Example 1 with VCMetaData
use of cbit.vcell.biomodel.meta.VCMetaData in project vcell by virtualcell.
the class ReactionRuleKineticsPropertiesPanel method changeFreeTextAnnotation.
private void changeFreeTextAnnotation() {
try {
if (reactionRule == null) {
return;
}
// set text from annotationTextField in free text annotation for species in vcMetaData (from model)
if (bioModel.getModel() != null && bioModel.getModel().getVcMetaData() != null) {
VCMetaData vcMetaData = bioModel.getModel().getVcMetaData();
String textAreaStr = (annotationTextArea.getText() == null || annotationTextArea.getText().length() == 0 ? null : annotationTextArea.getText());
if (!Compare.isEqualOrNull(vcMetaData.getFreeTextAnnotation(reactionRule), textAreaStr)) {
vcMetaData.setFreeTextAnnotation(reactionRule, textAreaStr);
}
}
} catch (Exception e) {
e.printStackTrace(System.out);
PopupGenerator.showErrorDialog(this, "Edit Reaction Rule Error\n" + e.getMessage(), e);
}
}
Also used :
VCMetaData(cbit.vcell.biomodel.meta.VCMetaData)
PropertyVetoException(java.beans.PropertyVetoException)
ExpressionBindingException(cbit.vcell.parser.ExpressionBindingException)
Example 2 with VCMetaData
use of cbit.vcell.biomodel.meta.VCMetaData in project vcell by virtualcell.
the class ReactionRuleKineticsPropertiesPanel method refreshInterface.
protected void refreshInterface() {
boolean bNonNullRule = reactionRule != null && bioModel != null;
annotationTextArea.setEditable(bNonNullRule);
if (bNonNullRule) {
VCMetaData vcMetaData = bioModel.getModel().getVcMetaData();
annotationTextArea.setText(vcMetaData.getFreeTextAnnotation(reactionRule));
nameTextField.setEditable(true);
nameTextField.setText(reactionRule.getName());
isReversibleCheckBox.setSelected(reactionRule.isReversible());
} else {
annotationTextArea.setText(null);
nameTextField.setEditable(false);
nameTextField.setText(null);
isReversibleCheckBox.setSelected(false);
}
listLinkedPathwayObjects();
}
Also used :
VCMetaData(cbit.vcell.biomodel.meta.VCMetaData)
Example 3 with VCMetaData
use of cbit.vcell.biomodel.meta.VCMetaData 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_MODELS = "SedMLModels";
final String BNG_UNIT_SYSTEM = "bngUnitSystem";
final String BMDB_DEFAULT_APPLICATION = "Deterministic";
/* 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);
hashTable.put("isBMDB", false);
hashTable.put("isSEDML", false);
// 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());
List<SedML> sedmls = new ArrayList<>();
sedmls.add(sedml);
hashTable.put(SEDML_MODELS, sedmls);
// 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));
List<SEDMLDocument> docs = ac.getSedmlDocuments();
List<SedML> sedmls = new ArrayList<>();
for (SEDMLDocument doc : docs) {
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());
}
sedmls.add(sedml);
}
// AbstractTask chosenTask = SEDMLChooserPanel.chooseTask(sedml, requester.getComponent(),
// file.getName());
hashTable.put(SEDML_MODELS, sedmls);
// 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;
List<VCDocument> docs = new ArrayList<>();
boolean isBMDB = false;
boolean isSEDML = false;
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);
// iterate through one or more SEDML objects
List<SedML> sedmls = (List<SedML>) hashTable.get(SEDML_MODELS);
for (SedML sedml : sedmls) {
// default to import all tasks
List<VCDocument> vcdocs = XmlHelper.sedmlToBioModel(transLogger, externalDocInfo, sedml, null, null, false);
for (VCDocument vcdoc : vcdocs) {
docs.add(vcdoc);
}
}
// treat the same since OMEX is just and archive with SED-ML file(s)
isSEDML = true;
} 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,
Element modelElement = childElementList.get(0);
// mathmodel or geometry.
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);
isBMDB = externalDocInfo.isBioModelsNet();
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)) {
// we know it is a single SedML since it is an actual XML source
List<SedML> sedmls = (List<SedML>) hashTable.get(SEDML_MODELS);
SedML sedml = sedmls.get(0);
// default to import all tasks
docs = XmlHelper.sedmlToBioModel(transLogger, externalDocInfo, sedml, null, externalDocInfo.getFile().getAbsolutePath(), false);
isSEDML = true;
} 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 && docs == 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("isBMDB", isBMDB);
hashTable.put("isSEDML", isSEDML);
if (!isSEDML) {
hashTable.put("doc", doc);
} else {
hashTable.put("docs", docs);
}
}
};
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) {
boolean isSEDML = (boolean) hashTable.get("isSEDML");
if (isSEDML) {
List<VCDocument> docs = (List<VCDocument>) hashTable.get("docs");
List<DocumentWindowManager> windowManagers = new ArrayList<DocumentWindowManager>();
for (VCDocument doc : docs) {
DocumentWindowManager windowManager = createDocumentWindowManager(doc);
getMdiManager().createNewDocumentWindow(windowManager);
windowManagers.add(windowManager);
}
hashTable.put("managers", windowManagers);
hashTable.put("docs", docs);
} else {
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);
} 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);
hashTable.put("doc", doc);
}
}
} catch (Exception ex) {
ex.printStackTrace();
// TODO: check why getMdiManager().createNewDocumentWindow(windowManager) fails sometimes
} 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 {
if (documentInfo instanceof ExternalDocInfo) {
ExternalDocInfo externalDocInfo = (ExternalDocInfo) documentInfo;
boolean isSEDML = (boolean) hashTable.get("isSEDML");
if (externalDocInfo.isBioModelsNet() || externalDocInfo.isFromXmlFile() || !isSEDML) {
DocumentWindowManager windowManager = (DocumentWindowManager) hashTable.get(WIN_MGR_KEY);
if (windowManager instanceof BioModelWindowManager) {
((BioModelWindowManager) windowManager).specialLayout();
}
}
if (isSEDML) {
List<DocumentWindowManager> windowManagers = (List<DocumentWindowManager>) hashTable.get("managers");
if (windowManagers != null) {
for (DocumentWindowManager manager : windowManagers) {
((BioModelWindowManager) manager).specialLayout();
}
}
}
}
}
};
AsynchClientTask task4 = new AsynchClientTaskFunction(ClientRequestManager::setWindowFocus, "Set window focus", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false, false);
AsynchClientTask task6 = new AsynchClientTask("Renaming, please wait...", // TASKTYPE_NONSWING_BLOCKING
AsynchClientTask.TASKTYPE_NONSWING_BLOCKING, // TASKTYPE_NONSWING_BLOCKING
false, // TASKTYPE_NONSWING_BLOCKING
false) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
VCDocument doc = (VCDocument) hashTable.get("doc");
if (!(doc instanceof BioModel)) {
return;
}
boolean isBMDB = (boolean) hashTable.get("isBMDB");
if (documentInfo instanceof ExternalDocInfo) {
if (isBMDB) {
idToNameConversion(doc);
}
}
if (isBMDB) {
BioModel bioModel = (BioModel) doc;
SimulationContext simulationContext = bioModel.getSimulationContext(0);
simulationContext.setName(BMDB_DEFAULT_APPLICATION);
MathMappingCallback callback = new MathMappingCallback() {
@Override
public void setProgressFraction(float fractionDone) {
}
@Override
public void setMessage(String message) {
}
@Override
public boolean isInterrupted() {
return false;
}
};
MathMapping mathMapping = simulationContext.createNewMathMapping(callback, NetworkGenerationRequirements.ComputeFullNoTimeout);
MathDescription mathDesc = null;
try {
mathDesc = mathMapping.getMathDescription(callback);
simulationContext.setMathDescription(mathDesc);
Simulation sim = new Simulation(mathDesc);
sim.setName(simulationContext.getBioModel().getFreeSimulationName());
simulationContext.addSimulation(sim);
bioModel.refreshDependencies();
} catch (MappingException | MathException | MatrixException | ExpressionException | ModelException e1) {
e1.printStackTrace();
}
hashTable.put("doc", doc);
}
}
};
ClientTaskDispatcher.dispatch(requester.getComponent(), hashTable, new AsynchClientTask[] { task0, task1, task6, task2, task3, task4 }, false);
}
Also used :
SetMathDescription(cbit.vcell.client.task.SetMathDescription)
MathDescription(cbit.vcell.math.MathDescription)
ArrayList(java.util.ArrayList)
UserCancelException(org.vcell.util.UserCancelException)
SpeciesContextSpec(cbit.vcell.mapping.SpeciesContextSpec)
ExpressionException(cbit.vcell.parser.ExpressionException)
MappingException(cbit.vcell.mapping.MappingException)
SedML(org.jlibsedml.SedML)
ExternalDocInfo(cbit.vcell.xml.ExternalDocInfo)
AsynchClientTaskFunction(cbit.vcell.client.task.AsynchClientTaskFunction)
MatrixException(cbit.vcell.matrix.MatrixException)
VCMetaData(cbit.vcell.biomodel.meta.VCMetaData)
BnglObjectConstructionVisitor(org.vcell.model.rbm.RbmUtils.BnglObjectConstructionVisitor)
RbmModelContainer(cbit.vcell.model.Model.RbmModelContainer)
GeometryInfo(cbit.vcell.geometry.GeometryInfo)
ArrayList(java.util.ArrayList)
List(java.util.List)
VCDocument(org.vcell.util.document.VCDocument)
MathMappingCallback(cbit.vcell.mapping.SimulationContext.MathMappingCallback)
ModelException(cbit.vcell.model.ModelException)
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)
MathMapping(cbit.vcell.mapping.MathMapping)
CSGObject(cbit.vcell.geometry.CSGObject)
ChooseFile(cbit.vcell.client.task.ChooseFile)
File(java.io.File)
AsynchClientTask(cbit.vcell.client.task.AsynchClientTask)
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)
MatrixException(cbit.vcell.matrix.MatrixException)
GeometryException(cbit.vcell.geometry.GeometryException)
IOException(java.io.IOException)
DataAccessException(org.vcell.util.DataAccessException)
MappingException(cbit.vcell.mapping.MappingException)
PropertyVetoException(java.beans.PropertyVetoException)
ImageException(cbit.image.ImageException)
UtilCancelException(org.vcell.util.UtilCancelException)
ModelException(cbit.vcell.model.ModelException)
DataFormatException(java.util.zip.DataFormatException)
ExpressionException(cbit.vcell.parser.ExpressionException)
MathException(cbit.vcell.math.MathException)
UserCancelException(org.vcell.util.UserCancelException)
Simulation(cbit.vcell.solver.Simulation)
VCDocumentInfo(org.vcell.util.document.VCDocumentInfo)
Expression(cbit.vcell.parser.Expression)
MathException(cbit.vcell.math.MathException)
BioModel(cbit.vcell.biomodel.BioModel)
XMLSource(cbit.vcell.xml.XMLSource)
Element(org.jdom.Element)
ASTModel(org.vcell.model.bngl.ASTModel)
Example 4 with VCMetaData
use of cbit.vcell.biomodel.meta.VCMetaData in project vcell by virtualcell.
the class ReactionCartoonTool method menuAction.
@Override
protected void menuAction(Shape shape, String menuAction) {
if (shape == null) {
return;
}
if (menuAction.equals(CartoonToolMiscActions.Properties.MENU_ACTION)) {
if (shape instanceof FluxReactionShape) {
// showFluxReactionPropertiesDialog((FluxReactionShape) shape);
} else if (shape instanceof SimpleReactionShape) {
// showSimpleReactionPropertiesDialog((SimpleReactionShape) shape);
} else if (shape instanceof ReactantShape) {
// Point locationOnScreen = shape.getSpaceManager().getAbsLoc();
// Point graphPaneLocation = getGraphPane().getLocationOnScreen();
// locationOnScreen.translate(graphPaneLocation.x,
// graphPaneLocation.y);
// showReactantPropertiesDialog((ReactantShape) shape,
// locationOnScreen);
} else if (shape instanceof ProductShape) {
// Point locationOnScreen = shape.getSpaceManager().getAbsLoc();
// Point graphPaneLocation = getGraphPane().getLocationOnScreen();
// locationOnScreen.translate(graphPaneLocation.x,
// graphPaneLocation.y);
// showProductPropertiesDialog((ProductShape) shape,
// locationOnScreen);
} else if (shape instanceof SpeciesContextShape) {
// showEditSpeciesDialog(getGraphPane(), getReactionCartoon()
// .getModel(), ((SpeciesContextShape) shape)
// .getSpeciesContext());
} else if (shape instanceof ReactionContainerShape) {
// ReactionContainerShape rcs = (ReactionContainerShape) shape;
// if (rcs.getStructure() instanceof Feature) {
// //
// // showFeaturePropertyDialog is invoked in two modes:
// //
// // 1) parent!=null and child==null
// // upon ok, it adds a new feature to the supplied parent.
// //
// // 2) parent==null and child!=null
// // upon ok, edits the feature name
// //
// showFeaturePropertiesDialog(getGraphPane(),
// (getReactionCartoon().getModel() == null ? null
// : getReactionCartoon().getModel()), null,
// (Feature) rcs.getStructure());
// } else if (rcs.getStructure() instanceof Membrane) {
// showMembranePropertiesDialog(getGraphPane(), (Membrane) rcs
// .getStructure());
// }
}
} else if (menuAction.equals(CartoonToolMiscActions.AddSpecies.MENU_ACTION)) {
if (shape instanceof ReactionContainerShape) {
getGraphModel().deselectShape(shape);
// showCreateSpeciesContextDialog(getGraphPane(),
// getReactionCartoon().getModel(),
// ((ReactionContainerShape) shape).getStructure(), null);
SpeciesContext speciesContext = getReactionCartoon().getModel().createSpeciesContext(((ReactionContainerShape) shape).getStructure());
getGraphModel().select(speciesContext);
}
} else if (menuAction.equals(CartoonToolEditActions.Copy.MENU_ACTION)) {
if (shape instanceof SpeciesContextShape || shape instanceof ReactionStepShape || // rule participants whose rule is not selected won't
shape instanceof RuleParticipantSignatureDiagramShape || // be copied since standalone they are meaningless
shape instanceof ReactionRuleDiagramShape) {
SpeciesContext[] spArray = getSelectedSpeciesContextArray();
ReactionStep[] rsArray = getSelectedReactionStepArray();
ReactionRule[] rrArray = getSelectedReactionRuleArray();
MolecularType[] mtArray = getSelectedMolecularTypeArray(rrArray, rsArray, spArray);
Structure[] structArray = getSelectedStructuresArray(rrArray, rsArray, spArray, mtArray);
Structure fromStruct = null;
ReactionContainerShape rcs = null;
Shape parentShape = shape.getParent();
if (parentShape instanceof ReactionContainerShape) {
rcs = (ReactionContainerShape) parentShape;
fromStruct = rcs.getStructure();
}
ReactionSpeciesCopy reactionSpeciesCopy = new ReactionSpeciesCopy(spArray, rsArray, rrArray, mtArray, fromStruct, structArray);
VCellTransferable.sendToClipboard(reactionSpeciesCopy);
}
} else if (/*menuAction.equals(CartoonToolEditActions.Paste.MENU_ACTION)
|| */
menuAction.equals(CartoonToolEditActions.PasteNew.MENU_ACTION)) {
if (shape instanceof ReactionContainerShape) {
pasteReactionsAndSpecies(getGraphPane().getRootPane(), ((ReactionContainerShape) shape).getStructure());
}
} else if (menuAction.equals(CartoonToolEditActions.Delete.MENU_ACTION)) {
try {
if (getGraphModel().getSelectedShape() instanceof ReactionContainerShape && menuAction.equals(CartoonToolEditActions.Delete.MENU_ACTION)) {
getModel().removeStructure(((ReactionContainerShape) getGraphModel().getSelectedShape()).getStructure());
return;
}
if (getSelectedReactionStepArray() != null || getSelectedSpeciesContextArray() != null) {
deleteReactionsAndSpecies(getGraphPane(), getSelectedReactionStepArray(), getSelectedSpeciesContextArray());
}
if (getSelectedReactionParticipantArray() != null && menuAction.equals(CartoonToolEditActions.Delete.MENU_ACTION)) {
ReactionParticipant[] reactionParticipantArr = getSelectedReactionParticipantArray();
if (ReactionCartoonTool.checkAllCatalyst(reactionParticipantArr)) {
DialogUtils.showWarningDialog(getGraphPane(), "Catalysts are determined automatically from the reaction kinetic expression.");
return;
}
String response = DialogUtils.showWarningDialog(getGraphPane(), "Delete " + reactionParticipantArr.length + " Reaction Stoichiometries", new String[] { RXSPECIES_DELETE, RXSPECIES_CANCEL }, RXSPECIES_CANCEL);
if (response != null && response.equals(RXSPECIES_DELETE)) {
for (int i = 0; i < reactionParticipantArr.length; i++) {
if (reactionParticipantArr[i] instanceof Catalyst) {
// Catalysts may only be deleted by editing kynetic / proxy parameters
continue;
}
ReactionStep reactionStep = reactionParticipantArr[i].getReactionStep();
reactionStep.removeReactionParticipant(reactionParticipantArr[i]);
}
}
}
} catch (UserCancelException uce) {
return;
} catch (PropertyVetoException e) {
DialogUtils.showErrorDialog(getGraphPane(), e.getMessage());
} catch (Exception e) {
DialogUtils.showErrorDialog(getGraphPane(), e.getMessage(), e);
}
} else if (menuAction.equals(CartoonToolMiscActions.SearchReactions.MENU_ACTION)) {
try {
if (shape instanceof ReactionContainerShape) {
showReactionBrowserDialog(((ReactionContainerShape) shape).getStructure(), null);
}
} catch (Exception e) {
DialogUtils.showErrorDialog(getGraphPane(), e.getMessage(), e);
}
} else if (menuAction.equals(CartoonToolSaveAsImageActions.MenuAction.MENU_ACTION)) {
try {
String resType = null;
if (shape instanceof ReactionContainerShape) {
showSaveReactionImageDialog();
}
} catch (Exception e) {
e.printStackTrace();
DialogUtils.showErrorDialog(getGraphPane(), e.getMessage(), e);
}
} else if (menuAction.equals(CartoonToolMiscActions.Annotate.MENU_ACTION)) {
if (shape instanceof ReactionStepShape) {
// MIRIAMHelper.showMIRIAMAnnotationDialog(((SimpleReactionShape)shape).getReactionStep());
// System.out.println("Menu action annotate activated...");
ReactionStep rs = ((ReactionStepShape) shape).getReactionStep();
VCMetaData vcMetaData = rs.getModel().getVcMetaData();
try {
String newAnnotation = DialogUtils.showAnnotationDialog(getGraphPane(), vcMetaData.getFreeTextAnnotation(rs));
vcMetaData.setFreeTextAnnotation(rs, newAnnotation);
} catch (UtilCancelException e) {
// Do Nothing
} catch (Throwable exc) {
exc.printStackTrace(System.out);
DialogUtils.showErrorDialog(getGraphPane(), "Failed to edit annotation!\n" + exc.getMessage(), exc);
}
}
} else {
// default action is to ignore
}
}
Also used :
ReactionSpeciesCopy(cbit.vcell.model.ReactionSpeciesCopy)
ReactionContainerShape(cbit.vcell.graph.ReactionContainerShape)
SpeciesContextShape(cbit.vcell.graph.SpeciesContextShape)
RubberBandRectShape(cbit.gui.graph.RubberBandRectShape)
ProductShape(cbit.vcell.graph.ProductShape)
ContainerShape(cbit.gui.graph.ContainerShape)
CatalystShape(cbit.vcell.graph.CatalystShape)
FluxReactionShape(cbit.vcell.graph.FluxReactionShape)
ContainerContainerShape(cbit.vcell.graph.ContainerContainerShape)
ReactantShape(cbit.vcell.graph.ReactantShape)
ElipseShape(cbit.gui.graph.ElipseShape)
SimpleReactionShape(cbit.vcell.graph.SimpleReactionShape)
ReactionStepShape(cbit.vcell.graph.ReactionStepShape)
ReactionContainerShape(cbit.vcell.graph.ReactionContainerShape)
Shape(cbit.gui.graph.Shape)
RuleParticipantSignatureDiagramShape(cbit.vcell.graph.RuleParticipantSignatureDiagramShape)
ReactionRuleDiagramShape(cbit.vcell.graph.ReactionRuleDiagramShape)
RubberBandEdgeShape(cbit.gui.graph.RubberBandEdgeShape)
ReactionParticipantShape(cbit.vcell.graph.ReactionParticipantShape)
ProductShape(cbit.vcell.graph.ProductShape)
UserCancelException(org.vcell.util.UserCancelException)
SimpleReactionShape(cbit.vcell.graph.SimpleReactionShape)
ReactantShape(cbit.vcell.graph.ReactantShape)
SpeciesContext(cbit.vcell.model.SpeciesContext)
VCMetaData(cbit.vcell.biomodel.meta.VCMetaData)
Structure(cbit.vcell.model.Structure)
UtilCancelException(org.vcell.util.UtilCancelException)
ReactionRule(cbit.vcell.model.ReactionRule)
SpeciesContextShape(cbit.vcell.graph.SpeciesContextShape)
ReactionRuleDiagramShape(cbit.vcell.graph.ReactionRuleDiagramShape)
ReactionStepShape(cbit.vcell.graph.ReactionStepShape)
Point(java.awt.Point)
PropertyVetoException(java.beans.PropertyVetoException)
UtilCancelException(org.vcell.util.UtilCancelException)
ExpressionException(cbit.vcell.parser.ExpressionException)
UserCancelException(org.vcell.util.UserCancelException)
FluxReactionShape(cbit.vcell.graph.FluxReactionShape)
MolecularType(org.vcell.model.rbm.MolecularType)
PropertyVetoException(java.beans.PropertyVetoException)
ReactionStep(cbit.vcell.model.ReactionStep)
RuleParticipantSignatureDiagramShape(cbit.vcell.graph.RuleParticipantSignatureDiagramShape)
ReactionParticipant(cbit.vcell.model.ReactionParticipant)
Catalyst(cbit.vcell.model.Catalyst)
Example 5 with VCMetaData
use of cbit.vcell.biomodel.meta.VCMetaData in project vcell by virtualcell.
the class BioModelEditor method setRightBottomPanelOnSelection.
@Override
protected void setRightBottomPanelOnSelection(Object[] selections) {
if (selections == null) {
return;
}
// TODO: here
JComponent bottomComponent = rightBottomEmptyPanel;
JComponent annotationComponent = rightBottomEmptyAnnotationsPanel;
// properties panel
int destComponentIndex = DocumentEditorTabID.object_properties.ordinal();
// annotations panel
int annComponentIndex = DocumentEditorTabID.annotations.ordinal();
boolean bShowInDatabaseProperties = false;
boolean bShowPathway = false;
if (selections.length == 1) {
annotationComponent = getAnnotationsPanel();
Object singleSelection = selections[0];
if (singleSelection instanceof ReactionStep) {
bottomComponent = getReactionPropertiesPanel();
} else if (singleSelection instanceof ReactionRule) {
bottomComponent = getReactionRulePropertiesPanel();
} else if (singleSelection instanceof SpeciesContext) {
bottomComponent = getSpeciesPropertiesPanel();
} else if (singleSelection instanceof MolecularType) {
bottomComponent = getMolecularTypePropertiesPanel();
} else if (singleSelection instanceof RbmObservable) {
bottomComponent = getObservablePropertiesPanel();
} else if (singleSelection instanceof Structure) {
bottomComponent = getStructurePropertiesPanel();
getStructurePropertiesPanel().setModel(bioModel.getModel());
} else if (singleSelection instanceof Parameter) {
bottomComponent = getParameterPropertiesPanel();
} else if (singleSelection instanceof SimulationContext) {
bottomComponent = getApplicationPropertiesPanel();
} else if (singleSelection instanceof ParameterEstimationTask) {
bottomComponent = parameterEstimationTaskPropertiesPanel;
} else if (singleSelection instanceof Product || singleSelection instanceof Reactant) {
bottomComponent = getReactionParticipantPropertiesPanel();
} else if (singleSelection instanceof BioModelNode.PublicationInfoNode) {
bShowInDatabaseProperties = true;
bottomComponent = bioModelMetaDataPanel;
} else if (singleSelection instanceof BioModelInfo) {
bShowInDatabaseProperties = true;
bottomComponent = bioModelMetaDataPanel;
} else if (singleSelection instanceof MathModelInfo) {
bShowInDatabaseProperties = true;
bottomComponent = mathModelMetaDataPanel;
} else if (singleSelection instanceof GeometryInfo) {
bShowInDatabaseProperties = true;
bottomComponent = geometryMetaDataPanel;
} else if (singleSelection instanceof SpeciesContextSpec) {
bottomComponent = getSpeciesContextSpecPanel();
} else if (singleSelection instanceof ReactionSpec) {
bottomComponent = getKineticsTypeTemplatePanel();
} else if (singleSelection instanceof ReactionRuleSpec) {
//
bottomComponent = getReactionRuleSpecPropertiesPanel();
} else if (singleSelection instanceof BioModelsNetModelInfo) {
bShowInDatabaseProperties = true;
bottomComponent = getBioModelsNetPropertiesPanel();
} else if (singleSelection instanceof Simulation) {
bottomComponent = getSimulationSummaryPanel();
} else if (singleSelection instanceof DataSymbol) {
bottomComponent = getDataSymbolsSpecPanel();
} else if (singleSelection instanceof BioEvent) {
bottomComponent = getEventPanel();
} else if (singleSelection instanceof SpatialObject) {
bottomComponent = getSpatialObjectPropertyPanel();
} else if (singleSelection instanceof SpatialProcess) {
bottomComponent = getSpatialProcessPropertyPanel();
} else if (singleSelection instanceof BioPaxObject) {
bottomComponent = bioPaxObjectPropertiesPanel;
} else if (singleSelection instanceof BioModel) {
// only contains Notes, is displayed in the Object Properties Panel
bottomComponent = bioModelEditorAnnotationPanel;
} else if (singleSelection instanceof VCMetaData) {
bottomComponent = bioModelEditorAnnotationPanel;
} else if (singleSelection instanceof PathwayData) {
bShowPathway = true;
bottomComponent = getBioModelEditorPathwayPanel();
} else if (singleSelection instanceof Model) {
} else if (singleSelection instanceof RuleParticipantSignature) {
bottomComponent = getReactionRuleParticipantSignaturePropertiesPanel();
} else if (singleSelection instanceof CSGObject) {
bottomComponent = csgObjectPropertiesPanel;
csgObjectPropertiesPanel.setSimulationContext(getSelectedSimulationContext());
} else if (singleSelection instanceof DocumentEditorTreeFolderNode) {
DocumentEditorTreeFolderClass folderClass = ((DocumentEditorTreeFolderNode) singleSelection).getFolderClass();
if ((folderClass == DocumentEditorTreeFolderClass.REACTIONS_NODE) && !(singleSelection instanceof ReactionRule)) {
bottomComponent = getReactionPropertiesPanel();
} else if ((folderClass == DocumentEditorTreeFolderClass.REACTIONS_NODE) && (singleSelection instanceof ReactionRule)) {
bottomComponent = getReactionRulePropertiesPanel();
} else if (folderClass == DocumentEditorTreeFolderClass.STRUCTURES_NODE) {
bottomComponent = getStructurePropertiesPanel();
} else if (folderClass == DocumentEditorTreeFolderClass.SPECIES_NODE) {
bottomComponent = getSpeciesPropertiesPanel();
} else if (folderClass == DocumentEditorTreeFolderClass.MOLECULAR_TYPES_NODE) {
bottomComponent = getMolecularTypePropertiesPanel();
} else if (folderClass == DocumentEditorTreeFolderClass.OBSERVABLES_NODE) {
bottomComponent = getObservablePropertiesPanel();
} else if (folderClass == DocumentEditorTreeFolderClass.APPLICATIONS_NODE) {
bottomComponent = getApplicationsPropertiesPanel();
getApplicationsPropertiesPanel().setBioModel(bioModel);
} else if (folderClass == DocumentEditorTreeFolderClass.PARAMETER_ESTIMATION_NODE) {
bottomComponent = parameterEstimationTaskPropertiesPanel;
}
} else if (singleSelection instanceof SelectionManager.AnnotationNavigator) {
Object entity = ((SelectionManager.AnnotationNavigator) singleSelection).getEntity();
if (entity instanceof ReactionStep) {
bottomComponent = getReactionPropertiesPanel();
} else if (entity instanceof SpeciesContext) {
bottomComponent = getSpeciesPropertiesPanel();
} else if (entity instanceof Structure) {
// Observables. MolecularType, Structures
bottomComponent = getStructurePropertiesPanel();
} else if (entity instanceof MolecularType) {
bottomComponent = getMolecularTypePropertiesPanel();
} else if (entity instanceof RbmObservable) {
bottomComponent = getObservablePropertiesPanel();
} else {
bottomComponent = bioModelEditorAnnotationPanel;
}
}
}
if (bShowPathway) {
int numTabs = rightBottomTabbedPane.getTabCount();
for (destComponentIndex = 0; destComponentIndex < numTabs; destComponentIndex++) {
Component current = rightBottomTabbedPane.getComponentAt(destComponentIndex);
if (current == bottomComponent) {
break;
}
}
String tabTitle = "Pathway Preview";
if (rightBottomTabbedPane.getTabCount() == destComponentIndex) {
rightBottomTabbedPane.addTab(tabTitle, new TabCloseIcon(), bottomComponent);
}
} else if (bShowInDatabaseProperties) {
for (destComponentIndex = 0; destComponentIndex < rightBottomTabbedPane.getTabCount(); destComponentIndex++) {
Component c = rightBottomTabbedPane.getComponentAt(destComponentIndex);
if (c == bioModelMetaDataPanel || c == mathModelMetaDataPanel || c == geometryMetaDataPanel || c == getBioModelsNetPropertiesPanel()) {
break;
}
}
if (rightBottomTabbedPane.getTabCount() == destComponentIndex) {
rightBottomTabbedPane.addTab(DATABASE_PROPERTIES_TAB_TITLE, new TabCloseIcon(), bottomComponent);
}
}
if (rightBottomTabbedPane.getComponentAt(destComponentIndex) != bottomComponent) {
bottomComponent.setBorder(GuiConstants.TAB_PANEL_BORDER);
annotationComponent.setBorder(GuiConstants.TAB_PANEL_BORDER);
rightBottomTabbedPane.setComponentAt(destComponentIndex, bottomComponent);
rightBottomTabbedPane.setComponentAt(annComponentIndex, annotationComponent);
rightSplitPane.repaint();
}
Component selectedComponent = rightBottomTabbedPane.getSelectedComponent();
if (selections.length == 1 && selections[0] instanceof BioModel && bottomComponent instanceof BioModelEditorAnnotationPanel) {
// if the biomodel name is selected in the upper left tree, we select the Annotations tab
rightBottomTabbedPane.setSelectedComponent(annotationComponent);
} else if (selections.length == 1 && selections[0] instanceof SelectionManager.AnnotationNavigator && selections[0] instanceof SelectionManager.AnnotationNavigator) {
// we want to navigate to the AnnotationPanel
rightBottomTabbedPane.setSelectedComponent(annotationComponent);
// } else if(selections.length == 1 && selections[0] instanceof SelectionManager.AnnotationNavigator && bottomComponent instanceof BioModelEditorAnnotationPanel) {
// // we want to navigate to the AnnotationPanel (old way)
// rightBottomTabbedPane.setSelectedComponent(annotationComponent);
} else if (selectedComponent != bottomComponent) /* && rightBottomTabbedPane.getSelectedComponent() != annotationComponent */
{
rightBottomTabbedPane.setSelectedComponent(bottomComponent);
}
}
Also used :
RuleParticipantSignature(cbit.vcell.model.RuleParticipantSignature)
BioPaxObject(org.vcell.pathway.BioPaxObject)
Product(cbit.vcell.model.Product)
PathwayData(cbit.vcell.client.desktop.biomodel.BioModelEditorPathwayCommonsPanel.PathwayData)
SpeciesContext(cbit.vcell.model.SpeciesContext)
SpeciesContextSpec(cbit.vcell.mapping.SpeciesContextSpec)
Reactant(cbit.vcell.model.Reactant)
SpatialObject(cbit.vcell.mapping.spatial.SpatialObject)
VCMetaData(cbit.vcell.biomodel.meta.VCMetaData)
SpatialProcess(cbit.vcell.mapping.spatial.processes.SpatialProcess)
GeometryInfo(cbit.vcell.geometry.GeometryInfo)
Structure(cbit.vcell.model.Structure)
CSGObject(cbit.vcell.geometry.CSGObject)
Component(java.awt.Component)
JComponent(javax.swing.JComponent)
PublicationInfoNode(cbit.vcell.desktop.BioModelNode.PublicationInfoNode)
ReactionRule(cbit.vcell.model.ReactionRule)
ReactionSpec(cbit.vcell.mapping.ReactionSpec)
ReactionRuleSpec(cbit.vcell.mapping.ReactionRuleSpec)
RbmObservable(cbit.vcell.model.RbmObservable)
JComponent(javax.swing.JComponent)
BioModelInfo(org.vcell.util.document.BioModelInfo)
DocumentEditorTreeFolderNode(cbit.vcell.client.desktop.biomodel.DocumentEditorTreeModel.DocumentEditorTreeFolderNode)
MathModelInfo(org.vcell.util.document.MathModelInfo)
SimulationContext(cbit.vcell.mapping.SimulationContext)
DocumentEditorTreeFolderClass(cbit.vcell.client.desktop.biomodel.DocumentEditorTreeModel.DocumentEditorTreeFolderClass)
MolecularType(org.vcell.model.rbm.MolecularType)
ParameterEstimationTask(cbit.vcell.modelopt.ParameterEstimationTask)
DataSymbol(cbit.vcell.data.DataSymbol)
Simulation(cbit.vcell.solver.Simulation)
ReactionStep(cbit.vcell.model.ReactionStep)
BioModel(cbit.vcell.biomodel.BioModel)
Model(cbit.vcell.model.Model)
ListSelectionModel(javax.swing.ListSelectionModel)
BioModel(cbit.vcell.biomodel.BioModel)
Parameter(cbit.vcell.model.Parameter)
BioPaxObject(org.vcell.pathway.BioPaxObject)
SpatialObject(cbit.vcell.mapping.spatial.SpatialObject)
CSGObject(cbit.vcell.geometry.CSGObject)
BioEvent(cbit.vcell.mapping.BioEvent)
Aggregations
VCMetaData (cbit.vcell.biomodel.meta.VCMetaData)21
PropertyVetoException (java.beans.PropertyVetoException)10
BioModel (cbit.vcell.biomodel.BioModel)5
SimulationContext (cbit.vcell.mapping.SimulationContext)4
Structure (cbit.vcell.model.Structure)4
ExpressionException (cbit.vcell.parser.ExpressionException)4
MiriamResource (cbit.vcell.biomodel.meta.MiriamManager.MiriamResource)3
Model (cbit.vcell.model.Model)3
ReactionStep (cbit.vcell.model.ReactionStep)3
Simulation (cbit.vcell.solver.Simulation)3
IOException (java.io.IOException)3
MolecularType (org.vcell.model.rbm.MolecularType)3
MiriamManager (cbit.vcell.biomodel.meta.MiriamManager)2
DocumentEditorTreeFolderClass (cbit.vcell.client.desktop.biomodel.DocumentEditorTreeModel.DocumentEditorTreeFolderClass)2
DocumentEditorTreeFolderNode (cbit.vcell.client.desktop.biomodel.DocumentEditorTreeModel.DocumentEditorTreeFolderNode)2
CSGObject (cbit.vcell.geometry.CSGObject)2
GeometryInfo (cbit.vcell.geometry.GeometryInfo)2
SpeciesContextSpec (cbit.vcell.mapping.SpeciesContextSpec)2
Catalyst (cbit.vcell.model.Catalyst)2
ReactionParticipant (cbit.vcell.model.ReactionParticipant)2
