src/jalview/gui/AnnotationExporter.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
   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 java.util.*;
  24 import java.util.List;
  25
  26 import java.awt.*;
  27 import java.awt.event.*;
  28 import javax.swing.*;
  29
  30 import jalview.datamodel.*;
  31 import jalview.io.*;
  32 import jalview.util.MessageManager;
  33
  34 /**
  35  *
  36  * GUI dialog for exporting features or alignment annotations depending upon
  37  * which method is called.
  38  *
  39  * @author AMW
  40  *
  41  */
  42 public class AnnotationExporter extends JPanel
  43 {
  44   JInternalFrame frame;
  45
  46   AlignmentPanel ap;
  47
  48   boolean features = true;
  49
  50   AlignmentAnnotation[] annotations;
  51
  52   List<SequenceGroup> sequenceGroups;
  53
  54   Hashtable alignmentProperties;
  55
  56   public AnnotationExporter()
  57   {
  58     try
  59     {
  60       jbInit();
  61     } catch (Exception ex)
  62     {
  63       ex.printStackTrace();
  64     }
  65
  66     frame = new JInternalFrame();
  67     frame.setContentPane(this);
  68     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  69     Desktop.addInternalFrame(frame, "", frame.getPreferredSize().width,
  70             frame.getPreferredSize().height);
  71   }
  72
  73   public void exportFeatures(AlignmentPanel ap)
  74   {
  75     this.ap = ap;
  76     features = true;
  77     CSVFormat.setVisible(false);
  78     frame.setTitle(MessageManager.getString("label.export_features"));
  79   }
  80
  81   public void exportAnnotations(AlignmentPanel ap,
  82           AlignmentAnnotation[] annotations, List<SequenceGroup> list,
  83           Hashtable alProperties)
  84   {
  85     this.ap = ap;
  86     features = false;
  87     GFFFormat.setVisible(false);
  88     CSVFormat.setVisible(true);
  89     this.annotations = annotations;
  90     this.sequenceGroups = list;
  91     this.alignmentProperties = alProperties;
  92     frame.setTitle(MessageManager.getString("label.export_annotations"));
  93   }
  94
  95   public void toFile_actionPerformed(ActionEvent e)
  96   {
  97     JalviewFileChooser chooser = new JalviewFileChooser(
  98             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
  99
 100     chooser.setFileView(new JalviewFileView());
 101     chooser.setDialogTitle(features ? MessageManager.getString("label.save_features_to_file")
 102             : MessageManager.getString("label.save_annotation_to_file"));
 103     chooser.setToolTipText(MessageManager.getString("action.save"));
 104
 105     int value = chooser.showSaveDialog(this);
 106
 107     if (value == JalviewFileChooser.APPROVE_OPTION)
 108     {
 109       String text = MessageManager.getString("label.no_features_on_alignment");
 110       if (features)
 111       {
 112         if (GFFFormat.isSelected())
 113         {
 114           text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
 115                   .getDataset().getSequencesArray(),
 116                   getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);
 117         }
 118         else
 119         {
 120           text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
 121                   .getDataset().getSequencesArray(),
 122                   getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);
 123         }
 124       }
 125       else
 126       {
 127         if (CSVFormat.isSelected())
 128         {
 129           text = new AnnotationFile().printCSVAnnotations(annotations);
 130         }
 131         else
 132         {
 133           text = new AnnotationFile().printAnnotations(annotations,
 134                   sequenceGroups, alignmentProperties);
 135         }
 136       }
 137
 138       try
 139       {
 140         java.io.PrintWriter out = new java.io.PrintWriter(
 141                 new java.io.FileWriter(chooser.getSelectedFile()));
 142
 143         out.print(text);
 144         out.close();
 145       } catch (Exception ex)
 146       {
 147         ex.printStackTrace();
 148       }
 149     }
 150
 151     close_actionPerformed(null);
 152   }
 153
 154   public void toTextbox_actionPerformed(ActionEvent e)
 155   {
 156     String text = MessageManager.getString("label.no_features_on_alignment");
 157     if (features)
 158     {
 159       if (GFFFormat.isSelected())
 160       {
 161         text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
 162                 .getDataset().getSequencesArray(),
 163                 getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
 164       }
 165       else
 166       {
 167         text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
 168                 .getDataset().getSequencesArray(),
 169                 getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
 170       }
 171     }
 172     else if (!features)
 173     {
 174       if (CSVFormat.isSelected())
 175       {
 176         text = new AnnotationFile().printCSVAnnotations(annotations);
 177       }
 178       else
 179       {
 180         text = new AnnotationFile().printAnnotations(annotations,
 181                 sequenceGroups, alignmentProperties);
 182       }
 183     }
 184
 185     CutAndPasteTransfer cap = new CutAndPasteTransfer();
 186     try
 187     {
 188       cap.setText(text);
 189       Desktop.addInternalFrame(
 190               cap,
 191               (features ? MessageManager.formatMessage(
 192                       "label.features_for_params", new String[]
 193                       { ap.alignFrame.getTitle() }) : MessageManager
 194                       .formatMessage("label.annotations_for_params",
 195                               new String[]
 196                               { ap.alignFrame.getTitle() })), 600, 500);
 197     } catch (OutOfMemoryError oom)
 198     {
 199       new OOMWarning((features ? MessageManager.formatMessage(
 200               "label.generating_features_for_params", new String[]
 201               { ap.alignFrame.getTitle() }) : MessageManager.formatMessage(
 202               "label.generating_annotations_for_params", new String[]
 203               { ap.alignFrame.getTitle() })), oom);
 204       cap.dispose();
 205     }
 206
 207     close_actionPerformed(null);
 208   }
 209
 210   private Hashtable getDisplayedFeatureCols()
 211   {
 212     Hashtable fcols = new Hashtable();
 213     if (ap.av.featuresDisplayed == null)
 214     {
 215       return fcols;
 216     }
 217     Enumeration en = ap.av.featuresDisplayed.keys();
 218     FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider
 219                                                                      // higher
 220                                                                      // level
 221                                                                      // method ?
 222     while (en.hasMoreElements())
 223     {
 224       Object col = en.nextElement();
 225       fcols.put(col, fr.featureColours.get(col));
 226     }
 227     return fcols;
 228   }
 229
 230   public void close_actionPerformed(ActionEvent e)
 231   {
 232     try
 233     {
 234       frame.setClosed(true);
 235     } catch (java.beans.PropertyVetoException ex)
 236     {
 237     }
 238   }
 239
 240   private void jbInit() throws Exception
 241   {
 242     this.setLayout(new BorderLayout());
 243
 244     toFile.setText(MessageManager.getString("label.to_file"));
 245     toFile.addActionListener(new ActionListener()
 246     {
 247       public void actionPerformed(ActionEvent e)
 248       {
 249         toFile_actionPerformed(e);
 250       }
 251     });
 252     toTextbox.setText(MessageManager.getString("label.to_textbox"));
 253     toTextbox.addActionListener(new ActionListener()
 254     {
 255       public void actionPerformed(ActionEvent e)
 256       {
 257         toTextbox_actionPerformed(e);
 258       }
 259     });
 260     close.setText(MessageManager.getString("action.close"));
 261     close.addActionListener(new ActionListener()
 262     {
 263       public void actionPerformed(ActionEvent e)
 264       {
 265         close_actionPerformed(e);
 266       }
 267     });
 268     jalviewFormat.setOpaque(false);
 269     jalviewFormat.setSelected(true);
 270     jalviewFormat.setText("Jalview");
 271     GFFFormat.setOpaque(false);
 272     GFFFormat.setText("GFF");
 273     CSVFormat.setOpaque(false);
 274     CSVFormat.setText(MessageManager.getString("label.csv_spreadsheet"));
 275     jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
 276     jLabel1.setText(MessageManager.getString("action.format") + " ");
 277     this.setBackground(Color.white);
 278     jPanel3.setBorder(BorderFactory.createEtchedBorder());
 279     jPanel3.setOpaque(false);
 280     jPanel1.setOpaque(false);
 281     jPanel1.add(toFile);
 282     jPanel1.add(toTextbox);
 283     jPanel1.add(close);
 284     jPanel3.add(jLabel1);
 285     jPanel3.add(jalviewFormat);
 286     jPanel3.add(GFFFormat);
 287     jPanel3.add(CSVFormat);
 288     buttonGroup.add(jalviewFormat);
 289     buttonGroup.add(GFFFormat);
 290     buttonGroup.add(CSVFormat);
 291     this.add(jPanel3, BorderLayout.CENTER);
 292     this.add(jPanel1, BorderLayout.SOUTH);
 293   }
 294
 295   JPanel jPanel1 = new JPanel();
 296
 297   JButton toFile = new JButton();
 298
 299   JButton toTextbox = new JButton();
 300
 301   JButton close = new JButton();
 302
 303   ButtonGroup buttonGroup = new ButtonGroup();
 304
 305   JRadioButton jalviewFormat = new JRadioButton();
 306
 307   JRadioButton GFFFormat = new JRadioButton();
 308
 309   JRadioButton CSVFormat = new JRadioButton();
 310
 311   JLabel jLabel1 = new JLabel();
 312
 313   JPanel jPanel3 = new JPanel();
 314
 315   FlowLayout flowLayout1 = new FlowLayout();
 316
 317 }