2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
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3 * Copyright (C) 2009 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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19 package jalview.gui;
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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 Vector 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, "", 260, 125);
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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, 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(jalview.bin.Cache
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93 .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.alignment
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110 .getDataset().getSequencesArray(),
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111 getDisplayedFeatureCols());//ap.av.featuresDisplayed//);
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115 text = new FeaturesFile().printJalviewFormat(ap.av.alignment
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116 .getDataset().getSequencesArray(),
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117 getDisplayedFeatureCols()); // 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.alignment
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157 .getDataset().getSequencesArray(), getDisplayedFeatureCols());
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161 text = new FeaturesFile().printJalviewFormat(ap.av.alignment
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162 .getDataset().getSequencesArray(), getDisplayedFeatureCols());
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165 else if (!features)
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167 if (CSVFormat.isSelected())
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169 text = new AnnotationFile().printCSVAnnotations(annotations);
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173 text = new AnnotationFile().printAnnotations(annotations,
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174 sequenceGroups, alignmentProperties);
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178 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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180 Desktop.addInternalFrame(cap, (features ? "Features for - "
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181 : "Annotations for - ")
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182 + ap.alignFrame.getTitle(), 600, 500);
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184 close_actionPerformed(null);
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187 private Hashtable getDisplayedFeatureCols()
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189 Hashtable fcols = new Hashtable();
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190 Enumeration en = ap.av.featuresDisplayed.keys();
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191 FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider higher level method ?
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192 while (en.hasMoreElements())
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194 Object col = en.nextElement();
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195 fcols.put(col, fr.featureColours.get(col));
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200 public void close_actionPerformed(ActionEvent e)
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204 frame.setClosed(true);
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205 } catch (java.beans.PropertyVetoException ex)
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210 private void jbInit() throws Exception
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212 this.setLayout(flowLayout1);
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213 toFile.setText("to File");
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214 toFile.addActionListener(new ActionListener()
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216 public void actionPerformed(ActionEvent e)
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218 toFile_actionPerformed(e);
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221 toTextbox.setText("to Textbox");
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222 toTextbox.addActionListener(new ActionListener()
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224 public void actionPerformed(ActionEvent e)
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226 toTextbox_actionPerformed(e);
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229 close.setText("Close");
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230 close.addActionListener(new ActionListener()
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232 public void actionPerformed(ActionEvent e)
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234 close_actionPerformed(e);
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237 jalviewFormat.setOpaque(false);
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238 jalviewFormat.setSelected(true);
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239 jalviewFormat.setText("Jalview");
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240 GFFFormat.setOpaque(false);
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241 GFFFormat.setText("GFF");
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242 CSVFormat.setOpaque(false);
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243 CSVFormat.setText("CSV(Spreadsheet)");
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244 jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
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245 jLabel1.setText("Format: ");
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246 this.setBackground(Color.white);
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247 jPanel3.setBorder(BorderFactory.createEtchedBorder());
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248 jPanel3.setOpaque(false);
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249 jPanel1.setOpaque(false);
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250 jPanel1.add(toFile);
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251 jPanel1.add(toTextbox);
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252 jPanel1.add(close);
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253 jPanel3.add(jLabel1);
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254 jPanel3.add(jalviewFormat);
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255 jPanel3.add(GFFFormat);
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256 jPanel3.add(CSVFormat);
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257 buttonGroup.add(jalviewFormat);
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258 buttonGroup.add(GFFFormat);
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259 buttonGroup.add(CSVFormat);
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260 this.add(jPanel3, null);
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261 this.add(jPanel1, null);
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264 JPanel jPanel1 = new JPanel();
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266 JButton toFile = new JButton();
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268 JButton toTextbox = new JButton();
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270 JButton close = new JButton();
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272 ButtonGroup buttonGroup = new ButtonGroup();
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274 JRadioButton jalviewFormat = new JRadioButton();
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276 JRadioButton GFFFormat = new JRadioButton();
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278 JRadioButton CSVFormat = new JRadioButton();
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280 JLabel jLabel1 = new JLabel();
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282 JPanel jPanel3 = new JPanel();
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284 FlowLayout flowLayout1 = new FlowLayout();
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