/*
* Copyright (c) 2010 The Jackson Laboratory
*
* This is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This software is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this software. If not, see <http://www.gnu.org/licenses/>.
*/
package org.jax.bham.io;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.io.File;
import java.io.FileReader;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.swing.JFileChooser;
import javax.swing.event.DocumentEvent;
import org.jax.bham.BhamApplication;
import org.jax.haplotype.io.GenomicFlatFileParser;
import org.jax.haplotype.io.HiddenMarkovModelStateParser;
import org.jax.util.concurrent.MultiTaskProgressPanel;
import org.jax.util.gui.MessageDialogUtilities;
import org.jax.util.gui.SimplifiedDocumentListener;
import org.jax.util.io.CommonFlatFileFormat;
import org.jax.util.io.FlatFileReader;
/**
* Dialog for converting a CSV HMM state data source into a binary
* HMM state data source
* @author <A HREF="mailto:keith.sheppard@jax.org">Keith Sheppard</A>
*/
public class ConvertCsvHMMStatesToBinaryDialog extends javax.swing.JDialog
{
/**
* every {@link java.io.Serializable} is supposed to have one of these
*/
private static final long serialVersionUID = 8134074414517961697L;
private static final Logger LOG = Logger.getLogger(
ConvertCsvHMMStatesToBinaryDialog.class.getName());
private static final String COLUMNS_NOT_AVAILABLE =
"Select Import Files First";
/**
* Constructor
* @param parent
* parent component
*/
public ConvertCsvHMMStatesToBinaryDialog(java.awt.Frame parent)
{
super(parent, "Convert CSV HMM Haplotype Data to Binary", false);
this.initComponents();
this.postGuiInit();
}
/**
* Do initialization after GUI builder is done
*/
private void postGuiInit()
{
this.importFilesButton.addActionListener(new ActionListener()
{
/**
* {@inheritDoc}
*/
public void actionPerformed(ActionEvent e)
{
ConvertCsvHMMStatesToBinaryDialog.this.browseImportFiles();
}
});
this.exportDirButton.addActionListener(new ActionListener()
{
/**
* {@inheritDoc}
*/
public void actionPerformed(ActionEvent e)
{
ConvertCsvHMMStatesToBinaryDialog.this.browseExportDirs();
}
});
this.helpButton.addActionListener(new ActionListener()
{
/**
* {@inheritDoc}
*/
public void actionPerformed(ActionEvent e)
{
ConvertCsvHMMStatesToBinaryDialog.this.showHelp();
}
});
this.okButton.addActionListener(new ActionListener()
{
/**
* {@inheritDoc}
*/
public void actionPerformed(ActionEvent e)
{
ConvertCsvHMMStatesToBinaryDialog.this.ok();
}
});
this.cancelButton.addActionListener(new ActionListener()
{
/**
* {@inheritDoc}
*/
public void actionPerformed(ActionEvent e)
{
ConvertCsvHMMStatesToBinaryDialog.this.cancel();
}
});
this.importFilesTextField.getDocument().addDocumentListener(new SimplifiedDocumentListener()
{
/**
* {@inheritDoc}
*/
@Override
protected void anyUpdate(DocumentEvent e)
{
ConvertCsvHMMStatesToBinaryDialog.this.importFilesChanged();
}
});
// to start with we have no valid columns to select
this.setImportFileColumnNames(null);
ItemListener chromoAndPositionItemListener = new ItemListener()
{
/**
* {@inheritDoc}
*/
public void itemStateChanged(ItemEvent e)
{
if(e.getStateChange() == ItemEvent.SELECTED)
{
ConvertCsvHMMStatesToBinaryDialog.this.chromosomeOrPositionColumnChanged();
}
}
};
this.chromosomeColumnComboBox.addItemListener(chromoAndPositionItemListener);
this.positionColumnComboBox.addItemListener(chromoAndPositionItemListener);
}
private void chromosomeOrPositionColumnChanged()
{
int maxChrPosIndex = Math.max(
this.chromosomeColumnComboBox.getSelectedIndex(),
this.positionColumnComboBox.getSelectedIndex());
int firstStrainIndex = this.firstStrainComboBox.getSelectedIndex();
if(maxChrPosIndex >= 0 && maxChrPosIndex >= firstStrainIndex)
{
int newIndex = maxChrPosIndex + 1;
if(newIndex < this.firstStrainComboBox.getItemCount())
{
this.firstStrainComboBox.setSelectedIndex(newIndex);
}
}
}
/**
* called when there is some change in the import files
*/
private void importFilesChanged()
{
try
{
String[] importFileNames = this.getImportFileNames();
if(importFileNames == null || importFileNames.length == 0)
{
this.setImportFileColumnNames(null);
}
else
{
File firstFile = new File(importFileNames[0]);
if(!firstFile.isFile())
{
this.setImportFileColumnNames(null);
}
else
{
FlatFileReader csvReader = new FlatFileReader(
new FileReader(firstFile),
CommonFlatFileFormat.CSV_RFC_4180);
String[] firstRow = csvReader.readRow();
this.setImportFileColumnNames(firstRow);
csvReader.close();
}
}
}
catch(Exception ex)
{
LOG.log(Level.WARNING,
"Failed to \"pre-parse\" CSV import file",
ex);
this.setImportFileColumnNames(null);
}
}
private void setImportFileColumnNames(String[] columnNames)
{
this.chromosomeColumnComboBox.removeAllItems();
this.positionColumnComboBox.removeAllItems();
this.firstStrainComboBox.removeAllItems();
if(columnNames == null || columnNames.length == 0)
{
this.chromosomeColumnComboBox.addItem(COLUMNS_NOT_AVAILABLE);
this.positionColumnComboBox.addItem(COLUMNS_NOT_AVAILABLE);
this.firstStrainComboBox.addItem(COLUMNS_NOT_AVAILABLE);
}
else
{
for(String columnName: columnNames)
{
this.chromosomeColumnComboBox.addItem(columnName);
this.positionColumnComboBox.addItem(columnName);
this.firstStrainComboBox.addItem(columnName);
}
// try to guess the right index to use
int chrIndexGuess = GenomicFlatFileParser.guessIndexOfChromosomeIdFromHeader(
columnNames);
if(chrIndexGuess >= 0)
{
this.chromosomeColumnComboBox.setSelectedIndex(chrIndexGuess);
}
int posIndexGuess = GenomicFlatFileParser.guessIndexOfBasePairPositionFromHeader(
columnNames);
if(posIndexGuess >= 0)
{
this.positionColumnComboBox.setSelectedIndex(posIndexGuess);
}
}
}
private void cancel()
{
this.dispose();
}
private void ok()
{
try
{
if(this.validateData())
{
File[] importFiles = this.getImportFiles();
File exportDir = this.getExportDirectory();
HiddenMarkovModelStateParser parser = new HiddenMarkovModelStateParser(
this.firstStrainComboBox.getSelectedIndex(),
this.chromosomeColumnComboBox.getSelectedIndex(),
this.positionColumnComboBox.getSelectedIndex());
ConvertCsvHMMStatesToBinaryTask conversionTask = new ConvertCsvHMMStatesToBinaryTask(
parser,
importFiles,
exportDir);
MultiTaskProgressPanel progressTracker =
BhamApplication.getInstance().getBhamFrame().getMultiTaskProgress();
progressTracker.addTaskToTrack(conversionTask, true);
new Thread(conversionTask).start();
this.dispose();
}
}
catch(Exception ex)
{
String title = "Failed to Convert CSV Data";
LOG.log(Level.SEVERE,
title,
ex);
MessageDialogUtilities.error(
this,
ex.getMessage(),
title);
}
}
private File getExportDirectory()
{
return new File(this.exportDirTextField.getText().trim());
}
private File[] getImportFiles()
{
String[] importFileNames = this.getImportFileNames();
File[] importFiles = new File[importFileNames.length];
for(int i = 0; i < importFileNames.length; i++)
{
importFiles[i] = new File(importFileNames[i]);
}
return importFiles;
}
private String[] getImportFileNames()
{
String importFilesString = this.importFilesTextField.getText().trim();
String[] importFileNames = importFilesString.split(",");
for(int i = 0; i < importFileNames.length; i++)
{
importFileNames[i] = importFileNames[i].trim();
}
return importFileNames;
}
/**
* Determine if the data is all valid
* @return
* true if the data is valid
*/
private boolean validateData()
{
String errorMessage = this.validateImportFiles();
if(errorMessage == null)
{
errorMessage = this.validateExportDirectory();
if(errorMessage == null)
{
int firstStrainIndex = this.firstStrainComboBox.getSelectedIndex();
int chrIndex = this.chromosomeColumnComboBox.getSelectedIndex();
int posIndex = this.positionColumnComboBox.getSelectedIndex();
if(chrIndex == posIndex)
{
errorMessage =
"The base pair position and chromosome columns must " +
"be different! Please either change your column " +
"selections or reformat your file if necessary.";
}
else if(firstStrainIndex <= Math.max(chrIndex, posIndex))
{
errorMessage =
"The first strain column must occur after the " +
"base pair position and chromosome columns. Please " +
"either change your column selections or reformat " +
"your file if necessary.";
}
}
}
if(errorMessage != null)
{
MessageDialogUtilities.warn(
this,
errorMessage,
"Validation Failed");
return false;
}
else
{
return true;
}
}
private String validateImportFiles()
{
String[] importFileNames = this.getImportFileNames();
if(importFileNames == null || importFileNames.length == 0)
{
return "The list of import files cannot be empty.";
}
else
{
for(int i = 0; i < importFileNames.length; i++)
{
if(importFileNames[i].length() == 0)
{
return "Found an empty filename in the import list.";
}
else
{
File currImportFile = new File(importFileNames[i]);
if(!currImportFile.exists())
{
return "\"" + importFileNames[i] + "\" is missing.";
}
else if(!currImportFile.isFile())
{
return "\"" + importFileNames[i] + "\" does not have " +
"a normal file type.";
}
}
}
}
return null;
}
private String validateExportDirectory()
{
String exportDirName = this.exportDirTextField.getText().trim();
if(exportDirName.length() == 0)
{
return "The export directory must be specified";
}
else
{
File exportDir = new File(exportDirName);
if(!exportDir.exists())
{
boolean userSaysCreate = MessageDialogUtilities.ask(
this,
"\"" + exportDirName + "\" does not currently exist. " +
"Should attempt to create a new directory?",
"Export Directory Does Not Exist");
if(userSaysCreate)
{
if(!exportDir.mkdirs())
{
return "Failed to create directory";
}
}
else
{
return "Cannot export to missing directory.";
}
}
else if(!exportDir.isDirectory())
{
return "\"" + exportDirName + "\" must be a directory.";
}
}
return null;
}
private void showHelp()
{
MessageDialogUtilities.inform(
this,
"Sorry, no help yet..",
"Help Not Implemented");
}
private void browseExportDirs()
{
JFileChooser outputDirectoryChooser = new JFileChooser();
outputDirectoryChooser.setDialogTitle(
"Select an Output Directory");
outputDirectoryChooser.setMultiSelectionEnabled(false);
outputDirectoryChooser.setFileSelectionMode(
JFileChooser.DIRECTORIES_ONLY);
int outputUserSelection =
outputDirectoryChooser.showOpenDialog(this);
if(outputUserSelection == JFileChooser.APPROVE_OPTION)
{
File selectedOutputDirectory =
outputDirectoryChooser.getSelectedFile();
this.exportDirTextField.setText(
selectedOutputDirectory.getAbsolutePath());
}
else
{
LOG.fine("user canceled export dir selection");
}
}
private void browseImportFiles()
{
JFileChooser inputFileChooser = new JFileChooser();
inputFileChooser.setDialogTitle("Select CSV Chromosome Input Files");
inputFileChooser.setMultiSelectionEnabled(true);
inputFileChooser.setFileSelectionMode(
JFileChooser.FILES_ONLY);
int userSelection = inputFileChooser.showOpenDialog(this);
if(userSelection == JFileChooser.APPROVE_OPTION)
{
File[] selectedInputFiles = inputFileChooser.getSelectedFiles();
StringBuffer selectedFilesText = new StringBuffer();
for(int i = 0; i < selectedInputFiles.length; i++)
{
if(i >= 1)
{
selectedFilesText.append(", ");
}
selectedFilesText.append(
selectedInputFiles[i].getAbsolutePath());
}
this.importFilesTextField.setText(selectedFilesText.toString());
}
else
{
LOG.fine("user canceled import file selection");
}
}
/**
* This method is called from within the constructor to
* initialize the form.
* WARNING: Do NOT modify this code. The content of this method is
* always regenerated by the Form Editor.
*/
@SuppressWarnings("all")
// <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
private void initComponents() {
contentPanel = new javax.swing.JPanel();
javax.swing.JLabel importFilesLabel = new javax.swing.JLabel();
importFilesTextField = new javax.swing.JTextField();
importFilesButton = new javax.swing.JButton();
javax.swing.JLabel exportDirLabel = new javax.swing.JLabel();
exportDirTextField = new javax.swing.JTextField();
exportDirButton = new javax.swing.JButton();
javax.swing.JLabel chromosomeColumnLabel = new javax.swing.JLabel();
chromosomeColumnComboBox = new javax.swing.JComboBox();
javax.swing.JLabel positionColumnLabel = new javax.swing.JLabel();
positionColumnComboBox = new javax.swing.JComboBox();
javax.swing.JLabel firstStrainLabel = new javax.swing.JLabel();
firstStrainComboBox = new javax.swing.JComboBox();
actionPanel = new javax.swing.JPanel();
okButton = new javax.swing.JButton();
cancelButton = new javax.swing.JButton();
helpButton = new javax.swing.JButton();
setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
importFilesLabel.setText("CSV File(s) To Import:");
importFilesButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/images/browse-16x16.png"))); // NOI18N
importFilesButton.setText("Browse...");
exportDirLabel.setText("Export Directory:");
exportDirButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/images/browse-16x16.png"))); // NOI18N
exportDirButton.setText("Browse...");
chromosomeColumnLabel.setText("Chromosome Column:");
positionColumnLabel.setText("Base Pair Column:");
firstStrainLabel.setText("First Strain Column:");
org.jdesktop.layout.GroupLayout contentPanelLayout = new org.jdesktop.layout.GroupLayout(contentPanel);
contentPanel.setLayout(contentPanelLayout);
contentPanelLayout.setHorizontalGroup(
contentPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
.add(contentPanelLayout.createSequentialGroup()
.addContainerGap()
.add(contentPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
.add(importFilesLabel)
.add(exportDirLabel)
.add(chromosomeColumnLabel)
.add(positionColumnLabel)
.add(firstStrainLabel))
.add(10, 10, 10)
.add(contentPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
.add(firstStrainComboBox, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
.add(positionColumnComboBox, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
.add(contentPanelLayout.createSequentialGroup()
.add(contentPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
.add(org.jdesktop.layout.GroupLayout.TRAILING, exportDirTextField, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 221, Short.MAX_VALUE)
.add(org.jdesktop.layout.GroupLayout.TRAILING, importFilesTextField, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 221, Short.MAX_VALUE))
.addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
.add(contentPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
.add(org.jdesktop.layout.GroupLayout.TRAILING, importFilesButton)
.add(org.jdesktop.layout.GroupLayout.TRAILING, exportDirButton)))
.add(chromosomeColumnComboBox, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
.addContainerGap())
);
contentPanelLayout.setVerticalGroup(
contentPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
.add(contentPanelLayout.createSequentialGroup()
.addContainerGap()
.add(contentPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
.add(importFilesLabel)
.add(importFilesTextField, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
.add(importFilesButton))
.addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
.add(contentPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
.add(exportDirLabel)
.add(exportDirTextField, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
.add(exportDirButton))
.addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
.add(contentPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
.add(chromosomeColumnLabel)
.add(chromosomeColumnComboBox, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
.add(contentPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
.add(positionColumnLabel)
.add(positionColumnComboBox, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
.add(contentPanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
.add(firstStrainLabel)
.add(firstStrainComboBox, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
.addContainerGap(org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
okButton.setText("OK");
actionPanel.add(okButton);
cancelButton.setText("Cancel");
actionPanel.add(cancelButton);
helpButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/images/help-16x16.png"))); // NOI18N
helpButton.setText("Help...");
actionPanel.add(helpButton);
org.jdesktop.layout.GroupLayout layout = new org.jdesktop.layout.GroupLayout(getContentPane());
getContentPane().setLayout(layout);
layout.setHorizontalGroup(
layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
.add(actionPanel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, 491, Short.MAX_VALUE)
.add(contentPanel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
);
layout.setVerticalGroup(
layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
.add(org.jdesktop.layout.GroupLayout.TRAILING, layout.createSequentialGroup()
.add(contentPanel, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
.add(actionPanel, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, org.jdesktop.layout.GroupLayout.DEFAULT_SIZE, org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
);
pack();
}// </editor-fold>//GEN-END:initComponents
// Variables declaration - do not modify//GEN-BEGIN:variables
private javax.swing.JPanel actionPanel;
private javax.swing.JButton cancelButton;
private javax.swing.JComboBox chromosomeColumnComboBox;
private javax.swing.JPanel contentPanel;
private javax.swing.JButton exportDirButton;
private javax.swing.JTextField exportDirTextField;
private javax.swing.JComboBox firstStrainComboBox;
private javax.swing.JButton helpButton;
private javax.swing.JButton importFilesButton;
private javax.swing.JTextField importFilesTextField;
private javax.swing.JButton okButton;
private javax.swing.JComboBox positionColumnComboBox;
// End of variables declaration//GEN-END:variables
}