Java tutorial
/** GenoMetric Space Explorer (GeMSE) Copyright (C) 2017 Vahid Jalili * This program 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 3 of the License, or * (at your option) any later version. * This program 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 this program; if not, write to the Free Software Foundation, * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA */ package GeMSE.GS.Analysis.Stats; import ExternalLibraries.HeatChart; import GeMSE.GlobalVariables; import java.awt.Color; import java.awt.Component; import java.awt.Dimension; import javax.swing.JTable; import javax.swing.ListSelectionModel; import javax.swing.table.DefaultTableModel; import javax.swing.table.TableCellRenderer; import javax.swing.table.TableColumn; import javax.swing.table.TableColumnModel; import org.apache.commons.math3.stat.correlation.Covariance; /** * * @author Vahid Jalili */ public final class OneSampleCovariancePanel extends javax.swing.JPanel { public OneSampleCovariancePanel() { initComponents(); Color.RGBtoHSB(214, 217, 223, bColor); _biasCorrected = false; BiasCorrectedCB.setSelected(_biasCorrected); } private double[][] _data; private Covariance _covariance; private Boolean _biasCorrected; float[] bColor = new float[3]; /** * This method is called from within the constructor to initialize the form. * WARNING: Do NOT modify this code. The content of this method is always * regenerated by the Form Editor. */ @SuppressWarnings("unchecked") // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents private void initComponents() { BiasCorrectedCB = new javax.swing.JCheckBox(); jTabbedPane1 = new javax.swing.JTabbedPane(); jPanel1 = new javax.swing.JPanel(); HeatmapL = new javax.swing.JLabel(); jScrollPane1 = new javax.swing.JScrollPane(); matrixDG = new javax.swing.JTable(); BiasCorrectedCB.setText("bias corrected"); BiasCorrectedCB.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { BiasCorrectedCBActionPerformed(evt); } }); HeatmapL.setHorizontalAlignment(javax.swing.SwingConstants.CENTER); HeatmapL.setText("GeMSE"); javax.swing.GroupLayout jPanel1Layout = new javax.swing.GroupLayout(jPanel1); jPanel1.setLayout(jPanel1Layout); jPanel1Layout .setHorizontalGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING) .addGroup(jPanel1Layout.createSequentialGroup().addContainerGap() .addComponent(HeatmapL, javax.swing.GroupLayout.DEFAULT_SIZE, 607, Short.MAX_VALUE) .addContainerGap())); jPanel1Layout.setVerticalGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING) .addGroup(jPanel1Layout.createSequentialGroup().addContainerGap() .addComponent(HeatmapL, javax.swing.GroupLayout.DEFAULT_SIZE, 444, Short.MAX_VALUE) .addContainerGap())); jTabbedPane1.addTab(" Heat Map ", jPanel1); matrixDG.setModel(new javax.swing.table.DefaultTableModel(new Object[][] { {}, {}, {}, {} }, new String[] { })); matrixDG.setAutoResizeMode(javax.swing.JTable.AUTO_RESIZE_OFF); matrixDG.setCellSelectionEnabled(true); matrixDG.setSelectionMode(javax.swing.ListSelectionModel.SINGLE_INTERVAL_SELECTION); jScrollPane1.setViewportView(matrixDG); jTabbedPane1.addTab(" Grid View ", jScrollPane1); javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this); this.setLayout(layout); layout.setHorizontalGroup( layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING) .addGroup(layout.createSequentialGroup().addContainerGap() .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING) .addGroup(layout.createSequentialGroup().addComponent(BiasCorrectedCB) .addGap(0, 0, Short.MAX_VALUE)) .addComponent(jTabbedPane1)) .addContainerGap())); layout.setVerticalGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING) .addGroup(layout.createSequentialGroup().addContainerGap().addComponent(BiasCorrectedCB) .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED) .addComponent(jTabbedPane1).addContainerGap())); }// </editor-fold>//GEN-END:initComponents private void BiasCorrectedCBActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_BiasCorrectedCBActionPerformed {//GEN-HEADEREND:event_BiasCorrectedCBActionPerformed _biasCorrected = BiasCorrectedCB.isSelected(); RunAnalysis(); }//GEN-LAST:event_BiasCorrectedCBActionPerformed // Variables declaration - do not modify//GEN-BEGIN:variables private javax.swing.JCheckBox BiasCorrectedCB; private javax.swing.JLabel HeatmapL; private javax.swing.JPanel jPanel1; private javax.swing.JScrollPane jScrollPane1; private javax.swing.JTabbedPane jTabbedPane1; private javax.swing.JTable matrixDG; // End of variables declaration//GEN-END:variables public void RunAnalysis(double[][] data) { if (data == null) return; if (data.length < 3 || data[0].length < 2) return; _data = data; RunAnalysis(); } private void RunAnalysis() { if (_data == null) return; _covariance = new Covariance(_data, _biasCorrected); double[][] matrix = (_covariance.getCovarianceMatrix()).getData(); Plot(matrix); GridView(matrix); } private void Plot(double[][] matrix) { HeatChart heatChart = new HeatChart(matrix); heatChart.setBackgroundColour(Color.getHSBColor(bColor[0], bColor[1], bColor[2])); heatChart.setChartMargin(10); Dimension dimension = new Dimension(HeatmapL.getSize().width - 50, HeatmapL.getSize().height - 50); dimension.height = (int) Math .round((dimension.height - (heatChart.getChartMargin() * 5.0)) / matrix.length); dimension.width = (int) Math .round((dimension.width - (heatChart.getChartMargin() * 5.0)) / matrix[0].length); if (dimension.height < 1) dimension.height = 1; if (dimension.width < 1) dimension.width = 1; String[] xValues = new String[matrix.length]; for (int i = 0; i < xValues.length; i++) xValues[i] = ""; heatChart.setXValues(xValues); String[] yValues = new String[matrix[0].length]; for (int i = 0; i < yValues.length; i++) yValues[i] = ""; heatChart.setYValues(yValues); heatChart.setHighValueColour(GlobalVariables.hightValueColor); heatChart.setLowValueColour(GlobalVariables.lowValueColor); heatChart.setCellSize(dimension); HeatmapL.setText(""); HeatmapL.setIcon(new javax.swing.ImageIcon(heatChart.getChartImage(false))); } private void GridView(double[][] matrix) { DefaultTableModel spaceTabMod = new DefaultTableModel() { @Override public boolean isCellEditable(int row, int column) { return false; } }; String[] columnTitle = new String[matrix[0].length + 1]; columnTitle[0] = ""; for (int col = 1; col < columnTitle.length; col++) columnTitle[col] = "Column " + String.valueOf(col); spaceTabMod.setColumnIdentifiers(columnTitle); int col = 0; for (int r = 0; r < matrix.length; r++) { String[] row = new String[matrix[0].length + 1]; row[0] = "Row " + Integer.toString(r); for (col = 0; col < matrix[0].length; col++) row[col + 1] = Double.toString(matrix[r][col]); spaceTabMod.addRow(row); } matrixDG.setModel(spaceTabMod); matrixDG.setAutoResizeMode(JTable.AUTO_RESIZE_OFF); matrixDG.setSelectionMode(ListSelectionModel.SINGLE_INTERVAL_SELECTION); ResizeColumnWidth(matrixDG); } public void ResizeColumnWidth(JTable table) { final TableColumnModel columnModel = table.getColumnModel(); for (int column = 0; column < table.getColumnCount(); column++) { int width = 50; // Min width TableColumn tableColumn = columnModel.getColumn(column); TableCellRenderer renderer = tableColumn.getHeaderRenderer(); if (renderer == null) renderer = table.getTableHeader().getDefaultRenderer(); Component component = renderer.getTableCellRendererComponent(table, tableColumn.getHeaderValue(), false, false, -1, column); width = Math.max(component.getPreferredSize().width + 5, width); for (int row = 0; row < table.getRowCount(); row++) { renderer = table.getCellRenderer(row, column); Component comp = table.prepareRenderer(renderer, row, column); width = Math.max(comp.getPreferredSize().width + 5, width); } if (width > 400) width = 400; columnModel.getColumn(column).setPreferredWidth(width); } } }