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

Example 1 with MathModelChildSummary

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

the class MathModel method createMathModelChildSummary.

public MathModelChildSummary createMathModelChildSummary() {
    MathType modelType = getMathDescription().getMathType();
    String geoName = getMathDescription().getGeometry().getName();
    int geoDim = getMathDescription().getGeometry().getDimension();
    Simulation[] sims = getSimulations();
    String[] simNames = new String[sims.length];
    String[] simAnnots = new String[sims.length];
    for (int i = 0; i < sims.length; i += 1) {
        simNames[i] = sims[i].getName();
        simAnnots[i] = sims[i].getDescription();
    }
    return new MathModelChildSummary(modelType, geoName, geoDim, simNames, simAnnots);
}

Example 2 with MathModelChildSummary

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

the class MathModelMetaDataTreeModel method createVersionSubTree.

/**
 * Insert the method's description here.
 * Creation date: (11/28/00 2:41:43 PM)
 * @param mathModelNode cbit.vcell.desktop.BioModelNode
 * @param mathModelInfo cbit.vcell.mathmodel.MathModelInfo
 */
private BioModelNode createVersionSubTree(MathModelInfo mathModelInfo) throws DataAccessException {
    BioModelNode versionNode = new BioModelNode(mathModelInfo, true);
    // 
    if (mathModelInfo.getVersion().getAnnot() != null && mathModelInfo.getVersion().getAnnot().trim().length() > 0) {
        versionNode.add(new BioModelNode(new Annotation(mathModelInfo.getVersion().getAnnot()), false));
    }
    MathModelChildSummary mathModelChildSummary = mathModelInfo.getMathModelChildSummary();
    if (mathModelChildSummary == null) {
        versionNode.add(new BioModelNode("SUMMARY INFORMATION NOT AVAILABLE", false));
    } else {
        int geomDim = mathModelChildSummary.getGeometryDimension();
        String geomName = mathModelChildSummary.getGeometryName();
        MathType modelType = mathModelChildSummary.getModelType();
        // add model type tree node
        BioModelNode modelTypeNode = new BioModelNode(modelType, false);
        modelTypeNode.setRenderHint("type", "AppType");
        versionNode.add(modelTypeNode);
        BioModelNode geometryNode = null;
        if (geomDim > 0) {
            geometryNode = new BioModelNode(geomName + " (" + geomDim + "D)", false);
        } else {
            geometryNode = new BioModelNode(BioModelChildSummary.COMPARTMENTAL_GEO_STR, false);
        }
        geometryNode.setRenderHint("type", "Geometry");
        geometryNode.setRenderHint("dimension", new Integer(geomDim));
        versionNode.add(geometryNode);
        // 
        // add simulations to simulationContext
        // 
        String[] simNames = mathModelChildSummary.getSimulationNames();
        String[] simAnnot = mathModelChildSummary.getSimulationAnnotations();
        for (int j = 0; j < simNames.length; j++) {
            BioModelNode simNode = new BioModelNode(simNames[j], true);
            simNode.setRenderHint("type", "Simulation");
            versionNode.add(simNode);
            if (simAnnot[j] != null && simAnnot[j].trim().length() > 0) {
                simNode.add(new BioModelNode(new Annotation(simAnnot[j]), false));
            }
        }
    }
    return versionNode;
}

Example 3 with MathModelChildSummary

use of org.vcell.util.document.MathModelChildSummary 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;
}