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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31 public class AnnotationExporter
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34 JInternalFrame frame;
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36 boolean features = true;
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37 AlignmentAnnotation[] annotations;
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38 Vector sequenceGroups;
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40 public AnnotationExporter()
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46 catch (Exception ex)
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48 ex.printStackTrace();
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51 frame = new JInternalFrame();
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52 frame.setContentPane(this);
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53 frame.setLayer(JLayeredPane.PALETTE_LAYER);
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54 Desktop.addInternalFrame(frame,
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59 public void exportFeatures(AlignmentPanel ap)
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63 frame.setTitle("Export Features");
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66 public void exportAnnotations(AlignmentPanel ap,
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67 AlignmentAnnotation[] annotations,
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68 Vector sequenceGroups)
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72 GFFFormat.setVisible(false);
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73 this.annotations = annotations;
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74 this.sequenceGroups = sequenceGroups;
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75 frame.setTitle("Export Annotations");
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78 public void toFile_actionPerformed(ActionEvent e)
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80 JalviewFileChooser chooser = new JalviewFileChooser(
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81 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
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83 chooser.setFileView(new JalviewFileView());
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84 chooser.setDialogTitle(
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85 features ? "Save Features to File" : "Save Annotation to File");
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86 chooser.setToolTipText("Save");
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88 int value = chooser.showSaveDialog(this);
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90 if (value == JalviewFileChooser.APPROVE_OPTION)
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92 String text = "No features found on alignment";
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95 if (GFFFormat.isSelected())
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97 text = new FeaturesFile().printGFFFormat(
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98 ap.av.alignment.getDataset().getSequencesArray(),
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99 ap.av.featuresDisplayed);
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103 text = new FeaturesFile().printJalviewFormat(
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104 ap.av.alignment.getDataset().getSequencesArray(),
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105 ap.av.featuresDisplayed);
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110 text = new AnnotationFile().printAnnotations(
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117 java.io.PrintWriter out = new java.io.PrintWriter(
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118 new java.io.FileWriter(chooser.getSelectedFile()));
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123 catch (Exception ex)
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125 ex.printStackTrace();
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130 public void toTextbox_actionPerformed(ActionEvent e)
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132 String text = "No features found on alignment";
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135 if (GFFFormat.isSelected())
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137 text = new FeaturesFile().printGFFFormat(
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138 ap.av.alignment.getDataset().getSequencesArray(),
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139 ap.av.featuresDisplayed);
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143 text = new FeaturesFile().printJalviewFormat(
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144 ap.av.alignment.getDataset().getSequencesArray(),
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145 ap.av.featuresDisplayed);
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148 else if (!features)
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150 text = new AnnotationFile().printAnnotations(
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155 CutAndPasteTransfer cap = new CutAndPasteTransfer();
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157 Desktop.addInternalFrame(cap,
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158 (features ? "Features for - " :
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159 "Annotations for - ")
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160 + ap.alignFrame.getTitle(),
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166 public void close_actionPerformed(ActionEvent e)
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170 frame.setClosed(true);
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172 catch (java.beans.PropertyVetoException ex)
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176 private void jbInit()
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179 this.setLayout(flowLayout1);
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180 toFile.setText("to File");
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181 toFile.addActionListener(new ActionListener()
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183 public void actionPerformed(ActionEvent e)
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185 toFile_actionPerformed(e);
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188 toTextbox.setText("to Textbox");
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189 toTextbox.addActionListener(new ActionListener()
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191 public void actionPerformed(ActionEvent e)
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193 toTextbox_actionPerformed(e);
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196 close.setText("Close");
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197 close.addActionListener(new ActionListener()
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199 public void actionPerformed(ActionEvent e)
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201 close_actionPerformed(e);
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204 jalviewFormat.setOpaque(false);
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205 jalviewFormat.setSelected(true);
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206 jalviewFormat.setText("Jalview");
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207 GFFFormat.setOpaque(false);
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208 GFFFormat.setText("GFF");
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209 jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
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210 jLabel1.setText("Format: ");
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211 this.setBackground(Color.white);
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212 jPanel3.setBorder(BorderFactory.createEtchedBorder());
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213 jPanel3.setOpaque(false);
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214 jPanel1.setOpaque(false);
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215 jPanel1.add(toFile);
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216 jPanel1.add(toTextbox);
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217 jPanel1.add(close);
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218 jPanel3.add(jLabel1);
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219 jPanel3.add(jalviewFormat);
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220 jPanel3.add(GFFFormat);
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221 buttonGroup.add(jalviewFormat);
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222 buttonGroup.add(GFFFormat);
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223 this.add(jPanel3, null);
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224 this.add(jPanel1, null);
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227 JPanel jPanel1 = new JPanel();
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228 JButton toFile = new JButton();
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229 JButton toTextbox = new JButton();
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230 JButton close = new JButton();
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231 ButtonGroup buttonGroup = new ButtonGroup();
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232 JRadioButton jalviewFormat = new JRadioButton();
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233 JRadioButton GFFFormat = new JRadioButton();
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234 JLabel jLabel1 = new JLabel();
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235 JPanel jPanel3 = new JPanel();
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236 FlowLayout flowLayout1 = new FlowLayout();
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