use of cbit.vcell.modelopt.ParameterEstimationTask in project vcell by virtualcell.
the class ParameterMappingPanel method setParameterEstimationTask.
/**
* Sets the parameterEstimationTask property (cbit.vcell.modelopt.ParameterEstimationTask) value.
* @param parameterEstimationTask The new value for the property.
* @see #getParameterEstimationTask
*/
public void setParameterEstimationTask(ParameterEstimationTask parameterEstimationTask) {
ParameterEstimationTask oldValue = fieldParameterEstimationTask;
fieldParameterEstimationTask = parameterEstimationTask;
firePropertyChange("parameterEstimationTask", oldValue, parameterEstimationTask);
}
use of cbit.vcell.modelopt.ParameterEstimationTask 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);
}
}
use of cbit.vcell.modelopt.ParameterEstimationTask in project vcell by virtualcell.
the class ParameterEstimationPanel method analysisTaskComboBox_ActionPerformed.
private void analysisTaskComboBox_ActionPerformed() {
ParameterEstimationTask selectedItem = (ParameterEstimationTask) getAnalysisTaskComboBox().getSelectedItem();
setParameterEstimationTask(selectedItem);
setSelectedObjects(new Object[] { selectedItem });
}
use of cbit.vcell.modelopt.ParameterEstimationTask in project vcell by virtualcell.
the class ParameterEstimationPanel method onSelectedObjectsChange.
@Override
protected void onSelectedObjectsChange(Object[] selectedObjects) {
if (selectedObjects == null || selectedObjects.length != 1 || !(selectedObjects[0] instanceof ParameterEstimationTask)) {
return;
}
ParameterEstimationTask parameterEstimationTask = (ParameterEstimationTask) selectedObjects[0];
setParameterEstimationTask(parameterEstimationTask);
}
use of cbit.vcell.modelopt.ParameterEstimationTask in project vcell by virtualcell.
the class SimulationContext method createDefaultParameterEstimationTask.
public void createDefaultParameterEstimationTask() {
if (applicationType == Application.NETWORK_DETERMINISTIC && this.getGeometry().getDimension() == 0 && fieldAnalysisTasks == null) {
try {
ParameterEstimationTask peTask = new ParameterEstimationTask(this);
peTask.setName(ParameterEstimationTask.defaultTaskName);
addAnalysisTask(peTask);
} catch (Exception e) {
// if cannot create parameter estimation task, we don't want to block the vcell running.
// it will leave an empty task, which users can actually use "new" button to create parameter estimation task later.
e.printStackTrace(System.out);
}
}
}
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