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Example 31 with GeometryInfo

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

the class ClientDocumentManager method setGroupPublic.

/**
 * Insert the method's description here.
 * Creation date: (11/28/00 5:43:44 PM)
 * @param bioModelInfo cbit.vcell.biomodel.BioModelInfo
 */
public GeometryInfo setGroupPublic(GeometryInfo geometryInfo) throws DataAccessException {
    try {
        // 
        // publish from database
        // 
        GeometryInfo newGeometryInfo = (GeometryInfo) setGroupPublic0(geometryInfo, VersionableType.Geometry, geoInfoHash);
        // //
        // // delete Geometry from cache
        // //
        // xmlHash.remove(geometryInfo.getVersion().getVersionKey());
        // //
        // // delete any MathModelMetaData's that use this GeometryInfo from cache
        // //
        // MathModelInfo referencedMathModelInfos[] = getMathModelReferences(geometryInfo);
        // for (int i = 0; i < referencedMathModelInfos.length; i++){
        // xmlHash.remove(referencedMathModelInfos[i].getVersion().getVersionKey());
        // }
        // //
        // // delete any BioModelMetaData's that use this GeometryInfo from cache
        // //
        // BioModelInfo referencedBioModelInfos[] = getBioModelReferences(geometryInfo);
        // for (int i = 0; i < referencedBioModelInfos.length; i++){
        // xmlHash.remove(referencedBioModelInfos[i].getVersion().getVersionKey());
        // }
        fireDatabaseUpdate(new DatabaseEvent(this, DatabaseEvent.UPDATE, geometryInfo, newGeometryInfo));
        return newGeometryInfo;
    } catch (RemoteProxyException e) {
        handleRemoteProxyException(e);
        throw new DataAccessException(e.getMessage());
    }
}
Also used : GeometryInfo(cbit.vcell.geometry.GeometryInfo) DataAccessException(org.vcell.util.DataAccessException) RemoteProxyException(cbit.vcell.message.server.bootstrap.client.RemoteProxyVCellConnectionFactory.RemoteProxyException)

Example 32 with GeometryInfo

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

the class ClientDocumentManager method getGeometryInfo.

/**
 * Insert the method's description here.
 * Creation date: (11/14/00 2:50:07 PM)
 * @return cbit.sql.Versionable
 * @param vType cbit.sql.VersionableType
 * @param key cbit.sql.KeyValue
 */
public synchronized GeometryInfo getGeometryInfo(KeyValue key) throws DataAccessException {
    if (key == null) {
        System.out.println("<<<NULL>>>> ClientDocumentManager.getGeometryInfo(" + key + ")");
        return null;
    }
    // 
    // first look in local cache for the Info object
    // 
    GeometryInfo geometryInfo = (GeometryInfo) geoInfoHash.get(key);
    if (geometryInfo != null) {
        // System.out.println("<<<IN CACHE>>> ClientDocumentManager.getGeometryInfo("+key+")");
        return geometryInfo;
    }
    // 
    // else get new list of info objects from database and stick in cache
    // 
    reloadGeometryInfos();
    // bGeometryInfosDirty = false;
    // 
    // now look in cache again (should be in there unless it was deleted from database).
    // 
    geometryInfo = (GeometryInfo) geoInfoHash.get(key);
    if (geometryInfo != null) {
        return geometryInfo;
    } else {
        throw new ObjectNotFoundException("GeometryInfo(" + key + ") not found");
    }
}
Also used : ObjectNotFoundException(org.vcell.util.ObjectNotFoundException) GeometryInfo(cbit.vcell.geometry.GeometryInfo)

Example 33 with GeometryInfo

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

the class ClientDocumentManager method removeUserFromGroup.

/**
 * Insert the method's description here.
 * Creation date: (11/28/00 5:43:44 PM)
 * @param bioModelInfo cbit.vcell.biomodel.BioModelInfo
 */
public GeometryInfo removeUserFromGroup(GeometryInfo geometryInfo, String userToRemove) throws DataAccessException {
    try {
        // 
        // publish from database
        // 
        GeometryInfo newGeometryInfo = (GeometryInfo) removeUserFromGroup0(geometryInfo, VersionableType.Geometry, geoInfoHash, userToRemove);
        // //
        // // delete Geometry from cache
        // //
        // xmlHash.remove(geometryInfo.getVersion().getVersionKey());
        // //
        // // delete any MathModelMetaData's that use this GeometryInfo from cache
        // //
        // MathModelInfo referencedMathModelInfos[] = getMathModelReferences(geometryInfo);
        // for (int i = 0; i < referencedMathModelInfos.length; i++){
        // xmlHash.remove(referencedMathModelInfos[i].getVersion().getVersionKey());
        // }
        // //
        // // delete any BioModelMetaData's that use this GeometryInfo from cache
        // //
        // BioModelInfo referencedBioModelInfos[] = getBioModelReferences(geometryInfo);
        // for (int i = 0; i < referencedBioModelInfos.length; i++){
        // xmlHash.remove(referencedBioModelInfos[i].getVersion().getVersionKey());
        // }
        fireDatabaseUpdate(new DatabaseEvent(this, DatabaseEvent.UPDATE, geometryInfo, newGeometryInfo));
        return newGeometryInfo;
    } catch (RemoteProxyException e) {
        handleRemoteProxyException(e);
        throw new DataAccessException(e.getMessage());
    }
}
Also used : GeometryInfo(cbit.vcell.geometry.GeometryInfo) DataAccessException(org.vcell.util.DataAccessException) RemoteProxyException(cbit.vcell.message.server.bootstrap.client.RemoteProxyVCellConnectionFactory.RemoteProxyException)

Example 34 with GeometryInfo

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

the class VCellBasicCellRenderer method getTreeCellRendererComponent.

/**
 * Insert the method's description here.
 * Creation date: (7/27/2000 6:41:57 PM)
 * @return java.awt.Component
 */
public java.awt.Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) {
    JLabel component = (JLabel) super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
    // 
    if (!leaf && expanded) {
        setIcon(fieldFolderOpenIcon);
    } else if (!leaf && !expanded) {
        setIcon(fieldFolderClosedIcon);
    }
    try {
        if (value instanceof BioModelNode) {
            BioModelNode node = (BioModelNode) value;
            boolean bLoaded = false;
            // 
            // Check if node is a SolverResultSetInfo
            // 
            Object userObject = node.getUserObject();
            if (userObject instanceof SimulationInfo) {
                // 
                // Check if node is a SimulationInfo
                // 
                setComponentProperties(component, (SimulationInfo) userObject);
                int maxErrorLevel = getMaxErrorLevel(node);
                if (maxErrorLevel == BioModelNode.ERROR_POSSIBLE) {
                    setIcon(fieldSimulationWarningIcon);
                    component.setToolTipText("Simulation contains possibly invalid results");
                } else if (maxErrorLevel == BioModelNode.ERROR_CONFIRMED) {
                    setIcon(fieldSimulationErrorIcon);
                    component.setToolTipText("Simulation contains invalid results");
                }
            } else if (userObject instanceof String && node.getChildCount() == 0) {
                component.setToolTipText(null);
                component.setText((String) userObject);
            } else if (userObject instanceof BioModelInfo) {
                // 
                // Check if node is a BioModelInfo
                // 
                setComponentProperties(component, (BioModelInfo) userObject);
                bLoaded = isLoaded((BioModelInfo) userObject);
                int maxErrorLevel = getMaxErrorLevel(node);
                if (maxErrorLevel == BioModelNode.ERROR_POSSIBLE) {
                    setIcon(fieldBioModelWarningIcon);
                    component.setToolTipText("BioModel version: Has possibly invalid simulation results");
                } else if (maxErrorLevel == BioModelNode.ERROR_CONFIRMED) {
                    setIcon(fieldBioModelErrorIcon);
                    component.setToolTipText("BioModel version: Has invalid simulation results");
                }
            } else if (userObject instanceof String && node.getChildCount() > 0 && ((BioModelNode) node.getChildAt(0)).getUserObject() instanceof BioModelInfo) {
                // 
                // Check if node is a BioModelName (String), with children (at least one version of biomodel), and if the child is a
                // BioModelInfo node
                // 
                String label = (String) userObject;
                component.setToolTipText("BioModel");
                component.setText(label);
                // 
                // check if child is loaded
                // 
                int maxErrorLevel = BioModelNode.ERROR_NONE;
                for (int i = 0; i < node.getChildCount(); i++) {
                    maxErrorLevel = Math.max(maxErrorLevel, getMaxErrorLevel((BioModelNode) node.getChildAt(i)));
                }
                if (maxErrorLevel == BioModelNode.ERROR_POSSIBLE) {
                    if (!leaf && expanded) {
                        setIcon(fieldFolderOpenWarningIcon);
                    } else if (!leaf && !expanded) {
                        setIcon(fieldFolderClosedWarningIcon);
                    }
                    component.setToolTipText("BioModel: one or more versions may have invalid simulation results");
                } else if (maxErrorLevel == BioModelNode.ERROR_CONFIRMED) {
                    if (!leaf && expanded) {
                        setIcon(fieldFolderOpenErrorIcon);
                    } else if (!leaf && !expanded) {
                        setIcon(fieldFolderClosedErrorIcon);
                    }
                    component.setToolTipText("BioModel: one or more versions have invalid simulation results");
                }
                // 
                for (int i = 0; i < node.getChildCount(); i++) {
                    BioModelInfo bioModelInfo = (BioModelInfo) ((BioModelNode) node.getChildAt(i)).getUserObject();
                    if (isLoaded(bioModelInfo)) {
                        bLoaded = true;
                    }
                }
            } else if (userObject instanceof User && node.getChildCount() > 0 && (((BioModelNode) node.getChildAt(0)).getUserObject() instanceof String) && ((BioModelNode) (node.getChildAt(0).getChildAt(0))).getUserObject() instanceof BioModelInfo) {
                // 
                // Check if node is a User, with at least one child which is a string (BioModel name)
                // and if the child's child is a BioModelInfo node
                // 
                String label = ((User) userObject).getName();
                component.setToolTipText("User Name");
                component.setText(label);
                if (isLoaded((User) userObject)) {
                    bLoaded = true;
                }
            } else if (userObject instanceof MathModelInfo) {
                // 
                // Check if node is a MathModelInfo node
                // 
                setComponentProperties(component, (MathModelInfo) userObject);
                bLoaded = isLoaded((MathModelInfo) userObject);
            } else if (userObject instanceof String && node.getChildCount() > 0 && ((BioModelNode) node.getChildAt(0)).getUserObject() instanceof MathModelInfo) {
                // 
                // Check if node is a MathModel name (String), with children (at least one version of mathmodel), and
                // if the child is a MathModelInfo node
                // 
                String label = (String) userObject;
                component.setToolTipText("Mathematical Model");
                component.setText(label);
                // 
                for (int i = 0; i < node.getChildCount(); i++) {
                    MathModelInfo mathModelInfo = (MathModelInfo) ((BioModelNode) node.getChildAt(i)).getUserObject();
                    if (isLoaded(mathModelInfo)) {
                        bLoaded = true;
                    }
                }
            } else if (userObject instanceof User && node.getChildCount() > 0 && (((BioModelNode) node.getChildAt(0)).getUserObject() instanceof String) && ((BioModelNode) (node.getChildAt(0).getChildAt(0))).getUserObject() instanceof MathModelInfo) {
                // 
                // Check if node is a User, with at least one child which is a string (Mathmodel name)
                // and if the child's child is a MathModelInfo node
                // 
                String label = ((User) userObject).getName();
                component.setToolTipText("User Name");
                component.setText(label);
                if (isLoaded((User) userObject)) {
                    bLoaded = true;
                }
            } else if (userObject instanceof cbit.vcell.geometry.GeometryInfo) {
                // 
                // Check if node is a GeometryInfo
                // 
                setComponentProperties(component, (GeometryInfo) userObject);
                bLoaded = isLoaded((GeometryInfo) userObject);
            } else if (userObject instanceof String && node.getChildCount() > 0 && ((BioModelNode) node.getChildAt(0)).getUserObject() instanceof GeometryInfo) {
                // 
                // Check if node is a Geometry name (String), with children (at least one version of Geometry), and
                // if the child is a GeometryInfo node
                // 
                String label = (String) userObject;
                component.setToolTipText("Geometry");
                component.setText(label);
                // 
                for (int i = 0; i < node.getChildCount(); i++) {
                    GeometryInfo geometryInfo = (GeometryInfo) ((BioModelNode) node.getChildAt(i)).getUserObject();
                    if (isLoaded(geometryInfo)) {
                        bLoaded = true;
                    }
                }
            } else if (userObject instanceof User && node.getChildCount() > 0 && (((BioModelNode) node.getChildAt(0)).getUserObject() instanceof String) && ((BioModelNode) (node.getChildAt(0).getChildAt(0))).getUserObject() instanceof GeometryInfo) {
                // 
                // Check if node is a User, with at least one child which is a string (Geometry name)
                // and if the child's child is a GeometryInfo node
                // 
                String label = ((User) userObject).getName();
                component.setToolTipText("User Name");
                component.setText(label);
                if (isLoaded((User) userObject)) {
                    bLoaded = true;
                }
            } else if (userObject instanceof String && node.getChildCount() > 0) {
                component.setToolTipText(null);
                component.setText((String) userObject);
            // }else if (node.getUserObject() instanceof MathInfo) {
            // setComponentProperties(component,(MathInfo)node.getUserObject());
            } else if (userObject instanceof VCImageInfo) {
                setComponentProperties(component, (VCImageInfo) userObject);
            } else if (userObject instanceof Extent) {
                setComponentProperties(component, (Extent) userObject);
            } else if (userObject instanceof Annotation) {
                setComponentProperties(component, (Annotation) userObject);
            } else if (userObject instanceof MathModel) {
                setComponentProperties(component, (MathModel) userObject);
            } else if (userObject instanceof BioModel) {
                setComponentProperties(component, (BioModel) userObject);
            } else if (userObject instanceof SimulationContext) {
                setComponentProperties(component, (SimulationContext) userObject);
                bLoaded = isLoaded((SimulationContext) userObject);
            } else if (userObject instanceof Simulation) {
                setComponentProperties(component, (Simulation) userObject);
            } else if (userObject instanceof MathDescription) {
                setComponentProperties(component, (MathDescription) userObject);
            } else if (userObject instanceof Geometry) {
                setComponentProperties(component, (Geometry) userObject);
            } else if (userObject instanceof User) {
                setComponentProperties(component, (User) userObject);
            } else {
                setComponentProperties(component, userObject);
            }
            if (selectedFont == null && component.getFont() != null) {
                selectedFont = component.getFont().deriveFont(Font.BOLD);
            }
            if (unselectedFont == null && component.getFont() != null) {
                unselectedFont = component.getFont().deriveFont(Font.PLAIN);
            }
            if (bLoaded) {
                component.setFont(selectedFont);
            } else {
                component.setFont(unselectedFont);
            }
        }
    } catch (Throwable e) {
        e.printStackTrace(System.out);
    }
    // 
    return component;
}
Also used : MathModel(cbit.vcell.mathmodel.MathModel) User(org.vcell.util.document.User) Extent(org.vcell.util.Extent) MathDescription(cbit.vcell.math.MathDescription) BioModelInfo(org.vcell.util.document.BioModelInfo) JLabel(javax.swing.JLabel) MathModelInfo(org.vcell.util.document.MathModelInfo) SimulationContext(cbit.vcell.mapping.SimulationContext) Geometry(cbit.vcell.geometry.Geometry) Simulation(cbit.vcell.solver.Simulation) BioModel(cbit.vcell.biomodel.BioModel) GeometryInfo(cbit.vcell.geometry.GeometryInfo) VCImageInfo(cbit.image.VCImageInfo) SimulationInfo(cbit.vcell.solver.SimulationInfo)

Example 35 with GeometryInfo

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

the class DeleteOldDocument method run.

/**
 * Insert the method's description here.
 * Creation date: (5/31/2004 6:04:14 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
public void run(Hashtable<String, Object> hashTable) throws java.lang.Exception {
    DocumentWindowManager dwm = (DocumentWindowManager) fetch(hashTable, DOCUMENT_WINDOW_MANAGER);
    VCDocument currentDocument = dwm.getVCDocument();
    DocumentManager documentManager = (DocumentManager) fetch(hashTable, DOCUMENT_MANAGER);
    switch(currentDocument.getDocumentType()) {
        case BIOMODEL_DOC:
            {
                // make the info
                BioModel oldBioModel = (BioModel) currentDocument;
                BioModelInfo oldBioModelInfo = documentManager.getBioModelInfo(oldBioModel.getVersion().getVersionKey());
                // delete document
                documentManager.delete(oldBioModelInfo);
                break;
            }
        case MATHMODEL_DOC:
            {
                // make the info
                MathModel oldMathModel = (MathModel) currentDocument;
                MathModelInfo oldMathModelInfo = documentManager.getMathModelInfo(oldMathModel.getVersion().getVersionKey());
                // delete document
                documentManager.delete(oldMathModelInfo);
                break;
            }
        case GEOMETRY_DOC:
            {
                // make the info
                Geometry oldGeometry = (Geometry) currentDocument;
                GeometryInfo oldGeometryInfo = documentManager.getGeometryInfo(oldGeometry.getVersion().getVersionKey());
                // delete document
                documentManager.delete(oldGeometryInfo);
                break;
            }
        default:
            break;
    }
}
Also used : Geometry(cbit.vcell.geometry.Geometry) MathModel(cbit.vcell.mathmodel.MathModel) VCDocument(org.vcell.util.document.VCDocument) DocumentWindowManager(cbit.vcell.client.DocumentWindowManager) BioModel(cbit.vcell.biomodel.BioModel) DocumentManager(cbit.vcell.clientdb.DocumentManager) BioModelInfo(org.vcell.util.document.BioModelInfo) GeometryInfo(cbit.vcell.geometry.GeometryInfo) MathModelInfo(org.vcell.util.document.MathModelInfo)

Aggregations

GeometryInfo (cbit.vcell.geometry.GeometryInfo)47 BioModelInfo (org.vcell.util.document.BioModelInfo)27 MathModelInfo (org.vcell.util.document.MathModelInfo)27 DataAccessException (org.vcell.util.DataAccessException)19 VCDocumentInfo (org.vcell.util.document.VCDocumentInfo)11 AsynchClientTask (cbit.vcell.client.task.AsynchClientTask)8 Hashtable (java.util.Hashtable)8 Geometry (cbit.vcell.geometry.Geometry)7 VCImageInfo (cbit.image.VCImageInfo)6 BioModel (cbit.vcell.biomodel.BioModel)6 User (org.vcell.util.document.User)6 VersionInfo (org.vcell.util.document.VersionInfo)6 CSGObject (cbit.vcell.geometry.CSGObject)5 SimulationContext (cbit.vcell.mapping.SimulationContext)5 RemoteProxyException (cbit.vcell.message.server.bootstrap.client.RemoteProxyVCellConnectionFactory.RemoteProxyException)5 Vector (java.util.Vector)5 ObjectNotFoundException (org.vcell.util.ObjectNotFoundException)5 ImageException (cbit.image.ImageException)4 DocumentManager (cbit.vcell.clientdb.DocumentManager)4 GeometryException (cbit.vcell.geometry.GeometryException)4