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

Example 46 with PeakList

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

the class PeakListTreeModel method valueForPathChanged.

public void valueForPathChanged(TreePath path, Object value) {
    DefaultMutableTreeNode node = (DefaultMutableTreeNode) path.getLastPathComponent();
    Object object = node.getUserObject();
    String newName = (String) value;
    if (object instanceof RawDataFile) {
        RawDataFile df = (RawDataFile) object;
        df.setName(newName);
    }
    if (object instanceof PeakList) {
        PeakList pl = (PeakList) object;
        pl.setName(newName);
    }
}

Example 47 with PeakList

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

the class PeakListTreeModel method addObject.

/**
 * This method must be called from Swing thread
 */
public void addObject(final Object object) {
    assert object != null;
    if (!SwingUtilities.isEventDispatchThread()) {
        throw new IllegalStateException("This method must be called from Swing thread");
    }
    // Create new node
    final DefaultMutableTreeNode newNode = new DefaultMutableTreeNode(object);
    treeObjects.put(object, newNode);
    if (object instanceof PeakList) {
        int childCount = getChildCount(rootNode);
        insertNodeInto(newNode, rootNode, childCount);
        final PeakList peakList = (PeakList) object;
        PeakListRow[] rows = peakList.getRows();
        for (int i = 0; i < rows.length; i++) {
            DefaultMutableTreeNode rowNode = new DefaultMutableTreeNode(rows[i]);
            treeObjects.put(rows[i], rowNode);
            insertNodeInto(rowNode, newNode, i);
        }
    }
    if (object instanceof MassList) {
        Scan scan = ((MassList) object).getScan();
        final DefaultMutableTreeNode scNode = treeObjects.get(scan);
        assert scNode != null;
        int index = scNode.getChildCount();
        insertNodeInto(newNode, scNode, index);
    }
}

Example 48 with PeakList

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

the class PeakListTreeModel method notifyObjectChanged.

public void notifyObjectChanged(Object object, boolean structureChanged) {
    if (rootNode.getUserObject() == object) {
        if (structureChanged)
            nodeStructureChanged(rootNode);
        else
            nodeChanged(rootNode);
        return;
    }
    Enumeration<?> nodes = rootNode.breadthFirstEnumeration();
    while (nodes.hasMoreElements()) {
        DefaultMutableTreeNode node = (DefaultMutableTreeNode) nodes.nextElement();
        if (node.getUserObject() == object) {
            if (structureChanged) {
                if (object instanceof PeakList) {
                    node.removeAllChildren();
                    PeakList peakList = (PeakList) object;
                    PeakListRow[] rows = peakList.getRows();
                    for (int i = 0; i < rows.length; i++) {
                        DefaultMutableTreeNode rowNode = new DefaultMutableTreeNode(rows[i]);
                        treeObjects.put(rows[i], rowNode);
                        insertNodeInto(rowNode, node, i);
                    }
                }
                nodeStructureChanged(node);
            } else
                nodeChanged(node);
            return;
        }
    }
}

Example 49 with PeakList

use of net.sf.mzmine.datamodel.PeakList 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;
}

Example 50 with PeakList

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

the class ProjectTreeMouseHandler method actionPerformed.

@Override
public void actionPerformed(ActionEvent e) {
    String command = e.getActionCommand();
    if (command.equals("SHOW_TIC")) {
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        TICVisualizerModule.setupNewTICVisualizer(selectedFiles);
    }
    if (command.equals("SHOW_SPECTRUM")) {
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        SpectraVisualizerModule module = MZmineCore.getModuleInstance(SpectraVisualizerModule.class);
        ParameterSet parameters = MZmineCore.getConfiguration().getModuleParameters(SpectraVisualizerModule.class);
        parameters.getParameter(SpectraVisualizerParameters.dataFiles).setValue(RawDataFilesSelectionType.SPECIFIC_FILES, selectedFiles);
        ExitCode exitCode = parameters.showSetupDialog(MZmineCore.getDesktop().getMainWindow(), true);
        MZmineProject project = MZmineCore.getProjectManager().getCurrentProject();
        if (exitCode == ExitCode.OK)
            module.runModule(project, parameters, new ArrayList<Task>());
    }
    if (command.equals("SHOW_IDA")) {
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        if (selectedFiles.length == 0)
            return;
        MsMsVisualizerModule.showIDAVisualizerSetupDialog(selectedFiles[0]);
    }
    if (command.equals("SHOW_2D")) {
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        if (selectedFiles.length == 0)
            return;
        TwoDVisualizerModule.show2DVisualizerSetupDialog(selectedFiles[0]);
    }
    if (command.equals("SHOW_3D")) {
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        if (selectedFiles.length == 0)
            return;
        Fx3DVisualizerModule.setupNew3DVisualizer(selectedFiles[0]);
    }
    if (command.equals("SORT_FILES")) {
        // save current selection
        TreePath[] savedSelection = tree.getSelectionPaths();
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        SortDataFilesModule module = MZmineCore.getModuleInstance(SortDataFilesModule.class);
        ParameterSet params = MZmineCore.getConfiguration().getModuleParameters(SortDataFilesModule.class);
        params.getParameter(SortDataFilesParameters.dataFiles).setValue(RawDataFilesSelectionType.SPECIFIC_FILES, selectedFiles);
        module.runModule(MZmineCore.getProjectManager().getCurrentProject(), params, new ArrayList<Task>());
        // restore selection
        tree.setSelectionPaths(savedSelection);
    }
    if (command.equals("REMOVE_EXTENSION")) {
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        for (RawDataFile file : selectedFiles) {
            file.setName(FilenameUtils.removeExtension(file.toString()));
        }
        tree.updateUI();
    }
    if (command.equals("EXPORT_FILE")) {
        RawDataExportModule exportModule = MZmineCore.getModuleInstance(RawDataExportModule.class);
        ParameterSet params = MZmineCore.getConfiguration().getModuleParameters(RawDataExportModule.class);
        ExitCode ec = params.showSetupDialog(null, true);
        if (ec == ExitCode.OK) {
            ParameterSet parametersCopy = params.cloneParameterSet();
            ArrayList<Task> tasks = new ArrayList<>();
            MZmineProject project = MZmineCore.getProjectManager().getCurrentProject();
            exportModule.runModule(project, parametersCopy, tasks);
            MZmineCore.getTaskController().addTasks(tasks.toArray(new Task[0]));
        }
    }
    if (command.equals("RENAME_FILE")) {
        TreePath path = tree.getSelectionPath();
        if (path == null)
            return;
        else
            tree.startEditingAtPath(path);
    }
    if (command.equals("REMOVE_FILE")) {
        RawDataFile[] selectedFiles = tree.getSelectedObjects(RawDataFile.class);
        PeakList[] allPeakLists = MZmineCore.getProjectManager().getCurrentProject().getPeakLists();
        for (RawDataFile file : selectedFiles) {
            for (PeakList peakList : allPeakLists) {
                if (peakList.hasRawDataFile(file)) {
                    String msg = "Cannot remove file " + file.getName() + ", because it is present in the feature list " + peakList.getName();
                    MZmineCore.getDesktop().displayErrorMessage(MZmineCore.getDesktop().getMainWindow(), msg);
                    return;
                }
            }
            MZmineCore.getProjectManager().getCurrentProject().removeFile(file);
        }
    }
    if (command.equals("SHOW_SCAN")) {
        Scan[] selectedScans = tree.getSelectedObjects(Scan.class);
        for (Scan scan : selectedScans) {
            SpectraVisualizerModule.showNewSpectrumWindow(scan.getDataFile(), scan.getScanNumber());
        }
    }
    if (command.equals("EXPORT_SCAN")) {
        Scan[] selectedScans = tree.getSelectedObjects(Scan.class);
        ExportScansModule.showSetupDialog(selectedScans);
    }
    if (command.equals("SHOW_MASSLIST")) {
        MassList[] selectedMassLists = tree.getSelectedObjects(MassList.class);
        for (MassList massList : selectedMassLists) {
            Scan scan = massList.getScan();
            SpectraVisualizerWindow window = SpectraVisualizerModule.showNewSpectrumWindow(scan.getDataFile(), scan.getScanNumber());
            MassListDataSet dataset = new MassListDataSet(massList);
            window.addDataSet(dataset, Color.green);
        }
    }
    if (command.equals("REMOVE_MASSLIST")) {
        MassList[] selectedMassLists = tree.getSelectedObjects(MassList.class);
        for (MassList massList : selectedMassLists) {
            Scan scan = massList.getScan();
            scan.removeMassList(massList);
        }
    }
    if (command.equals("REMOVE_ALL_MASSLISTS")) {
        MassList[] selectedMassLists = tree.getSelectedObjects(MassList.class);
        for (MassList massList : selectedMassLists) {
            String massListName = massList.getName();
            RawDataFile[] dataFiles = MZmineCore.getProjectManager().getCurrentProject().getDataFiles();
            for (RawDataFile dataFile : dataFiles) {
                int[] scanNumbers = dataFile.getScanNumbers();
                for (int scanNum : scanNumbers) {
                    Scan scan = dataFile.getScan(scanNum);
                    MassList ml = scan.getMassList(massListName);
                    if (ml != null)
                        scan.removeMassList(ml);
                }
            }
        }
    }
    if (command.equals("SHOW_PEAKLIST_TABLES")) {
        PeakList[] selectedPeakLists = tree.getSelectedObjects(PeakList.class);
        for (PeakList peakList : selectedPeakLists) {
            PeakListTableModule.showNewPeakListVisualizerWindow(peakList);
        }
    }
    if (command.equals("SHOW_PEAKLIST_INFO")) {
        PeakList[] selectedPeakLists = tree.getSelectedObjects(PeakList.class);
        for (PeakList peakList : selectedPeakLists) {
            InfoVisualizerModule.showNewPeakListInfo(peakList);
        }
    }
    if (command.equals("SHOW_SCATTER_PLOT")) {
        PeakList[] selectedPeakLists = tree.getSelectedObjects(PeakList.class);
        for (PeakList peakList : selectedPeakLists) {
            ScatterPlotVisualizerModule.showNewScatterPlotWindow(peakList);
        }
    }
    if (command.equals("SORT_PEAKLISTS")) {
        // save current selection
        TreePath[] savedSelection = tree.getSelectionPaths();
        PeakList[] selectedPeakLists = tree.getSelectedObjects(PeakList.class);
        SortPeakListsModule module = MZmineCore.getModuleInstance(SortPeakListsModule.class);
        ParameterSet params = MZmineCore.getConfiguration().getModuleParameters(SortPeakListsModule.class);
        params.getParameter(SortPeakListsParameters.peakLists).setValue(PeakListsSelectionType.SPECIFIC_PEAKLISTS, selectedPeakLists);
        module.runModule(MZmineCore.getProjectManager().getCurrentProject(), params, new ArrayList<Task>());
        // restore selection
        tree.setSelectionPaths(savedSelection);
    }
    if (command.equals("RENAME_FEATURELIST")) {
        TreePath path = tree.getSelectionPath();
        if (path == null)
            return;
        else
            tree.startEditingAtPath(path);
    }
    if (command.equals("REMOVE_PEAKLIST")) {
        PeakList[] selectedPeakLists = tree.getSelectedObjects(PeakList.class);
        for (PeakList peakList : selectedPeakLists) MZmineCore.getProjectManager().getCurrentProject().removePeakList(peakList);
    }
    if (command.equals("SHOW_PEAK_SUMMARY")) {
        PeakListRow[] selectedRows = tree.getSelectedObjects(PeakListRow.class);
        for (PeakListRow row : selectedRows) {
            PeakSummaryVisualizerModule.showNewPeakSummaryWindow(row);
        }
    }
}