src/jalview/gui/AnnotationExporter.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ 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.api.FeatureColourI;
  24 import jalview.datamodel.AlignmentAnnotation;
  25 import jalview.datamodel.SequenceI;
  26 import jalview.io.AnnotationFile;
  27 import jalview.io.FeaturesFile;
  28 import jalview.io.JalviewFileChooser;
  29 import jalview.io.JalviewFileView;
  30 import jalview.util.MessageManager;
  31
  32 import java.awt.BorderLayout;
  33 import java.awt.Color;
  34 import java.awt.FlowLayout;
  35 import java.awt.event.ActionEvent;
  36 import java.awt.event.ActionListener;
  37 import java.util.Map;
  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   private AlignmentAnnotation[] annotations;
  66
  67   private boolean wholeView;
  68
  69   public AnnotationExporter()
  70   {
  71     try
  72     {
  73       jbInit();
  74     } catch (Exception ex)
  75     {
  76       ex.printStackTrace();
  77     }
  78
  79     frame = new JInternalFrame();
  80     frame.setContentPane(this);
  81     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  82     Desktop.addInternalFrame(frame, "", frame.getPreferredSize().width,
  83             frame.getPreferredSize().height);
  84   }
  85
  86   public void exportFeatures(AlignmentPanel ap)
  87   {
  88     this.ap = ap;
  89     features = true;
  90     CSVFormat.setVisible(false);
  91     frame.setTitle(MessageManager.getString("label.export_features"));
  92   }
  93
  94   public void exportAnnotations(AlignmentPanel ap)
  95   {
  96     this.ap = ap;
  97     annotations = ap.av.isShowAnnotation() ? null : ap.av.getAlignment()
  98             .getAlignmentAnnotation();
  99     wholeView = true;
 100     startExportAnnotation();
 101   }
 102
 103   public void exportAnnotations(AlignmentPanel alp,
 104           AlignmentAnnotation[] toExport)
 105   {
 106     ap = alp;
 107     annotations = toExport;
 108     wholeView = false;
 109     startExportAnnotation();
 110   }
 111
 112   private void startExportAnnotation()
 113   {
 114     features = false;
 115     GFFFormat.setVisible(false);
 116     CSVFormat.setVisible(true);
 117     frame.setTitle(MessageManager.getString("label.export_annotations"));
 118   }
 119
 120   public void toFile_actionPerformed(ActionEvent e)
 121   {
 122     JalviewFileChooser chooser = new JalviewFileChooser(
 123             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 124
 125     chooser.setFileView(new JalviewFileView());
 126     chooser.setDialogTitle(features ? MessageManager
 127             .getString("label.save_features_to_file") : MessageManager
 128             .getString("label.save_annotation_to_file"));
 129     chooser.setToolTipText(MessageManager.getString("action.save"));
 130
 131     int value = chooser.showSaveDialog(this);
 132
 133     if (value == JalviewFileChooser.APPROVE_OPTION)
 134     {
 135       String text = getFileContents();
 136
 137       try
 138       {
 139         java.io.PrintWriter out = new java.io.PrintWriter(
 140                 new java.io.FileWriter(chooser.getSelectedFile()));
 141
 142         out.print(text);
 143         out.close();
 144       } catch (Exception ex)
 145       {
 146         ex.printStackTrace();
 147       }
 148     }
 149
 150     close_actionPerformed(null);
 151   }
 152
 153   private String getFileContents()
 154   {
 155     String text = MessageManager
 156             .getString("label.no_features_on_alignment");
 157     if (features)
 158     {
 159       FeaturesFile formatter = new FeaturesFile();
 160       SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
 161       Map<String, FeatureColourI> featureColours = ap.getFeatureRenderer()
 162               .getDisplayedFeatureCols();
 163       boolean includeNonPositional = ap.av.isShowNPFeats();
 164       if (GFFFormat.isSelected())
 165       {
 166         text = formatter.printGffFormat(sequences, featureColours,
 167                 includeNonPositional);
 168       }
 169       else
 170       {
 171         text = formatter.printJalviewFormat(sequences, featureColours,
 172                 includeNonPositional);
 173       }
 174     }
 175     else
 176     {
 177       if (CSVFormat.isSelected())
 178       {
 179         text = new AnnotationFile().printCSVAnnotations(annotations);
 180       }
 181       else
 182       {
 183         if (wholeView)
 184         {
 185           text = new AnnotationFile().printAnnotationsForView(ap.av);
 186         }
 187         else
 188         {
 189           text = new AnnotationFile().printAnnotations(annotations, null,
 190                   null);
 191         }
 192       }
 193     }
 194     return text;
 195   }
 196
 197   public void toTextbox_actionPerformed(ActionEvent e)
 198   {
 199     CutAndPasteTransfer cap = new CutAndPasteTransfer();
 200
 201     try
 202     {
 203       String text = getFileContents();
 204       cap.setText(text);
 205       Desktop.addInternalFrame(
 206               cap,
 207               (features ? MessageManager.formatMessage(
 208                       "label.features_for_params",
 209                       new String[] { ap.alignFrame.getTitle() })
 210                       : MessageManager.formatMessage(
 211                               "label.annotations_for_params",
 212                               new String[] { ap.alignFrame.getTitle() })),
 213               600, 500);
 214     } catch (OutOfMemoryError oom)
 215     {
 216       new OOMWarning((features ? MessageManager.formatMessage(
 217               "label.generating_features_for_params",
 218               new String[] { ap.alignFrame.getTitle() })
 219               : MessageManager.formatMessage(
 220                       "label.generating_annotations_for_params",
 221                       new String[] { ap.alignFrame.getTitle() })), oom);
 222       cap.dispose();
 223     }
 224
 225     close_actionPerformed(null);
 226   }
 227
 228   public void close_actionPerformed(ActionEvent e)
 229   {
 230     try
 231     {
 232       frame.setClosed(true);
 233     } catch (java.beans.PropertyVetoException ex)
 234     {
 235     }
 236   }
 237
 238   private void jbInit() throws Exception
 239   {
 240     this.setLayout(new BorderLayout());
 241
 242     toFile.setText(MessageManager.getString("label.to_file"));
 243     toFile.addActionListener(new ActionListener()
 244     {
 245       @Override
 246       public void actionPerformed(ActionEvent e)
 247       {
 248         toFile_actionPerformed(e);
 249       }
 250     });
 251     toTextbox.setText(MessageManager.getString("label.to_textbox"));
 252     toTextbox.addActionListener(new ActionListener()
 253     {
 254       @Override
 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       @Override
 264       public void actionPerformed(ActionEvent e)
 265       {
 266         close_actionPerformed(e);
 267       }
 268     });
 269     jalviewFormat.setOpaque(false);
 270     jalviewFormat.setSelected(true);
 271     jalviewFormat.setText("Jalview");
 272     GFFFormat.setOpaque(false);
 273     GFFFormat.setText("GFF");
 274     CSVFormat.setOpaque(false);
 275     CSVFormat.setText(MessageManager.getString("label.csv_spreadsheet"));
 276     jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
 277     jLabel1.setText(MessageManager.getString("action.format") + " ");
 278     this.setBackground(Color.white);
 279     jPanel3.setBorder(BorderFactory.createEtchedBorder());
 280     jPanel3.setOpaque(false);
 281     jPanel1.setOpaque(false);
 282     jPanel1.add(toFile);
 283     jPanel1.add(toTextbox);
 284     jPanel1.add(close);
 285     jPanel3.add(jLabel1);
 286     jPanel3.add(jalviewFormat);
 287     jPanel3.add(GFFFormat);
 288     jPanel3.add(CSVFormat);
 289     buttonGroup.add(jalviewFormat);
 290     buttonGroup.add(GFFFormat);
 291     buttonGroup.add(CSVFormat);
 292     this.add(jPanel3, BorderLayout.CENTER);
 293     this.add(jPanel1, BorderLayout.SOUTH);
 294   }
 295
 296   JPanel jPanel1 = new JPanel();
 297
 298   JButton toFile = new JButton();
 299
 300   JButton toTextbox = new JButton();
 301
 302   JButton close = new JButton();
 303
 304   ButtonGroup buttonGroup = new ButtonGroup();
 305
 306   JRadioButton jalviewFormat = new JRadioButton();
 307
 308   JRadioButton GFFFormat = new JRadioButton();
 309
 310   JRadioButton CSVFormat = new JRadioButton();
 311
 312   JLabel jLabel1 = new JLabel();
 313
 314   JPanel jPanel3 = new JPanel();
 315
 316   FlowLayout flowLayout1 = new FlowLayout();
 317 }