Examples with UtilCancelException org.vcell.util.UtilCancelException used on opensource projects

Example 11 with UtilCancelException

use of org.vcell.util.UtilCancelException in project vcell by virtualcell.

the class ClientRequestManager method getISizeFromUser.

public static ISize getISizeFromUser(Component guiParent, ISize initISize, String textMessage) throws UserCancelException {
    Integer imageDimension = (initISize == null ? null : (initISize.getX() != 1 ? 1 : 0) + (initISize.getY() != 1 ? 1 : 0) + (initISize.getZ() != 1 ? 1 : 0));
    if (imageDimension != null && (imageDimension < 1 || imageDimension > 3)) {
        throw new IllegalArgumentException("Dimension must be 1, 2 or 3.");
    }
    try {
        int xsize = (imageDimension == null ? -1 : initISize.getX());
        int ysize = (imageDimension == null ? -1 : initISize.getY());
        int zsize = (imageDimension == null ? -1 : initISize.getZ());
        do {
            String result = (imageDimension == null ? "256,256,8" : xsize + "," + ysize + "," + zsize);
            result = DialogUtils.showInputDialog0(guiParent, textMessage, result);
            String tempResult = result;
            try {
                if (result == null || result.length() == 0) {
                    result = "";
                    throw new Exception("No size values entered.");
                }
                xsize = Integer.parseInt(tempResult.substring(0, tempResult.indexOf(",")));
                tempResult = tempResult.substring(tempResult.indexOf(",") + 1, tempResult.length());
                ysize = Integer.parseInt(tempResult.substring(0, tempResult.indexOf(",")));
                tempResult = tempResult.substring(tempResult.indexOf(",") + 1, tempResult.length());
                zsize = Integer.parseInt(tempResult);
                if (imageDimension != null) {
                    if (imageDimension == 2 && zsize != 1) {
                        throw new Exception("Dimension " + imageDimension + " must have z = 1.");
                    } else if (imageDimension == 1 && zsize != 1 && ysize != 1) {
                        throw new Exception("Dimension " + imageDimension + " must have z = 1 and y = 1.");
                    }
                }
                ISize isize = new ISize(xsize, ysize, zsize);
                if (isize.getXYZ() <= 0) {
                    throw new Exception("Total pixels (" + xsize + "*" + ysize + "*" + zsize + ") cannot be <=0.");
                }
                return isize;
            } catch (Exception e) {
                DialogUtils.showErrorDialog(guiParent, "Error entering starting sizes\n" + e.getMessage(), e);
            }
        } while (true);
    } catch (UtilCancelException e2) {
        throw UserCancelException.CANCEL_GENERIC;
    }
}

Example 12 with UtilCancelException

use of org.vcell.util.UtilCancelException in project vcell by virtualcell.

the class BioModelEditorPathwayDiagramPanel method groupBioPaxObjects.

private void groupBioPaxObjects() {
    HashSet<BioPaxObject> selected = new HashSet<BioPaxObject>();
    selected.addAll(getSelectedBioPaxObjects());
    if (selected.size() == 0)
        return;
    if (bioModel == null || bioModel.getPathwayModel() == null)
        return;
    PathwayGrouping pathwayGrouping = new PathwayGrouping();
    ArrayList<String> names = new ArrayList<String>();
    String id = pathwayGrouping.groupIdGenerator(bioModel.getPathwayModel());
    String newName = null;
    try {
        newName = DialogUtils.showInputDialog0(this, "Name of the GroupObject", id);
    } catch (UtilCancelException ex) {
    // user canceled; it's ok
    }
    if (newName != null) {
        if (newName.length() == 0) {
            PopupGenerator.showErrorDialog(this, "The Name of the GroupObject should be provided.");
        } else {
            names.add(newName);
            GroupObject groupObject = pathwayGrouping.createGroupObject(bioModel.getPathwayModel(), names, id, selected, GroupObject.Type.GROUPEDBIOPAXOBJECTS);
            if (groupObject == null) {
                // error message
                DialogUtils.showErrorDialog(this, "The set of selected objects is a subset of one group object in the model. They will not be grouped together again.");
            } else {
                bioModel.getPathwayModel().add(groupObject);
                bioModel.getPathwayModel().refreshGroupMap();
                // set the grouped object to be selected
                graphCartoonTool.getGraphModel().setSelectedObjects(new GroupObject[] { groupObject });
            }
        }
    }
    pathwayGraphModel.refreshAll();
}

Example 13 with UtilCancelException

use of org.vcell.util.UtilCancelException in project vcell by virtualcell.

the class DocumentWindow method showEditAnnotationWindow.

// /**
// * Comment
// */
// private void  showBNGWindow() {
// getWindowManager().showBNGWindow();
// }
/**
 * Comment
 */
private void showEditAnnotationWindow() {
    try {
        if (getWindowManager() != null) {
            VCDocument vcDoc = getWindowManager().getVCDocument();
            if (vcDoc != null) {
                try {
                    // initialize fields - different for biomodel and mathmodel, geometry
                    String oldAnnotation = null;
                    if (vcDoc instanceof BioModel) {
                        oldAnnotation = ((BioModel) vcDoc).getVCMetaData().getFreeTextAnnotation((BioModel) vcDoc);
                    } else {
                        oldAnnotation = vcDoc.getDescription();
                    }
                    // show the editor
                    String newAnnotation = DialogUtils.showAnnotationDialog(this, oldAnnotation);
                    if (org.vcell.util.BeanUtils.triggersPropertyChangeEvent(oldAnnotation, newAnnotation)) {
                        // if VCDocument is a Biomodel, set the vcMetadata, else edit VCDoc.description for now
                        if (vcDoc instanceof BioModel) {
                            // update free text annotation in VCMetaData
                            VCMetaData vcMetaData = ((BioModel) vcDoc).getVCMetaData();
                            vcMetaData.setFreeTextAnnotation((BioModel) vcDoc, newAnnotation);
                        } else {
                            // Update VCDocument annotation
                            vcDoc.setDescription(newAnnotation);
                        }
                    }
                } catch (UtilCancelException e) {
                // Do Nothing
                }
            } else {
                throw new Exception("No Document to Edit");
            }
        }
    } catch (Throwable exc) {
        exc.printStackTrace(System.out);
        PopupGenerator.showErrorDialog(this, "Failed to edit annotation!\n" + exc.getMessage(), exc);
    }
}

Example 14 with UtilCancelException

use of org.vcell.util.UtilCancelException in project vcell by virtualcell.

the class NetworkProxyPreferences method setProxyPrefs.

public static void setProxyPrefs(Component requester, RestartWarningProvider restartWarningProvider) throws UtilCancelException {
    Preferences prefs = Preferences.userNodeForPackage(RemoteProxyVCellConnectionFactory.class);
    String proxyType = prefs.get(prefProxyType, prefProxyType);
    String proxyHost = prefs.get(prefProxyHost, prefProxyHost);
    String proxyPort = prefs.get(prefProxyPort, prefProxyPort);
    do {
        try {
            String init = proxyType + ":" + proxyHost + ":" + proxyPort;
            String s = DialogUtils.showInputDialog0(requester, "Enter 3 : separated values, " + PROXY_FORMAT, init);
            String proxyTypeNew = null;
            String proxyHostNew = null;
            String proxyPortNew = null;
            if (s == null || s.trim().length() == 0) {
                // clear proxy info
                prefs.remove(prefProxyType);
                prefs.remove(prefProxyHost);
                prefs.remove(prefProxyPort);
            } else {
                StringTokenizer st = new StringTokenizer(s, ":");
                proxyTypeNew = st.nextToken().toLowerCase();
                if (!proxyTypeNew.equals("http") && !proxyTypeNew.equals("socks")) {
                    throw new IllegalArgumentException("Unkown proxyType='" + proxyTypeNew + "'");
                }
                proxyHostNew = st.nextToken();
                proxyPortNew = st.nextToken();
                prefs.put(prefProxyType, proxyTypeNew);
                prefs.put(prefProxyHost, proxyHostNew);
                prefs.put(prefProxyPort, Integer.parseInt(proxyPortNew) + "");
            }
            break;
        } catch (UtilCancelException uce) {
            // User didn't set proxy info
            throw uce;
        } catch (NumberFormatException nfe) {
            nfe.printStackTrace();
            DialogUtils.showErrorDialog(requester, nfe.getMessage() + "\nportNumber must be integer between 0 and 65535");
        } catch (IllegalArgumentException iae) {
            iae.printStackTrace();
            DialogUtils.showErrorDialog(requester, iae.getMessage() + "\nProxy type must be 'http' or 'socks'");
        } catch (Exception e) {
            e.printStackTrace();
            DialogUtils.showErrorDialog(requester, e.getMessage() + "\nEntry must be of form (" + PROXY_FORMAT + ")");
        }
    } while (true);
    NetworkProxyUtils.setProxyProperties(true, restartWarningProvider, proxyType, proxyHost, proxyPort, prefs.get(prefProxyType, prefProxyType), prefs.get(prefProxyHost, prefProxyHost), prefs.get(prefProxyPort, prefProxyPort));
}

Example 15 with UtilCancelException

use of org.vcell.util.UtilCancelException in project vcell by virtualcell.

the class ParameterEstimationPanel method newParameterEstimationTaskButton_ActionPerformed.

private void newParameterEstimationTaskButton_ActionPerformed() {
    try {
        String parameterEstimationName = "task0";
        if (simulationContext == null) {
            return;
        }
        AnalysisTask[] analysisTasks = simulationContext.getAnalysisTasks();
        boolean found = true;
        while (found) {
            found = false;
            parameterEstimationName = TokenMangler.getNextEnumeratedToken(parameterEstimationName);
            for (int i = 0; analysisTasks != null && i < analysisTasks.length; i++) {
                if (analysisTasks[i].getName().equals(parameterEstimationName)) {
                    found = true;
                    continue;
                }
            }
        }
        String newParameterEstimationName = null;
        try {
            newParameterEstimationName = DialogUtils.showInputDialog0(this, "name for new parameter estimation set", parameterEstimationName);
        } catch (UtilCancelException ex) {
        // user canceled; it's ok
        }
        if (newParameterEstimationName != null) {
            if (newParameterEstimationName.length() == 0) {
                PopupGenerator.showErrorDialog(this, "Error:\n name for new parameter estimation can't be empty");
            } else {
                final String finalname = newParameterEstimationName;
                AsynchClientTask task1 = new AsynchClientTask("init task", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

                    @Override
                    public void run(Hashtable<String, Object> hashTable) throws Exception {
                        ParameterEstimationTask newParameterEstimationTask = new ParameterEstimationTask(simulationContext);
                        newParameterEstimationTask.setName(finalname);
                        hashTable.put("newParameterEstimationTask", newParameterEstimationTask);
                    }
                };
                AsynchClientTask task2 = new AsynchClientTask("add task", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

                    @Override
                    public void run(Hashtable<String, Object> hashTable) throws Exception {
                        ParameterEstimationTask newParameterEstimationTask = (ParameterEstimationTask) hashTable.get("newParameterEstimationTask");
                        simulationContext.addAnalysisTask(newParameterEstimationTask);
                        getAnalysisTaskComboBox().setSelectedItem(newParameterEstimationTask);
                        refreshAnalysisTaskEnables();
                    }
                };
                ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
            }
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        DialogUtils.showErrorDialog(this, e.getMessage(), e);
    }
}