Java tutorial
/* * Copyright 2007-2013 VTT Biotechnology * This file is part of Guineu. * * Guineu 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. * * Guineu 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 * Guineu; if not, write to the Free Software Foundation, Inc., 51 Franklin St, * Fifth Floor, Boston, MA 02110-1301 USA */ package guineu.modules.dataanalysis.PCA; import guineu.data.Dataset; import guineu.data.PeakListRow; import guineu.data.impl.datasets.SimpleBasicDataset; import guineu.data.impl.peaklists.SimplePeakListRowOther; import guineu.main.GuineuCore; import guineu.parameters.ParameterSet; import java.awt.Color; import java.awt.Font; import java.text.NumberFormat; import org.jfree.chart.ChartFactory; import org.jfree.chart.ChartPanel; import org.jfree.chart.JFreeChart; import org.jfree.chart.LegendItem; import org.jfree.chart.LegendItemCollection; import org.jfree.chart.axis.NumberAxis; import org.jfree.chart.plot.PlotOrientation; import org.jfree.chart.plot.XYPlot; import org.jfree.chart.title.TextTitle; import org.jfree.ui.RectangleInsets; /** * @author Taken from MZmine2 http://mzmine.sourceforge.net/ * */ public class ProjectionPlotPanel extends ChartPanel { private static final Color gridColor = Color.lightGray; private static final Font titleFont = new Font("SansSerif", Font.PLAIN, 11); private static final float dataPointAlpha = 0.8f; private JFreeChart chart; private XYPlot plot; private ProjectionPlotItemLabelGenerator itemLabelGenerator; private ProjectionPlotRenderer spotRenderer; public ProjectionPlotPanel(ProjectionPlotWindow masterFrame, ProjectionPlotDataset dataset, ParameterSet parameters) { super(null); boolean createLegend = true; if (dataset.getNumberOfGroups() > 20) { createLegend = false; } chart = ChartFactory.createXYAreaChart("", dataset.getXLabel(), dataset.getYLabel(), dataset, PlotOrientation.VERTICAL, createLegend, false, false); chart.setBackgroundPaint(Color.white); setChart(chart); // title TextTitle chartTitle = chart.getTitle(); chartTitle.setMargin(5, 0, 0, 0); chartTitle.setFont(titleFont); chart.removeSubtitle(chartTitle); // disable maximum size (we don't want scaling) setMaximumDrawWidth(Integer.MAX_VALUE); setMaximumDrawHeight(Integer.MAX_VALUE); // set the plot properties plot = chart.getXYPlot(); plot.setBackgroundPaint(Color.white); plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0)); // set grid properties plot.setDomainGridlinePaint(gridColor); plot.setRangeGridlinePaint(gridColor); // set crosshair (selection) properties plot.setDomainCrosshairVisible(false); plot.setRangeCrosshairVisible(false); plot.setForegroundAlpha(dataPointAlpha); NumberFormat numberFormat = NumberFormat.getNumberInstance(); // set the X axis (component 1) properties NumberAxis xAxis = (NumberAxis) plot.getDomainAxis(); xAxis.setNumberFormatOverride(numberFormat); // set the Y axis (component 2) properties NumberAxis yAxis = (NumberAxis) plot.getRangeAxis(); yAxis.setNumberFormatOverride(numberFormat); plot.setDataset(dataset); spotRenderer = new ProjectionPlotRenderer(plot, dataset); itemLabelGenerator = new ProjectionPlotItemLabelGenerator(parameters); spotRenderer.setBaseItemLabelGenerator(itemLabelGenerator); spotRenderer.setBaseItemLabelsVisible(true); spotRenderer.setBaseToolTipGenerator(new ProjectionPlotToolTipGenerator(parameters)); plot.setRenderer(spotRenderer); // Setup legend if (createLegend) { LegendItemCollection legendItemsCollection = new LegendItemCollection(); for (int groupNumber = 0; groupNumber < dataset.getNumberOfGroups(); groupNumber++) { Object paramValue = dataset.getGroupParameterValue(groupNumber); if (paramValue == null) { // No parameter value available: search for raw data files // within this group, and use their names as group's name String fileNames = new String(); for (int itemNumber = 0; itemNumber < dataset.getItemCount(0); itemNumber++) { String rawDataFile = dataset.getRawDataFile(itemNumber); if (dataset.getGroupNumber(itemNumber) == groupNumber) { fileNames = fileNames.concat(rawDataFile); } } if (fileNames.length() == 0) { fileNames = "Empty group"; } paramValue = fileNames; } Color nextColor = (Color) spotRenderer.getGroupPaint(groupNumber); Color groupColor = new Color(nextColor.getRed(), nextColor.getGreen(), nextColor.getBlue(), (int) Math.round(255 * dataPointAlpha)); legendItemsCollection.add(new LegendItem(paramValue.toString(), "-", null, null, spotRenderer.getDataPointsShape(), groupColor)); } plot.setFixedLegendItems(legendItemsCollection); } else { Dataset legends = new SimpleBasicDataset("Legends"); legends.addColumnName("Samples"); for (int groupNumber = 0; groupNumber < dataset.getNumberOfGroups(); groupNumber++) { Object paramValue = dataset.getGroupParameterValue(groupNumber); if (paramValue == null) { // No parameter value available: search for raw data files // within this group, and use their names as group's name String fileNames = new String(); for (int itemNumber = 0; itemNumber < dataset.getItemCount(0); itemNumber++) { String rawDataFile = dataset.getRawDataFile(itemNumber); if (dataset.getGroupNumber(itemNumber) == groupNumber) { fileNames = fileNames.concat(rawDataFile.toString()); } } if (fileNames.length() == 0) { fileNames = "Empty group"; } paramValue = fileNames; } Color nextColor = (Color) spotRenderer.getGroupPaint(groupNumber); Color groupColor = new Color(nextColor.getRed(), nextColor.getGreen(), nextColor.getBlue(), (int) Math.round(255 * dataPointAlpha)); PeakListRow row = new SimplePeakListRowOther(); row.setPeak("Samples", paramValue.toString()); legends.addRow(row); legends.addRowColor(groupColor); } GuineuCore.getDesktop().AddNewFile(legends); } } protected void cycleItemLabelMode() { itemLabelGenerator.cycleLabelMode(); spotRenderer.setBaseItemLabelsVisible(true); } }