/* $Id: ESTsSubmitter.java 67 2008-12-21 22:00:12Z weizhongli $
* $Author: weizhongli $
* ======================================================================
* Batch ESTs submitter to dbEST
* ====================================================================== */
package easiest;
import java.awt.event.ActionListener;
import java.awt.event.ActionEvent;
import java.awt.BorderLayout;
import javax.swing.SwingConstants;
import javax.swing.SwingUtilities;
import java.awt.Point;
import javax.swing.ImageIcon;
import javax.swing.JFileChooser;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JMenuItem;
import javax.swing.JMenuBar;
import javax.swing.JMenu;
import javax.swing.JFrame;
import javax.swing.JDialog;
import javax.swing.JTabbedPane;
import java.awt.Rectangle;
import javax.swing.JComboBox;
import javax.swing.JTextField;
import javax.swing.JButton;
import javax.swing.event.DocumentEvent;
import javax.swing.event.DocumentListener;
import javax.swing.table.DefaultTableModel;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.awt.Dimension;
import javax.swing.JScrollPane;
import javax.swing.JTable;
public class ESTsSubmitter {
private JFrame jFrame = null; // @jve:decl-index=0:visual-constraint="10,10"
private JMenuBar jJMenuBar = null;
private JMenu fileMenu = null;
private JMenu helpMenu = null;
private JMenuItem exitMenuItem = null;
private JMenuItem aboutMenuItem = null;
private JDialog aboutDialog = null;
private JDialog errorDialog = null; // @jve:decl-index=0:visual-constraint="188,531"
private JPanel aboutContentPane = null;
private JPanel errorContentPane = null;
private JLabel aboutVersionLabel = null;
private JLabel errorVersionLabel = null;
private JTabbedPane jTabbedPane = null;
private JPanel jPanel = null;
private JPanel jPanel1 = null;
private JPanel jPanel2 = null;
private JPanel jPanel3 = null;
private JLabel jLabel = null;
private JLabel jLabel1 = null;
private JLabel jLabel2 = null;
private JLabel jLabel3 = null;
private JLabel jLabel4 = null;
private JLabel jLabel5 = null;
private JLabel jLabel6 = null;
private JLabel jLabel7 = null;
private JComboBox jComboBoxCont = null;
private JTextField jTextFieldName = null;
private JTextField jTextFieldFax = null;
private JTextField jTextFieldTel = null;
private JTextField jTextFieldEmail = null;
private JTextField jTextFieldLab = null;
private JTextField jTextFieldInst = null;
private JTextField jTextFieldAddr = null;
private static JButton jButtonCont = null;
private JLabel jLabel8 = null;
private JLabel jLabel9 = null;
private JLabel jLabel10 = null;
private JLabel jLabel11 = null;
private JLabel jLabel12 = null;
private JLabel jLabel13 = null;
private JLabel jLabel14 = null;
private JLabel jLabel15 = null;
private JLabel jLabel16 = null;
private JLabel jLabel17 = null;
private JLabel jLabel18 = null;
private JLabel jLabel19 = null;
private JComboBox jComboBoxPub = null;
private JTextField jTextFieldMed = null;
private JTextField jTextFieldTitle = null;
private JTextField jTextFieldAuthors = null;
private JTextField jTextFieldJournal = null;
private JTextField jTextFieldVolume = null;
private JTextField jTextFieldSuppl = null;
private JTextField jTextFieldIssue = null;
private JTextField jTextFieldI_Suppl = null;
private JTextField jTextFieldPages = null;
private JTextField jTextFieldYear = null;
private JComboBox jComboBoxStatus = null;
private JLabel jLabel20 = null;
private JLabel jLabel21 = null;
private JLabel jLabel22 = null;
private JLabel jLabel23 = null;
private JLabel jLabel24 = null;
private JLabel jLabel25 = null;
private JLabel jLabel26 = null;
private JLabel jLabel27 = null;
private JLabel jLabel28 = null;
private JLabel jLabel29 = null;
private JLabel jLabel30 = null;
private JLabel jLabel31 = null;
private JLabel jLabel32 = null;
private JLabel jLabel33 = null;
private JLabel jLabel34 = null;
private JLabel jLabel35 = null;
private JLabel jLabel36 = null;
private JLabel jLabel37 = null;
private JComboBox jComboBoxLib = null;
private JTextField jTextFieldLibName = null;
private JTextField jTextFieldOrganism = null;
private JTextField jTextFieldStrain = null;
private JTextField jTextFieldCultivar = null;
private JTextField jTextFieldIsolate = null;
private JComboBox jComboBoxSex = null;
private JTextField jTextFieldOrgan = null;
private JTextField jTextFieldTissue = null;
private JTextField jTextFieldCell_Type = null;
private JTextField jTextFieldCell_Line = null;
private JTextField jTextFieldStage = null;
private JTextField jTextFieldHost = null;
private JTextField jTextFieldVector = null;
private JComboBox jComboBoxV_Type = null;
private JTextField jTextFieldRE_1 = null;
private JTextField jTextFieldRE_2 = null;
private JTextField jTextFieldDescr = null;
private JLabel jLabel38 = null;
private JLabel jLabel39 = null;
private JLabel jLabel40 = null;
private JLabel jLabel41 = null;
private JLabel jLabel42 = null;
private JLabel jLabel43 = null;
private JLabel jLabel44 = null;
private JLabel jLabel45 = null;
private JLabel jLabel46 = null;
private JLabel jLabel47 = null;
private JLabel jLabel48 = null;
private JLabel jLabel49 = null;
private JLabel jLabel50 = null;
private JLabel jLabel51 = null;
private JLabel jLabel52 = null;
private JLabel jLabel53 = null;
private JLabel jLabel54 = null;
private JLabel jLabel55 = null;
private JLabel jLabel56 = null;
private JLabel jLabel57 = null;
private JLabel jLabel58 = null;
private JLabel jLabel59 = null;
private JLabel jLabel60 = null;
private JLabel jLabel61 = null;
private JLabel jLabel62 = null;
private JLabel jLabel63 = null;
private JLabel jLabel64 = null;
private JLabel jLabel65 = null;
private JLabel jLabel66 = null;
private JLabel jLabel67 = null;
private JLabel jLabel68 = null;
private JLabel jLabel69 = null;
private JLabel jLabel70 = null;
private JLabel jLabel71 = null;
private JLabel jLabel72 = null;
private JLabel jLabel73 = null;
private JComboBox jComboBoxEST = null;
private JComboBox jComboBoxStatusEST = null;
private JTextField jTextFieldContEST = null;
private JTextField jTextFieldCitationEST = null;
private JTextField jTextFieldLibEST = null;
private JTextField jTextFieldPublic = null;
private JPanel jPanelStart = null;
private JLabel jLabel75 = null;
private JLabel jLabel76 = null;
private JTextField jTextFieldDir = null;
private JButton jButtonDir = null;
private JLabel jLabel77 = null;
private JPanel jPanelFinish = null;
private static JButton jButtonPub = null;
private String filePath = null;
private String contactFilePath =null;
private String publicationFilePath =null;
private String libraryFilePath =null;
private String estFilePath =null;
private PrintWriter outputContact = null;
private PrintWriter outputPublication = null;
private PrintWriter outputLibrary = null;
private PrintWriter outputEst = null;
private BufferedReader inputFasta =null;
private JLabel jLabel78 = null;
private static JButton jButtonLib = null;
private JLabel jLabel79 = null;
private JLabel jLabel80 = null;
private JTextField jTextFieldDna_Type = null;
private JTextField jTextFieldComment = null;
private JTextField jTextFieldSeq_Primer = null;
private JTextField jTextFieldP_End = null;
private JFrame jFrameAdvanced = null;
private JPanel jContentPaneAdvance = null;
private static JButton jButtonAdvanced = null;
private JScrollPane jScrollPane = null;
private JTable jTable = null;
private JTextField jTextFieldInputFasta = null;
private JLabel jLabel74 = null;
private JButton jButtonFasta = null;
private JButton jButtonLoad = null;
private static JButton jButtonEst = null;
private JLabel jLabel82 = null;
private JLabel jLabel83 = null;
private JLabel jLabel84 = null;
private JLabel jLabel85 = null;
private JLabel jLabel81 = null;
private JLabel jLabel86 = null;
private JLabel jLabel87 = null;
private JLabel jLabel88 = null;
private JLabel jLabel89 = null;
private JLabel jLabel90 = null;
/**
* This method initializes jFrame
*
* @return javax.swing.JFrame
*/
private JFrame getJFrame() {
if (jFrame == null) {
jFrame = new JFrame();
jFrame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
jFrame.setJMenuBar(getJJMenuBar());
jFrame.setSize(824, 511);
jFrame.setContentPane(getJTabbedPane());
jFrame.setTitle("ESTsSubmitter");
}
return jFrame;
}
/**
* This method initializes jJMenuBar
*
* @return javax.swing.JMenuBar
*/
private JMenuBar getJJMenuBar() {
if (jJMenuBar == null) {
jJMenuBar = new JMenuBar();
jJMenuBar.add(getFileMenu());
jJMenuBar.add(getHelpMenu());
}
return jJMenuBar;
}
/**
* This method initializes jMenu
*
* @return javax.swing.JMenu
*/
private JMenu getFileMenu() {
if (fileMenu == null) {
fileMenu = new JMenu();
fileMenu.setText("File");
fileMenu.add(getExitMenuItem());
}
return fileMenu;
}
/**
* This method initializes jMenu
*
* @return javax.swing.JMenu
*/
private JMenu getHelpMenu() {
if (helpMenu == null) {
helpMenu = new JMenu();
helpMenu.setText("Help");
helpMenu.add(getAboutMenuItem());
}
return helpMenu;
}
/**
* This method initializes jMenuItem
*
* @return javax.swing.JMenuItem
*/
private JMenuItem getExitMenuItem() {
if (exitMenuItem == null) {
exitMenuItem = new JMenuItem();
exitMenuItem.setText("Exit");
exitMenuItem.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
System.exit(0);
}
});
}
return exitMenuItem;
}
/**
* This method initializes jMenuItem
*
* @return javax.swing.JMenuItem
*/
private JMenuItem getAboutMenuItem() {
if (aboutMenuItem == null) {
aboutMenuItem = new JMenuItem();
aboutMenuItem.setText("About");
aboutMenuItem.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
JDialog aboutDialog = getAboutDialog();
aboutDialog.pack();
Point loc = getJFrame().getLocation();
loc.translate(20, 20);
aboutDialog.setLocation(loc);
aboutDialog.setVisible(true);
}
});
}
return aboutMenuItem;
}
/**
* This method initializes aboutDialog
*
* @return javax.swing.JDialog
*/
private JDialog getAboutDialog() {
if (aboutDialog == null) {
aboutDialog = new JDialog(getJFrame(), true);
aboutDialog.setTitle("About");
aboutDialog.setContentPane(getAboutContentPane());
}
return aboutDialog;
}
/**
* This method initializes errorDialog
*
* @return javax.swing.JDialog
*/
private JDialog getErrorDialog() {
if (errorDialog == null) {
errorDialog = new JDialog(getJFrame(), true);
errorDialog.setTitle("Error");
errorDialog.setSize(new Dimension(325, 183));
errorDialog.setContentPane(getErrorContentPane());
}
return errorDialog;
}
/**
* This method initializes aboutContentPane
*
* @return javax.swing.JPanel
*/
private JPanel getAboutContentPane() {
if (aboutContentPane == null) {
aboutContentPane = new JPanel();
aboutContentPane.setLayout(new BorderLayout());
aboutContentPane.add(getAboutVersionLabel(), BorderLayout.CENTER);
}
return aboutContentPane;
}
/**
* This method initializes aboutContentPane
*
* @return javax.swing.JPanel
*/
private JPanel getErrorContentPane() {
if (errorContentPane == null) {
errorContentPane = new JPanel();
errorContentPane.setLayout(new BorderLayout());
errorContentPane.add(getErrorVersionLabel(), BorderLayout.CENTER);
}
return errorContentPane;
}
/**
* This method initializes aboutVersionLabel
*
* @return javax.swing.JLabel
*/
private JLabel getAboutVersionLabel() {
if (aboutVersionLabel == null) {
aboutVersionLabel = new JLabel();
aboutVersionLabel.setText("ESTsSubmitter Version 0.1 in easiEST");
aboutVersionLabel.setHorizontalAlignment(SwingConstants.CENTER);
}
return aboutVersionLabel;
}
/**
* This method initializes aboutVersionLabel
*
* @return javax.swing.JLabel
*/
private JLabel getErrorVersionLabel() {
if (errorVersionLabel == null) {
errorVersionLabel = new JLabel();
errorVersionLabel.setText(" You missed the required fileds with *. ");
errorVersionLabel.setBounds(new Rectangle(17, 70, 270, 16));
errorVersionLabel.setHorizontalAlignment(SwingConstants.CENTER);
}
return errorVersionLabel;
}
/**
* This method initializes jTabbedPane
*
* @return javax.swing.JTabbedPane
*/
private JTabbedPane getJTabbedPane() {
if (jTabbedPane == null) {
jTabbedPane = new JTabbedPane();
jTabbedPane.setTabPlacement(JTabbedPane.LEFT);
jTabbedPane.addTab("Start Project ", new ImageIcon("icons/n1.png"), getJPanelStart(), null);
jTabbedPane.addTab("CONTACT File ", new ImageIcon("icons/n2.png"), getJPanel(), null);
jTabbedPane.addTab("PUBLICATION File", new ImageIcon("icons/n3.png"), getJPanel1(), null);
jTabbedPane.addTab("LIBRARY File ", new ImageIcon("icons/n4.png"), getJPanel2(), null);
jTabbedPane.addTab("EST File ", new ImageIcon("icons/n5.png"), getJPanel3(), null);
jTabbedPane.addTab("Finish ", new ImageIcon("icons/n6.png"), getJPanelFinish(), null);
}
return jTabbedPane;
}
/**
* This method initializes jPanel
*
* @return javax.swing.JPanel
*/
private JPanel getJPanel() {
if (jPanel == null) {
jLabel79 = new JLabel();
jLabel79.setBounds(new Rectangle(122, 296, 176, 18));
jLabel79.setText("*: Field required");
jLabel7 = new JLabel();
jLabel7.setBounds(new Rectangle(46, 241, 73, 16));
jLabel7.setToolTipText("Address string, comma delineation");
jLabel7.setText("Address");
jLabel6 = new JLabel();
jLabel6.setBounds(new Rectangle(46, 212, 77, 16));
jLabel6.setToolTipText("Institution name");
jLabel6.setText("Institute");
jLabel5 = new JLabel();
jLabel5.setBounds(new Rectangle(45, 179, 76, 16));
jLabel5.setToolTipText("Laboratory providing EST");
jLabel5.setText("Laboratory");
jLabel4 = new JLabel();
jLabel4.setBounds(new Rectangle(46, 152, 38, 16));
jLabel4.setToolTipText("Email address");
jLabel4.setText("Email");
jLabel3 = new JLabel();
jLabel3.setBounds(new Rectangle(44, 118, 68, 16));
jLabel3.setToolTipText("Telephone number as string of digits");
jLabel3.setText("Telephone");
jLabel2 = new JLabel();
jLabel2.setBounds(new Rectangle(46, 90, 38, 16));
jLabel2.setToolTipText("Fax number as string of digits");
jLabel2.setText("Fax");
jLabel1 = new JLabel();
jLabel1.setBounds(new Rectangle(45, 60, 56, 16));
jLabel1.setToolTipText("Name of person submitting the EST");
jLabel1.setText("Name*");
jLabel = new JLabel();
jLabel.setBounds(new Rectangle(43, 31, 62, 16));
jLabel.setToolTipText("Entry type (obligatory field)");
jLabel.setText("Type*");
jPanel = new JPanel();
jPanel.setLayout(null);
jPanel.add(jLabel, null);
jPanel.add(jLabel1, null);
jPanel.add(jLabel2, null);
jPanel.add(jLabel3, null);
jPanel.add(jLabel4, null);
jPanel.add(jLabel5, null);
jPanel.add(jLabel6, null);
jPanel.add(jLabel7, null);
jPanel.add(getJComboBoxCont(), null);
jPanel.add(getJTextFieldName(), null);
jPanel.add(getJTextFieldFax(), null);
jPanel.add(getJTextFieldTel(), null);
jPanel.add(getJTextFieldEmail(), null);
jPanel.add(getJTextFieldLab(), null);
jPanel.add(getJTextFieldInst(), null);
jPanel.add(getJTextFieldAddr(), null);
jPanel.add(getJButtonCont(), null);
jPanel.add(jLabel79, null);
}
return jPanel;
}
/**
* This method initializes jPanel1
*
* @return javax.swing.JPanel
*/
private JPanel getJPanel1() {
if (jPanel1 == null) {
jLabel80 = new JLabel();
jLabel80.setBounds(new Rectangle(135, 413, 152, 16));
jLabel80.setText("*: Field required");
jLabel78 = new JLabel();
jLabel78.setBounds(new Rectangle(195, 362, 342, 16));
jLabel78.setText("1: Unpublished; 2: Submitted; 3: In press; 4: Published");
jLabel19 = new JLabel();
jLabel19.setBounds(new Rectangle(43, 358, 53, 21));
jLabel19.setToolTipText("Publication status (Obligatory field)");
jLabel19.setText("Status*");
jLabel18 = new JLabel();
jLabel18.setBounds(new Rectangle(44, 329, 44, 16));
jLabel18.setToolTipText("Year of publication (Obligatory field)");
jLabel18.setText("Year*");
jLabel17 = new JLabel();
jLabel17.setBounds(new Rectangle(45, 299, 38, 16));
jLabel17.setToolTipText("Page, format: 123-9");
jLabel17.setText("Pages");
jLabel16 = new JLabel();
jLabel16.setBounds(new Rectangle(45, 270, 68, 20));
jLabel16.setToolTipText("Issue supplement number");
jLabel16.setText("I_Suppl");
jLabel15 = new JLabel();
jLabel15.setBounds(new Rectangle(43, 239, 65, 21));
jLabel15.setToolTipText("Issue number");
jLabel15.setText("Issue");
jLabel14 = new JLabel();
jLabel14.setBounds(new Rectangle(45, 209, 61, 18));
jLabel14.setToolTipText("Supplement number");
jLabel14.setText("Suppl");
jLabel13 = new JLabel();
jLabel13.setBounds(new Rectangle(46, 180, 60, 20));
jLabel13.setToolTipText("Volume number");
jLabel13.setText("Volume");
jLabel12 = new JLabel();
jLabel12.setBounds(new Rectangle(45, 151, 62, 21));
jLabel12.setToolTipText("Journal name");
jLabel12.setText("Journal");
jLabel11 = new JLabel();
jLabel11.setBounds(new Rectangle(46, 120, 64, 19));
jLabel11.setToolTipText("Author name, format: Name,I.I.; Name2,I.I.; Name3,I.I. (Obligatory field)");
jLabel11.setText("Authors*");
jLabel10 = new JLabel();
jLabel10.setBounds(new Rectangle(45, 89, 49, 18));
jLabel10.setToolTipText("Title of article (Obligatory field)");
jLabel10.setText("Title*");
jLabel9 = new JLabel();
jLabel9.setBounds(new Rectangle(46, 60, 49, 17));
jLabel9.setToolTipText("Medline unique identifier");
jLabel9.setText("MEDUID");
jLabel8 = new JLabel();
jLabel8.setBounds(new Rectangle(44, 30, 38, 16));
jLabel8.setToolTipText("Entry type (obligatory field)");
jLabel8.setText("Type*");
jPanel1 = new JPanel();
jPanel1.setLayout(null);
jPanel1.add(jLabel8, null);
jPanel1.add(jLabel9, null);
jPanel1.add(jLabel10, null);
jPanel1.add(jLabel11, null);
jPanel1.add(jLabel12, null);
jPanel1.add(jLabel13, null);
jPanel1.add(jLabel14, null);
jPanel1.add(jLabel15, null);
jPanel1.add(jLabel16, null);
jPanel1.add(jLabel17, null);
jPanel1.add(jLabel18, null);
jPanel1.add(jLabel19, null);
jPanel1.add(getJComboBoxPub(), null);
jPanel1.add(getJTextFieldMed(), null);
jPanel1.add(getJTextFieldTitle(), null);
jPanel1.add(getJTextFieldAuthors(), null);
jPanel1.add(getJTextFieldJournal(), null);
jPanel1.add(getJTextFieldVolume(), null);
jPanel1.add(getJTextFieldSuppl(), null);
jPanel1.add(getJTextFieldIssue(), null);
jPanel1.add(getJTextFieldI_Suppl(), null);
jPanel1.add(getJTextFieldPages(), null);
jPanel1.add(getJTextFieldYear(), null);
jPanel1.add(getJComboBoxStatus(), null);
jPanel1.add(getJButtonPub(), null);
jPanel1.add(jLabel78, null);
jPanel1.add(jLabel80, null);
}
return jPanel1;
}
/**
* This method initializes jPanel2
*
* @return javax.swing.JPanel
*/
private JPanel getJPanel2() {
if (jPanel2 == null) {
jLabel84 = new JLabel();
jLabel84.setBounds(new Rectangle(121, 389, 89, 16));
jLabel84.setText("*: Field required");
jLabel37 = new JLabel();
jLabel37.setBounds(new Rectangle(344, 206, 38, 16));
jLabel37.setToolTipText("Description of library preparation methods, vector, etc");
jLabel37.setText("Descr");
jLabel36 = new JLabel();
jLabel36.setBounds(new Rectangle(345, 176, 38, 16));
jLabel36.setToolTipText("Restriction enzyme at site2 of vector");
jLabel36.setText("RE_2");
jLabel35 = new JLabel();
jLabel35.setBounds(new Rectangle(345, 146, 38, 16));
jLabel35.setToolTipText("Restriction enzyme at site1 of vector");
jLabel35.setText("RE_1");
jLabel34 = new JLabel();
jLabel34.setBounds(new Rectangle(345, 115, 82, 16));
jLabel34.setToolTipText("Type of vector");
jLabel34.setText("Vector_Type");
jLabel33 = new JLabel();
jLabel33.setBounds(new Rectangle(345, 86, 47, 16));
jLabel33.setToolTipText("Name of vector");
jLabel33.setText("Vector");
jLabel32 = new JLabel();
jLabel32.setBounds(new Rectangle(345, 57, 38, 16));
jLabel32.setToolTipText("Laboratory host");
jLabel32.setText("Host");
jLabel31 = new JLabel();
jLabel31.setBounds(new Rectangle(344, 239, 38, 16));
jLabel31.setToolTipText("Developmental stage");
jLabel31.setText("Stage");
jLabel30 = new JLabel();
jLabel30.setBounds(new Rectangle(45, 330, 60, 16));
jLabel30.setToolTipText("Name of cell line");
jLabel30.setText("Cell_Line");
jLabel29 = new JLabel();
jLabel29.setBounds(new Rectangle(46, 300, 60, 16));
jLabel29.setToolTipText("Cell type");
jLabel29.setText("Cell_Type");
jLabel28 = new JLabel();
jLabel28.setBounds(new Rectangle(45, 270, 46, 16));
jLabel28.setToolTipText("Tissue type");
jLabel28.setText("Tissue");
jLabel27 = new JLabel();
jLabel27.setBounds(new Rectangle(45, 240, 38, 16));
jLabel27.setToolTipText("Organ name");
jLabel27.setText("Organ");
jLabel26 = new JLabel();
jLabel26.setBounds(new Rectangle(46, 210, 38, 16));
jLabel26.setToolTipText("Sex of organism");
jLabel26.setText("Sex");
jLabel25 = new JLabel();
jLabel25.setBounds(new Rectangle(45, 179, 60, 16));
jLabel25.setToolTipText("Individual isolate from which the sequence was obtained");
jLabel25.setText("Isolate");
jLabel24 = new JLabel();
jLabel24.setBounds(new Rectangle(46, 150, 61, 16));
jLabel24.setToolTipText("Plant cultivar");
jLabel24.setText("Cultivar");
jLabel23 = new JLabel();
jLabel23.setBounds(new Rectangle(46, 119, 38, 16));
jLabel23.setToolTipText("Organism strain");
jLabel23.setText("Strain");
jLabel22 = new JLabel();
jLabel22.setBounds(new Rectangle(46, 90, 70, 16));
jLabel22.setToolTipText("Scientific name of Organism from which library prepared (Obligatory field)");
jLabel22.setText("Organism*");
jLabel21 = new JLabel();
jLabel21.setBounds(new Rectangle(45, 61, 48, 16));
jLabel21.setToolTipText("Name of library (Obligatory field)");
jLabel21.setText("Name*");
jLabel20 = new JLabel();
jLabel20.setBounds(new Rectangle(45, 31, 38, 16));
jLabel20.setToolTipText("Entry type (obligatory field)");
jLabel20.setText("Type*");
jPanel2 = new JPanel();
jPanel2.setLayout(null);
jPanel2.add(jLabel20, null);
jPanel2.add(jLabel21, null);
jPanel2.add(jLabel22, null);
jPanel2.add(jLabel23, null);
jPanel2.add(jLabel24, null);
jPanel2.add(jLabel25, null);
jPanel2.add(jLabel26, null);
jPanel2.add(jLabel27, null);
jPanel2.add(jLabel28, null);
jPanel2.add(jLabel29, null);
jPanel2.add(jLabel30, null);
jPanel2.add(jLabel31, null);
jPanel2.add(jLabel32, null);
jPanel2.add(jLabel33, null);
jPanel2.add(jLabel34, null);
jPanel2.add(jLabel35, null);
jPanel2.add(jLabel36, null);
jPanel2.add(jLabel37, null);
jPanel2.add(getJComboBoxLib(), null);
jPanel2.add(getJTextFieldLibName(), null);
jPanel2.add(getJTextFieldOrganism(), null);
jPanel2.add(getJTextFieldStrain(), null);
jPanel2.add(getJTextFieldCultivar(), null);
jPanel2.add(getJTextFieldIsolate(), null);
jPanel2.add(getJComboBoxSex(), null);
jPanel2.add(getJTextFieldOrgan(), null);
jPanel2.add(getJTextFieldTissue(), null);
jPanel2.add(getJTextFieldCell_Type(), null);
jPanel2.add(getJTextFieldCell_Line(), null);
jPanel2.add(getJTextFieldStage(), null);
jPanel2.add(getJTextFieldHost(), null);
jPanel2.add(getJTextFieldVector(), null);
jPanel2.add(getJComboBoxV_Type(), null);
jPanel2.add(getJTextFieldRE_1(), null);
jPanel2.add(getJTextFieldRE_2(), null);
jPanel2.add(getJTextFieldDescr(), null);
jPanel2.add(getJButtonLib(), null);
jPanel2.add(jLabel84, null);
}
return jPanel2;
}
/**
* This method initializes jPanel3
*
* @return javax.swing.JPanel
*/
private JPanel getJPanel3() {
if (jPanel3 == null) {
jLabel85 = new JLabel();
jLabel85.setBounds(new Rectangle(298, 413, 88, 16));
jLabel85.setText("*: Field required");
jLabel82 = new JLabel();
jLabel82.setBounds(new Rectangle(133, 225, 376, 21));
jLabel82.setText("The first word in the sequence header will be used as EST#.");
jLabel74 = new JLabel();
jLabel74.setBounds(new Rectangle(44, 194, 89, 23));
jLabel74.setText("Input Fasta file*");
jLabel73 = new JLabel();
jLabel73.setBounds(new Rectangle(344, 121, 61, 15));
jLabel73.setToolTipText("Comments about EST.");
jLabel73.setText("Comment");
jLabel72 = new JLabel();
jLabel72.setToolTipText("Y or N to indicate if a polyA tail was or was not found in the EST sequence.");
jLabel72.setBounds(new Rectangle(480, 85, 38, 16));
jLabel72.setText("PolyA");
jLabel71 = new JLabel();
jLabel71.setToolTipText("The actual sequence of the library tag found in the EST read. If the tag was searched for and not found, put 'Not found' in this field.");
jLabel71.setBounds(new Rectangle(480, 54, 56, 19));
jLabel71.setText("Tag_Seq");
jLabel70 = new JLabel();
jLabel70.setToolTipText("Tissue that was source for the tagged library, if a library tag was found.");
jLabel70.setBounds(new Rectangle(389, 86, 76, 16));
jLabel70.setText("Tag_Tissue");
jLabel69 = new JLabel();
jLabel69.setToolTipText("Name of library whose tag is found in this sequence");
jLabel69.setBounds(new Rectangle(389, 55, 62, 16));
jLabel69.setText("Tag_Lib");
jLabel68 = new JLabel();
jLabel68.setToolTipText("Putative identification of sequence by submitter");
jLabel68.setBounds(new Rectangle(339, 86, 38, 16));
jLabel68.setText("Put_ID");
jLabel67 = new JLabel();
jLabel67.setBounds(new Rectangle(343, 91, 46, 16));
jLabel67.setToolTipText("Date of public release. Leave blank for immediate release.Format: 9/11/1994 (MM/DD/YYYY). Obligatory field.");
jLabel67.setText("Public*");
jLabel66 = new JLabel();
jLabel66.setBounds(new Rectangle(45, 121, 62, 16));
jLabel66.setToolTipText("cDNA (default), Genomic, Viral, Synthetic, Other");
jLabel66.setText("DNA_Type");
jLabel65 = new JLabel();
jLabel65.setToolTipText("Base position of last base of highest quality sequence");
jLabel65.setBounds(new Rectangle(458, 26, 122, 16));
jLabel65.setText("HiQual_Stop");
jLabel64 = new JLabel();
jLabel64.setToolTipText("Base position of start of highest quality sequence (default=1)");
jLabel64.setBounds(new Rectangle(309, 22, 119, 20));
jLabel64.setText("HiQual_Start");
jLabel63 = new JLabel();
jLabel63.setBounds(new Rectangle(345, 150, 38, 16));
jLabel63.setToolTipText("Which end sequenced e.g. 5'");
jLabel63.setText("P_End");
jLabel62 = new JLabel();
jLabel62.setBounds(new Rectangle(43, 150, 74, 16));
jLabel62.setToolTipText("Sequencing primer description or sequence");
jLabel62.setText("Seq_Primer");
jLabel61 = new JLabel();
jLabel61.setToolTipText("Column number or letter");
jLabel61.setBounds(new Rectangle(65, 35, 51, 16));
jLabel61.setText("Column");
jLabel60 = new JLabel();
jLabel60.setToolTipText("Row number or letter");
jLabel60.setBounds(new Rectangle(23, 34, 38, 16));
jLabel60.setText("Row");
jLabel59 = new JLabel();
jLabel59.setToolTipText("Plate number or code");
jLabel59.setBounds(new Rectangle(85, 18, 38, 16));
jLabel59.setText("Plate");
jLabel58 = new JLabel();
jLabel58.setToolTipText("Estimated error in insert length (bases)");
jLabel58.setBounds(new Rectangle(287, 89, 38, 16));
jLabel58.setText("Error");
jLabel57 = new JLabel();
jLabel57.setToolTipText("Insert length (in bases)");
jLabel57.setBounds(new Rectangle(287, 61, 78, 17));
jLabel57.setText("Insert Length");
jLabel56 = new JLabel();
jLabel56.setToolTipText("Backward PCR primer sequence");
jLabel56.setBounds(new Rectangle(212, 125, 47, 16));
jLabel56.setText("PCR_B");
jLabel55 = new JLabel();
jLabel55.setToolTipText("Forward PCR primer sequence");
jLabel55.setBounds(new Rectangle(212, 94, 48, 16));
jLabel55.setText("PCR_F");
jLabel54 = new JLabel();
jLabel54.setToolTipText("Database cross-reference accession");
jLabel54.setBounds(new Rectangle(211, 65, 61, 16));
jLabel54.setText("DBXRef");
jLabel53 = new JLabel();
jLabel53.setToolTipText("Database name for cross-reference to another database");
jLabel53.setBounds(new Rectangle(221, 141, 62, 16));
jLabel53.setText("DBName");
jLabel52 = new JLabel();
jLabel52.setToolTipText("Other ESTs on this clone");
jLabel52.setBounds(new Rectangle(141, 143, 62, 16));
jLabel52.setText("Other_EST");
jLabel51 = new JLabel();
jLabel51.setToolTipText("Source id number for the clone stored in the host");
jLabel51.setBounds(new Rectangle(128, 110, 90, 16));
jLabel51.setText("Source_InHost");
jLabel50 = new JLabel();
jLabel50.setToolTipText("Source id number for the clone as pure DNA");
jLabel50.setBounds(new Rectangle(128, 80, 76, 16));
jLabel50.setText("Source_DNA");
jLabel49 = new JLabel();
jLabel49.setToolTipText("Source providing clone e.g. ATCC");
jLabel49.setBounds(new Rectangle(58, 113, 48, 16));
jLabel49.setText("Source");
jLabel48 = new JLabel();
jLabel48.setToolTipText("Clone id");
jLabel48.setBounds(new Rectangle(15, 19, 59, 16));
jLabel48.setText("Clone ID");
jLabel47 = new JLabel();
jLabel47.setToolTipText("Genome database Dsegment number");
jLabel47.setBounds(new Rectangle(57, 83, 76, 16));
jLabel47.setText("GDB_DSEG");
jLabel46 = new JLabel();
jLabel46.setToolTipText("Genome database accession number");
jLabel46.setBounds(new Rectangle(9, 116, 38, 16));
jLabel46.setText("GDB#");
jLabel45 = new JLabel();
jLabel45.setToolTipText("Secondary GenBank accessions");
jLabel45.setBounds(new Rectangle(9, 86, 48, 16));
jLabel45.setText("GB_SEC");
jLabel44 = new JLabel();
jLabel44.setToolTipText("GenBank accession number");
jLabel44.setBounds(new Rectangle(9, 57, 38, 16));
jLabel44.setText("GB#");
jLabel43 = new JLabel();
jLabel43.setBounds(new Rectangle(44, 225, 38, 16));
jLabel43.setToolTipText("EST id assigned by contact lab (Obligatory field)");
jLabel43.setText("EST# *");
jLabel42 = new JLabel();
jLabel42.setBounds(new Rectangle(343, 61, 47, 16));
jLabel42.setToolTipText("Library name (must be identical string to library name entry, obligatory field)");
jLabel42.setText("Library*");
jLabel41 = new JLabel();
jLabel41.setBounds(new Rectangle(46, 90, 61, 16));
jLabel41.setToolTipText("Journal citation (must be identical string to the publication title, obligatory field)");
jLabel41.setText("Citation*");
jLabel40 = new JLabel();
jLabel40.setBounds(new Rectangle(45, 60, 76, 16));
jLabel40.setToolTipText("Name of contact (must be identical string to the contact entry, obligatory field)");
jLabel40.setText("Cont_Name*");
jLabel39 = new JLabel();
jLabel39.setBounds(new Rectangle(344, 33, 49, 16));
jLabel39.setToolTipText("Status of EST entry - \"New\" or \"Update\" (obligatory field)");
jLabel39.setText("Status*");
jLabel38 = new JLabel();
jLabel38.setBounds(new Rectangle(45, 31, 38, 16));
jLabel38.setToolTipText("Entry type (obligatory field)");
jLabel38.setText("Type*");
jPanel3 = new JPanel();
jPanel3.setLayout(null);
jPanel3.add(jLabel38, null);
jPanel3.add(jLabel39, null);
jPanel3.add(jLabel40, null);
jPanel3.add(jLabel41, null);
jPanel3.add(jLabel42, null);
jPanel3.add(jLabel43, null);
jPanel3.add(jLabel62, null);
jPanel3.add(jLabel63, null);
jPanel3.add(jLabel66, null);
jPanel3.add(jLabel67, null);
jPanel3.add(jLabel73, null);
jPanel3.add(getJComboBoxEST(), null);
jPanel3.add(getJComboBoxStatusEST(), null);
jPanel3.add(getJTextFieldContEST(), null);
jPanel3.add(getJTextFieldCitationEST(), null);
jPanel3.add(getJTextFieldLibEST(), null);
jPanel3.add(getJTextFieldPublic(), null);
jPanel3.add(getJTextFieldDna_Type(), null);
jPanel3.add(getJTextFieldComment(), null);
jPanel3.add(getJTextFieldSeq_Primer(), null);
jPanel3.add(getJTextFieldP_End(), null);
// Do not show the advanced option in this version
//jPanel3.add(getJButtonAdvanced(), null);
jPanel3.add(getJScrollPane(), null);
jPanel3.add(getJTextFieldInputFasta(), null);
jPanel3.add(jLabel74, null);
jPanel3.add(getJButtonFasta(), null);
jPanel3.add(getJButtonLoad(), null);
jPanel3.add(getJButtonEst(), null);
jPanel3.add(jLabel82, null);
jPanel3.add(jLabel85, null);
}
return jPanel3;
}
/**
* This method initializes jComboBoxCont
*
* @return javax.swing.JComboBox
*/
private JComboBox getJComboBoxCont() {
if (jComboBoxCont == null) {
jComboBoxCont = new JComboBox(new String[]{"Cont"});
jComboBoxCont.setBounds(new Rectangle(121, 29, 69, 25));
}
return jComboBoxCont;
}
/**
* This method initializes jTextFieldName
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldName() {
if (jTextFieldName == null) {
jTextFieldName = new JTextField();
jTextFieldName.setBounds(new Rectangle(121, 60, 211, 20));
jTextFieldName.getDocument().addDocumentListener(new DocumentListener () {
public void changedUpdate(DocumentEvent arg0) {
}
public void insertUpdate(DocumentEvent arg0) {
jTextFieldContEST.setText(jTextFieldName.getText());
}
public void removeUpdate(DocumentEvent arg0) {
jTextFieldContEST.setText(jTextFieldName.getText());
}
});
}
return jTextFieldName;
}
/**
* This method initializes jTextFieldFax
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldFax() {
if (jTextFieldFax == null) {
jTextFieldFax = new JTextField();
jTextFieldFax.setBounds(new Rectangle(121, 91, 211, 20));
}
return jTextFieldFax;
}
/**
* This method initializes jTextFieldTel
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldTel() {
if (jTextFieldTel == null) {
jTextFieldTel = new JTextField();
jTextFieldTel.setBounds(new Rectangle(121, 119, 209, 19));
}
return jTextFieldTel;
}
/**
* This method initializes jTextFieldEmail
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldEmail() {
if (jTextFieldEmail == null) {
jTextFieldEmail = new JTextField();
jTextFieldEmail.setBounds(new Rectangle(120, 150, 211, 19));
}
return jTextFieldEmail;
}
/**
* This method initializes jTextFieldLab
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldLab() {
if (jTextFieldLab == null) {
jTextFieldLab = new JTextField();
jTextFieldLab.setBounds(new Rectangle(121, 177, 210, 19));
}
return jTextFieldLab;
}
/**
* This method initializes jTextFieldInst
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldInst() {
if (jTextFieldInst == null) {
jTextFieldInst = new JTextField();
jTextFieldInst.setBounds(new Rectangle(120, 209, 212, 19));
}
return jTextFieldInst;
}
/**
* This method initializes jTextFieldAddr
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldAddr() {
if (jTextFieldAddr == null) {
jTextFieldAddr = new JTextField();
jTextFieldAddr.setBounds(new Rectangle(120, 239, 360, 21));
}
return jTextFieldAddr;
}
/**
* This method initializes jButtonCont
*
* @return javax.swing.JButton
*/
private JButton getJButtonCont() {
if (jButtonCont == null) {
jButtonCont = new JButton();
jButtonCont.setBounds(new Rectangle(121, 268, 179, 20));
jButtonCont.setText("Generate CONTACT File");
jButtonCont.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent e) {
if (jTextFieldName.getText().equalsIgnoreCase("") ) {
errorDialog = getErrorDialog();
errorDialog.pack();
Point loc = getJFrame().getLocation();
loc.translate(60, 60);
errorDialog.setLocation(loc);
errorDialog.setVisible(true);
}
else {
contactFilePath = filePath+ "/CONTACT";
try {
outputContact = new PrintWriter(new FileWriter(contactFilePath));
} catch (IOException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
String contactInfo = getContactInfo();
outputContact.println(contactInfo);
outputContact.close();
}
}
});
}
return jButtonCont;
}
/**
* This method getContactInfo
*
* @return String
*/
private String getContactInfo() {
String contactInfo;
contactInfo = "TYPE: Cont\n";
if (!jTextFieldName.getText().equalsIgnoreCase("")) {
contactInfo = contactInfo + "NAME: " + jTextFieldName.getText() + "\n";
}
if (!jTextFieldFax.getText().equalsIgnoreCase("")) {
contactInfo = contactInfo + "FAX: " + jTextFieldFax.getText() + "\n";
}
if (!jTextFieldTel.getText().equalsIgnoreCase("") ) {
contactInfo = contactInfo + "TEL: " + jTextFieldTel.getText() + "\n";
}
if (!jTextFieldEmail.getText().equalsIgnoreCase("") ) {
contactInfo = contactInfo + "EMAIL:" + jTextFieldEmail.getText() + "\n";
}
if (!jTextFieldLab.getText().equalsIgnoreCase("") ) {
contactInfo = contactInfo + "LAB: " + jTextFieldLab.getText() + "\n";
}
if (!jTextFieldInst.getText().equalsIgnoreCase("") ) {
contactInfo = contactInfo + "INST: " + jTextFieldInst.getText() + "\n";
}
if (!jTextFieldAddr.getText().equalsIgnoreCase("") ) {
contactInfo = contactInfo + "ADDR: " + jTextFieldAddr.getText() + "\n";
}
contactInfo = contactInfo + "||" + "\n";
return contactInfo;
}
/**
* This method initializes jComboBoxPub
*
* @return javax.swing.JComboBox
*/
private JComboBox getJComboBoxPub() {
if (jComboBoxPub == null) {
jComboBoxPub = new JComboBox(new String [] {"Pub"});
jComboBoxPub.setBounds(new Rectangle(135, 31, 66, 21));
}
return jComboBoxPub;
}
/**
* This method initializes jTextFieldMed
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldMed() {
if (jTextFieldMed == null) {
jTextFieldMed = new JTextField();
jTextFieldMed.setBounds(new Rectangle(134, 60, 68, 21));
}
return jTextFieldMed;
}
/**
* This method initializes jTextFieldTitle
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldTitle() {
if (jTextFieldTitle == null) {
jTextFieldTitle = new JTextField();
jTextFieldTitle.setBounds(new Rectangle(135, 91, 361, 18));
jTextFieldTitle.getDocument().addDocumentListener(new DocumentListener () {
public void changedUpdate(DocumentEvent arg0) {
}
public void insertUpdate(DocumentEvent arg0) {
jTextFieldCitationEST.setText(jTextFieldTitle.getText());
}
public void removeUpdate(DocumentEvent arg0) {
jTextFieldCitationEST.setText(jTextFieldTitle.getText());
}
});
}
return jTextFieldTitle;
}
/**
* This method initializes jTextFieldAuthors
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldAuthors() {
if (jTextFieldAuthors == null) {
jTextFieldAuthors = new JTextField();
jTextFieldAuthors.setBounds(new Rectangle(134, 121, 361, 19));
}
return jTextFieldAuthors;
}
/**
* This method initializes jTextFieldJournal
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldJournal() {
if (jTextFieldJournal == null) {
jTextFieldJournal = new JTextField();
jTextFieldJournal.setBounds(new Rectangle(136, 151, 357, 20));
}
return jTextFieldJournal;
}
/**
* This method initializes jTextFieldVolume
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldVolume() {
if (jTextFieldVolume == null) {
jTextFieldVolume = new JTextField();
jTextFieldVolume.setBounds(new Rectangle(135, 179, 54, 20));
}
return jTextFieldVolume;
}
/**
* This method initializes jTextFieldSuppl
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldSuppl() {
if (jTextFieldSuppl == null) {
jTextFieldSuppl = new JTextField();
jTextFieldSuppl.setBounds(new Rectangle(135, 209, 55, 20));
}
return jTextFieldSuppl;
}
/**
* This method initializes jTextFieldIssue
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldIssue() {
if (jTextFieldIssue == null) {
jTextFieldIssue = new JTextField();
jTextFieldIssue.setBounds(new Rectangle(136, 240, 54, 23));
}
return jTextFieldIssue;
}
/**
* This method initializes jTextFieldI_Suppl
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldI_Suppl() {
if (jTextFieldI_Suppl == null) {
jTextFieldI_Suppl = new JTextField();
jTextFieldI_Suppl.setBounds(new Rectangle(135, 271, 56, 21));
}
return jTextFieldI_Suppl;
}
/**
* This method initializes jTextFieldPages
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldPages() {
if (jTextFieldPages == null) {
jTextFieldPages = new JTextField();
jTextFieldPages.setBounds(new Rectangle(135, 299, 56, 19));
}
return jTextFieldPages;
}
/**
* This method initializes jTextFieldYear
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldYear() {
if (jTextFieldYear == null) {
jTextFieldYear = new JTextField();
jTextFieldYear.setBounds(new Rectangle(135, 330, 56, 21));
}
return jTextFieldYear;
}
/**
* This method initializes jComboBoxStatus
*
* @return javax.swing.JComboBox
*/
private JComboBox getJComboBoxStatus() {
if (jComboBoxStatus == null) {
jComboBoxStatus = new JComboBox(new String [] {"1", "2", "3", "4"} );
jComboBoxStatus.setBounds(new Rectangle(136, 361, 55, 21));
}
return jComboBoxStatus;
}
/**
* This method initializes jComboBoxLib
*
* @return javax.swing.JComboBox
*/
private JComboBox getJComboBoxLib() {
if (jComboBoxLib == null) {
jComboBoxLib = new JComboBox(new String [] {"Lib"} );
jComboBoxLib.setBounds(new Rectangle(121, 32, 77, 17));
}
return jComboBoxLib;
}
/**
* This method initializes jTextFieldLibName
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldLibName() {
if (jTextFieldLibName == null) {
jTextFieldLibName = new JTextField();
jTextFieldLibName.setBounds(new Rectangle(120, 60, 180, 19));
jTextFieldLibName.getDocument().addDocumentListener(new DocumentListener () {
public void changedUpdate(DocumentEvent arg0) {
}
public void insertUpdate(DocumentEvent arg0) {
jTextFieldLibEST.setText(jTextFieldLibName.getText());
}
public void removeUpdate(DocumentEvent arg0) {
jTextFieldLibEST.setText(jTextFieldLibName.getText());
}
});
}
return jTextFieldLibName;
}
/**
* This method initializes jTextFieldOrganism
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldOrganism() {
if (jTextFieldOrganism == null) {
jTextFieldOrganism = new JTextField();
jTextFieldOrganism.setBounds(new Rectangle(120, 90, 181, 21));
}
return jTextFieldOrganism;
}
/**
* This method initializes jTextFieldStrain
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldStrain() {
if (jTextFieldStrain == null) {
jTextFieldStrain = new JTextField();
jTextFieldStrain.setBounds(new Rectangle(120, 120, 180, 20));
}
return jTextFieldStrain;
}
/**
* This method initializes jTextFieldCultivar
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldCultivar() {
if (jTextFieldCultivar == null) {
jTextFieldCultivar = new JTextField();
jTextFieldCultivar.setBounds(new Rectangle(120, 149, 181, 20));
}
return jTextFieldCultivar;
}
/**
* This method initializes jTextFieldIsolate
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldIsolate() {
if (jTextFieldIsolate == null) {
jTextFieldIsolate = new JTextField();
jTextFieldIsolate.setBounds(new Rectangle(120, 180, 181, 19));
}
return jTextFieldIsolate;
}
/**
* This method initializes jComboBoxSex
*
* @return javax.swing.JComboBox
*/
private JComboBox getJComboBoxSex() {
if (jComboBoxSex == null) {
jComboBoxSex = new JComboBox(new String [] {
"", "female", "male", "hermaphrodite"} );
jComboBoxSex.setBounds(new Rectangle(121, 209, 137, 16));
}
return jComboBoxSex;
}
/**
* This method initializes jTextFieldOrgan
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldOrgan() {
if (jTextFieldOrgan == null) {
jTextFieldOrgan = new JTextField();
jTextFieldOrgan.setBounds(new Rectangle(120, 240, 180, 20));
}
return jTextFieldOrgan;
}
/**
* This method initializes jTextFieldTissue
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldTissue() {
if (jTextFieldTissue == null) {
jTextFieldTissue = new JTextField();
jTextFieldTissue.setBounds(new Rectangle(120, 270, 180, 20));
}
return jTextFieldTissue;
}
/**
* This method initializes jTextFieldCell_Type
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldCell_Type() {
if (jTextFieldCell_Type == null) {
jTextFieldCell_Type = new JTextField();
jTextFieldCell_Type.setBounds(new Rectangle(120, 301, 180, 20));
}
return jTextFieldCell_Type;
}
/**
* This method initializes jTextFieldCell_Line
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldCell_Line() {
if (jTextFieldCell_Line == null) {
jTextFieldCell_Line = new JTextField();
jTextFieldCell_Line.setBounds(new Rectangle(121, 330, 180, 20));
}
return jTextFieldCell_Line;
}
/**
* This method initializes jTextFieldStage
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldStage() {
if (jTextFieldStage == null) {
jTextFieldStage = new JTextField();
jTextFieldStage.setBounds(new Rectangle(434, 239, 165, 20));
}
return jTextFieldStage;
}
/**
* This method initializes jTextFieldHost
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldHost() {
if (jTextFieldHost == null) {
jTextFieldHost = new JTextField();
jTextFieldHost.setBounds(new Rectangle(435, 56, 168, 20));
}
return jTextFieldHost;
}
/**
* This method initializes jTextFieldVector
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldVector() {
if (jTextFieldVector == null) {
jTextFieldVector = new JTextField();
jTextFieldVector.setBounds(new Rectangle(434, 86, 168, 20));
}
return jTextFieldVector;
}
/**
* This method initializes jComboBoxV_Type
*
* @return javax.swing.JComboBox
*/
private JComboBox getJComboBoxV_Type() {
if (jComboBoxV_Type == null) {
jComboBoxV_Type = new JComboBox(new String [] {
"", "Cosmid", "Phage", "Plasmid", "YAC", "other"});
jComboBoxV_Type.setBounds(new Rectangle(434, 116, 135, 17));
}
return jComboBoxV_Type;
}
/**
* This method initializes jTextFieldRE_1
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldRE_1() {
if (jTextFieldRE_1 == null) {
jTextFieldRE_1 = new JTextField();
jTextFieldRE_1.setBounds(new Rectangle(436, 145, 165, 19));
}
return jTextFieldRE_1;
}
/**
* This method initializes jTextFieldRE_2
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldRE_2() {
if (jTextFieldRE_2 == null) {
jTextFieldRE_2 = new JTextField();
jTextFieldRE_2.setBounds(new Rectangle(435, 176, 169, 20));
}
return jTextFieldRE_2;
}
/**
* This method initializes jTextFieldDescr
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldDescr() {
if (jTextFieldDescr == null) {
jTextFieldDescr = new JTextField();
jTextFieldDescr.setBounds(new Rectangle(435, 207, 167, 20));
}
return jTextFieldDescr;
}
/**
* This method initializes jComboBoxEST
*
* @return javax.swing.JComboBox
*/
private JComboBox getJComboBoxEST() {
if (jComboBoxEST == null) {
jComboBoxEST = new JComboBox(new String [] {"EST"} );
jComboBoxEST.setBounds(new Rectangle(134, 32, 79, 18));
jComboBoxEST.setEnabled(true);
}
return jComboBoxEST;
}
/**
* This method initializes jComboBoxStatusEST
*
* @return javax.swing.JComboBox
*/
private JComboBox getJComboBoxStatusEST() {
if (jComboBoxStatusEST == null) {
jComboBoxStatusEST = new JComboBox(new String [] {"New", "Update"} );
jComboBoxStatusEST.setBounds(new Rectangle(405, 31, 81, 18));
}
return jComboBoxStatusEST;
}
/**
* This method initializes jTextFieldContEST
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldContEST() {
if (jTextFieldContEST == null) {
jTextFieldContEST = new JTextField();
jTextFieldContEST.setBounds(new Rectangle(133, 58, 183, 20));
jTextFieldContEST.setEditable(false);
}
return jTextFieldContEST;
}
/**
* This method initializes jTextFieldCitationEST
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldCitationEST() {
if (jTextFieldCitationEST == null) {
jTextFieldCitationEST = new JTextField();
jTextFieldCitationEST.setBounds(new Rectangle(133, 90, 184, 20));
jTextFieldCitationEST.setEditable(false);
}
return jTextFieldCitationEST;
}
/**
* This method initializes jTextFieldLibEST
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldLibEST() {
if (jTextFieldLibEST == null) {
jTextFieldLibEST = new JTextField();
jTextFieldLibEST.setBounds(new Rectangle(404, 61, 198, 20));
jTextFieldLibEST.setEditable(false);
}
return jTextFieldLibEST;
}
/**
* This method initializes jTextFieldPublic
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldPublic() {
if (jTextFieldPublic == null) {
jTextFieldPublic = new JTextField();
jTextFieldPublic.setBounds(new Rectangle(403, 91, 198, 17));
}
return jTextFieldPublic;
}
/**
* This method initializes jPanelStart
*
* @return javax.swing.JPanel
*/
private JPanel getJPanelStart() {
if (jPanelStart == null) {
jLabel89 = new JLabel();
jLabel89.setBounds(new Rectangle(46, 240, 511, 16));
jLabel89.setToolTipText("Tips: Move the mouse on the labels of fields for tips when inputting data. \");");
jLabel89.setText("Tips: Move the mouse on the labels of fields for tips when inputting data. ");
jLabel83 = new JLabel();
jLabel83.setBounds(new Rectangle(45, 135, 511, 19));
jLabel83.setText("*: Field required. You have to set a directory firstly, otherwise you can not do anything. ");
jLabel77 = new JLabel();
jLabel77.setBounds(new Rectangle(44, 195, 512, 16));
jLabel77.setText("Then please create files of CONTACT, PUBLICATION, LIBRARY and EST step by step. ");
jLabel76 = new JLabel();
jLabel76.setBounds(new Rectangle(46, 75, 511, 15));
jLabel76.setText("To start a project, please firstly indicate a directory for the output files * :");
jLabel75 = new JLabel();
jLabel75.setBounds(new Rectangle(45, 30, 211, 18));
jLabel75.setText("Welcome to ESTsSubmitter!");
jPanelStart = new JPanel();
jPanelStart.setLayout(null);
jPanelStart.add(jLabel75, null);
jPanelStart.add(jLabel76, null);
jPanelStart.add(getJTextFieldDir(), null);
jPanelStart.add(getJButtonDir(), null);
jPanelStart.add(jLabel77, null);
jPanelStart.add(jLabel83, null);
jPanelStart.add(jLabel89, null);
}
return jPanelStart;
}
/**
* This method initializes jTextFieldDir
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldDir() {
if (jTextFieldDir == null) {
jTextFieldDir = new JTextField();
jTextFieldDir.setBounds(new Rectangle(45, 105, 407, 23));
}
return jTextFieldDir;
}
/**
* This method initializes jButtonDir
*
* @return javax.swing.JButton
*/
private JButton getJButtonDir() {
if (jButtonDir == null) {
jButtonDir = new JButton();
jButtonDir.setBounds(new Rectangle(466, 105, 90, 20));
jButtonDir.setText("Browse");
jButtonDir.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent e) {
if (filePath == null) {
filePath = new String(".");
}
JFileChooser fc = new JFileChooser(filePath);
fc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
fc.showOpenDialog(jButtonDir);
File projectDir = fc.getSelectedFile();
String projectDirPath = projectDir.getAbsolutePath();
jTextFieldDir.setText(projectDirPath);
filePath = projectDirPath;
if (projectDirPath != null) {
jButtonCont.setEnabled(true);
jButtonPub.setEnabled(true);
jButtonLib.setEnabled(true);
jButtonEst.setEnabled(true);
}
}
});
}
return jButtonDir;
}
/**
* This method initializes jPanelFinish
*
* @return javax.swing.JPanel
*/
private JPanel getJPanelFinish() {
if (jPanelFinish == null) {
jLabel90 = new JLabel();
jLabel90.setBounds(new Rectangle(45, 64, 520, 16));
jLabel90.setText("For submission, mail the 4 files to dbEST (batch-sub@ncbi.nlm.nih.gov).");
jLabel88 = new JLabel();
jLabel88.setBounds(new Rectangle(45, 253, 189, 12));
jLabel88.setText("Dec 2008");
jLabel87 = new JLabel();
jLabel87.setBounds(new Rectangle(44, 224, 233, 17));
jLabel87.setText("Weizhong Li");
jLabel86 = new JLabel();
jLabel86.setBounds(new Rectangle(46, 120, 314, 22));
jLabel86.setText("Thanks for using ESTsSubmitter!");
jLabel81 = new JLabel();
jLabel81.setBounds(new Rectangle(44, 30, 521, 21));
jLabel81.setText("To see the result in your project, just go to the fold you specified in the Step 1. ");
jPanelFinish = new JPanel();
jPanelFinish.setLayout(null);
jPanelFinish.add(jLabel81, null);
jPanelFinish.add(jLabel86, null);
jPanelFinish.add(jLabel87, null);
jPanelFinish.add(jLabel88, null);
jPanelFinish.add(jLabel90, null);
}
return jPanelFinish;
}
/**
* This method initializes jButtonPub
*
* @return javax.swing.JButton
*/
private JButton getJButtonPub() {
if (jButtonPub == null) {
jButtonPub = new JButton();
jButtonPub.setBounds(new Rectangle(135, 389, 196, 22));
jButtonPub.setText("Generate PUBLICATION File");
jButtonPub.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent e) {
if (jTextFieldTitle.getText().equalsIgnoreCase("")
|| jTextFieldAuthors.getText().equalsIgnoreCase("")
|| jTextFieldYear.getText().equalsIgnoreCase("") ) {
errorDialog = getErrorDialog();
errorDialog.pack();
Point loc = getJFrame().getLocation();
loc.translate(60, 60);
errorDialog.setLocation(loc);
errorDialog.setVisible(true);
}
else {
publicationFilePath = filePath+ "/PUBLICATION";
try {
outputPublication = new PrintWriter(new FileWriter(publicationFilePath));
} catch (IOException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
String publicationInfo = getPublicationInfo();
outputPublication.println(publicationInfo);
outputPublication.close();
}
}
});
}
return jButtonPub;
}
/**
* This method getPublicationInfo
*
* @return String
*/
private String getPublicationInfo() {
String publicationInfo;
publicationInfo = "TYPE: Pub\n";
if (!jTextFieldMed.getText().equalsIgnoreCase("") ) {
publicationInfo = publicationInfo + "MEDUID: " + jTextFieldMed.getText() + "\n";
}
if (!jTextFieldTitle.getText().equalsIgnoreCase("") ) {
publicationInfo = publicationInfo + "TITLE: \n";
publicationInfo = publicationInfo + jTextFieldTitle.getText() + "\n";
}
if (!jTextFieldAuthors.getText().equalsIgnoreCase("") ) {
publicationInfo = publicationInfo + "AUTHORS: \n";
publicationInfo = publicationInfo + jTextFieldAuthors.getText() + "\n";
}
if (!jTextFieldJournal.getText().equalsIgnoreCase("") ) {
publicationInfo = publicationInfo + "JOURNAL: " + jTextFieldJournal.getText() + "\n";
}
if (!jTextFieldVolume.getText().equalsIgnoreCase("") ) {
publicationInfo = publicationInfo + "VOLUME: " + jTextFieldVolume.getText() + "\n";
}
if (!jTextFieldSuppl.getText().equalsIgnoreCase("") ) {
publicationInfo = publicationInfo + "Suppl: " + jTextFieldSuppl.getText() + "\n";
}
if (!jTextFieldIssue.getText().equalsIgnoreCase("") ) {
publicationInfo = publicationInfo + "ISSUE: " + jTextFieldIssue.getText() + "\n";
}
if (!jTextFieldI_Suppl.getText().equalsIgnoreCase("") ) {
publicationInfo = publicationInfo + "I_Suppl: " + jTextFieldI_Suppl.getText() + "\n";
}
if (!jTextFieldPages.getText().equalsIgnoreCase("") ) {
publicationInfo = publicationInfo + "PAGES: " + jTextFieldPages.getText() + "\n";
}
if (!jTextFieldYear.getText().equalsIgnoreCase("") ) {
publicationInfo = publicationInfo + "YEAR: " + jTextFieldYear.getText() + "\n";
}
if (!((String) jComboBoxStatus.getSelectedItem()).equalsIgnoreCase("") ) {
publicationInfo = publicationInfo + "STATUS: " + jComboBoxStatus.getSelectedItem() + "\n";
}
publicationInfo = publicationInfo + "||" + "\n";
return publicationInfo;
}
/**
* This method initializes jButtonLib
*
* @return javax.swing.JButton
*/
private JButton getJButtonLib() {
if (jButtonLib == null) {
jButtonLib = new JButton();
jButtonLib.setBounds(new Rectangle(121, 359, 190, 23));
jButtonLib.setText("Generate LIBRARY File");
jButtonLib.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent e) {
if (jTextFieldLibName.getText().equalsIgnoreCase("")
|| jTextFieldOrganism.getText().equalsIgnoreCase("") ) {
errorDialog = getErrorDialog();
errorDialog.pack();
Point loc = getJFrame().getLocation();
loc.translate(60, 60);
errorDialog.setLocation(loc);
errorDialog.setVisible(true);
}
else {
libraryFilePath = filePath+ "/LIBRARY";
try {
outputLibrary = new PrintWriter(new FileWriter(libraryFilePath));
} catch (IOException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
String libraryInfo = getLibraryInfo();
outputLibrary.println(libraryInfo);
outputLibrary.close();
}
}
});
}
return jButtonLib;
}
/**
* This method getLibraryInfo
*
* @return String
*/
private String getLibraryInfo() {
String libraryInfo;
libraryInfo = "TYPE: Lib\n";
if (!jTextFieldLibName.getText().equalsIgnoreCase("") ) {
libraryInfo = libraryInfo + "NAME: " + jTextFieldLibName.getText() + "\n";
}
if (!jTextFieldOrganism.getText().equalsIgnoreCase("") ) {
libraryInfo = libraryInfo + "ORGANISM: " + jTextFieldOrganism.getText() + "\n";
}
if (!jTextFieldStrain.getText().equalsIgnoreCase("") ) {
libraryInfo = libraryInfo + "STRAIN: " + jTextFieldStrain.getText() + "\n";
}
if (!jTextFieldCultivar.getText().equalsIgnoreCase("") ) {
libraryInfo = libraryInfo + "CULTIVAR: " + jTextFieldCultivar.getText() + "\n";
}
if (!jTextFieldIsolate.getText().equalsIgnoreCase("") ) {
libraryInfo = libraryInfo + "ISOLATE: " + jTextFieldIsolate.getText() + "\n";
}
if (!((String) jComboBoxSex.getSelectedItem()).equalsIgnoreCase("") ) {
libraryInfo = libraryInfo + "SEX: " + jComboBoxSex.getSelectedItem() + "\n";
}
if (!jTextFieldOrgan.getText().equalsIgnoreCase("") ) {
libraryInfo = libraryInfo + "ORGAN: " + jTextFieldOrgan.getText() + "\n";
}
if (!jTextFieldTissue.getText().equalsIgnoreCase("") ) {
libraryInfo = libraryInfo + "TISSUE: " + jTextFieldTissue.getText() + "\n";
}
if (!jTextFieldCell_Type.getText().equalsIgnoreCase("") ) {
libraryInfo = libraryInfo + "CELL_TYPE: " + jTextFieldCell_Type.getText() + "\n";
}
if (!jTextFieldCell_Line.getText().equalsIgnoreCase("") ) {
libraryInfo = libraryInfo + "CELL_LINE: " + jTextFieldCell_Line.getText() + "\n";
}
if (!jTextFieldStage.getText().equalsIgnoreCase("") ) {
libraryInfo = libraryInfo + "STAGE: " + jTextFieldStage.getText() + "\n";
}
if (!jTextFieldHost.getText().equalsIgnoreCase("") ) {
libraryInfo = libraryInfo + "HOST: " + jTextFieldHost.getText() + "\n";
}
if (!jTextFieldVector.getText().equalsIgnoreCase("") ) {
libraryInfo = libraryInfo + "VECTOR: " + jTextFieldVector.getText() + "\n";
}
if (!((String) jComboBoxV_Type.getSelectedItem()).equalsIgnoreCase("") ) {
libraryInfo = libraryInfo + "V_TYPE: " + jComboBoxV_Type.getSelectedItem() + "\n";
}
if (!jTextFieldRE_1.getText().equalsIgnoreCase("") ) {
libraryInfo = libraryInfo + "RE_1: " + jTextFieldRE_1.getText() + "\n";
}
if (!jTextFieldRE_2.getText().equalsIgnoreCase("") ) {
libraryInfo = libraryInfo + "RE_2: " + jTextFieldRE_2.getText() + "\n";
}
if (!jTextFieldDescr.getText().equalsIgnoreCase("") ) {
libraryInfo = libraryInfo + "DESCR: \n";
libraryInfo = libraryInfo + jTextFieldDescr.getText() + "\n";
}
libraryInfo = libraryInfo + "||" + "\n";
return libraryInfo;
}
/**
* This method initializes jTextFieldDna_Type
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldDna_Type() {
if (jTextFieldDna_Type == null) {
jTextFieldDna_Type = new JTextField();
jTextFieldDna_Type.setBounds(new Rectangle(132, 119, 185, 22));
}
return jTextFieldDna_Type;
}
/**
* This method initializes jTextFieldComment
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldComment() {
if (jTextFieldComment == null) {
jTextFieldComment = new JTextField();
jTextFieldComment.setBounds(new Rectangle(405, 120, 197, 17));
}
return jTextFieldComment;
}
/**
* This method initializes jTextFieldSeq_Primer
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldSeq_Primer() {
if (jTextFieldSeq_Primer == null) {
jTextFieldSeq_Primer = new JTextField();
jTextFieldSeq_Primer.setBounds(new Rectangle(134, 148, 182, 21));
}
return jTextFieldSeq_Primer;
}
/**
* This method initializes jTextFieldP_End
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldP_End() {
if (jTextFieldP_End == null) {
jTextFieldP_End = new JTextField();
jTextFieldP_End.setBounds(new Rectangle(405, 150, 199, 17));
}
return jTextFieldP_End;
}
/**
* This method initializes jFrameAdvanced
*
* @return javax.swing.JFrame
*/
private JFrame getJFrameAdvanced() {
if (jFrameAdvanced == null) {
jFrameAdvanced = new JFrame();
jFrameAdvanced.setSize(new Dimension(585, 208));
jFrameAdvanced.setTitle("Advanced options for EST");
jFrameAdvanced.setContentPane(getJContentPaneAdvance());
}
return jFrameAdvanced;
}
/**
* This method initializes jContentPaneAdvance
*
* @return javax.swing.JPanel
*/
private JPanel getJContentPaneAdvance() {
if (jContentPaneAdvance == null) {
jContentPaneAdvance = new JPanel();
jContentPaneAdvance.setLayout(null);
jContentPaneAdvance.add(jLabel44, null);
jContentPaneAdvance.add(jLabel45, null);
jContentPaneAdvance.add(jLabel46, null);
jContentPaneAdvance.add(jLabel47, null);
jContentPaneAdvance.add(jLabel49, null);
jContentPaneAdvance.add(jLabel50, null);
jContentPaneAdvance.add(jLabel51, null);
jContentPaneAdvance.add(jLabel54, null);
jContentPaneAdvance.add(jLabel55, null);
jContentPaneAdvance.add(jLabel56, null);
jContentPaneAdvance.add(jLabel53, null);
jContentPaneAdvance.add(jLabel64, null);
jContentPaneAdvance.add(jLabel57, null);
jContentPaneAdvance.add(jLabel58, null);
jContentPaneAdvance.add(jLabel68, null);
jContentPaneAdvance.add(jLabel69, null);
jContentPaneAdvance.add(jLabel70, null);
jContentPaneAdvance.add(jLabel65, null);
jContentPaneAdvance.add(jLabel71, null);
jContentPaneAdvance.add(jLabel72, null);
jContentPaneAdvance.add(jLabel52, null);
jContentPaneAdvance.add(jLabel48, null);
jContentPaneAdvance.add(jLabel59, null);
jContentPaneAdvance.add(jLabel60, null);
jContentPaneAdvance.add(jLabel61, null);
}
return jContentPaneAdvance;
}
/**
* This method initializes jButtonAdvanced
*
* @return javax.swing.JButton
*/
private JButton getJButtonAdvanced() {
if (jButtonAdvanced == null) {
jButtonAdvanced = new JButton();
jButtonAdvanced.setBounds(new Rectangle(446, 290, 156, 25));
jButtonAdvanced.setText("Advanced Options");
jButtonAdvanced.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent e) {
getJFrameAdvanced();
Point loc = getJFrame().getLocation();
loc.translate(100, 100);
jFrameAdvanced.setLocation(loc);
jFrameAdvanced.setVisible(true);
}
});
}
return jButtonAdvanced;
}
/**
* This method initializes jScrollPane
*
* @return javax.swing.JScrollPane
*/
private JScrollPane getJScrollPane() {
if (jScrollPane == null) {
jScrollPane = new JScrollPane();
jScrollPane.setBounds(new Rectangle(134, 289, 281, 118));
jScrollPane.setViewportView(getJTable());
}
return jScrollPane;
}
/**
* This method initializes jTable
*
* @return javax.swing.JTable
*/
private JTable getJTable() {
if (jTable == null) {
jTable = new JTable();
jTable.setToolTipText("In the table, EST id assigned by contact lab (Obligatory field); ");
String[] columnNames = {"EST#"};
Object[][] data = { };
DefaultTableModel model = new DefaultTableModel(data,columnNames);
jTable.setModel(model);
}
return jTable;
}
/**
* This method initializes jTextFieldInputFasta
*
* @return javax.swing.JTextField
*/
private JTextField getJTextFieldInputFasta() {
if (jTextFieldInputFasta == null) {
jTextFieldInputFasta = new JTextField();
jTextFieldInputFasta.setBounds(new Rectangle(135, 195, 374, 21));
}
return jTextFieldInputFasta;
}
/**
* This method initializes jButtonFasta
*
* @return javax.swing.JButton
*/
private JButton getJButtonFasta() {
if (jButtonFasta == null) {
jButtonFasta = new JButton();
jButtonFasta.setBounds(new Rectangle(522, 194, 80, 24));
jButtonFasta.setText("Browse");
jButtonFasta.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent e) {
if (filePath == null) {
filePath = new String(".");
}
JFileChooser fc = new JFileChooser(filePath);
fc.showOpenDialog(jButtonFasta);
File fastaFile = fc.getSelectedFile();
String fastaPath = fastaFile.getAbsolutePath();
jTextFieldInputFasta.setText(fastaPath);
jButtonLoad.setEnabled(true);
}
});
}
return jButtonFasta;
}
/**
* This method initializes jButtonLoad
*
* @return javax.swing.JButton
*/
private JButton getJButtonLoad() {
if (jButtonLoad == null) {
jButtonLoad = new JButton();
jButtonLoad.setBounds(new Rectangle(135, 261, 182, 24));
jButtonLoad.setText("Preview EST# in Table");
if (jTextFieldInputFasta.getText().equalsIgnoreCase("")) {
jButtonLoad.setEnabled(false);
}
jButtonLoad.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent e) {
String[] columnNames = {"EST#"};
Object[][] data = {{}};
DefaultTableModel model = new DefaultTableModel(data,columnNames);
try {
inputFasta = new BufferedReader(
new FileReader(jTextFieldInputFasta.getText()));
} catch (FileNotFoundException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
String inputLine;
int row_num = 0;
try {
while ((inputLine = inputFasta.readLine()) != null) {
if (inputLine.startsWith(">")) {
// print EST# etc
row_num++;
String[] seqAcc = inputLine.substring(1).split(" ");
String[] current_row = {seqAcc[0]};
model.insertRow(row_num, current_row);
jTable.setModel(model);
}
}
} catch (IOException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
// Close file handles
try {
inputFasta.close();
} catch (IOException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
}
});
}
return jButtonLoad;
}
/**
* This method initializes jButtonEst
*
* @return javax.swing.JButton
*/
private JButton getJButtonEst() {
if (jButtonEst == null) {
jButtonEst = new JButton();
jButtonEst.setBounds(new Rectangle(135, 411, 153, 24));
jButtonEst.setText("Generate EST File");
jButtonEst.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent e) {
if (jTextFieldContEST.getText().equalsIgnoreCase("")
|| jTextFieldCitationEST.getText().equalsIgnoreCase("")
|| jTextFieldLibEST.getText().equalsIgnoreCase("")
|| jTextFieldPublic.getText().equalsIgnoreCase("")
|| jTextFieldInputFasta.getText().equalsIgnoreCase("")
) {
errorDialog = getErrorDialog();
errorDialog.pack();
Point loc = getJFrame().getLocation();
loc.translate(60, 60);
errorDialog.setLocation(loc);
errorDialog.setVisible(true);
}
else {
estFilePath = filePath+ "/EST";
try {
outputEst = new PrintWriter(new FileWriter(estFilePath));
} catch (IOException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
try {
inputFasta = new BufferedReader(
new FileReader(jTextFieldInputFasta.getText()));
} catch (FileNotFoundException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
String inputLine;
int sequence_num = 0;
try {
while ((inputLine = inputFasta.readLine()) != null) {
if (inputLine.startsWith(">")) {
//Print recodr separator
if (sequence_num > 0) {
outputEst.print("||" + "\n");
}
// Ptint part 1
String estInfoPart1 = getEstInfoPart1();
outputEst.print(estInfoPart1);
// print EST# etc
String[] seqAcc = inputLine.substring(1).split(" ");
outputEst.print("EST: " + seqAcc[0] + "\n");
// Print part 2
String estInfoPart2 = getEstInfoPart2();
outputEst.print(estInfoPart2);
sequence_num++;
}
// Print sequence
else {
outputEst.print(inputLine+ "\n");
}
}
} catch (IOException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
// Close file handles
outputEst.close();
try {
inputFasta.close();
} catch (IOException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
}
}
});
}
return jButtonEst;
}
/**
* This method getEstInfoPart1
*
* @return String
*/
private String getEstInfoPart1() {
String estInfo;
estInfo = "TYPE: EST\n";
if (!((String) jComboBoxStatusEST.getSelectedItem()).equalsIgnoreCase("") ) {
estInfo = estInfo + "Status: " + jComboBoxStatusEST.getSelectedItem() + "\n";
}
if (!jTextFieldContEST.getText().equalsIgnoreCase("") ) {
estInfo = estInfo + "CONT_NAME: " + jTextFieldContEST.getText() + "\n";
}
if (!jTextFieldCitationEST.getText().equalsIgnoreCase("") ) {
estInfo = estInfo + "CITATION: " + jTextFieldCitationEST.getText() + "\n";
}
if (!jTextFieldLibEST.getText().equalsIgnoreCase("") ) {
estInfo = estInfo + "LIBRARY: " + jTextFieldLibEST.getText() + "\n";
}
return estInfo;
}
/**
* This method getEstInfoPart2
*
* @return String
*/
private String getEstInfoPart2() {
String estInfo;
estInfo = "";
if (!jTextFieldSeq_Primer.getText().equalsIgnoreCase("") ) {
estInfo = estInfo + "SEQ_PRIMER:" + jTextFieldSeq_Primer.getText() + "\n";
}
if (!jTextFieldP_End.getText().equalsIgnoreCase("") ) {
estInfo = estInfo + "P_END: " + jTextFieldP_End.getText() + "\n";
}
if (!jTextFieldDna_Type.getText().equalsIgnoreCase("") ) {
estInfo = estInfo + "DNA_TYPE: " + jTextFieldDna_Type.getText() + "\n";
}
if (!jTextFieldPublic.getText().equalsIgnoreCase("") ) {
estInfo = estInfo + "PUBLIC: " + jTextFieldPublic.getText() + "\n";
}
if (!jTextFieldComment.getText().equalsIgnoreCase("") ) {
estInfo = estInfo + "Comment:" + "\n";
estInfo = estInfo + jTextFieldComment.getText() + "\n";
}
estInfo = estInfo + "SEQUENCE:" + "\n";
return estInfo;
}
/**
* Launches this application
*/
public static void main(String[] args) {
SwingUtilities.invokeLater(new Runnable() {
public void run() {
ESTsSubmitter application = new ESTsSubmitter();
application.getJFrame().setVisible(true);
jButtonCont.setEnabled(false);
jButtonPub.setEnabled(false);
jButtonLib.setEnabled(false);
jButtonEst.setEnabled(false);
}
});
}
}