Java tutorial
/* * Copyright 2006-2015 The MZmine 2 Development Team * * This file is part of MZmine 2. * * MZmine 2 is free software; you can redistribute it and/or modify it under the * terms of the GNU General Public License as published by the Free Software * Foundation; either version 2 of the License, or (at your option) any later * version. * * MZmine 2 is distributed in the hope that it will be useful, but WITHOUT ANY * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR * A PARTICULAR PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License along with * MZmine 2; if not, write to the Free Software Foundation, Inc., 51 Franklin * St, Fifth Floor, Boston, MA 02110-1301 USA */ package net.sf.mzmine.modules.visualization.ida; import java.awt.Color; import java.awt.Dimension; import java.awt.Font; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.util.Collections; import java.util.Vector; import java.util.logging.Logger; import javax.swing.Box; import javax.swing.BoxLayout; import javax.swing.JComboBox; import javax.swing.JPanel; import javax.swing.JTextField; import javax.swing.SwingConstants; import javax.swing.border.EmptyBorder; import javax.swing.event.TreeModelEvent; import javax.swing.event.TreeModelListener; import javax.swing.tree.DefaultMutableTreeNode; import org.jfree.chart.plot.XYPlot; import net.sf.mzmine.datamodel.Feature; import net.sf.mzmine.datamodel.PeakList; import net.sf.mzmine.datamodel.PeakListRow; import net.sf.mzmine.datamodel.RawDataFile; import net.sf.mzmine.datamodel.impl.SimplePeakList; import net.sf.mzmine.main.MZmineCore; import net.sf.mzmine.parameters.ParameterSet; import net.sf.mzmine.util.GUIUtils; import net.sf.mzmine.util.PeakListRowSorter; import net.sf.mzmine.util.SortingDirection; import net.sf.mzmine.util.SortingProperty; import com.google.common.collect.Range; /** * IDA visualizer's bottom panel */ class IDABottomPanel extends JPanel implements TreeModelListener, ActionListener { private static final long serialVersionUID = 1L; private Logger logger = Logger.getLogger(this.getClass().getName()); private static final Font smallFont = new Font("SansSerif", Font.PLAIN, 10); private JComboBox<PeakList> peakListSelector; private JComboBox<?> thresholdCombo; private JTextField peakTextField; private PeakThresholdParameter thresholdSettings; private IDAVisualizerWindow masterFrame; private RawDataFile dataFile; IDABottomPanel(IDAVisualizerWindow masterFrame, RawDataFile dataFile, ParameterSet parameters) { this.dataFile = dataFile; this.masterFrame = masterFrame; setLayout(new BoxLayout(this, BoxLayout.X_AXIS)); setBackground(Color.white); setBorder(new EmptyBorder(5, 5, 5, 0)); add(Box.createHorizontalGlue()); GUIUtils.addLabel(this, "Show: ", SwingConstants.RIGHT); thresholdCombo = new JComboBox<Object>(PeakThresholdMode.values()); thresholdCombo.setSelectedItem(PeakThresholdMode.NONE); thresholdCombo.setBackground(Color.white); thresholdCombo.setFont(smallFont); thresholdCombo.addActionListener(this); add(thresholdCombo); JPanel peakThresholdPanel = new JPanel(); peakThresholdPanel.setBackground(Color.white); peakThresholdPanel.setLayout(new BoxLayout(peakThresholdPanel, BoxLayout.X_AXIS)); GUIUtils.addLabel(peakThresholdPanel, "Value: ", SwingConstants.RIGHT); peakTextField = new JTextField(); peakTextField.setPreferredSize(new Dimension(50, 15)); peakTextField.setFont(smallFont); peakTextField.addActionListener(this); peakThresholdPanel.add(peakTextField); add(peakThresholdPanel); GUIUtils.addLabel(this, " from peak list: ", SwingConstants.RIGHT); peakListSelector = new JComboBox<PeakList>(); peakListSelector.setBackground(Color.white); peakListSelector.setFont(smallFont); peakListSelector.addActionListener(masterFrame); peakListSelector.setActionCommand("PEAKLIST_CHANGE"); add(peakListSelector); thresholdSettings = parameters.getParameter(IDAParameters.peakThresholdSettings); thresholdCombo.setSelectedItem(thresholdSettings.getMode()); add(Box.createHorizontalStrut(10)); add(Box.createHorizontalGlue()); } /** * Returns a peak list different peaks depending on the selected option of * the "peak Threshold" combo box */ PeakList getPeaksInThreshold() { PeakList selectedPeakList = (PeakList) peakListSelector.getSelectedItem(); PeakThresholdMode mode = (PeakThresholdMode) thresholdCombo.getSelectedItem(); switch (mode) { case ABOVE_INTENSITY_PEAKS: double threshold = thresholdSettings.getIntensityThreshold(); return getIntensityThresholdPeakList(threshold); case ALL_PEAKS: return selectedPeakList; case TOP_PEAKS: case TOP_PEAKS_AREA: int topPeaks = thresholdSettings.getTopPeaksThreshold(); return getTopThresholdPeakList(topPeaks); } return null; } /** * Returns a peak list with the peaks which intensity is above the parameter * "intensity" */ PeakList getIntensityThresholdPeakList(double intensity) { PeakList selectedPeakList = (PeakList) peakListSelector.getSelectedItem(); if (selectedPeakList == null) return null; SimplePeakList newList = new SimplePeakList(selectedPeakList.getName(), selectedPeakList.getRawDataFiles()); for (PeakListRow peakRow : selectedPeakList.getRows()) { Feature peak = peakRow.getPeak(dataFile); if (peak == null) continue; if (peak.getRawDataPointsIntensityRange().upperEndpoint() > intensity) { newList.addRow(peakRow); } } return newList; } /** * Returns a peak list with the top peaks defined by the parameter * "threshold" */ PeakList getTopThresholdPeakList(int threshold) { PeakList selectedPeakList = (PeakList) peakListSelector.getSelectedItem(); if (selectedPeakList == null) return null; SimplePeakList newList = new SimplePeakList(selectedPeakList.getName(), selectedPeakList.getRawDataFiles()); Vector<PeakListRow> peakRows = new Vector<PeakListRow>(); Range<Double> mzRange = selectedPeakList.getRowsMZRange(); Range<Double> rtRange = selectedPeakList.getRowsRTRange(); PeakThresholdMode selectedPeakOption = (PeakThresholdMode) thresholdCombo.getSelectedItem(); if (selectedPeakOption == PeakThresholdMode.TOP_PEAKS_AREA) { XYPlot xyPlot = masterFrame.getPlot().getXYPlot(); org.jfree.data.Range yAxis = xyPlot.getRangeAxis().getRange(); org.jfree.data.Range xAxis = xyPlot.getDomainAxis().getRange(); rtRange = Range.closed(xAxis.getLowerBound(), xAxis.getUpperBound()); mzRange = Range.closed(yAxis.getLowerBound(), yAxis.getUpperBound()); } for (PeakListRow peakRow : selectedPeakList.getRows()) { if (mzRange.contains(peakRow.getAverageMZ()) && rtRange.contains(peakRow.getAverageRT())) { peakRows.add(peakRow); } } Collections.sort(peakRows, new PeakListRowSorter(SortingProperty.Intensity, SortingDirection.Descending)); if (threshold > peakRows.size()) threshold = peakRows.size(); for (int i = 0; i < threshold; i++) { newList.addRow(peakRows.elementAt(i)); } return newList; } /** * Returns selected peak list */ PeakList getSelectedPeakList() { PeakList selectedPeakList = (PeakList) peakListSelector.getSelectedItem(); return selectedPeakList; } /** * Reloads peak lists from the project to the selector combo box */ void rebuildPeakListSelector() { logger.finest("Rebuilding the peak list selector"); PeakList selectedPeakList = (PeakList) peakListSelector.getSelectedItem(); PeakList currentPeakLists[] = MZmineCore.getProjectManager().getCurrentProject().getPeakLists(dataFile); peakListSelector.removeAllItems(); for (int i = currentPeakLists.length - 1; i >= 0; i--) { peakListSelector.addItem(currentPeakLists[i]); } if (selectedPeakList != null) peakListSelector.setSelectedItem(selectedPeakList); } @Override public void actionPerformed(ActionEvent e) { Object src = e.getSource(); if (src == thresholdCombo) { PeakThresholdMode mode = (PeakThresholdMode) this.thresholdCombo.getSelectedItem(); switch (mode) { case ABOVE_INTENSITY_PEAKS: peakTextField.setText(String.valueOf(thresholdSettings.getIntensityThreshold())); peakTextField.setEnabled(true); break; case ALL_PEAKS: peakTextField.setEnabled(false); break; case TOP_PEAKS: case TOP_PEAKS_AREA: peakTextField.setText(String.valueOf(thresholdSettings.getTopPeaksThreshold())); peakTextField.setEnabled(true); break; } thresholdSettings.setMode(mode); } if (src == peakTextField) { PeakThresholdMode mode = (PeakThresholdMode) this.thresholdCombo.getSelectedItem(); String value = peakTextField.getText(); switch (mode) { case ABOVE_INTENSITY_PEAKS: double topInt = Double.parseDouble(value); thresholdSettings.setIntensityThreshold(topInt); break; case TOP_PEAKS: case TOP_PEAKS_AREA: int topPeaks = Integer.parseInt(value); thresholdSettings.setTopPeaksThreshold(topPeaks); break; default: break; } } PeakList selectedPeakList = getPeaksInThreshold(); if (selectedPeakList != null) masterFrame.getPlot().loadPeakList(selectedPeakList); } @Override public void treeNodesChanged(TreeModelEvent event) { DefaultMutableTreeNode node = (DefaultMutableTreeNode) event.getTreePath().getLastPathComponent(); if (node.getUserObject() instanceof PeakList) rebuildPeakListSelector(); } @Override public void treeNodesInserted(TreeModelEvent event) { DefaultMutableTreeNode node = (DefaultMutableTreeNode) event.getTreePath().getLastPathComponent(); if (node.getUserObject() instanceof PeakList) rebuildPeakListSelector(); } @Override public void treeNodesRemoved(TreeModelEvent event) { DefaultMutableTreeNode node = (DefaultMutableTreeNode) event.getTreePath().getLastPathComponent(); if (node.getUserObject() instanceof PeakList) rebuildPeakListSelector(); } @Override public void treeStructureChanged(TreeModelEvent event) { DefaultMutableTreeNode node = (DefaultMutableTreeNode) event.getTreePath().getLastPathComponent(); if (node.getUserObject() instanceof PeakList) rebuildPeakListSelector(); } }