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       Map<String, FeatureColourI> displayedFeatureColours = ap
 160               .getFeatureRenderer().getDisplayedFeatureCols();
 161       FeaturesFile formatter = new FeaturesFile();
 162       SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
 163       Map<String, FeatureColourI> featureColours = ap.getFeatureRenderer()
 164               .getDisplayedFeatureCols();
 165       boolean includeNonPositional = ap.av.isShowNPFeats();
 166       if (GFFFormat.isSelected())
 167       {
 168         text = new FeaturesFile().printGffFormat(ap.av.getAlignment()
 169                 .getDataset().getSequencesArray(), displayedFeatureColours,
 170                 true, ap.av.isShowNPFeats());
 171         text = formatter.printGffFormat(sequences, featureColours, true,
 172                 includeNonPositional);
 173       }
 174       else
 175       {
 176         text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
 177                 .getDataset().getSequencesArray(), displayedFeatureColours, true, ap.av.isShowNPFeats()); // ap.av.featuresDisplayed);
 178         text = formatter.printJalviewFormat(sequences, featureColours,
 179                 true, includeNonPositional);
 180       }
 181     }
 182     else
 183     {
 184       if (CSVFormat.isSelected())
 185       {
 186         text = new AnnotationFile().printCSVAnnotations(annotations);
 187       }
 188       else
 189       {
 190         if (wholeView)
 191         {
 192           text = new AnnotationFile().printAnnotationsForView(ap.av);
 193         }
 194         else
 195         {
 196           text = new AnnotationFile().printAnnotations(annotations, null,
 197                   null);
 198         }
 199       }
 200     }
 201     return text;
 202   }
 203
 204   public void toTextbox_actionPerformed(ActionEvent e)
 205   {
 206     CutAndPasteTransfer cap = new CutAndPasteTransfer();
 207
 208     try
 209     {
 210       String text = getFileContents();
 211       cap.setText(text);
 212       Desktop.addInternalFrame(
 213               cap,
 214               (features ? MessageManager.formatMessage(
 215                       "label.features_for_params",
 216                       new String[] { ap.alignFrame.getTitle() })
 217                       : MessageManager.formatMessage(
 218                               "label.annotations_for_params",
 219                               new String[] { ap.alignFrame.getTitle() })),
 220               600, 500);
 221     } catch (OutOfMemoryError oom)
 222     {
 223       new OOMWarning((features ? MessageManager.formatMessage(
 224               "label.generating_features_for_params",
 225               new String[] { ap.alignFrame.getTitle() })
 226               : MessageManager.formatMessage(
 227                       "label.generating_annotations_for_params",
 228                       new String[] { ap.alignFrame.getTitle() })), oom);
 229       cap.dispose();
 230     }
 231
 232     close_actionPerformed(null);
 233   }
 234
 235   public void close_actionPerformed(ActionEvent e)
 236   {
 237     try
 238     {
 239       frame.setClosed(true);
 240     } catch (java.beans.PropertyVetoException ex)
 241     {
 242     }
 243   }
 244
 245   private void jbInit() throws Exception
 246   {
 247     this.setLayout(new BorderLayout());
 248
 249     toFile.setText(MessageManager.getString("label.to_file"));
 250     toFile.addActionListener(new ActionListener()
 251     {
 252       @Override
 253       public void actionPerformed(ActionEvent e)
 254       {
 255         toFile_actionPerformed(e);
 256       }
 257     });
 258     toTextbox.setText(MessageManager.getString("label.to_textbox"));
 259     toTextbox.addActionListener(new ActionListener()
 260     {
 261       @Override
 262       public void actionPerformed(ActionEvent e)
 263       {
 264         toTextbox_actionPerformed(e);
 265       }
 266     });
 267     close.setText(MessageManager.getString("action.close"));
 268     close.addActionListener(new ActionListener()
 269     {
 270       @Override
 271       public void actionPerformed(ActionEvent e)
 272       {
 273         close_actionPerformed(e);
 274       }
 275     });
 276     jalviewFormat.setOpaque(false);
 277     jalviewFormat.setSelected(true);
 278     jalviewFormat.setText("Jalview");
 279     GFFFormat.setOpaque(false);
 280     GFFFormat.setText("GFF");
 281     CSVFormat.setOpaque(false);
 282     CSVFormat.setText(MessageManager.getString("label.csv_spreadsheet"));
 283     jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
 284     jLabel1.setText(MessageManager.getString("action.format") + " ");
 285     this.setBackground(Color.white);
 286     jPanel3.setBorder(BorderFactory.createEtchedBorder());
 287     jPanel3.setOpaque(false);
 288     jPanel1.setOpaque(false);
 289     jPanel1.add(toFile);
 290     jPanel1.add(toTextbox);
 291     jPanel1.add(close);
 292     jPanel3.add(jLabel1);
 293     jPanel3.add(jalviewFormat);
 294     jPanel3.add(GFFFormat);
 295     jPanel3.add(CSVFormat);
 296     buttonGroup.add(jalviewFormat);
 297     buttonGroup.add(GFFFormat);
 298     buttonGroup.add(CSVFormat);
 299     this.add(jPanel3, BorderLayout.CENTER);
 300     this.add(jPanel1, BorderLayout.SOUTH);
 301   }
 302
 303   JPanel jPanel1 = new JPanel();
 304
 305   JButton toFile = new JButton();
 306
 307   JButton toTextbox = new JButton();
 308
 309   JButton close = new JButton();
 310
 311   ButtonGroup buttonGroup = new ButtonGroup();
 312
 313   JRadioButton jalviewFormat = new JRadioButton();
 314
 315   JRadioButton GFFFormat = new JRadioButton();
 316
 317   JRadioButton CSVFormat = new JRadioButton();
 318
 319   JLabel jLabel1 = new JLabel();
 320
 321   JPanel jPanel3 = new JPanel();
 322
 323   FlowLayout flowLayout1 = new FlowLayout();
 324 }