mappingmicroarrayprobestotheratgenomeviaapersistentindex
Class MappingMicroarrayProbestotheRatGenomeviaaPersistentIndexView

java.lang.Object
  extended by FrameView
      extended by mappingmicroarrayprobestotheratgenomeviaapersistentindex.MappingMicroarrayProbestotheRatGenomeviaaPersistentIndexView

public class MappingMicroarrayProbestotheRatGenomeviaaPersistentIndexView
extends FrameView

This class creates the interface for the software


Field Summary
private  javax.swing.JDialog aboutBox
           
private  javax.swing.JButton buildIndexButton
           
private  javax.swing.JPanel buildIndexPanel
           
private  int busyIconIndex
           
private  javax.swing.Icon[] busyIcons
           
private  javax.swing.Timer busyIconTimer
           
private  javax.swing.ButtonGroup buttonGroup1
           
private  javax.swing.ButtonGroup buttonGroup2
           
private  javax.swing.ButtonGroup buttonGroup3
           
private  javax.swing.JButton chromosomeControlDATFilesDestinationBrowseButton
           
private  javax.swing.JLabel chromosomesControlDATFilesDestinationLabel
           
private  javax.swing.JTextField chromosomesControlDATFilesDestinationTextField
           
private  javax.swing.JButton chromosomesLocationBrowseButton
           
private  javax.swing.JLabel chromosomesLocationLabel
           
private  javax.swing.JTextField chromosomesLocationTextField
           
private  java.sql.Connection conn
           
private  java.lang.String dbName
           
private  java.lang.String genome
           
private  javax.swing.Icon idleIcon
           
private  javax.swing.JTextArea indexProgressInformationTextArea
           
private  javax.swing.JLabel indexProgressLabel
           
private  javax.swing.JLabel indexTimingLabel
           
private  javax.swing.JLabel jLabel1
           
private  javax.swing.JScrollPane jScrollPane1
           
private  javax.swing.JScrollPane jScrollPane2
           
private  javax.swing.JScrollPane jScrollPane3
           
private  javax.swing.JTabbedPane jTabbedPane1
           
private  javax.swing.JTabbedPane jTabbedPane2
           
private  javax.swing.JButton locationOfProbesBrowseButton
           
private  javax.swing.JPanel mainPanel
           
private  javax.swing.JMenuBar menuBar
           
private  javax.swing.Timer messageTimer
           
private  javax.swing.JRadioButton nineteenExRadioButton
           
private  javax.swing.JRadioButton nineteenK1RadioButton
           
private  javax.swing.JRadioButton nineteenK3RadioButton
           
private  XMLParser parser
           
private  java.lang.String password
           
private  javax.swing.JButton probesControlDATFilesDestinationBrowseButton
           
private  javax.swing.JLabel probesControlDATFilesDestinationLabel
           
private  javax.swing.JTextField probesControlDATFilesDestinationTextField
           
private  javax.swing.JLabel probesLocationLabel
           
private  javax.swing.JTextField probesLocationTextField
           
private  javax.swing.JTextArea probesProgressInformationTextArea
           
private  javax.swing.JLabel probesProgressLabel
           
private  javax.swing.JProgressBar progressBar
           
private  javax.swing.JPanel runSearchesPanel
           
private  javax.swing.JButton searchButton
           
private  javax.swing.JLabel searchesAvailableLabel
           
private  javax.swing.JTextArea searchProgressInformationTextArea
           
private  javax.swing.JLabel searchProgressLabel
           
private  javax.swing.JRadioButton sixteenExRadioButton
           
private  javax.swing.JLabel statusAnimationLabel
           
private  javax.swing.JLabel statusMessageLabel
           
private  javax.swing.JPanel statusPanel
           
private  javax.swing.JButton storeProbesButton
           
private  javax.swing.JPanel storeProbesPanel
           
private  javax.swing.JTabbedPane tabs
           
private  java.lang.String url
           
private  java.lang.String username
           
 
Constructor Summary
MappingMicroarrayProbestotheRatGenomeviaaPersistentIndexView(SingleFrameApplication app)
           
 
Method Summary
private  void buildIndexButtonActionPerformed(java.awt.event.ActionEvent evt)
          Performs the action when the build index buttion is pressed
private  void chromosomeControlDATFilesDestinationBrowseButtonActionPerformed(java.awt.event.ActionEvent evt)
          Performs the action when the chromosomes control and dat files location browse buttion is pressed
private  void chromosomesLocationBrowseButtonActionPerformed(java.awt.event.ActionEvent evt)
          Performs the action when the chromosomes location browse buttion is pressed
private  void createGeneratedVariantsTable(java.lang.String query)
          Creates the GeneratedVariants table in the database
private  void initComponents()
          This method is called from within the constructor to initialize the form.
static boolean isCtlFile(java.io.File f)
          Checks to see if file f is a ctl file
private  void loadJavaFunctions()
          Loads the required Java functions into the database
private  void locationOfProbesBrowseButtonActionPerformed(java.awt.event.ActionEvent evt)
          Performs the action when the probes location browse buttion is pressed
private  void probesControlDATFilesDestinationBrowseButtonActionPerformed(java.awt.event.ActionEvent evt)
          Performs the action when the probes control and dat files location browse buttion is pressed
private  void search16ex()
          Performs the 16ex search
private  void search19ex()
          Performs the 19ex search
private  void search19k1()
          Performs the 19k1 search
private  void search19k3()
          Performs the 19k3 search
private  void searchButtonActionPerformed(java.awt.event.ActionEvent evt)
          Performs the action when the search buttion is pressed
 void showAboutBox()
          
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

buildIndexButton

private javax.swing.JButton buildIndexButton

buildIndexPanel

private javax.swing.JPanel buildIndexPanel

buttonGroup1

private javax.swing.ButtonGroup buttonGroup1

buttonGroup2

private javax.swing.ButtonGroup buttonGroup2

buttonGroup3

private javax.swing.ButtonGroup buttonGroup3

chromosomeControlDATFilesDestinationBrowseButton

private javax.swing.JButton chromosomeControlDATFilesDestinationBrowseButton

chromosomesControlDATFilesDestinationLabel

private javax.swing.JLabel chromosomesControlDATFilesDestinationLabel

chromosomesControlDATFilesDestinationTextField

private javax.swing.JTextField chromosomesControlDATFilesDestinationTextField

chromosomesLocationBrowseButton

private javax.swing.JButton chromosomesLocationBrowseButton

chromosomesLocationLabel

private javax.swing.JLabel chromosomesLocationLabel

chromosomesLocationTextField

private javax.swing.JTextField chromosomesLocationTextField

indexProgressInformationTextArea

private javax.swing.JTextArea indexProgressInformationTextArea

indexProgressLabel

private javax.swing.JLabel indexProgressLabel

indexTimingLabel

private javax.swing.JLabel indexTimingLabel

jLabel1

private javax.swing.JLabel jLabel1

jScrollPane1

private javax.swing.JScrollPane jScrollPane1

jScrollPane2

private javax.swing.JScrollPane jScrollPane2

jScrollPane3

private javax.swing.JScrollPane jScrollPane3

jTabbedPane1

private javax.swing.JTabbedPane jTabbedPane1

jTabbedPane2

private javax.swing.JTabbedPane jTabbedPane2

locationOfProbesBrowseButton

private javax.swing.JButton locationOfProbesBrowseButton

mainPanel

private javax.swing.JPanel mainPanel

menuBar

private javax.swing.JMenuBar menuBar

nineteenExRadioButton

private javax.swing.JRadioButton nineteenExRadioButton

nineteenK1RadioButton

private javax.swing.JRadioButton nineteenK1RadioButton

nineteenK3RadioButton

private javax.swing.JRadioButton nineteenK3RadioButton

probesControlDATFilesDestinationBrowseButton

private javax.swing.JButton probesControlDATFilesDestinationBrowseButton

probesControlDATFilesDestinationLabel

private javax.swing.JLabel probesControlDATFilesDestinationLabel

probesControlDATFilesDestinationTextField

private javax.swing.JTextField probesControlDATFilesDestinationTextField

probesLocationLabel

private javax.swing.JLabel probesLocationLabel

probesLocationTextField

private javax.swing.JTextField probesLocationTextField

probesProgressInformationTextArea

private javax.swing.JTextArea probesProgressInformationTextArea

probesProgressLabel

private javax.swing.JLabel probesProgressLabel

progressBar

private javax.swing.JProgressBar progressBar

runSearchesPanel

private javax.swing.JPanel runSearchesPanel

searchButton

private javax.swing.JButton searchButton

searchProgressInformationTextArea

private javax.swing.JTextArea searchProgressInformationTextArea

searchProgressLabel

private javax.swing.JLabel searchProgressLabel

searchesAvailableLabel

private javax.swing.JLabel searchesAvailableLabel

sixteenExRadioButton

private javax.swing.JRadioButton sixteenExRadioButton

statusAnimationLabel

private javax.swing.JLabel statusAnimationLabel

statusMessageLabel

private javax.swing.JLabel statusMessageLabel

statusPanel

private javax.swing.JPanel statusPanel

storeProbesButton

private javax.swing.JButton storeProbesButton

storeProbesPanel

private javax.swing.JPanel storeProbesPanel

tabs

private javax.swing.JTabbedPane tabs

messageTimer

private final javax.swing.Timer messageTimer

busyIconTimer

private final javax.swing.Timer busyIconTimer

idleIcon

private final javax.swing.Icon idleIcon

busyIcons

private final javax.swing.Icon[] busyIcons

busyIconIndex

private int busyIconIndex

aboutBox

private javax.swing.JDialog aboutBox

conn

private java.sql.Connection conn

genome

private java.lang.String genome

parser

private XMLParser parser

url

private java.lang.String url

dbName

private java.lang.String dbName

username

private java.lang.String username

password

private java.lang.String password
Constructor Detail

MappingMicroarrayProbestotheRatGenomeviaaPersistentIndexView

public MappingMicroarrayProbestotheRatGenomeviaaPersistentIndexView(SingleFrameApplication app)
Method Detail

showAboutBox


initComponents

private void initComponents()
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.


chromosomesLocationBrowseButtonActionPerformed

private void chromosomesLocationBrowseButtonActionPerformed(java.awt.event.ActionEvent evt)
Performs the action when the chromosomes location browse buttion is pressed

Parameters:
evt - the ActionEvent

chromosomeControlDATFilesDestinationBrowseButtonActionPerformed

private void chromosomeControlDATFilesDestinationBrowseButtonActionPerformed(java.awt.event.ActionEvent evt)
Performs the action when the chromosomes control and dat files location browse buttion is pressed

Parameters:
evt - the ActionEvent

buildIndexButtonActionPerformed

private void buildIndexButtonActionPerformed(java.awt.event.ActionEvent evt)
Performs the action when the build index buttion is pressed

Parameters:
evt - the ActionEvent

locationOfProbesBrowseButtonActionPerformed

private void locationOfProbesBrowseButtonActionPerformed(java.awt.event.ActionEvent evt)
Performs the action when the probes location browse buttion is pressed

Parameters:
evt - the ActionEvent

probesControlDATFilesDestinationBrowseButtonActionPerformed

private void probesControlDATFilesDestinationBrowseButtonActionPerformed(java.awt.event.ActionEvent evt)
Performs the action when the probes control and dat files location browse buttion is pressed

Parameters:
evt - the ActionEvent

storeProbesButtonActionPerformed

private void storeProbesButtonActionPerformed(java.awt.event.ActionEvent evt)
Performs the action when the store probes buttion is pressed

Parameters:
evt - the ActionEvent

isCtlFile

public static boolean isCtlFile(java.io.File f)
Checks to see if file f is a ctl file

Parameters:
f - the file to be checked
Returns:
true if file f is a ctl file, false otherwise

strip

public static java.lang.String strip(java.lang.String f)
Returns the name of the file f after removing the file extension

Parameters:
f - the file
Returns:
the name of the file after removing the file extension

createGeneratedVariantsTable

private void createGeneratedVariantsTable(java.lang.String query)
Creates the GeneratedVariants table in the database

Parameters:
query - the query to create the table

loadJavaFunctions

private void loadJavaFunctions()
Loads the required Java functions into the database


search19ex

private void search19ex()
Performs the 19ex search


search19k1

private void search19k1()
Performs the 19k1 search


search19k3

private void search19k3()
Performs the 19k3 search


search16ex

private void search16ex()
Performs the 16ex search


searchButtonActionPerformed

private void searchButtonActionPerformed(java.awt.event.ActionEvent evt)
Performs the action when the search buttion is pressed

Parameters:
evt - the ActionEvent