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1 /**
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2 *****************************************************************************
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3 * <p>
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4 * Copyright (c) Regents of the University of Minnesota. All Rights Reserved.
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5 * <p>
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6 * Author: Kevin Murray University of Minnesota - (murra668@umn.edu)
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7 * <p>
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8 *****************************************************************************
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9 */
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10 package kinamine;
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11
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12 import java.io.File;
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13 import java.net.URL;
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14 import java.util.ArrayList;
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15 import java.util.ResourceBundle;
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16 import javafx.event.ActionEvent;
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17 import javafx.fxml.FXML;
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18 import javafx.fxml.Initializable;
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19 import javafx.geometry.Pos;
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20 import javafx.scene.Scene;
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21 import javafx.scene.control.Button;
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22 import javafx.scene.control.Label;
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23 import javafx.scene.control.TextField;
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24 import javafx.scene.layout.VBox;
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25 import javafx.stage.DirectoryChooser;
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26 import javafx.stage.FileChooser;
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27 import javafx.stage.FileChooser.ExtensionFilter;
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28 import javafx.stage.Modality;
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29 import javafx.stage.Stage;
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30
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31 /**
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32 * Controller class for KinaMine GUI. Implements ActionEvents for GUI FXML frame
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33 * - built in Scene Builder.
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34 *
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35 * @version 1.0
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36 * @author murra668
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37 */
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38 public class KinaMineGUIController implements Initializable {
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39
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40 /**
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41 * Textfields for Peptide Report path, FASTA Database path, Output
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42 * Directory, FDR Score and Output Group Name.
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43 */
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44 @FXML
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45 private TextField pepPath, fastaPath, outPath, fdrScore, outGroup;
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46
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47 /** Debug */
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48 private boolean debug;
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49
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50 /** Location of last directory visited. */
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51 @FXML
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52 File lastDirectory;
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53
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54 /**
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55 * Handles ActionEvent of pepBrowseButton being pressed. Opens file browser
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56 * for selection of peptide report tabular file. Stores location of the pep
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57 * report in the PepPath Textfield.
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58 *
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59 * @param event
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60 */
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61 @FXML
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62 public void pepSearchClicked(ActionEvent event) {
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63
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64 /** Creates new FileChooser. */
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65 final FileChooser fileChooser = new FileChooser();
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66
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67 /** Creates new ExtensionFilter for selection of tabular file. */
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68 ExtensionFilter filter
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69 = new ExtensionFilter("Tabular", "*.tabular", "*.txt");
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70
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71 /** Configures FileChooser with parameters and last directory. */
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72 configFileChooser(fileChooser, lastDirectory, filter);
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73
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74 /** Opens FileChooser window. */
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75 final File selectedFile
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76 = fileChooser.showOpenDialog(KinaMine.stage);
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77
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78 /**
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79 * If the selected file is non-null, set the text of the pepPath
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80 * TextField to the absolute path of the file. Update last directory.
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81 */
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82 if (selectedFile != null) {
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83 lastDirectory = new File(selectedFile.getParent());
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84 pepPath.setText(selectedFile.getAbsolutePath());
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85
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86 }
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87 }
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88
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89 /**
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90 * Handles ActionEvent of fastaSearchButton being pressed. Opens a file
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91 * browser for the selection of a FASTA database and stores the location of
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92 * the file in the fastaPath Textfield.
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93 *
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94 * @param event
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95 */
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96 @FXML
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97 public void fastaSearchClicked(ActionEvent event) {
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98
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99 /** Initialize new filechosoer. */
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100 final FileChooser fileChooser = new FileChooser();
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101
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102 /** Create new extension filter */
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103 ExtensionFilter filter
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104 = new ExtensionFilter("Database", "*.fasta", "*.tabular");
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105
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106 /** Configure file chooser */
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107 configFileChooser(fileChooser, lastDirectory, filter);
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108
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109 /** Open file select window. */
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110 final File selectedFile
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111 = fileChooser.showOpenDialog(KinaMine.stage);
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112
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113 /** Update fastapath and last directory, if not null */
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114 if (selectedFile != null) {
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115 lastDirectory = new File(selectedFile.getParent());
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116 fastaPath.setText(selectedFile.getAbsolutePath());
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117
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118 }
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119 }
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120
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121 /**
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122 * Configures FileChooser.
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123 *
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124 * @param fileChooser
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125 * @param lastDir
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126 * @param filter
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127 */
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128 private static void configFileChooser(final FileChooser fileChooser,
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129 File lastDir, ExtensionFilter filter) {
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130
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131 fileChooser.setTitle("Open File");
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132
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133 fileChooser.getExtensionFilters().add(filter);
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134
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135 /** If last directory exists, start file selection from there. */
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136 if (lastDir == null) {
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137 fileChooser.setInitialDirectory(
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138 new File(System.getProperty("user.home")));
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139 } else {
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140 fileChooser.setInitialDirectory(lastDir);
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141 }
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142 }
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143
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144 /**
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145 * Handles ActionEvent that browse output was clicked. Opens directory
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146 * chooser and records path to directory chosen.
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147 *
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148 * @param event
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149 */
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150 public void browseFolderClicked(ActionEvent event) {
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151
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152 /** Initialize new DirectoryChooser */
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153 final DirectoryChooser dirChooser = new DirectoryChooser();
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154
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155 dirChooser.setTitle("Choose Output Location");
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156
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157 /** Configure starting location for directory chooser. */
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158 if (lastDirectory != null) {
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159 dirChooser.setInitialDirectory(lastDirectory);
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160 } else {
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161 dirChooser.setInitialDirectory(new File(System.getProperty("user.home")));
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162 }
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163
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164 /** Opens directory chooser window. */
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165 final File output = dirChooser.showDialog(KinaMine.stage);
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166
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167 /** Set path if file not null */
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168 if (output != null) {
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169 outPath.setText(output.getAbsolutePath());
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170 }
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171
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172 }
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173
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174 /**
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175 * Handles event that submit button is clicked. Collects are required inputs
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176 * for KineMineDriver.
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177 *
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178 * @param event
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179 */
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180 public void submitButtonClicked(ActionEvent event) {
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181
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182 /** Collect arguments */
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183 String args[] = new String[5];
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184 args[0] = pepPath.getText();
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185 args[1] = fastaPath.getText();
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186 args[2] = outPath.getText();
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187 args[3] = fdrScore.getText();
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188 args[4] = outGroup.getText();
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189
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190 ArrayList<String> error = checkForErrors(args);
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191
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192 /** Handle errors */
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193 if (error.isEmpty()) {
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194 boolean status = KinaMineDriver.run(args, debug = true);
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195 completeWindow();
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196 } else {
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197 alertError(error);
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198 }
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199 }
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200
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201 public ArrayList<String> checkForErrors(String[] args) {
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202
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203 ArrayList<String> error = new ArrayList<>();
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204
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205 File pep = new File(args[0]);
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206 File fasta = new File(args[1]);
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207 File dir = new File(args[2]);
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208 String score = args[3];
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209
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210 if (!pep.isFile()) {
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211 error.add(args[0] + " is not a file.");
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212 }
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213 if (!pep.canRead()) {
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214 error.add("Can't read peptide report: " + args[0]);
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215 }
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216 if (!fasta.isFile()) {
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217 error.add(args[1] + " is not a file.");
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218 }
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219 if (!fasta.canRead()) {
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220 error.add("Can't read database: " + args[0]);
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221 }
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222 if (!dir.isDirectory()){
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223 error.add(dir + " is not a directory.");
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224 }
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225 if (!score.matches("[-+]?\\d*\\.?\\d+")) {
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226 error.add("FDR Score: " + score + " is not a number.");
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227 }
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228
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229 return error;
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230 }
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231
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232 /**
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233 * If error in arguments for KinaMineDriver, open error window and write
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234 * error message to user.
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235 *
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236 * @param errors list of errors
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237 */
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238 public void alertError(ArrayList<String> errors) {
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239
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240 /** Format window. */
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241 Stage window = new Stage();
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242 window.initModality(Modality.APPLICATION_MODAL);
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243 window.setTitle("Error");
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244 window.setMinWidth(250);
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245
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246 /** Format message*/
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247 String message = "";
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248 for (String error : errors) {
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249 message += error + "\n";
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250 }
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251 Label label = new Label(message);
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252
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253 /** Format Button */
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254 Button closeButton = new Button("Close\n");
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255 closeButton.setOnAction(e -> window.close());
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256
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257 /** Format layout */
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258 VBox layout = new VBox(10);
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259 layout.getChildren().addAll(label, closeButton);
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260 layout.setAlignment(Pos.CENTER);
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261
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262 /** Set scene */
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263 Scene scene = new Scene(layout);
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264 window.setScene(scene);
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265 window.showAndWait();
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266
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267 }
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268
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269 /**
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270 * Opens window when Run is complete.
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271 */
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272 public void completeWindow() {
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273
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274 /** Format window. */
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275 Stage window = new Stage();
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276 window.initModality(Modality.APPLICATION_MODAL);
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277 window.setMinWidth(250);
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278
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279 /** Format close button */
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280 Label label = new Label("Run Complete");
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281 Button closeButton = new Button("Done");
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282 closeButton.setOnAction(e -> window.close());
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283
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284 /** Format layout */
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285 VBox layout = new VBox(10);
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286 layout.getChildren().addAll(label, closeButton);
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287 layout.setAlignment(Pos.CENTER);
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288
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289 /** Set scene */
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290 Scene scene = new Scene(layout);
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291 window.setScene(scene);
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292 window.showAndWait();
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293
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294 }
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295
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296 /**
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297 * Initialize method for KinaMineGUI. Initializes all paths.
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298 *
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299 * @param url
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300 * @param rb
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301 */
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302 @Override
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303 public void initialize(URL url, ResourceBundle rb) {
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304 System.out.println("Initializing...");
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305 lastDirectory = null;
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306 assert pepPath != null : "fx:id=\"pepPath\" was not injected: check your FXML file 'KinaMineGUI.fxml'.";
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307 assert fastaPath != null : "fx:id=\"fastaPath\" was not injected: check your FXML file 'KinaMineGUI.fxml'.";
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308 assert outPath != null : "fx:id=\"outPath\" was not injected: check your FXML file 'KinaMineGUI.fxml'.";
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309
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310 }
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311
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312 }
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