src/jalview/gui/AnnotationExporter.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.datamodel.AlignmentAnnotation;
  24 import jalview.datamodel.SequenceGroup;
  25 import jalview.io.AnnotationFile;
  26 import jalview.io.FeaturesFile;
  27 import jalview.io.JalviewFileChooser;
  28 import jalview.io.JalviewFileView;
  29 import jalview.util.MessageManager;
  30
  31 import java.awt.BorderLayout;
  32 import java.awt.Color;
  33 import java.awt.FlowLayout;
  34 import java.awt.event.ActionEvent;
  35 import java.awt.event.ActionListener;
  36 import java.util.Enumeration;
  37 import java.util.Hashtable;
  38 import java.util.List;
  39
  40 import javax.swing.BorderFactory;
  41 import javax.swing.ButtonGroup;
  42 import javax.swing.JButton;
  43 import javax.swing.JInternalFrame;
  44 import javax.swing.JLabel;
  45 import javax.swing.JLayeredPane;
  46 import javax.swing.JPanel;
  47 import javax.swing.JRadioButton;
  48 import javax.swing.SwingConstants;
  49
  50 /**
  51  *
  52  * GUI dialog for exporting features or alignment annotations depending upon
  53  * which method is called.
  54  *
  55  * @author AMW
  56  *
  57  */
  58 public class AnnotationExporter extends JPanel
  59 {
  60   JInternalFrame frame;
  61
  62   AlignmentPanel ap;
  63
  64   boolean features = true;
  65
  66   AlignmentAnnotation[] annotations;
  67
  68   List<SequenceGroup> sequenceGroups;
  69
  70   Hashtable alignmentProperties;
  71
  72   public AnnotationExporter()
  73   {
  74     try
  75     {
  76       jbInit();
  77     } catch (Exception ex)
  78     {
  79       ex.printStackTrace();
  80     }
  81
  82     frame = new JInternalFrame();
  83     frame.setContentPane(this);
  84     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  85     Desktop.addInternalFrame(frame, "", frame.getPreferredSize().width,
  86             frame.getPreferredSize().height);
  87   }
  88
  89   public void exportFeatures(AlignmentPanel ap)
  90   {
  91     this.ap = ap;
  92     features = true;
  93     CSVFormat.setVisible(false);
  94     frame.setTitle(MessageManager.getString("label.export_features"));
  95   }
  96
  97   public void exportAnnotations(AlignmentPanel ap,
  98           AlignmentAnnotation[] annotations, List<SequenceGroup> list,
  99           Hashtable alProperties)
 100   {
 101     this.ap = ap;
 102     features = false;
 103     GFFFormat.setVisible(false);
 104     CSVFormat.setVisible(true);
 105     this.annotations = annotations;
 106     this.sequenceGroups = list;
 107     this.alignmentProperties = alProperties;
 108     frame.setTitle(MessageManager.getString("label.export_annotations"));
 109   }
 110
 111   public void toFile_actionPerformed(ActionEvent e)
 112   {
 113     JalviewFileChooser chooser = new JalviewFileChooser(
 114             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 115
 116     chooser.setFileView(new JalviewFileView());
 117     chooser.setDialogTitle(features ? MessageManager.getString("label.save_features_to_file")
 118             : MessageManager.getString("label.save_annotation_to_file"));
 119     chooser.setToolTipText(MessageManager.getString("action.save"));
 120
 121     int value = chooser.showSaveDialog(this);
 122
 123     if (value == JalviewFileChooser.APPROVE_OPTION)
 124     {
 125       String text = MessageManager.getString("label.no_features_on_alignment");
 126       if (features)
 127       {
 128         if (GFFFormat.isSelected())
 129         {
 130           text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
 131                   .getDataset().getSequencesArray(),
 132                   getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);
 133         }
 134         else
 135         {
 136           text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
 137                   .getDataset().getSequencesArray(),
 138                   getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);
 139         }
 140       }
 141       else
 142       {
 143         if (CSVFormat.isSelected())
 144         {
 145           text = new AnnotationFile().printCSVAnnotations(annotations);
 146         }
 147         else
 148         {
 149           text = new AnnotationFile().printAnnotations(annotations,
 150                   sequenceGroups, alignmentProperties);
 151         }
 152       }
 153
 154       try
 155       {
 156         java.io.PrintWriter out = new java.io.PrintWriter(
 157                 new java.io.FileWriter(chooser.getSelectedFile()));
 158
 159         out.print(text);
 160         out.close();
 161       } catch (Exception ex)
 162       {
 163         ex.printStackTrace();
 164       }
 165     }
 166
 167     close_actionPerformed(null);
 168   }
 169
 170   public void toTextbox_actionPerformed(ActionEvent e)
 171   {
 172     String text = MessageManager.getString("label.no_features_on_alignment");
 173     if (features)
 174     {
 175       if (GFFFormat.isSelected())
 176       {
 177         text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
 178                 .getDataset().getSequencesArray(),
 179                 getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
 180       }
 181       else
 182       {
 183         text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
 184                 .getDataset().getSequencesArray(),
 185                 getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
 186       }
 187     }
 188     else if (!features)
 189     {
 190       if (CSVFormat.isSelected())
 191       {
 192         text = new AnnotationFile().printCSVAnnotations(annotations);
 193       }
 194       else
 195       {
 196         text = new AnnotationFile().printAnnotations(annotations,
 197                 sequenceGroups, alignmentProperties);
 198       }
 199     }
 200
 201     CutAndPasteTransfer cap = new CutAndPasteTransfer();
 202     try
 203     {
 204       cap.setText(text);
 205       Desktop.addInternalFrame(
 206               cap,
 207               (features ? MessageManager.formatMessage(
 208                       "label.features_for_params", new String[]
 209                       { ap.alignFrame.getTitle() }) : MessageManager
 210                       .formatMessage("label.annotations_for_params",
 211                               new String[]
 212                               { ap.alignFrame.getTitle() })), 600, 500);
 213     } catch (OutOfMemoryError oom)
 214     {
 215       new OOMWarning((features ? MessageManager.formatMessage(
 216               "label.generating_features_for_params", new String[]
 217               { ap.alignFrame.getTitle() }) : MessageManager.formatMessage(
 218               "label.generating_annotations_for_params", new String[]
 219               { ap.alignFrame.getTitle() })), oom);
 220       cap.dispose();
 221     }
 222
 223     close_actionPerformed(null);
 224   }
 225
 226   private Hashtable getDisplayedFeatureCols()
 227   {
 228     Hashtable fcols = new Hashtable();
 229     if (ap.av.getFeaturesDisplayed() == null)
 230     {
 231       return fcols;
 232     }
 233
 234     Enumeration en = ap.av.getFeaturesDisplayed().keys();
 235     FeatureRenderer fr = ap.getSeqPanel().seqCanvas.getFeatureRenderer(); // consider
 236                                                                      // higher
 237                                                                      // level
 238                                                                      // method ?
 239     while (en.hasMoreElements())
 240     {
 241       Object col = en.nextElement();
 242       fcols.put(col, fr.featureColours.get(col));
 243     }
 244     return fcols;
 245   }
 246
 247   public void close_actionPerformed(ActionEvent e)
 248   {
 249     try
 250     {
 251       frame.setClosed(true);
 252     } catch (java.beans.PropertyVetoException ex)
 253     {
 254     }
 255   }
 256
 257   private void jbInit() throws Exception
 258   {
 259     this.setLayout(new BorderLayout());
 260
 261     toFile.setText(MessageManager.getString("label.to_file"));
 262     toFile.addActionListener(new ActionListener()
 263     {
 264       public void actionPerformed(ActionEvent e)
 265       {
 266         toFile_actionPerformed(e);
 267       }
 268     });
 269     toTextbox.setText(MessageManager.getString("label.to_textbox"));
 270     toTextbox.addActionListener(new ActionListener()
 271     {
 272       public void actionPerformed(ActionEvent e)
 273       {
 274         toTextbox_actionPerformed(e);
 275       }
 276     });
 277     close.setText(MessageManager.getString("action.close"));
 278     close.addActionListener(new ActionListener()
 279     {
 280       public void actionPerformed(ActionEvent e)
 281       {
 282         close_actionPerformed(e);
 283       }
 284     });
 285     jalviewFormat.setOpaque(false);
 286     jalviewFormat.setSelected(true);
 287     jalviewFormat.setText("Jalview");
 288     GFFFormat.setOpaque(false);
 289     GFFFormat.setText("GFF");
 290     CSVFormat.setOpaque(false);
 291     CSVFormat.setText(MessageManager.getString("label.csv_spreadsheet"));
 292     jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
 293     jLabel1.setText(MessageManager.getString("action.format") + " ");
 294     this.setBackground(Color.white);
 295     jPanel3.setBorder(BorderFactory.createEtchedBorder());
 296     jPanel3.setOpaque(false);
 297     jPanel1.setOpaque(false);
 298     jPanel1.add(toFile);
 299     jPanel1.add(toTextbox);
 300     jPanel1.add(close);
 301     jPanel3.add(jLabel1);
 302     jPanel3.add(jalviewFormat);
 303     jPanel3.add(GFFFormat);
 304     jPanel3.add(CSVFormat);
 305     buttonGroup.add(jalviewFormat);
 306     buttonGroup.add(GFFFormat);
 307     buttonGroup.add(CSVFormat);
 308     this.add(jPanel3, BorderLayout.CENTER);
 309     this.add(jPanel1, BorderLayout.SOUTH);
 310   }
 311
 312   JPanel jPanel1 = new JPanel();
 313
 314   JButton toFile = new JButton();
 315
 316   JButton toTextbox = new JButton();
 317
 318   JButton close = new JButton();
 319
 320   ButtonGroup buttonGroup = new ButtonGroup();
 321
 322   JRadioButton jalviewFormat = new JRadioButton();
 323
 324   JRadioButton GFFFormat = new JRadioButton();
 325
 326   JRadioButton CSVFormat = new JRadioButton();
 327
 328   JLabel jLabel1 = new JLabel();
 329
 330   JPanel jPanel3 = new JPanel();
 331
 332   FlowLayout flowLayout1 = new FlowLayout();
 333
 334 }