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 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("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("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 ? "Save Features to File"
 102             : "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 = "No features found on alignment";
 110       if (features)
 111       {
 112         if (GFFFormat.isSelected())
 113         {
 114           text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
 115                   .getDataset().getSequencesArray(), ap
 116                   .getFeatureRenderer().getDisplayedFeatureCols(), true,
 117                   ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);
 118         }
 119         else
 120         {
 121           text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
 122                   .getDataset().getSequencesArray(), ap
 123                   .getFeatureRenderer().getDisplayedFeatureCols(), true,
 124                   ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);
 125         }
 126       }
 127       else
 128       {
 129         if (CSVFormat.isSelected())
 130         {
 131           text = new AnnotationFile().printCSVAnnotations(annotations);
 132         }
 133         else
 134         {
 135           text = new AnnotationFile().printAnnotations(annotations,
 136                   sequenceGroups, alignmentProperties);
 137         }
 138       }
 139
 140       try
 141       {
 142         java.io.PrintWriter out = new java.io.PrintWriter(
 143                 new java.io.FileWriter(chooser.getSelectedFile()));
 144
 145         out.print(text);
 146         out.close();
 147       } catch (Exception ex)
 148       {
 149         ex.printStackTrace();
 150       }
 151     }
 152
 153     close_actionPerformed(null);
 154   }
 155
 156   public void toTextbox_actionPerformed(ActionEvent e)
 157   {
 158     String text = "No features found on alignment";
 159     if (features)
 160     {
 161       if (GFFFormat.isSelected())
 162       {
 163         text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
 164                 .getDataset().getSequencesArray(), ap.getFeatureRenderer()
 165                 .getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
 166       }
 167       else
 168       {
 169         text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
 170                 .getDataset().getSequencesArray(), ap.getFeatureRenderer()
 171                 .getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
 172       }
 173     }
 174     else if (!features)
 175     {
 176       if (CSVFormat.isSelected())
 177       {
 178         text = new AnnotationFile().printCSVAnnotations(annotations);
 179       }
 180       else
 181       {
 182         text = new AnnotationFile().printAnnotations(annotations,
 183                 sequenceGroups, alignmentProperties);
 184       }
 185     }
 186
 187     CutAndPasteTransfer cap = new CutAndPasteTransfer();
 188     try
 189     {
 190       cap.setText(text);
 191       Desktop.addInternalFrame(
 192               cap,
 193               (features ? MessageManager.formatMessage(
 194                       "label.features_for_params", new String[]
 195                       { ap.alignFrame.getTitle() }) : MessageManager
 196                       .formatMessage("label.annotations_for_params",
 197                               new String[]
 198                               { ap.alignFrame.getTitle() })), 600, 500);
 199     } catch (OutOfMemoryError oom)
 200     {
 201       new OOMWarning((features ? MessageManager.formatMessage(
 202               "label.generating_features_for_params", new String[]
 203               { ap.alignFrame.getTitle() }) : MessageManager.formatMessage(
 204               "label.generating_annotations_for_params", new String[]
 205               { ap.alignFrame.getTitle() })), oom);
 206       cap.dispose();
 207     }
 208
 209     close_actionPerformed(null);
 210   }
 211
 212   public void close_actionPerformed(ActionEvent e)
 213   {
 214     try
 215     {
 216       frame.setClosed(true);
 217     } catch (java.beans.PropertyVetoException ex)
 218     {
 219     }
 220   }
 221
 222   private void jbInit() throws Exception
 223   {
 224     this.setLayout(new BorderLayout());
 225
 226     toFile.setText(MessageManager.getString("label.to_file"));
 227     toFile.addActionListener(new ActionListener()
 228     {
 229       public void actionPerformed(ActionEvent e)
 230       {
 231         toFile_actionPerformed(e);
 232       }
 233     });
 234     toTextbox.setText(MessageManager.getString("label.to_textbox"));
 235     toTextbox.addActionListener(new ActionListener()
 236     {
 237       public void actionPerformed(ActionEvent e)
 238       {
 239         toTextbox_actionPerformed(e);
 240       }
 241     });
 242     close.setText(MessageManager.getString("action.close"));
 243     close.addActionListener(new ActionListener()
 244     {
 245       public void actionPerformed(ActionEvent e)
 246       {
 247         close_actionPerformed(e);
 248       }
 249     });
 250     jalviewFormat.setOpaque(false);
 251     jalviewFormat.setSelected(true);
 252     jalviewFormat.setText("Jalview");
 253     GFFFormat.setOpaque(false);
 254     GFFFormat.setText("GFF");
 255     CSVFormat.setOpaque(false);
 256     CSVFormat.setText(MessageManager.getString("label.csv_spreadsheet"));
 257     jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
 258     jLabel1.setText(MessageManager.getString("action.format") + " ");
 259     this.setBackground(Color.white);
 260     jPanel3.setBorder(BorderFactory.createEtchedBorder());
 261     jPanel3.setOpaque(false);
 262     jPanel1.setOpaque(false);
 263     jPanel1.add(toFile);
 264     jPanel1.add(toTextbox);
 265     jPanel1.add(close);
 266     jPanel3.add(jLabel1);
 267     jPanel3.add(jalviewFormat);
 268     jPanel3.add(GFFFormat);
 269     jPanel3.add(CSVFormat);
 270     buttonGroup.add(jalviewFormat);
 271     buttonGroup.add(GFFFormat);
 272     buttonGroup.add(CSVFormat);
 273     this.add(jPanel3, BorderLayout.CENTER);
 274     this.add(jPanel1, BorderLayout.SOUTH);
 275   }
 276
 277   JPanel jPanel1 = new JPanel();
 278
 279   JButton toFile = new JButton();
 280
 281   JButton toTextbox = new JButton();
 282
 283   JButton close = new JButton();
 284
 285   ButtonGroup buttonGroup = new ButtonGroup();
 286
 287   JRadioButton jalviewFormat = new JRadioButton();
 288
 289   JRadioButton GFFFormat = new JRadioButton();
 290
 291   JRadioButton CSVFormat = new JRadioButton();
 292
 293   JLabel jLabel1 = new JLabel();
 294
 295   JPanel jPanel3 = new JPanel();
 296
 297   FlowLayout flowLayout1 = new FlowLayout();
 298
 299 }