2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
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3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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11 * Jalview is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty
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13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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14 * PURPOSE. See the GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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18 package jalview.gui;
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21 import java.util.List;
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24 import java.awt.event.*;
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25 import javax.swing.*;
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27 import jalview.datamodel.*;
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28 import jalview.io.*;
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32 * GUI dialog for exporting features or alignment annotations depending upon
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33 * which method is called.
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38 public class AnnotationExporter extends JPanel
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40 JInternalFrame frame;
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44 boolean features = true;
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46 AlignmentAnnotation[] annotations;
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48 List<SequenceGroup> sequenceGroups;
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50 Hashtable alignmentProperties;
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52 public AnnotationExporter()
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57 } catch (Exception ex)
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59 ex.printStackTrace();
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62 frame = new JInternalFrame();
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63 frame.setContentPane(this);
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64 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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65 Desktop.addInternalFrame(frame, "", frame.getPreferredSize().width, frame.getPreferredSize().height);
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68 public void exportFeatures(AlignmentPanel ap)
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72 CSVFormat.setVisible(false);
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73 frame.setTitle("Export Features");
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76 public void exportAnnotations(AlignmentPanel ap,
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77 AlignmentAnnotation[] annotations, List<SequenceGroup> list,
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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 = list;
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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(features ? "Save Features to File"
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97 : "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(ap.av.getAlignment()
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110 .getDataset().getSequencesArray(),
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111 getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);
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115 text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
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116 .getDataset().getSequencesArray(),
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117 getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // 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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128 text = new AnnotationFile().printAnnotations(annotations,
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129 sequenceGroups, 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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140 } catch (Exception ex)
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142 ex.printStackTrace();
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146 close_actionPerformed(null);
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149 public void toTextbox_actionPerformed(ActionEvent e)
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151 String text = "No features found on alignment";
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154 if (GFFFormat.isSelected())
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156 text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
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157 .getDataset().getSequencesArray(),
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158 getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
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162 text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
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163 .getDataset().getSequencesArray(),
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164 getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
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167 else if (!features)
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169 if (CSVFormat.isSelected())
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171 text = new AnnotationFile().printCSVAnnotations(annotations);
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175 text = new AnnotationFile().printAnnotations(annotations,
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176 sequenceGroups, alignmentProperties);
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180 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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184 Desktop.addInternalFrame(cap, (features ? "Features for - "
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185 : "Annotations for - ") + ap.alignFrame.getTitle(), 600, 500);
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186 } catch (OutOfMemoryError oom)
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188 new OOMWarning("generating "
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189 + (features ? "Features for - " : "Annotations for - ")
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190 + ap.alignFrame.getTitle(), oom);
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194 close_actionPerformed(null);
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197 private Hashtable getDisplayedFeatureCols()
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199 Hashtable fcols = new Hashtable();
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200 if (ap.av.featuresDisplayed == null)
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204 Enumeration en = ap.av.featuresDisplayed.keys();
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205 FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider
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209 while (en.hasMoreElements())
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211 Object col = en.nextElement();
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212 fcols.put(col, fr.featureColours.get(col));
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217 public void close_actionPerformed(ActionEvent e)
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221 frame.setClosed(true);
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222 } catch (java.beans.PropertyVetoException ex)
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227 private void jbInit() throws Exception
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229 this.setLayout(new BorderLayout());
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231 toFile.setText("to File");
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232 toFile.addActionListener(new ActionListener()
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234 public void actionPerformed(ActionEvent e)
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236 toFile_actionPerformed(e);
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239 toTextbox.setText("to Textbox");
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240 toTextbox.addActionListener(new ActionListener()
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242 public void actionPerformed(ActionEvent e)
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244 toTextbox_actionPerformed(e);
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247 close.setText("Close");
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248 close.addActionListener(new ActionListener()
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250 public void actionPerformed(ActionEvent e)
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252 close_actionPerformed(e);
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255 jalviewFormat.setOpaque(false);
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256 jalviewFormat.setSelected(true);
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257 jalviewFormat.setText("Jalview");
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258 GFFFormat.setOpaque(false);
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259 GFFFormat.setText("GFF");
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260 CSVFormat.setOpaque(false);
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261 CSVFormat.setText("CSV(Spreadsheet)");
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262 jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
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263 jLabel1.setText("Format: ");
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264 this.setBackground(Color.white);
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265 jPanel3.setBorder(BorderFactory.createEtchedBorder());
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266 jPanel3.setOpaque(false);
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267 jPanel1.setOpaque(false);
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268 jPanel1.add(toFile);
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269 jPanel1.add(toTextbox);
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270 jPanel1.add(close);
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271 jPanel3.add(jLabel1);
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272 jPanel3.add(jalviewFormat);
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273 jPanel3.add(GFFFormat);
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274 jPanel3.add(CSVFormat);
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275 buttonGroup.add(jalviewFormat);
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276 buttonGroup.add(GFFFormat);
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277 buttonGroup.add(CSVFormat);
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278 this.add(jPanel3, BorderLayout.CENTER);
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279 this.add(jPanel1, BorderLayout.SOUTH);
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282 JPanel jPanel1 = new JPanel();
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284 JButton toFile = new JButton();
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286 JButton toTextbox = new JButton();
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288 JButton close = new JButton();
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290 ButtonGroup buttonGroup = new ButtonGroup();
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292 JRadioButton jalviewFormat = new JRadioButton();
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294 JRadioButton GFFFormat = new JRadioButton();
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296 JRadioButton CSVFormat = new JRadioButton();
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298 JLabel jLabel1 = new JLabel();
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300 JPanel jPanel3 = new JPanel();
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302 FlowLayout flowLayout1 = new FlowLayout();
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