Java tutorial
/* * The Gemma project * * Copyright (c) 2006 University of British Columbia * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * */ package chibi.gemmaanalysis.cli.deprecated; import java.awt.GridBagConstraints; import java.awt.GridBagLayout; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.io.BufferedWriter; import java.io.File; import java.io.FileInputStream; import java.io.FileNotFoundException; import java.io.FileWriter; import java.io.IOException; import java.sql.SQLException; import java.util.Collection; import java.util.Map; import javax.swing.JButton; import javax.swing.JComboBox; import javax.swing.JFileChooser; import javax.swing.JFrame; import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JTextField; import javax.swing.UIManager; import javax.swing.UnsupportedLookAndFeelException; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation; import ubic.gemma.model.genome.sequenceAnalysis.ThreePrimeDistanceMethod; /** * @author pavlidis * @version $Id$ */ @Deprecated public class ProbeMapperGui extends JFrame { /** * */ private static final long serialVersionUID = -7060936185884039602L; private static Log log = LogFactory.getLog(ProbeMapperGui.class.getName()); private javax.swing.JPanel jContentPane = null; private JPanel topButtonPanel = null; private JPanel fileNamesPanel = null; private JPanel bottomPanel = null; private JButton okButton = null; private JButton cancelButton = null; private JPanel inputFileNamePanel = null; private JPanel outputFileNamePanel = null; private JTextField inputFileNameTextField = null; private JButton inputFileBrowseButton = null; private JTextField outputFileNameTextField = null; private JButton outputFileBrowseButton = null; private JPanel locationMethodPanel = null; private JLabel locationMethodLabel = null; JComboBox<String> locationMethodComboBox = null; ThreePrimeDistanceMethod method = ThreePrimeDistanceMethod.RIGHT; protected File inputFile; protected File outputFile; /** * This method initializes jPanel * * @return javax.swing.JPanel */ private JPanel getTopButtonPanel() { if (topButtonPanel == null) { topButtonPanel = new JPanel(); topButtonPanel.setLayout(null); topButtonPanel.add(getLocationMethodPanel(), null); } return topButtonPanel; } /** * This method initializes jPanel * * @return javax.swing.JPanel */ private JPanel getFileNamesPanel() { if (fileNamesPanel == null) { fileNamesPanel = new JPanel(); fileNamesPanel.setLayout(null); fileNamesPanel.add(getInputFileNamePanel(), null); fileNamesPanel.add(getOutputFileNamePanel(), null); } return fileNamesPanel; } /** * This method initializes jPanel1 * * @return javax.swing.JPanel */ private JPanel getBottomPanel() { if (bottomPanel == null) { bottomPanel = new JPanel(); bottomPanel.setLayout(null); bottomPanel.add(getOkButton(), null); bottomPanel.add(getCancelButton(), null); } return bottomPanel; } /** * This method initializes jButton * * @return javax.swing.JButton */ private JButton getOkButton() { if (okButton == null) { okButton = new JButton(); okButton.setText("OK"); okButton.setBounds(200, 13, 51, 26); okButton.addActionListener(new ActionListener() { @Override @SuppressWarnings({ "synthetic-access" }) public void actionPerformed(ActionEvent e) { inputFile = new File(inputFileNameTextField.getText()); outputFile = new File(outputFileNameTextField.getText()); if (inputFile != null || outputFile != null) { run(); } else { log.error("Must provide file names"); } } }); } return okButton; } /** * */ @SuppressWarnings("resource") protected void run() { ProbeMapperCli ptpl = new ProbeMapperCli(); try { String bestOutputFileName = outputFile.getAbsolutePath().replaceFirst("\\.", ".best."); log.info("Saving best to " + bestOutputFileName); Map<String, Collection<BlatAssociation>> results = ptpl.runOnBlatResults(new FileInputStream(inputFile), new BufferedWriter(new FileWriter(outputFile))); File o = new File(bestOutputFileName); ptpl.printBestResults(results, new BufferedWriter(new FileWriter(o))); } catch (FileNotFoundException e) { log.error(e, e); } catch (IOException e) { log.error(e, e); } catch (SQLException e) { log.error(e, e); } } /** * This method initializes jButton1 * * @return javax.swing.JButton */ private JButton getCancelButton() { if (cancelButton == null) { cancelButton = new JButton(); cancelButton.setText("Cancel"); cancelButton.setBounds(256, 13, 73, 26); cancelButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { exit(); } }); } return cancelButton; } /** * */ protected void exit() { System.exit(0); } /** * This method initializes jPanel1 * * @return javax.swing.JPanel */ private JPanel getInputFileNamePanel() { if (inputFileNamePanel == null) { inputFileNamePanel = new JPanel(); inputFileNamePanel.setLayout(null); inputFileNamePanel.setBounds(16, 22, 544, 41); inputFileNamePanel.add(getInputFileNameTextField(), null); inputFileNamePanel.add(getInputFileBrowseButton(), null); } return inputFileNamePanel; } /** * This method initializes jPanel2 * * @return javax.swing.JPanel */ private JPanel getOutputFileNamePanel() { if (outputFileNamePanel == null) { outputFileNamePanel = new JPanel(); outputFileNamePanel.setLayout(null); outputFileNamePanel.setBounds(15, 71, 548, 35); outputFileNamePanel.add(getOutputFileNameTextField(), null); outputFileNamePanel.add(getOutputFileBrowseButton(), null); } return outputFileNamePanel; } /** * This method initializes getInputFileNameTextField * * @return javax.swing.JTextField */ private JTextField getInputFileNameTextField() { if (inputFileNameTextField == null) { inputFileNameTextField = new JTextField(); inputFileNameTextField.setPreferredSize(new java.awt.Dimension(200, 20)); inputFileNameTextField.setLocation(5, 12); inputFileNameTextField.setSize(440, 20); inputFileNameTextField.setText("Input File"); } return inputFileNameTextField; } /** * This method initializes InputFileBrowseButton * * @return javax.swing.JButton */ private JButton getInputFileBrowseButton() { if (inputFileBrowseButton == null) { inputFileBrowseButton = new JButton(); inputFileBrowseButton.setText("Browse..."); inputFileBrowseButton.setActionCommand("inputFileBrowse"); inputFileBrowseButton.setBounds(451, 8, 87, 26); inputFileBrowseButton.addActionListener(new ActionListener() { @Override @SuppressWarnings({ "synthetic-access" }) public void actionPerformed(ActionEvent e) { JFileChooser fc = new JFileChooser(); fc.showOpenDialog(jContentPane.getParent()); File selectedFile = fc.getSelectedFile(); if (selectedFile != null) { getInputFileNameTextField().setText(selectedFile.getAbsolutePath()); if (!selectedFile.canRead()) { // error } else { inputFile = selectedFile; } } } }); } return inputFileBrowseButton; } /** * This method initializes OutputFileNameTextField * * @return javax.swing.JTextField */ private JTextField getOutputFileNameTextField() { if (outputFileNameTextField == null) { outputFileNameTextField = new JTextField(); outputFileNameTextField.setPreferredSize(new java.awt.Dimension(200, 20)); outputFileNameTextField.setText("Output file"); outputFileNameTextField.setBounds(6, 8, 440, 20); } return outputFileNameTextField; } /** * @return javax.swing.JButton */ private JButton getOutputFileBrowseButton() { if (outputFileBrowseButton == null) { outputFileBrowseButton = new JButton(); outputFileBrowseButton.setText("Browse..."); outputFileBrowseButton.setBounds(454, 4, 87, 26); outputFileBrowseButton.addActionListener(new ActionListener() { @Override @SuppressWarnings({ "synthetic-access" }) public void actionPerformed(ActionEvent e) { JFileChooser fc = new JFileChooser(); fc.showSaveDialog(jContentPane.getParent()); File selectedFile = fc.getSelectedFile(); if (selectedFile != null) { getOutputFileNameTextField().setText(selectedFile.getAbsolutePath()); if (selectedFile.canRead()) { outputFile = selectedFile; } else { // error } } } }); } return outputFileBrowseButton; } /** * This method initializes jPanel3 * * @return javax.swing.JPanel */ private JPanel getLocationMethodPanel() { if (locationMethodPanel == null) { locationMethodLabel = new JLabel(); locationMethodPanel = new JPanel(); locationMethodPanel.setLayout(null); locationMethodLabel.setText("Location Method"); locationMethodLabel.setBounds(81, 19, 123, 16); locationMethodLabel.setFont(new java.awt.Font("Dialog", java.awt.Font.PLAIN, 12)); locationMethodPanel.setBounds(0, 0, 594, 46); locationMethodPanel.add(locationMethodLabel, null); locationMethodPanel.add(getLocationMethodComboBox(), null); } return locationMethodPanel; } /** * This method initializes jComboBox * * @return javax.swing.JComboBox */ private JComboBox<String> getLocationMethodComboBox() { if (locationMethodComboBox == null) { locationMethodComboBox = new JComboBox<String>(); locationMethodComboBox.setBounds(209, 17, 234, 20); locationMethodComboBox.addItem("Center"); locationMethodComboBox.addItem("3' end"); locationMethodComboBox.addActionListener(new java.awt.event.ActionListener() { @Override public void actionPerformed(java.awt.event.ActionEvent e) { if (((String) locationMethodComboBox.getSelectedItem()) .equals(ThreePrimeDistanceMethod.MIDDLE)) { method = ThreePrimeDistanceMethod.MIDDLE; } else if (((String) locationMethodComboBox.getSelectedItem()) .equals(ThreePrimeDistanceMethod.RIGHT)) { method = ThreePrimeDistanceMethod.RIGHT; } } }); } return locationMethodComboBox; } /** * @param args */ public static void main(String[] args) { try { UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); } catch (ClassNotFoundException e) { e.printStackTrace(); } catch (InstantiationException e) { e.printStackTrace(); } catch (IllegalAccessException e) { e.printStackTrace(); } catch (UnsupportedLookAndFeelException e) { e.printStackTrace(); } ProbeMapperGui pgmg = new ProbeMapperGui(); pgmg.pack(); pgmg.setVisible(true); } /** * This is the default constructor */ public ProbeMapperGui() { super(); initialize(); } /** * This method initializes this * * @return void */ private void initialize() { this.setDefaultCloseOperation(javax.swing.JFrame.EXIT_ON_CLOSE); this.setSize(602, 472); this.setContentPane(getJContentPane()); this.setTitle("ProbeMapper"); } /** * This method initializes jContentPane * * @return javax.swing.JPanel */ private javax.swing.JPanel getJContentPane() { if (jContentPane == null) { GridBagConstraints gridBagConstraints5 = new GridBagConstraints(); GridBagConstraints gridBagConstraints4 = new GridBagConstraints(); GridBagConstraints gridBagConstraints3 = new GridBagConstraints(); jContentPane = new javax.swing.JPanel(); jContentPane.setLayout(new GridBagLayout()); gridBagConstraints3.insets = new java.awt.Insets(0, 0, 18, 0); gridBagConstraints3.gridx = 0; gridBagConstraints3.gridy = 0; gridBagConstraints3.ipadx = 593; gridBagConstraints3.ipady = 219; gridBagConstraints4.insets = new java.awt.Insets(19, 0, 4, 0); gridBagConstraints4.gridx = 0; gridBagConstraints4.gridy = 1; gridBagConstraints4.ipadx = 593; gridBagConstraints4.ipady = 124; gridBagConstraints5.insets = new java.awt.Insets(5, 37, 1, 31); gridBagConstraints5.gridx = 0; gridBagConstraints5.gridy = 2; gridBagConstraints5.ipadx = 525; gridBagConstraints5.ipady = 50; jContentPane.add(getTopButtonPanel(), gridBagConstraints3); jContentPane.add(getFileNamesPanel(), gridBagConstraints4); jContentPane.add(getBottomPanel(), gridBagConstraints5); } return jContentPane; } } // @jve:decl-index=0:visual-constraint="10,10"