2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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20 package jalview.gui;
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25 import java.awt.event.*;
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26 import javax.swing.*;
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28 import jalview.datamodel.*;
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29 import jalview.io.*;
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33 * GUI dialog for exporting features or alignment annotations depending upon which method is called.
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38 public class AnnotationExporter
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41 JInternalFrame frame;
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43 boolean features = true;
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44 AlignmentAnnotation[] annotations;
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45 Vector sequenceGroups;
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46 Hashtable alignmentProperties;
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48 public AnnotationExporter()
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54 catch (Exception ex)
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56 ex.printStackTrace();
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59 frame = new JInternalFrame();
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60 frame.setContentPane(this);
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61 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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62 Desktop.addInternalFrame(frame,
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67 public void exportFeatures(AlignmentPanel ap)
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71 CSVFormat.setVisible(false);
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72 frame.setTitle("Export Features");
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75 public void exportAnnotations(AlignmentPanel ap,
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76 AlignmentAnnotation[] annotations,
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77 Vector sequenceGroups,
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78 Hashtable alProperties)
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82 GFFFormat.setVisible(false);
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83 CSVFormat.setVisible(true);
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84 this.annotations = annotations;
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85 this.sequenceGroups = sequenceGroups;
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86 this.alignmentProperties = alProperties;
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87 frame.setTitle("Export Annotations");
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90 public void toFile_actionPerformed(ActionEvent e)
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92 JalviewFileChooser chooser = new JalviewFileChooser(
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93 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
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95 chooser.setFileView(new JalviewFileView());
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96 chooser.setDialogTitle(
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97 features ? "Save Features to File" : "Save Annotation to File");
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98 chooser.setToolTipText("Save");
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100 int value = chooser.showSaveDialog(this);
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102 if (value == JalviewFileChooser.APPROVE_OPTION)
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104 String text = "No features found on alignment";
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107 if (GFFFormat.isSelected())
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109 text = new FeaturesFile().printGFFFormat(
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110 ap.av.alignment.getDataset().getSequencesArray(),
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111 ap.av.featuresDisplayed);
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115 text = new FeaturesFile().printJalviewFormat(
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116 ap.av.alignment.getDataset().getSequencesArray(),
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117 ap.av.featuresDisplayed);
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122 if (CSVFormat.isSelected())
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124 text = new AnnotationFile().printCSVAnnotations(annotations);
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126 text = new AnnotationFile().printAnnotations(
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129 alignmentProperties);
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135 java.io.PrintWriter out = new java.io.PrintWriter(
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136 new java.io.FileWriter(chooser.getSelectedFile()));
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141 catch (Exception ex)
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143 ex.printStackTrace();
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147 close_actionPerformed(null);
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150 public void toTextbox_actionPerformed(ActionEvent e)
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152 String text = "No features found on alignment";
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155 if (GFFFormat.isSelected())
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157 text = new FeaturesFile().printGFFFormat(
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158 ap.av.alignment.getDataset().getSequencesArray(),
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159 ap.av.featuresDisplayed);
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163 text = new FeaturesFile().printJalviewFormat(
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164 ap.av.alignment.getDataset().getSequencesArray(),
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165 ap.av.featuresDisplayed);
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168 else if (!features)
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170 if (CSVFormat.isSelected())
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172 text = new AnnotationFile().printCSVAnnotations(annotations);
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174 text = new AnnotationFile().printAnnotations(
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177 alignmentProperties);
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181 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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183 Desktop.addInternalFrame(cap,
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184 (features ? "Features for - " :
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185 "Annotations for - ")
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186 + ap.alignFrame.getTitle(),
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190 close_actionPerformed(null);
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193 public void close_actionPerformed(ActionEvent e)
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197 frame.setClosed(true);
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199 catch (java.beans.PropertyVetoException ex)
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203 private void jbInit()
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206 this.setLayout(flowLayout1);
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207 toFile.setText("to File");
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208 toFile.addActionListener(new ActionListener()
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210 public void actionPerformed(ActionEvent e)
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212 toFile_actionPerformed(e);
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215 toTextbox.setText("to Textbox");
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216 toTextbox.addActionListener(new ActionListener()
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218 public void actionPerformed(ActionEvent e)
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220 toTextbox_actionPerformed(e);
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223 close.setText("Close");
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224 close.addActionListener(new ActionListener()
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226 public void actionPerformed(ActionEvent e)
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228 close_actionPerformed(e);
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231 jalviewFormat.setOpaque(false);
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232 jalviewFormat.setSelected(true);
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233 jalviewFormat.setText("Jalview");
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234 GFFFormat.setOpaque(false);
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235 GFFFormat.setText("GFF");
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236 CSVFormat.setOpaque(false);
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237 CSVFormat.setText("CSV(Spreadsheet)");
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238 jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
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239 jLabel1.setText("Format: ");
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240 this.setBackground(Color.white);
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241 jPanel3.setBorder(BorderFactory.createEtchedBorder());
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242 jPanel3.setOpaque(false);
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243 jPanel1.setOpaque(false);
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244 jPanel1.add(toFile);
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245 jPanel1.add(toTextbox);
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246 jPanel1.add(close);
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247 jPanel3.add(jLabel1);
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248 jPanel3.add(jalviewFormat);
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249 jPanel3.add(GFFFormat);
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250 jPanel3.add(CSVFormat);
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251 buttonGroup.add(jalviewFormat);
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252 buttonGroup.add(GFFFormat);
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253 buttonGroup.add(CSVFormat);
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254 this.add(jPanel3, null);
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255 this.add(jPanel1, null);
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258 JPanel jPanel1 = new JPanel();
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259 JButton toFile = new JButton();
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260 JButton toTextbox = new JButton();
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261 JButton close = new JButton();
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262 ButtonGroup buttonGroup = new ButtonGroup();
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263 JRadioButton jalviewFormat = new JRadioButton();
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264 JRadioButton GFFFormat = new JRadioButton();
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265 JRadioButton CSVFormat = new JRadioButton();
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266 JLabel jLabel1 = new JLabel();
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267 JPanel jPanel3 = new JPanel();
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268 FlowLayout flowLayout1 = new FlowLayout();
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