Examples with BioModel cbit.vcell.biomodel.BioModel used on opensource projects

Example 96 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class TestingFrameworkWindowManager method getDataInfoProvider.

private DataInfoProvider getDataInfoProvider(VCDocument document, PDEDataContext pdeDataContext, String refSimName) throws ObjectNotFoundException {
    SimulationWorkspaceModelInfo simulationWorkspaceModelInfo = null;
    if (document instanceof MathModel) {
        MathModel mathModel = (MathModel) document;
        Simulation[] sims = mathModel.getSimulations();
        for (int i = 0; i < sims.length; i++) {
            if (refSimName.equals(sims[i].getName())) {
                simulationWorkspaceModelInfo = new SimulationWorkspaceModelInfo(mathModel, sims[i].getName());
                break;
            }
        }
    } else {
        BioModel bioModel = (BioModel) document;
        Simulation[] sims = bioModel.getSimulations();
        for (int i = 0; i < sims.length; i++) {
            if (refSimName.equals(sims[i].getName())) {
                simulationWorkspaceModelInfo = new SimulationWorkspaceModelInfo(bioModel.getSimulationContext(sims[i]), sims[i].getName());
                break;
            }
        }
    }
    DataInfoProvider dataInfoProvider = new DataInfoProvider(pdeDataContext, simulationWorkspaceModelInfo);
    return dataInfoProvider;
}

Example 97 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class TopLevelWindowManager method prepareDocumentToLoad.

public void prepareDocumentToLoad(VCDocument doc, boolean bInNewWindow) throws Exception {
    if (doc instanceof BioModel) {
        Simulation[] simulations = ((BioModel) doc).getSimulations();
        ArrayList<VCSimulationIdentifier> simIDs = new ArrayList<VCSimulationIdentifier>();
        for (int i = 0; i < simulations.length; i++) {
            SimulationInfo simulationInfo = simulations[i].getSimulationInfo();
            if (simulationInfo != null) {
                simIDs.add(simulationInfo.getAuthoritativeVCSimulationIdentifier());
            }
        }
        RequestManager rm = getRequestManager();
        ConnectionStatus stat = rm.getConnectionStatus();
        if (stat.getStatus() == ConnectionStatus.CONNECTED) {
            rm.getDocumentManager().preloadSimulationStatus(simIDs.toArray(new VCSimulationIdentifier[0]));
        }
    } else if (doc instanceof MathModel) {
        Geometry geometry = ((MathModel) doc).getMathDescription().getGeometry();
        geometry.precomputeAll(new GeometryThumbnailImageFactoryAWT());
        Simulation[] simulations = ((MathModel) doc).getSimulations();
        // VCSimulationIdentifier simIDs[] = new VCSimulationIdentifier[simulations.length];
        ArrayList<VCSimulationIdentifier> simIDs = new ArrayList<>();
        for (int i = 0; i < simulations.length; i++) {
            if (simulations[i].getSimulationInfo() != null) {
                simIDs.add(simulations[i].getSimulationInfo().getAuthoritativeVCSimulationIdentifier());
            }
        }
        getRequestManager().getDocumentManager().preloadSimulationStatus(simIDs.toArray(new VCSimulationIdentifier[0]));
    } else if (doc instanceof Geometry) {
        ((Geometry) doc).precomputeAll(new GeometryThumbnailImageFactoryAWT());
    }
}

Example 98 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class BioModelEditorReactionTableModel method bioModelChange.

@Override
protected void bioModelChange(PropertyChangeEvent evt) {
    super.bioModelChange(evt);
    // ownerTable.getColumnModel().getColumn(COLUMN_STRUCTURE).setCellEditor(getStructureComboBoxEditor());
    // updateStructureComboBox();
    BioModel oldValue = (BioModel) evt.getOldValue();
    if (oldValue != null) {
        for (ModelProcess p : oldValue.getModel().getModelProcesses()) {
            p.removePropertyChangeListener(this);
        }
    }
    BioModel newValue = (BioModel) evt.getNewValue();
    if (newValue != null) {
        for (ModelProcess p : newValue.getModel().getModelProcesses()) {
            p.addPropertyChangeListener(this);
        }
    }
}

Example 99 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class BioModelEditorRightSidePanel method setBioModel.

public void setBioModel(BioModel newValue) {
    BioModel oldValue = bioModel;
    bioModel = newValue;
    firePropertyChange(PROPERTY_NAME_BIO_MODEL, oldValue, newValue);
}

Example 100 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class BioModelEditorRightSideTableModel method setBioModel.

public void setBioModel(BioModel newValue) {
    BioModel oldValue = bioModel;
    bioModel = newValue;
    firePropertyChange(PROPERTY_NAME_BIO_MODEL, oldValue, newValue);
}