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(),
 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 = "No features found 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(cap, (features ? MessageManager.formatMessage("label.features_for_params", new String[]{ap.alignFrame.getTitle()})
 190               : MessageManager.formatMessage("label.annotations_for_params", new String[]{ap.alignFrame.getTitle()})), 600, 500);
 191     } catch (OutOfMemoryError oom)
 192     {
 193       new OOMWarning((features ? MessageManager.formatMessage("label.generating_features_for_params", new String[]{ap.alignFrame.getTitle()}) : MessageManager.formatMessage("label.generating_annotations_for_params", new String[]{ap.alignFrame.getTitle()}))
 194               , oom);
 195       cap.dispose();
 196     }
 197
 198     close_actionPerformed(null);
 199   }
 200
 201   private Hashtable getDisplayedFeatureCols()
 202   {
 203     Hashtable fcols = new Hashtable();
 204     if (ap.av.featuresDisplayed == null)
 205     {
 206       return fcols;
 207     }
 208     Enumeration en = ap.av.featuresDisplayed.keys();
 209     FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider
 210                                                                      // higher
 211                                                                      // level
 212                                                                      // method ?
 213     while (en.hasMoreElements())
 214     {
 215       Object col = en.nextElement();
 216       fcols.put(col, fr.featureColours.get(col));
 217     }
 218     return fcols;
 219   }
 220
 221   public void close_actionPerformed(ActionEvent e)
 222   {
 223     try
 224     {
 225       frame.setClosed(true);
 226     } catch (java.beans.PropertyVetoException ex)
 227     {
 228     }
 229   }
 230
 231   private void jbInit() throws Exception
 232   {
 233     this.setLayout(new BorderLayout());
 234
 235     toFile.setText(MessageManager.getString("label.to_file"));
 236     toFile.addActionListener(new ActionListener()
 237     {
 238       public void actionPerformed(ActionEvent e)
 239       {
 240         toFile_actionPerformed(e);
 241       }
 242     });
 243     toTextbox.setText(MessageManager.getString("label.to_textbox"));
 244     toTextbox.addActionListener(new ActionListener()
 245     {
 246       public void actionPerformed(ActionEvent e)
 247       {
 248         toTextbox_actionPerformed(e);
 249       }
 250     });
 251     close.setText(MessageManager.getString("action.close"));
 252     close.addActionListener(new ActionListener()
 253     {
 254       public void actionPerformed(ActionEvent e)
 255       {
 256         close_actionPerformed(e);
 257       }
 258     });
 259     jalviewFormat.setOpaque(false);
 260     jalviewFormat.setSelected(true);
 261     jalviewFormat.setText("Jalview");
 262     GFFFormat.setOpaque(false);
 263     GFFFormat.setText("GFF");
 264     CSVFormat.setOpaque(false);
 265     CSVFormat.setText(MessageManager.getString("label.csv_spreadsheet"));
 266     jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
 267     jLabel1.setText(MessageManager.getString("action.format") + " ");
 268     this.setBackground(Color.white);
 269     jPanel3.setBorder(BorderFactory.createEtchedBorder());
 270     jPanel3.setOpaque(false);
 271     jPanel1.setOpaque(false);
 272     jPanel1.add(toFile);
 273     jPanel1.add(toTextbox);
 274     jPanel1.add(close);
 275     jPanel3.add(jLabel1);
 276     jPanel3.add(jalviewFormat);
 277     jPanel3.add(GFFFormat);
 278     jPanel3.add(CSVFormat);
 279     buttonGroup.add(jalviewFormat);
 280     buttonGroup.add(GFFFormat);
 281     buttonGroup.add(CSVFormat);
 282     this.add(jPanel3, BorderLayout.CENTER);
 283     this.add(jPanel1, BorderLayout.SOUTH);
 284   }
 285
 286   JPanel jPanel1 = new JPanel();
 287
 288   JButton toFile = new JButton();
 289
 290   JButton toTextbox = new JButton();
 291
 292   JButton close = new JButton();
 293
 294   ButtonGroup buttonGroup = new ButtonGroup();
 295
 296   JRadioButton jalviewFormat = new JRadioButton();
 297
 298   JRadioButton GFFFormat = new JRadioButton();
 299
 300   JRadioButton CSVFormat = new JRadioButton();
 301
 302   JLabel jLabel1 = new JLabel();
 303
 304   JPanel jPanel3 = new JPanel();
 305
 306   FlowLayout flowLayout1 = new FlowLayout();
 307
 308 }