Examples with Geometry cbit.vcell.geometry.Geometry used on opensource projects

Example 51 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class StructureMappingTableModel method propertyChange.

/**
 * This method gets called when a bound property is changed.
 * @param evt A PropertyChangeEvent object describing the event source
 *   and the property that has changed.
 */
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    if (evt.getSource() == this && evt.getPropertyName().equals(PROPERTY_GEOMETRY_CONTEXT)) {
        GeometryContext oldValue = (GeometryContext) evt.getOldValue();
        if (oldValue != null) {
            oldValue.removePropertyChangeListener(this);
            StructureMapping[] oldStructureMappings = oldValue.getStructureMappings();
            for (int i = 0; i < oldStructureMappings.length; i++) {
                oldStructureMappings[i].removePropertyChangeListener(this);
            }
            SubVolume[] subvols = oldValue.getGeometry().getGeometrySpec().getSubVolumes();
            for (int i = 0; i < subvols.length; i++) {
                subvols[i].removePropertyChangeListener(this);
            }
        }
        GeometryContext newValue = (GeometryContext) evt.getNewValue();
        if (newValue != null) {
            newValue.addPropertyChangeListener(this);
            StructureMapping[] newStructureMappings = newValue.getStructureMappings();
            for (int i = 0; i < newStructureMappings.length; i++) {
                newStructureMappings[i].addPropertyChangeListener(this);
            }
            SubVolume[] subvols = newValue.getGeometry().getGeometrySpec().getSubVolumes();
            for (int i = 0; i < subvols.length; i++) {
                subvols[i].addPropertyChangeListener(this);
            }
        }
        update();
    }
    if (evt.getSource() == getGeometryContext() && evt.getPropertyName().equals(GeometryOwner.PROPERTY_NAME_GEOMETRY)) {
        SubVolume[] subvols = ((Geometry) evt.getOldValue()).getGeometrySpec().getSubVolumes();
        for (int i = 0; i < subvols.length; i++) {
            subvols[i].removePropertyChangeListener(this);
        }
        subvols = ((Geometry) evt.getNewValue()).getGeometrySpec().getSubVolumes();
        for (int i = 0; i < subvols.length; i++) {
            subvols[i].addPropertyChangeListener(this);
        }
        update();
    }
    // subvolume name change
    if (evt.getSource() instanceof SubVolume) {
        update();
    }
    if (evt.getSource() instanceof GeometryContext && evt.getPropertyName().equals(GeometryContext.PROPERTY_STRUCTURE_MAPPINGS)) {
        StructureMapping[] oldStructureMappings = (StructureMapping[]) evt.getOldValue();
        StructureMapping[] newStructureMappings = (StructureMapping[]) evt.getNewValue();
        for (int i = 0; oldStructureMappings != null && i < oldStructureMappings.length; i++) {
            oldStructureMappings[i].removePropertyChangeListener(this);
        }
        for (int i = 0; newStructureMappings != null && i < newStructureMappings.length; i++) {
            newStructureMappings[i].addPropertyChangeListener(this);
        }
        update();
    }
    if (evt.getSource() instanceof StructureMapping) {
        fireTableRowsUpdated(0, getRowCount() - 1);
    }
}

Example 52 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class MathDebuggerPanel method main.

public static void main(java.lang.String[] args) {
    try {
        javax.swing.JFrame frame = new javax.swing.JFrame();
        MathDebuggerPanel aMathDebuggerPanel;
        aMathDebuggerPanel = new MathDebuggerPanel();
        frame.setContentPane(aMathDebuggerPanel);
        frame.setTitle("Math Descriptions Comparator");
        frame.setSize(aMathDebuggerPanel.getSize());
        frame.addWindowListener(new java.awt.event.WindowAdapter() {

            public void windowClosing(java.awt.event.WindowEvent e) {
                System.exit(0);
            }
        });
        MathModel mathModel1 = new MathModel(null);
        mathModel1.setName("math1");
        Geometry geometry1 = new Geometry("geo", 0);
        MathDescription mathDesc1 = mathModel1.getMathDescription();
        mathDesc1.setGeometry(geometry1);
        mathDesc1.addSubDomain(new CompartmentSubDomain("Compartment", CompartmentSubDomain.NON_SPATIAL_PRIORITY));
        MathModel mathModel2 = new MathModel(null);
        mathModel2.setName("math2");
        Geometry geometry2 = new Geometry("geo", 0);
        MathDescription mathDesc2 = mathModel2.getMathDescription();
        mathDesc2.setGeometry(geometry2);
        mathDesc2.addSubDomain(new CompartmentSubDomain("Compartment", CompartmentSubDomain.NON_SPATIAL_PRIORITY));
        aMathDebuggerPanel.setMathModel1(mathModel1);
        aMathDebuggerPanel.setMathModel2(mathModel2);
        frame.setSize(1500, 800);
        frame.setVisible(true);
    } catch (Throwable exception) {
        System.err.println("Exception occurred in main() of javax.swing.JPanel");
        exception.printStackTrace(System.out);
    }
}

Example 53 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class GeomDbDriver method getGeometry.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.model.Model
 * @param rset java.sql.ResultSet
 */
private Geometry getGeometry(QueryHashtable dbc, Connection con, User user, ResultSet rset) throws SQLException, DataAccessException {
    // 
    // get Image reference
    // 
    java.math.BigDecimal bigD = rset.getBigDecimal(geomTable.imageRef.toString());
    KeyValue imageRef = null;
    if (!rset.wasNull()) {
        imageRef = new KeyValue(bigD);
    }
    // 
    // get geometry object
    // 
    Geometry tempGeometry = null;
    try {
        tempGeometry = geomTable.getGeometry(rset, con);
    } catch (PropertyVetoException e) {
        throw new DataAccessException(e.getMessage());
    }
    Geometry geom = null;
    // 
    // get image for this geometry
    // 
    VCImage vcImage = null;
    if (imageRef != null) {
        // permission checking for the image is disabled because it is a child of this geometry
        vcImage = getVCImage(dbc, con, user, imageRef, false);
    }
    if (vcImage != null) {
        geom = new Geometry(tempGeometry, vcImage);
    } else {
        geom = tempGeometry;
    }
    // 
    // get SubVolumes for this geometry
    // 
    SubVolume[] subVolumes = getSubVolumesFromGeometry(dbc, con, geom.getVersion().getVersionKey());
    if (subVolumes != null) {
        try {
            geom.getGeometrySpec().setSubVolumes(subVolumes);
        } catch (java.beans.PropertyVetoException e) {
            lg.error(e.getMessage(), e);
            throw new DataAccessException(e.getMessage());
        }
    }
    // 
    if (geom.getDimension() > 0) {
        getSurfaceDescription(con, geom);
    }
    // 
    if (geom.getDimension() > 0) {
        getFilaments(con, geom);
    }
    // 
    // get SurfaceClasses for this geometry
    // 
    SurfaceClass[] surfaceClasses = getSurfaceClassesFromGeometry(dbc, con, geom.getVersion().getVersionKey());
    if (surfaceClasses != null) {
        try {
            geom.getGeometrySurfaceDescription().setSurfaceClasses(surfaceClasses);
        } catch (java.beans.PropertyVetoException e) {
            lg.error(e.getMessage(), e);
            throw new DataAccessException(e.getMessage());
        }
    }
    return geom;
}

Example 54 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class GeometryTable method getGeometry.

/**
 * This method was created in VisualAge.
 * @return Model
 * @param rset ResultSet
 * @param log SessionLog
 */
public Geometry getGeometry(ResultSet rset, Connection con) throws SQLException, DataAccessException, PropertyVetoException {
    int dim = rset.getInt(dimension.toString());
    double ox = rset.getBigDecimal(originX.toString()).doubleValue();
    double oy = rset.getBigDecimal(originY.toString()).doubleValue();
    double oz = rset.getBigDecimal(originZ.toString()).doubleValue();
    double ex = rset.getBigDecimal(ExtentTable.table.extentX.toString()).doubleValue();
    double ey = rset.getBigDecimal(ExtentTable.table.extentY.toString()).doubleValue();
    double ez = rset.getBigDecimal(ExtentTable.table.extentZ.toString()).doubleValue();
    java.math.BigDecimal groupid = rset.getBigDecimal(VersionTable.privacy_ColumnName);
    Version version = getVersion(rset, DbDriver.getGroupAccessFromGroupID(con, groupid));
    Geometry geometry = new Geometry(version, dim);
    geometry.getGeometrySpec().setOrigin(new org.vcell.util.Origin(ox, oy, oz));
    geometry.getGeometrySpec().setExtent(new org.vcell.util.Extent(ex, ey, ez));
    return geometry;
}

Example 55 with Geometry

use of cbit.vcell.geometry.Geometry in project vcell by virtualcell.

the class MathDescriptionDbDriver method getMathDescriptionSQL.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.math.MathDescription
 * @param user cbit.vcell.server.User
 * @param mathDescKey cbit.sql.KeyValue
 */
private MathDescription getMathDescriptionSQL(QueryHashtable dbc, Connection con, User user, KeyValue mathDescKey) throws SQLException, DataAccessException, ObjectNotFoundException {
    String sql;
    Field[] f = { userTable.userid, new cbit.sql.StarField(mathDescTable) };
    Table[] t = { mathDescTable, userTable };
    String condition = mathDescTable.id.getQualifiedColName() + " = " + mathDescKey + " AND " + userTable.id.getQualifiedColName() + " = " + mathDescTable.ownerRef.getQualifiedColName();
    sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, (OuterJoin) null, condition, null, dbSyntax);
    // System.out.println(sql);
    MathDescription mathDescription = null;
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            // 
            // note: must call mathDescTable.getMathDescription() first (rset.getBytes(language) must be called first)
            // 
            mathDescription = mathDescTable.getMathDescription(rset, con, dbSyntax);
            // 
            // get Geometry reference and assign to mathDescription
            // 
            java.math.BigDecimal bigD = rset.getBigDecimal(MathDescTable.table.geometryRef.toString());
            KeyValue geomRef = null;
            if (!rset.wasNull()) {
                geomRef = new KeyValue(bigD);
            } else {
                throw new DataAccessException("Error:  Geometry Reference Cannot be Null for MathDescription");
            }
            Geometry geom = (Geometry) geomDB.getVersionable(dbc, con, user, VersionableType.Geometry, geomRef, false);
            try {
                mathDescription.setGeometry(geom);
            } catch (java.beans.PropertyVetoException e) {
                e.printStackTrace(System.out);
                throw new DataAccessException("DataAccess Exception: " + e.getMessage());
            }
        } else {
            throw new ObjectNotFoundException("MathDescription id=" + mathDescKey + " not found for user '" + user + "'");
        }
    } finally {
        // Release resources include resultset
        stmt.close();
    }
    return mathDescription;
}