Examples with BioModelInfo org.vcell.util.document.BioModelInfo used on opensource projects

Example 66 with BioModelInfo

use of org.vcell.util.document.BioModelInfo in project vcell by virtualcell.

the class BioModelDbTreePanel method treeSelection.

/**
 * Comment
 */
protected void treeSelection() {
    TreePath treePath = getJTree1().getSelectionPath();
    if (treePath == null) {
        setSelectedVersionInfo(null);
        return;
    }
    BioModelNode bioModelNode = (BioModelNode) treePath.getLastPathComponent();
    Object object = bioModelNode.getUserObject();
    if (object instanceof BioModelInfo) {
        setSelectedVersionInfo((VersionInfo) object);
    } else if (object instanceof VCDocumentInfoNode && bioModelNode.getChildCount() > 0 && ((BioModelNode) bioModelNode.getChildAt(0)).getUserObject() instanceof BioModelInfo) {
        BioModelInfo bioModelInfo = (BioModelInfo) ((BioModelNode) bioModelNode.getChildAt(0)).getUserObject();
        setSelectedVersionInfo(bioModelInfo);
    } else if (object instanceof BioModelMetaData) {
        BioModelInfo bioModelInfo = (BioModelInfo) ((BioModelNode) bioModelNode.getParent()).getUserObject();
        setSelectedVersionInfo(bioModelInfo);
    } else {
        setSelectedVersionInfo(null);
    }
}

Example 67 with BioModelInfo

use of org.vcell.util.document.BioModelInfo in project vcell by virtualcell.

the class BioModelInfoTreeModel method setBioModelInfo.

/**
 * Sets the bioModelInfo property (cbit.vcell.biomodel.BioModelInfo) value.
 * @param bioModelInfo The new value for the property.
 * @see #getBioModelInfo
 */
public void setBioModelInfo(BioModelInfo bioModelInfo) {
    if (bioModelInfo == fieldBioModelInfo) {
        return;
    }
    BioModelInfo oldValue = fieldBioModelInfo;
    fieldBioModelInfo = bioModelInfo;
    firePropertyChange("bioModelInfo", oldValue, bioModelInfo);
    refreshTree();
}

Example 68 with BioModelInfo

use of org.vcell.util.document.BioModelInfo in project vcell by virtualcell.

the class ClientRequestManager method createNewDocument.

/**
 * Insert the method's description here.
 * Creation date: (5/10/2004 3:48:16 PM)
 */
public AsynchClientTask[] createNewDocument(final TopLevelWindowManager requester, final VCDocument.DocumentCreationInfo documentCreationInfo) {
    // throws UserCancelException, Exception {
    /* asynchronous and not blocking any window */
    AsynchClientTask[] taskArray = null;
    final int createOption = documentCreationInfo.getOption();
    switch(documentCreationInfo.getDocumentType()) {
        case BIOMODEL_DOC:
            {
                AsynchClientTask task1 = new AsynchClientTask("creating biomodel", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                    @Override
                    public void run(Hashtable<String, Object> hashTable) throws Exception {
                        BioModel bioModel = createDefaultBioModelDocument(null);
                        hashTable.put("doc", bioModel);
                    }
                };
                taskArray = new AsynchClientTask[] { task1 };
                break;
            }
        case MATHMODEL_DOC:
            {
                if ((createOption == VCDocument.MATH_OPTION_NONSPATIAL) || (createOption == VCDocument.MATH_OPTION_SPATIAL_EXISTS)) {
                    AsynchClientTask task2 = new AsynchClientTask("creating mathmodel", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                        @Override
                        public void run(Hashtable<String, Object> hashTable) throws Exception {
                            Geometry geometry = null;
                            if (createOption == VCDocument.MATH_OPTION_NONSPATIAL) {
                                geometry = new Geometry("Untitled", 0);
                            } else {
                                geometry = (Geometry) hashTable.get(GEOMETRY_KEY);
                            }
                            MathModel mathModel = createMathModel("Untitled", geometry);
                            mathModel.setName("MathModel" + (getMdiManager().getNumCreatedDocumentWindows() + 1));
                            hashTable.put("doc", mathModel);
                        }
                    };
                    if (createOption == VCDocument.MATH_OPTION_SPATIAL_EXISTS) {
                        AsynchClientTask task1 = createSelectDocTask(requester);
                        AsynchClientTask task1b = createSelectLoadGeomTask(requester);
                        taskArray = new AsynchClientTask[] { task1, task1b, task2 };
                    } else {
                        taskArray = new AsynchClientTask[] { task2 };
                    }
                    break;
                } else if (createOption == VCDocument.MATH_OPTION_FROMBIOMODELAPP) {
                    AsynchClientTask task1 = new AsynchClientTask("select biomodel application", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

                        @Override
                        public void run(Hashtable<String, Object> hashTable) throws Exception {
                            // spatial or non-spatial
                            BioModelInfo bioModelInfo = (BioModelInfo) DialogUtils.getDBTreePanelSelection(requester.getComponent(), getMdiManager().getDatabaseWindowManager().getBioModelDbTreePanel(), "Open", "Select BioModel");
                            if (bioModelInfo != null) {
                                // may throw UserCancelException
                                hashTable.put("bioModelInfo", bioModelInfo);
                            }
                        }
                    };
                    AsynchClientTask task2 = new AsynchClientTask("find sim contexts in biomodel application", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                        @Override
                        public void run(Hashtable<String, Object> hashTable) throws Exception {
                            // spatial or non-spatial
                            // Get the simContexts in the corresponding BioModel
                            BioModelInfo bioModelInfo = (BioModelInfo) hashTable.get("bioModelInfo");
                            SimulationContext[] simContexts = getDocumentManager().getBioModel(bioModelInfo).getSimulationContexts();
                            if (simContexts != null) {
                                // may throw UserCancelException
                                hashTable.put("simContexts", simContexts);
                            }
                        }
                    };
                    AsynchClientTask task3 = new AsynchClientTask("create math model from biomodel application", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

                        @Override
                        public void run(Hashtable<String, Object> hashTable) throws Exception {
                            SimulationContext[] simContexts = (SimulationContext[]) hashTable.get("simContexts");
                            String[] simContextNames = new String[simContexts.length];
                            if (simContextNames.length == 0) {
                                throw new RuntimeException("no application is available");
                            } else {
                                for (int i = 0; i < simContexts.length; i++) {
                                    simContextNames[i] = simContexts[i].getName();
                                }
                                Component component = requester.getComponent();
                                // Get the simContext names, so that user can choose which simContext math to import
                                String simContextChoice = (String) PopupGenerator.showListDialog(component, simContextNames, "Please select Application");
                                if (simContextChoice == null) {
                                    throw UserCancelException.CANCEL_DB_SELECTION;
                                }
                                SimulationContext chosenSimContext = null;
                                for (int i = 0; i < simContexts.length; i++) {
                                    if (simContexts[i].getName().equals(simContextChoice)) {
                                        chosenSimContext = simContexts[i];
                                        break;
                                    }
                                }
                                Objects.requireNonNull(chosenSimContext);
                                BioModelInfo bioModelInfo = (BioModelInfo) hashTable.get("bioModelInfo");
                                // Get corresponding mathDesc to create new mathModel and return.
                                String newName = bioModelInfo.getVersion().getName() + "_" + chosenSimContext.getName();
                                MathDescription bioMathDesc = chosenSimContext.getMathDescription();
                                MathDescription newMathDesc = null;
                                newMathDesc = new MathDescription(newName + "_" + (new Random()).nextInt());
                                newMathDesc.setGeometry(bioMathDesc.getGeometry());
                                newMathDesc.read_database(new CommentStringTokenizer(bioMathDesc.getVCML_database()));
                                newMathDesc.isValid();
                                MathModel newMathModel = new MathModel(null);
                                newMathModel.setName(newName);
                                newMathModel.setMathDescription(newMathDesc);
                                hashTable.put("doc", newMathModel);
                            }
                        }
                    };
                    taskArray = new AsynchClientTask[] { task1, task2, task3 };
                    break;
                } else {
                    throw new RuntimeException("Unknown MathModel Document creation option value=" + documentCreationInfo.getOption());
                }
            }
        case GEOMETRY_DOC:
            {
                if (createOption == VCDocument.GEOM_OPTION_1D || createOption == VCDocument.GEOM_OPTION_2D || createOption == VCDocument.GEOM_OPTION_3D) {
                    // analytic
                    AsynchClientTask task1 = new AsynchClientTask("creating analytic geometry", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                        @Override
                        public void run(Hashtable<String, Object> hashTable) throws Exception {
                            Geometry geometry = new Geometry("Geometry" + (getMdiManager().getNumCreatedDocumentWindows() + 1), documentCreationInfo.getOption());
                            geometry.getGeometrySpec().addSubVolume(new AnalyticSubVolume("subdomain0", new Expression(1.0)));
                            geometry.precomputeAll(new GeometryThumbnailImageFactoryAWT());
                            hashTable.put("doc", geometry);
                        }
                    };
                    taskArray = new AsynchClientTask[] { task1 };
                    break;
                }
                if (createOption == VCDocument.GEOM_OPTION_CSGEOMETRY_3D) {
                    // constructed solid geometry
                    AsynchClientTask task1 = new AsynchClientTask("creating constructed solid geometry", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                        @Override
                        public void run(Hashtable<String, Object> hashTable) throws Exception {
                            Geometry geometry = new Geometry("Geometry" + (getMdiManager().getNumCreatedDocumentWindows() + 1), 3);
                            Extent extent = geometry.getExtent();
                            if (extent != null) {
                                // create a CSGPrimitive of type cube and scale it to the 'extent' components. Use this as the default or background CSGObject (subdomain).
                                // This can be considered as the equivalent of subdomain (with expression) 1.0 for analyticSubvolume.
                                // basic cube
                                CSGPrimitive cube = new CSGPrimitive("cube", CSGPrimitive.PrimitiveType.CUBE);
                                // scaled cube
                                double x = extent.getX();
                                double y = extent.getY();
                                double z = extent.getZ();
                                CSGScale scaledCube = new CSGScale("scale", new Vect3d(x / 2.0, y / 2.0, z / 2.0));
                                scaledCube.setChild(cube);
                                // translated scaled cube
                                CSGTranslation translatedScaledCube = new CSGTranslation("translation", new Vect3d(x / 2, y / 2, z / 2));
                                translatedScaledCube.setChild(scaledCube);
                                CSGObject csgObject = new CSGObject(null, "subdomain0", 0);
                                csgObject.setRoot(translatedScaledCube);
                                geometry.getGeometrySpec().addSubVolume(csgObject, false);
                                geometry.precomputeAll(new GeometryThumbnailImageFactoryAWT());
                                hashTable.put("doc", geometry);
                            }
                        }
                    };
                    taskArray = new AsynchClientTask[] { task1 };
                    break;
                } else {
                    throw new RuntimeException("Unknown Geometry Document creation option value=" + documentCreationInfo.getOption());
                }
            }
        default:
            {
                throw new RuntimeException("Unknown default document type: " + documentCreationInfo.getDocumentType());
            }
    }
    return taskArray;
}

Example 69 with BioModelInfo

use of org.vcell.util.document.BioModelInfo in project vcell by virtualcell.

the class ClientRequestManager method compareWithOther.

/**
 * Processes the model comparison request.
 * Creation date: (6/9/2004 1:07:09 PM)
 * @param vcDocument cbit.vcell.document.VCDocument
 */
public XmlTreeDiff compareWithOther(final VCDocumentInfo docInfo1, final VCDocumentInfo docInfo2) {
    VCDocument document1, document2;
    try {
        // get the VCDocument versions from documentManager
        if (docInfo1 instanceof BioModelInfo && docInfo2 instanceof BioModelInfo) {
            document1 = getDocumentManager().getBioModel((BioModelInfo) docInfo1);
            document2 = getDocumentManager().getBioModel((BioModelInfo) docInfo2);
        } else if (docInfo1 instanceof MathModelInfo && docInfo2 instanceof MathModelInfo) {
            document1 = getDocumentManager().getMathModel((MathModelInfo) docInfo1);
            document2 = getDocumentManager().getMathModel((MathModelInfo) docInfo2);
        } else if (docInfo1 instanceof GeometryInfo && docInfo2 instanceof GeometryInfo) {
            document1 = getDocumentManager().getGeometry((GeometryInfo) docInfo1);
            document2 = getDocumentManager().getGeometry((GeometryInfo) docInfo2);
        } else {
            throw new IllegalArgumentException("The two documents are invalid or of different types.");
        }
        return compareDocuments(document1, document2, DiffConfiguration.COMPARE_DOCS_OTHER);
    } catch (Exception e) {
        e.printStackTrace();
        throw new RuntimeException(e.getMessage());
    }
}

Example 70 with BioModelInfo

use of org.vcell.util.document.BioModelInfo in project vcell by virtualcell.

the class ClientRequestManager method getGeometryFromDocumentSelection.

public Geometry getGeometryFromDocumentSelection(Component parentComponent, VCDocumentInfo vcDocumentInfo, boolean bClearVersion) throws Exception, UserCancelException {
    Geometry geom = null;
    if (vcDocumentInfo.getVersionType().equals(VersionableType.BioModelMetaData)) /*documentType == VCDocument.BIOMODEL_DOC*/
    {
        BioModelInfo bioModelInfo = getDocumentManager().getBioModelInfo(vcDocumentInfo.getVersion().getVersionKey());
        BioModelChildSummary bioModelChildSummary = bioModelInfo.getBioModelChildSummary();
        if (bioModelChildSummary != null && bioModelChildSummary.getSimulationContextNames() != null) {
            Vector<Integer> spatialV = new Vector<Integer>();
            for (int i = 0; i < bioModelChildSummary.getSimulationContextNames().length; i++) {
                if (bioModelChildSummary.getGeometryDimensions()[i] > 0) {
                    spatialV.add(i);
                }
            }
            if (spatialV.size() > 0) {
                String[] columnNames = new String[] { "Application", "Geometry", "Dimension" };
                String[][] rowData = new String[spatialV.size()][3];
                for (int i = 0; i < spatialV.size(); i++) {
                    rowData[i][0] = bioModelChildSummary.getSimulationContextNames()[spatialV.elementAt(i)];
                    rowData[i][1] = bioModelChildSummary.getGeometryNames()[spatialV.elementAt(i)];
                    rowData[i][2] = bioModelChildSummary.getGeometryDimensions()[spatialV.elementAt(i)] + "";
                }
                int[] selection = DialogUtils.showComponentOKCancelTableList(JOptionPane.getFrameForComponent(parentComponent), "Select Geometry", columnNames, rowData, ListSelectionModel.SINGLE_SELECTION);
                ModelGeometryOPResults modelGeometryOPResults = (ModelGeometryOPResults) getDocumentManager().getSessionManager().getUserMetaDbServer().doTestSuiteOP(new ModelGeometryOP((BioModelInfo) vcDocumentInfo, rowData[selection[0]][0]));
                geom = getDocumentManager().getGeometry(modelGeometryOPResults.getGeometryKey());
            // BioModel bioModel = getDocumentManager().getBioModel((BioModelInfo)vcDocumentInfo);
            // for (int i = 0; i < bioModel.getSimulationContexts().length; i++) {
            // if(bioModel.getSimulationContexts()[i].getName().equals(rowData[selection[0]][0])){
            // geom = bioModel.getSimulationContexts()[i].getGeometry();
            // break;
            // }
            // }
            } else {
                throw new Exception("BioModel '" + bioModelInfo.getVersion().getName() + "' contains no spatial geometries.");
            }
        } else {
            throw new Exception("BioModel '" + bioModelInfo.getVersion().getName() + "' contains no spatial geometries.");
        }
    } else if (vcDocumentInfo.getVersionType().equals(VersionableType.MathModelMetaData)) /*documentType == VCDocument.MATHMODEL_DOC*/
    {
        MathModelInfo mathModelInfo = getDocumentManager().getMathModelInfo(vcDocumentInfo.getVersion().getVersionKey());
        MathModelChildSummary mathModelChildSummary = mathModelInfo.getMathModelChildSummary();
        if (mathModelChildSummary != null) {
            if (mathModelChildSummary.getGeometryDimension() > 0) {
                ModelGeometryOPResults modelGeometryOPResults = (ModelGeometryOPResults) getDocumentManager().getSessionManager().getUserMetaDbServer().doTestSuiteOP(new ModelGeometryOP((MathModelInfo) vcDocumentInfo));
                geom = getDocumentManager().getGeometry(modelGeometryOPResults.getGeometryKey());
            // MathModel mathModel = getDocumentManager().getMathModel(mathModelInfo);
            // geom = mathModel.getMathDescription().getGeometry();
            } else {
                throw new Exception("MathModel '" + mathModelInfo.getVersion().getName() + "' contains no spatial geometry.");
            }
        } else {
            throw new Exception("MathModel '" + mathModelInfo.getVersion().getName() + "' contains no spatial geometry.");
        }
    } else if (vcDocumentInfo.getVersionType().equals(VersionableType.Geometry)) {
        geom = getDocumentManager().getGeometry((GeometryInfo) vcDocumentInfo);
        if (geom.getDimension() == 0) {
            throw new Exception("Error, Only spatial geometries allowed (dimension > 0).");
        }
    } else {
        throw new IllegalArgumentException("Error selecting geometry from document type " + vcDocumentInfo.getVersionType() + ". Must be BioModel,MathModel or Geometry.");
    }
    if (geom == null) {
        throw new Exception("error selecting geometry");
    }
    if (bClearVersion) {
        geom.clearVersion();
    }
    return geom;
}