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

Example 96 with Geometry

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

the class GeometryFilamentCurvePanel method setGeometry2.

/**
 * Set the Geometry2 to a new value.
 * @param newValue cbit.vcell.geometry.Geometry
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private void setGeometry2(cbit.vcell.geometry.Geometry newValue) {
    if (ivjGeometry2 != newValue) {
        try {
            cbit.vcell.geometry.Geometry oldValue = getGeometry2();
            ivjGeometry2 = newValue;
            connPtoP9SetSource();
            connEtoM2(ivjGeometry2);
            firePropertyChange("geometry", oldValue, newValue);
        // user code begin {1}
        // user code end
        } catch (java.lang.Throwable ivjExc) {
            // user code begin {2}
            // user code end
            handleException(ivjExc);
        }
    }
    ;
// user code begin {3}
// user code end
}

Example 97 with Geometry

use of cbit.vcell.geometry.Geometry 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;
}

Example 98 with Geometry

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

the class BioModelCellRenderer 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);
    // 
    try {
        if (value instanceof DateNode) {
            DateNode dateNode = (DateNode) value;
            AnnotationQualifier qualifier = dateNode.getDateQualifier();
            String colorString = (sel) ? "white" : "black";
            component.setText("<html>" + qualifier.getDescription() + "&nbsp;<font color=\"" + colorString + "\">" + dateNode.getDate().getDateString() + "</font></html>");
        } else if (value instanceof LinkNode) {
            LinkNode ln = (LinkNode) value;
            String link = ln.getLink();
            String text = ln.getText();
            String qualifier = ln.getMiriamQualifier().getDescription();
            if (link != null) {
                String colorString = (sel) ? "white" : "blue";
                component.setToolTipText("Double-click to open link");
                component.setText("<html>" + qualifier + "&nbsp;<font color=\"" + colorString + "\"><a href=" + link + ">" + text + "</a></font></html>");
            } else {
                String colorString = (sel) ? "white" : "black";
                component.setText("<html>" + qualifier + "&nbsp;<font color=\"" + colorString + "\">" + text + "</font></html>");
            }
        } else if (value instanceof BioModelNode) {
            BioModelNode node = (BioModelNode) value;
            Object userObject = node.getUserObject();
            if (userObject instanceof User) {
                String label = null;
                if (sessionUser != null && sessionUser.compareEqual((User) userObject)) {
                    label = "My BioModels (" + ((User) userObject).getName() + ") (" + node.getChildCount() + ")";
                } else {
                    label = ((User) userObject).getName() + "(abcdefghijklmnopq)(000000)";
                }
                component.setToolTipText(label);
                component.setText(label);
            } else if (userObject instanceof BioModelInfo) {
                BioModelInfo biomodelInfo = (BioModelInfo) userObject;
                if (biomodelInfo.getVersion().getFlag().compareEqual(org.vcell.util.document.VersionFlag.Archived)) {
                    component.setText("(Archived) " + component.getText());
                } else if (biomodelInfo.getVersion().getFlag().compareEqual(org.vcell.util.document.VersionFlag.Published)) {
                    component.setText("(Published) " + component.getText());
                }
            } else if (userObject instanceof Geometry) {
                Geometry geo = (Geometry) userObject;
                String label = "";
                // geomety info, when spatial--shows name+1D/2D/3D
                if (geo.getDimension() > 0) {
                    label = geo.getName() + " (" + geo.getDimension() + "D)";
                } else {
                    label = BioModelChildSummary.COMPARTMENTAL_GEO_STR;
                }
                component.setToolTipText("Geometry");
                component.setText(label);
                setIcon(fieldGeometryIcon);
            } else if (userObject instanceof String && "AppType".equals(node.getRenderHint("type"))) {
                String label = (String) userObject;
                component.setToolTipText("Application type");
                component.setText(label);
                setIcon(VCellIcons.mathTypeIcon);
            } else if (userObject instanceof VCDocumentInfoNode) {
                VCDocumentInfoNode infonode = (VCDocumentInfoNode) userObject;
                User nodeUser = infonode.getVCDocumentInfo().getVersion().getOwner();
                String modelName = infonode.getVCDocumentInfo().getVersion().getName();
                String username = nodeUser.getName();
                if (nodeUser.compareEqual(sessionUser) || username.equals(VCDocumentDbTreeModel.USER_tutorial) || username.equals(VCDocumentDbTreeModel.USER_Education) || username.equals(VCDocumentDbTreeModel.USER_tutorial610) || username.equals(VCDocumentDbTreeModel.USER_tutorial611)) {
                    component.setText(modelName);
                } else {
                    component.setText("<html><b>" + username + " </b> : " + modelName + "</html>");
                }
            }
        }
    } catch (Throwable e) {
        e.printStackTrace(System.out);
    }
    // 
    if (component.getToolTipText() == null || component.getToolTipText().length() == 0) {
        component.setToolTipText(component.getText());
    }
    return component;
}

Example 99 with Geometry

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

the class BioModelWindowManager method actionPerformed.

/**
 * Invoked when an action occurs.
 */
public void actionPerformed(java.awt.event.ActionEvent e) {
    String actionCommand = e.getActionCommand();
    final Object source = e.getSource();
    if (source instanceof GeometryViewer && (actionCommand.equals(GuiConstants.ACTIONCMD_CREATE_GEOMETRY) || actionCommand.equals(GuiConstants.ACTIONCMD_EDITCURRENTSPATIAL_GEOMETRY))) {
        final GeometryViewer geometryViewer = (GeometryViewer) source;
        AsynchClientTask precomputeAllTask = new AsynchClientTask("precomputeAll geometry", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                Geometry newGeom = (Geometry) hashTable.get("doc");
                if (newGeom != null) {
                    newGeom.precomputeAll(new GeometryThumbnailImageFactoryAWT());
                }
            }
        };
        AsynchClientTask setGeomOnSimContextTask = new AsynchClientTask("Setting geometry on application", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                Geometry newGeom = (Geometry) hashTable.get("doc");
                for (SimulationContext simulationContext : getBioModel().getSimulationContexts()) {
                    if (simulationContext == geometryViewer.getGeometryOwner()) {
                        if (newGeom.getName() == null) {
                            newGeom.setName(getBioModel().getName() + "_" + (simulationContext.getName() + "_" + BeanUtils.generateDateTimeString()));
                        }
                        simulationContext.setGeometry(newGeom);
                        return;
                    }
                }
                Geometry origGeom = geometryViewer.getGeometryOwner().getGeometry();
                throw new IllegalArgumentException("Couldn't find matching application editor for orig geom '" + origGeom.getName() + "' key=" + origGeom.getKey() + " in application hash.");
            }
        };
        Geometry currentGeometry = geometryViewer.getGeometryOwner().getGeometry();
        createGeometry(currentGeometry, new AsynchClientTask[] { /*oldEditorTask,*/
        precomputeAllTask, setGeomOnSimContextTask }, TopLevelWindowManager.DEFAULT_CREATEGEOM_SELECT_DIALOG_TITLE, TopLevelWindowManager.APPLY_GEOMETRY_BUTTON_TEXT, (actionCommand.equals(GuiConstants.ACTIONCMD_EDITCURRENTSPATIAL_GEOMETRY) ? new DocumentWindowManager.GeometrySelectionInfo() : null));
    }
    if (source instanceof MathematicsPanel && actionCommand.equals(GuiConstants.ACTIONCMD_CREATE_MATH_MODEL)) {
        SimulationContext sc = ((MathematicsPanel) source).getSimulationContext();
        getRequestManager().createMathModelFromApplication(this, "Untitled", sc);
    }
    if (source instanceof GeometryViewer && actionCommand.equals(GuiConstants.ACTIONCMD_CHANGE_GEOMETRY)) {
        final GeometryViewer geometryViewer = (GeometryViewer) source;
        getRequestManager().changeGeometry(this, (SimulationContext) geometryViewer.getGeometryOwner());
    }
}

Example 100 with Geometry

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

the class ClientRequestManager method isDifferentFromBlank.

/**
 * Insert the method's description here.
 * Creation date: (5/10/2004 3:48:16 PM)
 */
public boolean isDifferentFromBlank(VCDocumentType documentType, VCDocument vcDocument) {
    if (documentType != vcDocument.getDocumentType()) {
        // we have to open the doc in a new window, hence return true;
        return true;
    }
    VCDocument blank = null;
    if (vcDocument.getDocumentType() != VCDocumentType.GEOMETRY_DOC) {
        // BioModel/MathModel
        blank = createDefaultDocument(vcDocument.getDocumentType());
        try {
            blank.setName(vcDocument.getName());
        }// ignore. doesn't happen
         catch (PropertyVetoException e) {
        }
        return !blank.compareEqual(vcDocument);
    } else {
        // Geometry
        blank = new Geometry(vcDocument.getName(), 1);
        if (blank.compareEqual(vcDocument)) {
            return false;
        }
        blank = new Geometry(vcDocument.getName(), 2);
        if (blank.compareEqual(vcDocument)) {
            return false;
        }
        blank = new Geometry(vcDocument.getName(), 3);
        if (blank.compareEqual(vcDocument)) {
            return false;
        }
        return true;
    }
}