Examples with BioModelWindowManager cbit.vcell.client.BioModelWindowManager used on opensource projects

Example 1 with BioModelWindowManager

use of cbit.vcell.client.BioModelWindowManager in project vcell by virtualcell.

the class NetworkFreePanel method createModel.

private void createModel() {
    DocumentWindow dw = (DocumentWindow) BeanUtils.findTypeParentOfComponent(this, DocumentWindow.class);
    BioModelWindowManager bmwm = (BioModelWindowManager) (dw.getTopLevelWindowManager());
    RequestManager rm = dw.getTopLevelWindowManager().getRequestManager();
    rm.createBioModelFromApplication(bmwm, "Test", fieldSimulationContext);
}

Example 2 with BioModelWindowManager

use of cbit.vcell.client.BioModelWindowManager in project vcell by virtualcell.

the class ApplicationSimulationsPanel method setBioModelWindowManager.

@Override
public void setBioModelWindowManager(BioModelWindowManager newValue) {
    super.setBioModelWindowManager(newValue);
    BioModelWindowManager oldValue = bioModelWindowManager;
    if (oldValue != null) {
        mathematicsPanel.removeActionListener(bioModelWindowManager);
    }
    bioModelWindowManager = newValue;
    if (newValue != null) {
        mathematicsPanel.addActionListener(newValue);
    }
}

Example 3 with BioModelWindowManager

use of cbit.vcell.client.BioModelWindowManager in project vcell by virtualcell.

the class NetworkConstraintsPanel method createModel.

private void createModel() {
    if (!checkBnglRequirements()) {
        return;
    }
    DocumentWindow dw = (DocumentWindow) BeanUtils.findTypeParentOfComponent(this, DocumentWindow.class);
    BioModelWindowManager bmwm = (BioModelWindowManager) (dw.getTopLevelWindowManager());
    RequestManager rm = dw.getTopLevelWindowManager().getRequestManager();
    rm.createBioModelFromApplication(bmwm, "Test", fieldSimulationContext);
}

Example 4 with BioModelWindowManager

use of cbit.vcell.client.BioModelWindowManager in project vcell by virtualcell.

the class VCellClientDataServiceImpl method getSimsFromOpenModels.

@Override
public List<SimulationDataSetRef> getSimsFromOpenModels() {
    ArrayList<SimulationDataSetRef> simulationDataSetRefs = new ArrayList<SimulationDataSetRef>();
    for (TopLevelWindowManager windowManager : vcellClient.getMdiManager().getWindowManagers()) {
        Simulation[] simulations = null;
        VCDocument modelDocument = null;
        if (windowManager instanceof BioModelWindowManager) {
            BioModelWindowManager selectedBioWindowManager = (BioModelWindowManager) windowManager;
            BioModel bioModel = selectedBioWindowManager.getBioModel();
            simulations = bioModel.getSimulations();
            modelDocument = bioModel;
        // simOwnerCount = bioModel.getNumSimulationContexts();
        } else if (windowManager instanceof MathModelWindowManager) {
            MathModelWindowManager selectedMathWindowManager = (MathModelWindowManager) windowManager;
            MathModel mathModel = selectedMathWindowManager.getMathModel();
            simulations = mathModel.getSimulations();
            modelDocument = mathModel;
        // simOwnerCount = 1;
        }
        if (simulations != null) {
            for (Simulation simulation : simulations) {
                if (!isVtkSupported(simulation)) {
                    continue;
                }
                Origin origin = simulation.getMathDescription().getGeometry().getOrigin();
                Extent extent = simulation.getMathDescription().getGeometry().getExtent();
                SimulationInfo simInfo = simulation.getSimulationInfo();
                SimulationStatus simStatus = vcellClient.getRequestManager().getServerSimulationStatus(simInfo);
                for (int jobIndex = 0; jobIndex < simulation.getScanCount(); jobIndex++) {
                    if (simStatus != null && simStatus.getHasData()) {
                        SimulationDataSetRef simulationDataSetReference = VCellClientDataServiceImpl.createSimulationDataSetRef(simulation, modelDocument, jobIndex, false);
                        simulationDataSetRefs.add(simulationDataSetReference);
                    }
                }
            }
        }
    }
    File localSimDir = ResourceUtil.getLocalSimDir(User.tempUser.getName());
    String[] simtaskFilenames = localSimDir.list((dir, name) -> (name.endsWith(".simtask.xml")));
    for (String simtaskFilename : simtaskFilenames) {
        try {
            SimulationTask simTask = XmlHelper.XMLToSimTask(org.apache.commons.io.FileUtils.readFileToString(new File(localSimDir, simtaskFilename)));
            VCDocument modelDocument = null;
            SimulationDataSetRef simulationDataSetReference = VCellClientDataServiceImpl.createSimulationDataSetRef(simTask.getSimulation(), modelDocument, simTask.getSimulationJob().getJobIndex(), true);
            simulationDataSetRefs.add(simulationDataSetReference);
        } catch (ExpressionException | XmlParseException | IOException e) {
            e.printStackTrace();
        }
    }
    return simulationDataSetRefs;
}

Example 5 with BioModelWindowManager

use of cbit.vcell.client.BioModelWindowManager in project vcell by virtualcell.

the class DocumentWindow method getJMenuItemMIRIAM.

/**
 * This method initializes jMenuItemMIRIAM
 *
 * @return javax.swing.JMenuItem
 */
private JMenuItem getJMenuItemMIRIAM() {
    if (jMenuItemMIRIAM == null) {
        jMenuItemMIRIAM = new JMenuItem();
        jMenuItemMIRIAM.setText("Model Annotation ...");
        jMenuItemMIRIAM.addActionListener(new java.awt.event.ActionListener() {

            public void actionPerformed(java.awt.event.ActionEvent e) {
                if (getTopLevelWindowManager() instanceof BioModelWindowManager) {
                    ((BioModelWindowManager) getTopLevelWindowManager()).showMIRIAMWindow();
                } else {
                    PopupGenerator.showInfoDialog(DocumentWindow.this, "Sorry, Currently only BioModels have a MIRIAM editor.");
                }
            }
        });
    }
    return jMenuItemMIRIAM;
}