined, xmlRolesToIgnore, newModel);
}
}
Element e1 = reactionRuleElement.getChild(XMLTags.RbmReactantPatternsListTag, vcNamespace);
getRbmReactantPatternsList(e1, reactionRule, newModel);
Element e2 = reactionRuleElement.getChild(XMLTags.RbmProductPatternsListTag, vcNamespace);
getRbmProductPatternsList(e2, reactionRule, newModel);
reactionRule.checkMatchConsistency();
return reactionRule;
} catch (PropertyVetoException | ExpressionException ex) {
ex.printStackTrace(System.out);
throw new RuntimeException("failed to parse kinetics for reaction rule '" + n + "': " + ex.getMessage(), ex);
}
}
Also used :
ReactionRule(cbit.vcell.model.ReactionRule)
HashMap(java.util.HashMap)
Element(org.jdom.Element)
RbmKineticLaw(cbit.vcell.model.RbmKineticLaw)
ExpressionException(cbit.vcell.parser.ExpressionException)
PropertyVetoException(java.beans.PropertyVetoException)
ParameterContext(cbit.vcell.mapping.ParameterContext)
RateLawType(cbit.vcell.model.RbmKineticLaw.RateLawType)
Structure(cbit.vcell.model.Structure)
ParameterRoleEnum(cbit.vcell.mapping.ParameterContext.ParameterRoleEnum)
HashSet(java.util.HashSet)
Example 13 with Structure
use of cbit.vcell.model.Structure in project vcell by virtualcell.
the class XmlReader method getRbmReactantPatternsList.
private void getRbmReactantPatternsList(Element e, ReactionRule r, Model newModel) {
if (e != null) {
List<Element> rpChildren = e.getChildren(XMLTags.RbmReactantPatternTag, vcNamespace);
for (Element rpElement : rpChildren) {
Structure structure = null;
String structureName = rpElement.getAttributeValue(XMLTags.StructureAttrTag);
if (structureName == null || structureName.isEmpty()) {
// the tag is missing
throw new RuntimeException("XMLReader: structure missing for reaction rule pattern.");
} else {
structure = newModel.getStructure(structureName);
}
Element spe = rpElement.getChild(XMLTags.RbmSpeciesPatternTag, vcNamespace);
SpeciesPattern s = getSpeciesPattern(spe, newModel);
if (s != null) {
r.addReactant(new ReactantPattern(s, structure), false);
}
}
// older models have the species pattern saved directly and using the structure or the rule
List<Element> spChildren = e.getChildren(XMLTags.RbmSpeciesPatternTag, vcNamespace);
for (Element element : spChildren) {
SpeciesPattern s = getSpeciesPattern(element, newModel);
if (s != null) {
r.addReactant(new ReactantPattern(s, r.getStructure()), false);
}
}
}
}
Also used :
Element(org.jdom.Element)
Structure(cbit.vcell.model.Structure)
ParticleSpeciesPattern(cbit.vcell.math.ParticleSpeciesPattern)
VolumeParticleSpeciesPattern(cbit.vcell.math.VolumeParticleSpeciesPattern)
SpeciesPattern(org.vcell.model.rbm.SpeciesPattern)
ReactantPattern(cbit.vcell.model.ReactantPattern)
Example 14 with Structure
use of cbit.vcell.model.Structure in project vcell by virtualcell.
the class RbmUtils method findStructure.
// not used; instead of this we should recover the structure of the rule that produced this reaction
@Deprecated
public static Structure findStructure(Model model, HashMap<Integer, String> speciesMap, BNGReaction forwardBNGReaction) {
Structure ours = null;
for (int j = 0; j < forwardBNGReaction.getReactants().length; j++) {
BNGSpecies s = forwardBNGReaction.getReactants()[j];
String scName = speciesMap.get(s.getNetworkFileIndex());
SpeciesContext sc = model.getSpeciesContext(scName);
Structure theirs = sc.getStructure();
if (ours == null || ours.getDimension() > theirs.getDimension()) {
ours = theirs;
}
}
for (int j = 0; j < forwardBNGReaction.getProducts().length; j++) {
BNGSpecies s = forwardBNGReaction.getProducts()[j];
String scName = speciesMap.get(s.getNetworkFileIndex());
SpeciesContext sc = model.getSpeciesContext(scName);
Structure theirs = sc.getStructure();
if (ours == null || ours.getDimension() > theirs.getDimension()) {
ours = theirs;
}
}
if (ours == null) {
ours = model.getStructure(0);
}
return ours;
}
Also used :
SpeciesContext(cbit.vcell.model.SpeciesContext)
Structure(cbit.vcell.model.Structure)
BNGSpecies(cbit.vcell.bionetgen.BNGSpecies)
Example 15 with Structure
use of cbit.vcell.model.Structure in project vcell by virtualcell.
the class RbmUtils method anchorToBnglString.
public static String anchorToBnglString(MolecularType molecularType) {
StringBuilder buffer = new StringBuilder(molecularType.getName());
buffer.append("(");
int i = 0;
for (Structure struct : molecularType.getAnchors()) {
if (i > 0) {
buffer.append(",");
}
buffer.append(struct.getName());
i++;
}
buffer.append(")");
return buffer.toString();
}
Also used :
Structure(cbit.vcell.model.Structure)
Aggregations
Structure (cbit.vcell.model.Structure)159
SpeciesContext (cbit.vcell.model.SpeciesContext)57
Membrane (cbit.vcell.model.Membrane)47
PropertyVetoException (java.beans.PropertyVetoException)42
Feature (cbit.vcell.model.Feature)36
Model (cbit.vcell.model.Model)35
ArrayList (java.util.ArrayList)35
ReactionStep (cbit.vcell.model.ReactionStep)33
Expression (cbit.vcell.parser.Expression)33
ReactionRule (cbit.vcell.model.ReactionRule)27
ExpressionException (cbit.vcell.parser.ExpressionException)27
BioModel (cbit.vcell.biomodel.BioModel)23
StructureMapping (cbit.vcell.mapping.StructureMapping)22
SpeciesPattern (org.vcell.model.rbm.SpeciesPattern)22
Species (cbit.vcell.model.Species)21
MolecularType (org.vcell.model.rbm.MolecularType)20
ReactionParticipant (cbit.vcell.model.ReactionParticipant)19
SimpleReaction (cbit.vcell.model.SimpleReaction)19
SimulationContext (cbit.vcell.mapping.SimulationContext)18
ModelException (cbit.vcell.model.ModelException)18
