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