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OTUStalkerGUI_UI.java
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OTUStalkerGUI_UI.java
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/*
* Copyright (c) 2015, Z. A. Dyson (zadyson@gmail.com) & L. B. M. Speirs
* Last updated May 27 2015
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* * Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
* * Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
*/
/**
* my.outstalkergui is a GUI version of the program OTUStalker designed for
* filtering PCR amplicon data by organism of interest.
*/
package my.otustalkergui;
import java.awt.Component;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintStream;
import java.io.PrintWriter;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
import java.util.Scanner;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.swing.JFileChooser;
import javax.swing.JOptionPane;
/**
* OTUStalkerGUI - Graphical User Interface (GUI) version of OTUStalker a
* program designed to filter PCR amplicon data by organism
*
* @author Z. A. Dyson & L. B. M. Speirs
* @version 0.0.1
*
*/
public class OTUStalkerGUI_UI extends javax.swing.JFrame {
private static Component frame;
boolean filesSelected = false;
File workingDirectory;
/**
* Creates new form OTUStalkerGUI_UI for GUI for OTUStalker program
*/
public OTUStalkerGUI_UI() {
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.
*/
@SuppressWarnings("unchecked")
// <editor-fold defaultstate="collapsed" desc="Generated Code">
private void initComponents() {
jButton1 = new javax.swing.JButton();
jButtonCancelOTUSTalker = new javax.swing.JButton();
jScrollPane2 = new javax.swing.JScrollPane();
jTextPane1 = new javax.swing.JTextPane();
jLabel11 = new javax.swing.JLabel();
jToolBar1 = new javax.swing.JToolBar();
jButtonRunOTUStalker = new javax.swing.JButton();
jLabel1 = new javax.swing.JLabel();
jTextFieldOrganism = new javax.swing.JTextField();
jLabel2 = new javax.swing.JLabel();
jScrollPane1 = new javax.swing.JScrollPane();
jTextAreaOTUStalkerOutput = new javax.swing.JTextArea();
jTextFieldTaxAssign = new javax.swing.JTextField();
jButtonTaxAssign = new javax.swing.JButton();
jSeparator1 = new javax.swing.JSeparator();
jLabel3 = new javax.swing.JLabel();
jProgressBar = new javax.swing.JProgressBar();
jLabel4 = new javax.swing.JLabel();
jLabel5 = new javax.swing.JLabel();
jTextFieldOTUList = new javax.swing.JTextField();
label1 = new java.awt.Label();
jButtonOTUList = new javax.swing.JButton();
jLabel6 = new javax.swing.JLabel();
jTextFieldDeMulSeq = new javax.swing.JTextField();
jLabel7 = new javax.swing.JLabel();
jTextFieldReadData = new javax.swing.JTextField();
jLabel8 = new javax.swing.JLabel();
jTextFieldReadScores = new javax.swing.JTextField();
jButtonDeMulSeq = new javax.swing.JButton();
jButtonReadData = new javax.swing.JButton();
jButtonReadScores = new javax.swing.JButton();
jLabel9 = new javax.swing.JLabel();
jSeparator2 = new javax.swing.JSeparator();
jLabel10 = new javax.swing.JLabel();
jTextFieldOutputDir = new javax.swing.JTextField();
jButtonOutputDir = new javax.swing.JButton();
jButtonQuit = new javax.swing.JButton();
jLabel12 = new javax.swing.JLabel();
jTextFieldRepSeq = new javax.swing.JTextField();
jButtonRepSeq = new javax.swing.JButton();
jMenuBar1 = new javax.swing.JMenuBar();
jButton1.setText("jButton1");
jButtonCancelOTUSTalker.setText("Cancel");
jButtonCancelOTUSTalker.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButtonCancelOTUSTalkerActionPerformed(evt);
}
});
jScrollPane2.setViewportView(jTextPane1);
jLabel11.setText("Time elapsed during run:");
setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);
setTitle("OTUStalker ");
setResizable(false);
jToolBar1.setRollover(true);
jButtonRunOTUStalker.setText("Start OTUStalking");
jButtonRunOTUStalker.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButtonRunOTUStalkerActionPerformed(evt);
}
});
jLabel1.setHorizontalAlignment(javax.swing.SwingConstants.RIGHT);
jLabel1.setText("Organism of interest ");
jLabel1.setToolTipText("A single nominated taxonomic group of interest. Query term is not case sensitive.");
jTextFieldOrganism.setText("e.g. Chloroflexi");
jTextFieldOrganism.setToolTipText("A single nominated taxonomic group of interest. Query term is not case sensitive.");
jTextFieldOrganism.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jTextFieldOrganismActionPerformed(evt);
}
});
jLabel2.setHorizontalAlignment(javax.swing.SwingConstants.RIGHT);
jLabel2.setText("Taxonomic Assignment file ");
jLabel2.setToolTipText("<html>This text file contains a line for each OTU created.<br> Each line then lists an OTU identifier followed by <br> its taxonomic assignment. This file<br> (eg: seqs_rep_set_tax_assignments.txt) is<br> generated by the script “assign_taxonomy.py”.</html>");
jTextAreaOTUStalkerOutput.setColumns(20);
jTextAreaOTUStalkerOutput.setRows(5);
jTextAreaOTUStalkerOutput.setText("Awaiting organism and file information...");
jTextAreaOTUStalkerOutput.setAutoscrolls(false);
jScrollPane1.setViewportView(jTextAreaOTUStalkerOutput);
jTextFieldTaxAssign.setText("e.g. seqs_rep_set_tax_assignments.txt");
jTextFieldTaxAssign.setToolTipText("<html>This text file contains a line for each OTU created.<br>\n Each line then lists an OTU identifier followed by <br>\nits taxonomic assignment. This file<br>\n (eg: seqs_rep_set_tax_assignments.txt) is<br>\n generated by the script “assign_taxonomy.py”.</html>");
jTextFieldTaxAssign.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jTextFieldTaxAssignActionPerformed(evt);
}
});
jButtonTaxAssign.setText("Select");
jButtonTaxAssign.setToolTipText("<html>This text file contains a line for each OTU created.<br> Each line then lists an OTU identifier followed by <br> its taxonomic assignment. This file<br> (eg: seqs_rep_set_tax_assignments.txt) is<br> generated by the script “assign_taxonomy.py”.</html>");
jButtonTaxAssign.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButtonTaxAssignActionPerformed(evt);
}
});
jLabel3.setFont(new java.awt.Font("Lucida Grande", 1, 13)); // NOI18N
jLabel3.setText("OTUStalker Run Status:");
jProgressBar.setFont(new java.awt.Font("Lucida Grande", 1, 13)); // NOI18N
jProgressBar.setStringPainted(true);
jLabel4.setText("Progress");
jLabel5.setHorizontalAlignment(javax.swing.SwingConstants.RIGHT);
jLabel5.setText("OTU Sequence List file ");
jTextFieldOTUList.setText("e.g. seqs_otus.txt");
jTextFieldOTUList.setToolTipText("<html>\nThis file contains a list of all the representative OTU <br> \nidentifiers and the corresponding individual sequences <br>\nthat contribute to each. This file is generated by the script <br>\n“pick_de_novo_otus.py” (or one of the alternative OTU<br>\npicking methods).");
label1.setText("Demultiplexed sequences file");
jButtonOTUList.setText("Select");
jButtonOTUList.setToolTipText("<html>\nThis file contains a list of all the representative OTU <br> \nidentifiers and the corresponding individual sequences <br>\nthat contribute to each. This file is generated by the script <br>\n“pick_de_novo_otus.py” (or one of the alternative OTU<br>\npicking methods).");
jButtonOTUList.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButtonOTUListActionPerformed(evt);
}
});
jLabel6.setFont(new java.awt.Font("Lucida Grande", 1, 13)); // NOI18N
jLabel6.setText("Select your files, and enter the name of your organism of intestet below:");
jTextFieldDeMulSeq.setText("e.g. seqs.fna");
jTextFieldDeMulSeq.setToolTipText("<html>\nThe script “split_libraries.py” will parse and rename <br> \neach read provided by the sequencing platform, with <br> \nthe appropriate Sample ID, therefore formatting the <br> \nsequence data for downstream analysis. This script <br> \ngenerates a file with the default name “seqs.fna”.");
jLabel7.setHorizontalAlignment(javax.swing.SwingConstants.RIGHT);
jLabel7.setText("Read data file ");
jTextFieldReadData.setText("e.g. HYPIJKO01.fna");
jTextFieldReadData.setToolTipText("<html>\nThis is the pyrosequencing platform generated <br> \nFASTA file (eg: ABCD.fna). The amplicon processing <br> \nsoftware attached to the pyrosequencing platform will <br>\ngenerate one of these files for each region of the PTP plate. ");
jTextFieldReadData.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jTextFieldReadDataActionPerformed(evt);
}
});
jLabel8.setHorizontalAlignment(javax.swing.SwingConstants.RIGHT);
jLabel8.setText("Read quality scores file ");
jTextFieldReadScores.setText("e.g. HYPIJKO01.qual");
jTextFieldReadScores.setToolTipText("<html>\nThis is the pyrosequencing platform generated <br>\nquality score file (eg: ABCD.qual), which contains<br>\na quality score for each base of each sequence<br>\nincluded in the FASTA (ie: ABCD.fna) file. Like the <br>\nfasta file mentioned above, the amplicon processing <br>\nsoftware will generate one of these files for each <br>\nregion of the PTP plate.");
jButtonDeMulSeq.setText("Select");
jButtonDeMulSeq.setToolTipText("<html>\nThe script “split_libraries.py” will parse and rename <br> \neach read provided by the sequencing platform, with <br> \nthe appropriate Sample ID, therefore formatting the <br> \nsequence data for downstream analysis. This script <br> \ngenerates a file with the default name “seqs.fna”.");
jButtonDeMulSeq.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButtonDeMulSeqActionPerformed(evt);
}
});
jButtonReadData.setText("Select");
jButtonReadData.setToolTipText("<html>\nThis is the pyrosequencing platform generated <br> \nFASTA file (eg: ABCD.fna). The amplicon processing <br> \nsoftware attached to the pyrosequencing platform will <br>\ngenerate one of these files for each region of the PTP plate. ");
jButtonReadData.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButtonReadDataActionPerformed(evt);
}
});
jButtonReadScores.setText("Select");
jButtonReadScores.setToolTipText("<html>\nThis is the pyrosequencing platform generated <br>\nquality score file (eg: ABCD.qual), which contains<br>\na quality score for each base of each sequence<br>\nincluded in the FASTA (ie: ABCD.fna) file. Like the <br>\nfasta file mentioned above, the amplicon processing <br>\nsoftware will generate one of these files for each <br>\nregion of the PTP plate.");
jButtonReadScores.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButtonReadScoresActionPerformed(evt);
}
});
jLabel9.setFont(new java.awt.Font("Lucida Grande", 1, 14)); // NOI18N
jLabel9.setText("Welcome to OTUStalker, a program designed to filter PCR amplicon data by organism!");
jLabel10.setHorizontalAlignment(javax.swing.SwingConstants.RIGHT);
jLabel10.setText("Output directory ");
jLabel10.setToolTipText("File path nominated by the OTUStalker user.");
jTextFieldOutputDir.setText("e.g. /home/speirs_dyson/putmydatahere/");
jTextFieldOutputDir.setToolTipText("File path nominated by the OTUStalker user.");
jTextFieldOutputDir.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jTextFieldOutputDirActionPerformed(evt);
}
});
jButtonOutputDir.setText("Select");
jButtonOutputDir.setToolTipText("File path nominated by the OTUStalker user");
jButtonOutputDir.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButtonOutputDirActionPerformed(evt);
}
});
jButtonQuit.setText("Quit");
jButtonQuit.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButtonQuitActionPerformed(evt);
}
});
jLabel12.setHorizontalAlignment(javax.swing.SwingConstants.RIGHT);
jLabel12.setText("Representative sequences file");
jTextFieldRepSeq.setText("e.g. seqs_rep_set.fasta");
jTextFieldRepSeq.setToolTipText("<html>\nThis file is created by the “pick_rep_set.py”.<br>\nIt is a FASTA file containing one sequence per <br>\nOTU. The default name of the output file will <br>\nbe (input_sequences_filepath)_rep_set.fasta.");
jTextFieldRepSeq.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jTextFieldRepSeqActionPerformed(evt);
}
});
jButtonRepSeq.setText("Select");
jButtonRepSeq.setToolTipText("<html>\nThis file is created by the “pick_rep_set.py”.<br>\nIt is a FASTA file containing one sequence per <br>\nOTU. The default name of the output file will <br>\nbe (input_sequences_filepath)_rep_set.fasta.");
jButtonRepSeq.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jButtonRepSeqActionPerformed(evt);
}
});
setJMenuBar(jMenuBar1);
javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
getContentPane().setLayout(layout);
layout.setHorizontalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(layout.createSequentialGroup()
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(layout.createSequentialGroup()
.addContainerGap()
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(jSeparator2)
.addComponent(jSeparator1, javax.swing.GroupLayout.Alignment.TRAILING)))
.addGroup(layout.createSequentialGroup()
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING, false)
.addGroup(layout.createSequentialGroup()
.addContainerGap()
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(jLabel9)
.addComponent(jLabel6, javax.swing.GroupLayout.PREFERRED_SIZE, 498, javax.swing.GroupLayout.PREFERRED_SIZE)))
.addGroup(layout.createSequentialGroup()
.addGap(15, 15, 15)
.addComponent(jLabel2))
.addGroup(layout.createSequentialGroup()
.addGap(54, 54, 54)
.addComponent(jLabel5)
.addGap(327, 327, 327)
.addComponent(jButtonOTUList))
.addGroup(layout.createSequentialGroup()
.addGap(62, 62, 62)
.addComponent(jLabel1)
.addGap(0, 0, 0)
.addComponent(jTextFieldOrganism, javax.swing.GroupLayout.PREFERRED_SIZE, 327, javax.swing.GroupLayout.PREFERRED_SIZE))
.addGroup(layout.createSequentialGroup()
.addGap(87, 87, 87)
.addComponent(jLabel10)
.addGap(0, 0, 0)
.addComponent(jTextFieldOutputDir, javax.swing.GroupLayout.PREFERRED_SIZE, 324, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(3, 3, 3)
.addComponent(jButtonOutputDir)))
.addGap(0, 0, Short.MAX_VALUE)))
.addContainerGap())
.addGroup(layout.createSequentialGroup()
.addGap(6, 6, 6)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(layout.createSequentialGroup()
.addComponent(jScrollPane1)
.addGap(6, 6, 6))
.addGroup(layout.createSequentialGroup()
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(layout.createSequentialGroup()
.addComponent(jLabel4)
.addGap(18, 18, 18)
.addComponent(jProgressBar, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
.addGroup(layout.createSequentialGroup()
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(layout.createSequentialGroup()
.addComponent(jButtonRunOTUStalker)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
.addComponent(jButtonQuit))
.addComponent(jLabel3))
.addGap(0, 0, Short.MAX_VALUE)))
.addGap(6, 6, 6))))
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
.addGroup(layout.createSequentialGroup()
.addComponent(jTextFieldTaxAssign, javax.swing.GroupLayout.PREFERRED_SIZE, 324, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(3, 3, 3)
.addComponent(jButtonTaxAssign))
.addGroup(layout.createSequentialGroup()
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING, false)
.addComponent(jTextFieldOTUList, javax.swing.GroupLayout.PREFERRED_SIZE, 324, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGroup(layout.createSequentialGroup()
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(layout.createSequentialGroup()
.addGap(103, 103, 103)
.addComponent(jLabel7))
.addGroup(layout.createSequentialGroup()
.addGap(42, 42, 42)
.addComponent(jLabel8)))
.addGap(0, 0, 0)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING, false)
.addComponent(jTextFieldDeMulSeq, javax.swing.GroupLayout.Alignment.TRAILING)
.addComponent(jTextFieldReadData)
.addComponent(jTextFieldReadScores, javax.swing.GroupLayout.DEFAULT_SIZE, 322, Short.MAX_VALUE)))
.addGroup(layout.createSequentialGroup()
.addContainerGap()
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(label1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGroup(layout.createSequentialGroup()
.addComponent(jLabel12)
.addGap(0, 2, Short.MAX_VALUE)
.addComponent(jTextFieldRepSeq, javax.swing.GroupLayout.PREFERRED_SIZE, 324, javax.swing.GroupLayout.PREFERRED_SIZE)))))
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(layout.createSequentialGroup()
.addGap(3, 3, 3)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(jButtonReadData)
.addComponent(jButtonDeMulSeq)
.addComponent(jButtonReadScores)))
.addGroup(layout.createSequentialGroup()
.addGap(3, 3, 3)
.addComponent(jButtonRepSeq)))))
);
layout.setVerticalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
.addGap(12, 12, 12)
.addComponent(jLabel9)
.addGap(18, 18, 18)
.addComponent(jLabel6)
.addGap(14, 14, 14)
.addComponent(jSeparator2, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jLabel1)
.addComponent(jTextFieldOrganism, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jTextFieldOutputDir, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(jLabel10)
.addComponent(jButtonOutputDir))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jLabel2)
.addComponent(jTextFieldTaxAssign, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(jButtonTaxAssign))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jTextFieldRepSeq, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(jLabel12)
.addComponent(jButtonRepSeq))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jButtonOTUList)
.addComponent(jTextFieldOTUList, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(jLabel5))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jTextFieldDeMulSeq, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(jButtonDeMulSeq))
.addComponent(label1, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jTextFieldReadData, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(jButtonReadData)
.addComponent(jLabel7))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jTextFieldReadScores, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(jButtonReadScores)
.addComponent(jLabel8))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(jSeparator1, javax.swing.GroupLayout.PREFERRED_SIZE, 10, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(jLabel3)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 7, Short.MAX_VALUE)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jButtonRunOTUStalker)
.addComponent(jButtonQuit))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(jScrollPane1, javax.swing.GroupLayout.PREFERRED_SIZE, 223, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(16, 16, 16)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(jLabel4)
.addComponent(jProgressBar, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addContainerGap(12, Short.MAX_VALUE))
);
label1.getAccessibleContext().setAccessibleName("Select file 3");
pack();
}// </editor-fold>
private void jButtonRunOTUStalkerActionPerformed(java.awt.event.ActionEvent evt) {
new Thread(new otustalkerthread1()).start();
jButtonRunOTUStalker.setEnabled(false);
}
private void jButtonTaxAssignActionPerformed(java.awt.event.ActionEvent evt) {
JFileChooser taxAssignChooser = new JFileChooser();
if (filesSelected == true) {
taxAssignChooser.setCurrentDirectory(workingDirectory);
}
taxAssignChooser.showOpenDialog(null);
File taxAssignFile = taxAssignChooser.getSelectedFile();
if (taxAssignFile != null) {
String taxAssignFilename = taxAssignFile.getAbsolutePath();
workingDirectory = taxAssignChooser.getCurrentDirectory();
jTextFieldTaxAssign.setText(taxAssignFilename);
filesSelected = true;
}
}
private void jButtonCancelOTUSTalkerActionPerformed(java.awt.event.ActionEvent evt) {
}
private void jTextFieldOrganismActionPerformed(java.awt.event.ActionEvent evt) {
}
private void jButtonDeMulSeqActionPerformed(java.awt.event.ActionEvent evt) {
JFileChooser deMulSeqChooser = new JFileChooser();
if (filesSelected == true) {
deMulSeqChooser.setCurrentDirectory(workingDirectory);
}
deMulSeqChooser.showOpenDialog(null);
File deMulSeqFile = deMulSeqChooser.getSelectedFile();
if (deMulSeqFile != null) {
String deMulSeqFilename = deMulSeqFile.getAbsolutePath();
workingDirectory = deMulSeqChooser.getCurrentDirectory();
jTextFieldDeMulSeq.setText(deMulSeqFilename);
filesSelected = true;
}
}
private void jTextFieldReadDataActionPerformed(java.awt.event.ActionEvent evt) {
}
private void jTextFieldTaxAssignActionPerformed(java.awt.event.ActionEvent evt) {
}
private void jButtonOTUListActionPerformed(java.awt.event.ActionEvent evt) {
JFileChooser otuListChooser = new JFileChooser();
if (filesSelected == true) {
otuListChooser.setCurrentDirectory(workingDirectory);
}
otuListChooser.showOpenDialog(null);
File otuListFile = otuListChooser.getSelectedFile();
if (otuListFile != null) {
String otuListFilename = otuListFile.getAbsolutePath();
workingDirectory = otuListChooser.getCurrentDirectory();
jTextFieldOTUList.setText(otuListFilename);
filesSelected = true;
}
}
private void jButtonReadScoresActionPerformed(java.awt.event.ActionEvent evt) {
JFileChooser readScoresChooser = new JFileChooser();
if (filesSelected == true) {
readScoresChooser.setCurrentDirectory(workingDirectory);
}
readScoresChooser.showOpenDialog(null);
File readScoresFile = readScoresChooser.getSelectedFile();
if (readScoresFile != null) {
String readScoresFilename = readScoresFile.getAbsolutePath();
workingDirectory = readScoresChooser.getCurrentDirectory();
jTextFieldReadScores.setText(readScoresFilename);
filesSelected = true;
}
}
private void jButtonOutputDirActionPerformed(java.awt.event.ActionEvent evt) {
JFileChooser outputDirectoryChooser = new JFileChooser();
if (filesSelected == true) {
outputDirectoryChooser.setCurrentDirectory(workingDirectory);
}
outputDirectoryChooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
outputDirectoryChooser.setAcceptAllFileFilterUsed(false);
outputDirectoryChooser.showOpenDialog(null);
File outputDirectoryFile = outputDirectoryChooser.getSelectedFile();
if (outputDirectoryFile != null) {
String outputDirectoryFilename = outputDirectoryFile.getAbsolutePath();
workingDirectory = outputDirectoryChooser.getCurrentDirectory();
jTextFieldOutputDir.setText(outputDirectoryFilename);
filesSelected = true;
}
}
private void jTextFieldOutputDirActionPerformed(java.awt.event.ActionEvent evt) {
}
private void jButtonQuitActionPerformed(java.awt.event.ActionEvent evt) {
System.exit(0);
}
private void jButtonReadDataActionPerformed(java.awt.event.ActionEvent evt) {
JFileChooser readDataChooser = new JFileChooser();
if (filesSelected == true) {
readDataChooser.setCurrentDirectory(workingDirectory);
}
readDataChooser.showOpenDialog(null);
File readDataFile = readDataChooser.getSelectedFile();
if (readDataFile != null) {
String readDataFilename = readDataFile.getAbsolutePath();
workingDirectory = readDataChooser.getCurrentDirectory();
jTextFieldReadData.setText(readDataFilename);
filesSelected = true;
}
}
private void jButtonRepSeqActionPerformed(java.awt.event.ActionEvent evt) {
JFileChooser repSeqChooser = new JFileChooser();
if (filesSelected == true) {
repSeqChooser.setCurrentDirectory(workingDirectory);
}
repSeqChooser.showOpenDialog(null);
File repSeqFile = repSeqChooser.getSelectedFile();
if (repSeqFile != null) {
String repSeqFilename = repSeqFile.getAbsolutePath();
workingDirectory = repSeqChooser.getCurrentDirectory();
jTextFieldRepSeq.setText(repSeqFilename);
filesSelected = true;
}
}
private void jTextFieldRepSeqActionPerformed(java.awt.event.ActionEvent evt) {
// TODO add your handling code here:
}
/**
* @param args the command line arguments
*/
public static void main(String args[]) {
/* Set the Nimbus look and feel */
//<editor-fold defaultstate="collapsed" desc=" Look and feel setting code (optional) ">
/* If Nimbus (introduced in Java SE 6) is not available, stay with the default look and feel.
* For details see http://download.oracle.com/javase/tutorial/uiswing/lookandfeel/plaf.html
*/
try {
for (javax.swing.UIManager.LookAndFeelInfo info : javax.swing.UIManager.getInstalledLookAndFeels()) {
if ("Nimbus".equals(info.getName())) {
javax.swing.UIManager.setLookAndFeel(info.getClassName());
break;
}
}
} catch (ClassNotFoundException ex) {
java.util.logging.Logger.getLogger(OTUStalkerGUI_UI.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
} catch (InstantiationException ex) {
java.util.logging.Logger.getLogger(OTUStalkerGUI_UI.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
} catch (IllegalAccessException ex) {
java.util.logging.Logger.getLogger(OTUStalkerGUI_UI.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
} catch (javax.swing.UnsupportedLookAndFeelException ex) {
java.util.logging.Logger.getLogger(OTUStalkerGUI_UI.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
}
//</editor-fold>
/* Create and display the form */
java.awt.EventQueue.invokeLater(new Runnable() {
@Override
public void run() {
new OTUStalkerGUI_UI().setVisible(true);
}
});
}
/**
* Retrieve the OTU numbers, and proportion of the organism of interest
* present, and number of representative sequences from the input data files
*
* @param outputDate Date of OTUStalker run
* @param searchOrganism the organism of interest, will be searched case
* independently
* @param repSet filename of taxonomic assignments file
* @param repSeq filename of the representative sequences file
* @param outputDir location of output directory selected by user
*
* @return finalResults total number of organisms, number of organism of
* interest, and the number of OTU representative sequences retrieved
*/
public static int[] getOrganismOTUNumsAndRepSeqs(
String outputDate, String searchOrganism, String repSet,
String repSeq, String outputDir) {
//Initialize variables
int organismCount = 0;
int totalOrganismCount = 0;
int seqMatchCount = 0;
String taxassignments;
try {
//Open data files
BufferedReader speciesDataIn = new BufferedReader(
new FileReader(repSet));
//Create output files
PrintWriter taxAssignDataOut = new PrintWriter(
new FileWriter(outputDir + outputDate
+ "_" + searchOrganism + "_Output/"
+ searchOrganism + "TaxAssignData.txt"));
PrintWriter repOTUListOut = new PrintWriter(
new FileWriter(outputDir + outputDate + "_"
+ searchOrganism + "_Output/"
+ searchOrganism + "OTUNumbers.txt"));
PrintWriter repSeqDataOut = new PrintWriter(
new FileWriter(outputDir + outputDate
+ "_" + searchOrganism + "_Output/All"
+ searchOrganism + "RepOTUs.fasta"));
//While there are new entries in the data file, keep screening
while ((taxassignments = speciesDataIn.readLine()) != null) {
totalOrganismCount++;
//Delimit file for screening
String splitarray[] = taxassignments.split("\t");
String taxassignotunumber = splitarray[0];
String secondentry = splitarray[1];
/*regular expression to search organism name regardless of lower
or upper case*/
boolean chloroflexiMatch = false;
if (secondentry.matches("(?i).*" + "_" + searchOrganism + ";" + ".*") || secondentry.matches("(?i).*" + "_" + searchOrganism)) {
chloroflexiMatch = true;
};
/*If the entry corresponds to the desired organism append
the entry to the output file and obtain representative sequence
data and output data*/
if (chloroflexiMatch) {
organismCount++;
/*Output taxonomic data and OTU numbers pertaining to the
organism of interest*/
taxAssignDataOut.println(taxassignments);
repOTUListOut.println(taxassignotunumber);
//Initalize variable for looping
String newToken;
boolean seqFound = false;
/* Open representative sequences data file and
retrieve relevant data */
Scanner repSeqIn = new Scanner(
new File(repSeq));
repSeqIn.useDelimiter(">");
StringBuffer tokenAdder = new StringBuffer();
while (repSeqIn.hasNext() && !seqFound) {
tokenAdder.append(repSeqIn.next());
newToken = tokenAdder.toString();
String splitarray2[] = newToken.split(" ");
String repfileotunumber = splitarray2[0];
if (repfileotunumber.matches(taxassignotunumber)) {
seqMatchCount++;
repSeqDataOut.append(
">" + tokenAdder.toString());
seqFound = true;
}
tokenAdder.delete(0, tokenAdder.length());
}
//Close scanner
repSeqIn.close();
}
}
//Close files
repOTUListOut.close();
repSeqDataOut.close();
taxAssignDataOut.close();
speciesDataIn.close();
//Exception handling
} catch (IOException ex) {
JOptionPane.showMessageDialog(frame,
"Taxonomic assignment or representative sequences "
+ "\nfiles not found, or output directory not selected"
+ "\nplease check these and try again.");
} catch (ArrayIndexOutOfBoundsException ex) {
JOptionPane.showMessageDialog(frame,
"Taxonimic assignment or representative sequences input"
+ " \nfile(s) format is not correct, please check file"
+ " format and try again.");
}
int[] finalResults = new int[]{
totalOrganismCount, organismCount, seqMatchCount};
return finalResults;
}
/**
* Retrieve sequence names for all OTUs pertaining to organism of interest
*
* @param outputDate Date of OTUStalker run
* @param searchOrganism the organism of interest, will be searched case
* independently
* @param seqsOTUs filename of OTU sequence list file
* @param outputDir location of output directory selected by user
*
* @return finalResults the number of matched OTUs, and the number of
* sequence names retrieved
*/
public static int[] getOTUSequenceNames(
String outputDate, String searchOrganism,
String seqsOTUs, String outputDir) {
//Initialize variables and data structures
int matchedOTUCount = 0;
int countSeqNamesListed = 0;
PrintWriter sequenceNamesOut;
try {
//Open data files and initialize output files
BufferedReader otuSequenceListIn = new BufferedReader(
new FileReader(seqsOTUs));
String otuSequenceList;
sequenceNamesOut = new PrintWriter(
new FileWriter(outputDir + outputDate + "_"
+ searchOrganism + "_Output/"
+ searchOrganism + "SequenceNames.txt"));
//While there are new entries in the data file, keep screening
while ((otuSequenceList = otuSequenceListIn.readLine()) != null) {
//Boolean for exiting while loop when a sequence name is located
boolean otuFound = false;
//Delimit the current entry by tab
String splitarray[] = otuSequenceList.split("\t");
String otuNumber = splitarray[0];
//Open data file
BufferedReader otuListIn = new BufferedReader(
new FileReader(
outputDir + outputDate + "_" + searchOrganism
+ "_Output/" + searchOrganism
+ "OTUNumbers.txt"));
String otuListEntry;
//Read through list of selected OTU numbers and attempt to match
//to the current entry in the seqs_otus data file
while ((otuListEntry = otuListIn.readLine()) != null
&& !otuFound) {
//If a match is found, output to data file and exit while loop
if (otuListEntry.matches(otuNumber)) {
matchedOTUCount++;
otuFound = true;
//Add all matching sequence names to the data file
int endOfArray = splitarray.length;
countSeqNamesListed = countSeqNamesListed
+ (endOfArray - 1);
for (int i = 1; i < endOfArray; i++) {
sequenceNamesOut.println(splitarray[i]);
}
}
}
}
//close files
sequenceNamesOut.close();
otuSequenceListIn.close();
//Exception handling
} catch (IOException ex) {
JOptionPane.showMessageDialog(frame,
"OTU Sequence List input file not found,\n"
+ "or output directory not selected"
+ "\nplease check these and try again.");
} catch (ArrayIndexOutOfBoundsException ex) {
JOptionPane.showMessageDialog(frame,
"OTU Sequence List input file format is not "
+ "\ncorrect, please check file format and try again.");
}
int[] finalResults = new int[]{matchedOTUCount, countSeqNamesListed};
return finalResults;
}
/**
* Retrieve all read names pertaining to organism of interest
*
* @param outputDate date of OTUStalker run
* @param searchOrganism organism of interest
* @param deMulSeq filename of demultiplexed sequences file
* @param outputDir location of output directory selected by user
* @return matchCount number of OTU numbers matched
*/
public static int getAllOTUReadNumbers(
String outputDate, String searchOrganism,
String deMulSeq, String outputDir) {
//Initialize counter
int matchCount = 0;
try {
//Initialize output files
PrintWriter otuSequenceDataOut = new PrintWriter(
new FileWriter(outputDir + outputDate
+ "_" + searchOrganism + "_Output/All"
+ searchOrganism + "OTUSequenceDataSEQS.fasta"));
PrintWriter otuSequenceReadTagsOut = new PrintWriter(
new FileWriter(outputDir + outputDate + "_"
+ searchOrganism + "_Output/All"
+ searchOrganism + "OTUReadNumbers.txt"));
//Open file seqs.fna and delimit entries by sequence
Scanner scanner2 = new Scanner(new File(deMulSeq));
scanner2.useDelimiter(">");
//While there are more entries in the data file, keep screening
while (scanner2.hasNext()) {
String newToken = scanner2.next().toString();
/* Boolean to allow exiting of loop when a match is found*/
Boolean sequenceFound = false;
//Select the read number from the entry
String scanner2Text = newToken;
String splitarray[] = scanner2Text.split("\n");
String firstentry = splitarray[0];
String splitarray2[] = firstentry.split(" ");
String firstentry2 = splitarray2[0];
String firstentry3 = splitarray2[1];
//Open data file
BufferedReader sequenceNamesIn = new BufferedReader(
new FileReader(
outputDir + outputDate + "_" + searchOrganism
+ "_Output/" + searchOrganism
+ "SequenceNames.txt"));
String nextTag;
/*While a match hasn't been found and there are more entries
in the data file keep reading the file*/
while ((nextTag = sequenceNamesIn.readLine()) != null
&& !sequenceFound) {
/*If a matching sequence name is found add the sequence
data and the read number to their respective data files*/
if (nextTag.matches(firstentry2)) {
matchCount++;
sequenceFound = true;
//Append new data to output files
otuSequenceDataOut.println(">" + scanner2Text);
otuSequenceReadTagsOut.println("" + firstentry3);
}
}
//Close file
sequenceNamesIn.close();
}
//Close files
otuSequenceDataOut.close();
otuSequenceReadTagsOut.close();
scanner2.close();
//Exception handling
} catch (IOException ex) {
JOptionPane.showMessageDialog(frame,
"Demultiplexed sequenced input file not found,\n"
+ "or output directory not selected"
+ "\nplease check these and try again.");
} catch (ArrayIndexOutOfBoundsException ex) {
JOptionPane.showMessageDialog(frame,
"Demultiplexed input file format is not "
+ "\ncorrect, please check file format and try again.");
}
return matchCount;
}
/**
* Retrieve all reads pertaining to the organism of interest and split the
* data by sample
*
* @param outputDate date of OTUStalker run
* @param searchOrganism organism of interest
* @param fnaFile filename of the read data file
* @param outputDir location of output directory selected by user
* @return finalResults the sample names and the number of samples present
* in the sequence data
*/
public static ArrayList[] getAllOTUSequences(String outputDate,
String searchOrganism, String fnaFile,
String outputDir) {
//Initialize variables and data structures
int newSampleNum = 1;
ArrayList sampleNames = new ArrayList();
ArrayList numSamples = new ArrayList();
ArrayList[] finalResults = new ArrayList[]{sampleNames, numSamples};
try {
//initialize variables and data structures
Boolean found = false;
int matchCount = 0;
Scanner scanner;
//Create output directory and files