Examples with MZmineProject net.sf.mzmine.datamodel.MZmineProject used on opensource projects

Example 1 with MZmineProject

use of net.sf.mzmine.datamodel.MZmineProject in project mzmine2 by mzmine.

the class ProjectParametersSetupDialog method copyParameterValuesToRawDataFiles.

private void copyParameterValuesToRawDataFiles() {
    MZmineProject currentProject = MZmineCore.getProjectManager().getCurrentProject();
    // Remove all previous parameters from project
    UserParameter<?, ?>[] parameters = currentProject.getParameters();
    for (UserParameter<?, ?> parameter : parameters) {
        currentProject.removeParameter(parameter);
    }
    // Add new parameters
    parameters = parameterValues.keySet().toArray(new UserParameter[0]);
    for (UserParameter<?, ?> parameter : parameters) {
        currentProject.addParameter(parameter);
    }
    // Set values for new parameters
    for (int columnIndex = 0; columnIndex < parameterValues.keySet().size(); columnIndex++) {
        UserParameter<?, ?> parameter = tablemodelParameterValues.getParameter(columnIndex + 1);
        for (int dataFileIndex = 0; dataFileIndex < dataFiles.length; dataFileIndex++) {
            RawDataFile file = dataFiles[dataFileIndex];
            Object value = tablemodelParameterValues.getValueAt(dataFileIndex, columnIndex + 1);
            if (parameter instanceof DoubleParameter) {
                Double doubleValue = null;
                if (value instanceof Double)
                    doubleValue = (Double) value;
                if (value instanceof String)
                    doubleValue = Double.parseDouble((String) value);
                currentProject.setParameterValue(parameter, file, doubleValue);
            }
            if (parameter instanceof StringParameter) {
                if (value == null)
                    value = "";
                currentProject.setParameterValue(parameter, file, (String) value);
            }
            if (parameter instanceof ComboParameter) {
                if (value == null)
                    value = "";
                currentProject.setParameterValue(parameter, file, (String) value);
            }
        }
    }
}

Example 2 with MZmineProject

use of net.sf.mzmine.datamodel.MZmineProject in project mzmine2 by mzmine.

the class ProjectParametersSetupDialog method copyParameterValuesFromRawDataFiles.

private void copyParameterValuesFromRawDataFiles() {
    MZmineProject currentProject = MZmineCore.getProjectManager().getCurrentProject();
    for (int dataFileIndex = 0; dataFileIndex < dataFiles.length; dataFileIndex++) {
        RawDataFile file = dataFiles[dataFileIndex];
        UserParameter<?, ?>[] parameters = currentProject.getParameters();
        // Loop through all parameters defined for this file
        for (UserParameter<?, ?> p : parameters) {
            // Check if this parameter has been seen before?
            Object[] values;
            if (!(parameterValues.containsKey(p))) {
                // No, initialize a new array of values for this parameter
                values = new Object[dataFiles.length];
                for (int i = 0; i < values.length; i++) values[i] = p.getValue();
                parameterValues.put(p, values);
            } else {
                values = parameterValues.get(p);
            }
            // Set value of this parameter for the current raw data file
            values[dataFileIndex] = currentProject.getParameterValue(p, file);
        }
    }
}

Example 3 with MZmineProject

use of net.sf.mzmine.datamodel.MZmineProject in project mzmine2 by mzmine.

the class ProjectCloseModule method runModule.

@Override
@Nonnull
public ExitCode runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet parameters, @Nonnull Collection<Task> tasks) {
    int selectedValue = JOptionPane.showInternalConfirmDialog(MZmineCore.getDesktop().getMainWindow().getContentPane(), "Are you sure you want to close the current project?", "Close project", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE);
    if (selectedValue != JOptionPane.YES_OPTION)
        return ExitCode.CANCEL;
    // Close all windows related to previous project
    GUIUtils.closeAllWindows();
    // Create a new, empty project
    MZmineProject newProject = new MZmineProjectImpl();
    // Replace the current project with the new one
    ProjectManager projectManager = MZmineCore.getProjectManager();
    projectManager.setCurrentProject(newProject);
    // Ask the garbage collector to free the previously used memory
    System.gc();
    logger.info("Project closed.");
    return ExitCode.OK;
}

Example 4 with MZmineProject

use of net.sf.mzmine.datamodel.MZmineProject in project mzmine2 by mzmine.

the class HeatMapParameters method showSetupDialog.

@Override
public ExitCode showSetupDialog(Window parent, boolean valueCheckRequired) {
    // Update the parameter choices
    MZmineProject project = MZmineCore.getProjectManager().getCurrentProject();
    UserParameter<?, ?>[] newChoices = project.getParameters();
    getParameter(HeatMapParameters.selectionData).setChoices(newChoices);
    if (newChoices.length > 0) {
        ArrayList<Object> values = new ArrayList<Object>();
        for (RawDataFile dataFile : project.getDataFiles()) {
            Object paramValue = project.getParameterValue(newChoices[0], dataFile);
            if (paramValue == null) {
                continue;
            }
            if (!values.contains(paramValue)) {
                values.add(paramValue);
            }
        }
        Object[] newValues = values.toArray();
        getParameter(HeatMapParameters.referenceGroup).setChoices(newValues);
    }
    HeatmapSetupDialog dialog = new HeatmapSetupDialog(parent, valueCheckRequired, this);
    dialog.setVisible(true);
    return dialog.getExitCode();
}

Example 5 with MZmineProject

use of net.sf.mzmine.datamodel.MZmineProject in project mzmine2 by mzmine.

the class ProjectTreeDnDHandler method importData.

public boolean importData(TransferSupport info) {
    if (!info.isDrop()) {
        return false;
    }
    ProjectTree projectTree = (ProjectTree) info.getComponent();
    DefaultTreeModel treeModel = (DefaultTreeModel) projectTree.getModel();
    MZmineProject project = MZmineCore.getProjectManager().getCurrentProject();
    JTree.DropLocation dl = (JTree.DropLocation) info.getDropLocation();
    TreePath dropPath = dl.getPath();
    DefaultMutableTreeNode droppedLocationNode = (DefaultMutableTreeNode) dropPath.getLastPathComponent();
    Object droppedLocationObject = droppedLocationNode.getUserObject();
    int childIndex = dl.getChildIndex();
    TreePath[] transferedPaths = projectTree.getSelectionPaths();
    // Check if the drop target is among the project data files
    if (droppedLocationObject == RawDataTreeModel.dataFilesNodeName) {
        for (TreePath path : transferedPaths) {
            DefaultMutableTreeNode node = (DefaultMutableTreeNode) path.getLastPathComponent();
            int currentIndex = node.getParent().getIndex(node);
            Object transferObject = node.getUserObject();
            if (transferObject instanceof RawDataFile) {
                treeModel.removeNodeFromParent(node);
                if (childIndex > currentIndex)
                    childIndex--;
                treeModel.insertNodeInto(node, droppedLocationNode, childIndex);
                childIndex++;
            }
        }
    }
    // Check if the drop target is AFTER the data files (last position)
    if ((droppedLocationObject == project) && (childIndex == 1)) {
        int numOfFiles = project.getDataFiles().length;
        DefaultMutableTreeNode filesNode = (DefaultMutableTreeNode) droppedLocationNode.getChildAt(0);
        for (TreePath path : transferedPaths) {
            DefaultMutableTreeNode node = (DefaultMutableTreeNode) path.getLastPathComponent();
            Object transferObject = node.getUserObject();
            if (transferObject instanceof RawDataFile) {
                treeModel.removeNodeFromParent(node);
                treeModel.insertNodeInto(node, filesNode, numOfFiles - 1);
            }
        }
    }
    // Check if the drop target is among the project feature lists
    if (droppedLocationObject == PeakListTreeModel.peakListsNodeName) {
        for (TreePath path : transferedPaths) {
            DefaultMutableTreeNode node = (DefaultMutableTreeNode) path.getLastPathComponent();
            int currentIndex = node.getParent().getIndex(node);
            Object transferObject = node.getUserObject();
            if (childIndex > currentIndex)
                childIndex--;
            if (transferObject instanceof PeakList) {
                treeModel.removeNodeFromParent(node);
                treeModel.insertNodeInto(node, droppedLocationNode, childIndex);
                childIndex++;
            }
        }
    }
    // Check if the drop target is AFTER the feature lists (last position)
    if ((droppedLocationObject == project) && (childIndex == 2)) {
        DefaultMutableTreeNode peakListsNode = (DefaultMutableTreeNode) droppedLocationNode.getChildAt(1);
        int numOfPeakLists = project.getPeakLists().length;
        for (TreePath path : transferedPaths) {
            DefaultMutableTreeNode node = (DefaultMutableTreeNode) path.getLastPathComponent();
            Object transferObject = node.getUserObject();
            if (transferObject instanceof PeakList) {
                treeModel.removeNodeFromParent(node);
                treeModel.insertNodeInto(node, peakListsNode, numOfPeakLists - 1);
            }
        }
    }
    return true;
}