src/jalview/gui/AnnotationExporter.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   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 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.gui;
  19
  20 import java.util.*;
  21 import java.util.List;
  22
  23 import java.awt.*;
  24 import java.awt.event.*;
  25 import javax.swing.*;
  26
  27 import jalview.datamodel.*;
  28 import jalview.io.*;
  29 import jalview.util.MessageManager;
  30
  31 /**
  32  *
  33  * GUI dialog for exporting features or alignment annotations depending upon
  34  * which method is called.
  35  *
  36  * @author AMW
  37  *
  38  */
  39 public class AnnotationExporter extends JPanel
  40 {
  41   JInternalFrame frame;
  42
  43   AlignmentPanel ap;
  44
  45   boolean features = true;
  46
  47   AlignmentAnnotation[] annotations;
  48
  49   List<SequenceGroup> sequenceGroups;
  50
  51   Hashtable alignmentProperties;
  52
  53   public AnnotationExporter()
  54   {
  55     try
  56     {
  57       jbInit();
  58     } catch (Exception ex)
  59     {
  60       ex.printStackTrace();
  61     }
  62
  63     frame = new JInternalFrame();
  64     frame.setContentPane(this);
  65     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  66     Desktop.addInternalFrame(frame, "", frame.getPreferredSize().width,
  67             frame.getPreferredSize().height);
  68   }
  69
  70   public void exportFeatures(AlignmentPanel ap)
  71   {
  72     this.ap = ap;
  73     features = true;
  74     CSVFormat.setVisible(false);
  75     frame.setTitle("Export Features");
  76   }
  77
  78   public void exportAnnotations(AlignmentPanel ap,
  79           AlignmentAnnotation[] annotations, List<SequenceGroup> list,
  80           Hashtable alProperties)
  81   {
  82     this.ap = ap;
  83     features = false;
  84     GFFFormat.setVisible(false);
  85     CSVFormat.setVisible(true);
  86     this.annotations = annotations;
  87     this.sequenceGroups = list;
  88     this.alignmentProperties = alProperties;
  89     frame.setTitle("Export Annotations");
  90   }
  91
  92   public void toFile_actionPerformed(ActionEvent e)
  93   {
  94     JalviewFileChooser chooser = new JalviewFileChooser(
  95             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
  96
  97     chooser.setFileView(new JalviewFileView());
  98     chooser.setDialogTitle(features ? "Save Features to File"
  99             : "Save Annotation to File");
 100     chooser.setToolTipText(MessageManager.getString("action.save"));
 101
 102     int value = chooser.showSaveDialog(this);
 103
 104     if (value == JalviewFileChooser.APPROVE_OPTION)
 105     {
 106       String text = "No features found on alignment";
 107       if (features)
 108       {
 109         if (GFFFormat.isSelected())
 110         {
 111           text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
 112                   .getDataset().getSequencesArray(),
 113                   getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);
 114         }
 115         else
 116         {
 117           text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
 118                   .getDataset().getSequencesArray(),
 119                   getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);
 120         }
 121       }
 122       else
 123       {
 124         if (CSVFormat.isSelected())
 125         {
 126           text = new AnnotationFile().printCSVAnnotations(annotations);
 127         }
 128         else
 129         {
 130           text = new AnnotationFile().printAnnotations(annotations,
 131                   sequenceGroups, alignmentProperties);
 132         }
 133       }
 134
 135       try
 136       {
 137         java.io.PrintWriter out = new java.io.PrintWriter(
 138                 new java.io.FileWriter(chooser.getSelectedFile()));
 139
 140         out.print(text);
 141         out.close();
 142       } catch (Exception ex)
 143       {
 144         ex.printStackTrace();
 145       }
 146     }
 147
 148     close_actionPerformed(null);
 149   }
 150
 151   public void toTextbox_actionPerformed(ActionEvent e)
 152   {
 153     String text = "No features found on alignment";
 154     if (features)
 155     {
 156       if (GFFFormat.isSelected())
 157       {
 158         text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
 159                 .getDataset().getSequencesArray(),
 160                 getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
 161       }
 162       else
 163       {
 164         text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
 165                 .getDataset().getSequencesArray(),
 166                 getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
 167       }
 168     }
 169     else if (!features)
 170     {
 171       if (CSVFormat.isSelected())
 172       {
 173         text = new AnnotationFile().printCSVAnnotations(annotations);
 174       }
 175       else
 176       {
 177         text = new AnnotationFile().printAnnotations(annotations,
 178                 sequenceGroups, alignmentProperties);
 179       }
 180     }
 181
 182     CutAndPasteTransfer cap = new CutAndPasteTransfer();
 183     try
 184     {
 185       cap.setText(text);
 186       Desktop.addInternalFrame(cap, (features ? MessageManager.formatMessage("label.features_for_params", new String[]{ap.alignFrame.getTitle()})
 187               : MessageManager.formatMessage("label.annotations_for_params", new String[]{ap.alignFrame.getTitle()})), 600, 500);
 188     } catch (OutOfMemoryError oom)
 189     {
 190       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()}))
 191               , oom);
 192       cap.dispose();
 193     }
 194
 195     close_actionPerformed(null);
 196   }
 197
 198   private Hashtable getDisplayedFeatureCols()
 199   {
 200     Hashtable fcols = new Hashtable();
 201     if (ap.av.featuresDisplayed == null)
 202     {
 203       return fcols;
 204     }
 205     Enumeration en = ap.av.featuresDisplayed.keys();
 206     FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider
 207                                                                      // higher
 208                                                                      // level
 209                                                                      // method ?
 210     while (en.hasMoreElements())
 211     {
 212       Object col = en.nextElement();
 213       fcols.put(col, fr.featureColours.get(col));
 214     }
 215     return fcols;
 216   }
 217
 218   public void close_actionPerformed(ActionEvent e)
 219   {
 220     try
 221     {
 222       frame.setClosed(true);
 223     } catch (java.beans.PropertyVetoException ex)
 224     {
 225     }
 226   }
 227
 228   private void jbInit() throws Exception
 229   {
 230     this.setLayout(new BorderLayout());
 231
 232     toFile.setText(MessageManager.getString("label.to_file"));
 233     toFile.addActionListener(new ActionListener()
 234     {
 235       public void actionPerformed(ActionEvent e)
 236       {
 237         toFile_actionPerformed(e);
 238       }
 239     });
 240     toTextbox.setText(MessageManager.getString("label.to_textbox"));
 241     toTextbox.addActionListener(new ActionListener()
 242     {
 243       public void actionPerformed(ActionEvent e)
 244       {
 245         toTextbox_actionPerformed(e);
 246       }
 247     });
 248     close.setText(MessageManager.getString("action.close"));
 249     close.addActionListener(new ActionListener()
 250     {
 251       public void actionPerformed(ActionEvent e)
 252       {
 253         close_actionPerformed(e);
 254       }
 255     });
 256     jalviewFormat.setOpaque(false);
 257     jalviewFormat.setSelected(true);
 258     jalviewFormat.setText("Jalview");
 259     GFFFormat.setOpaque(false);
 260     GFFFormat.setText("GFF");
 261     CSVFormat.setOpaque(false);
 262     CSVFormat.setText(MessageManager.getString("label.csv_spreadsheet"));
 263     jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
 264     jLabel1.setText(MessageManager.getString("action.format") + " ");
 265     this.setBackground(Color.white);
 266     jPanel3.setBorder(BorderFactory.createEtchedBorder());
 267     jPanel3.setOpaque(false);
 268     jPanel1.setOpaque(false);
 269     jPanel1.add(toFile);
 270     jPanel1.add(toTextbox);
 271     jPanel1.add(close);
 272     jPanel3.add(jLabel1);
 273     jPanel3.add(jalviewFormat);
 274     jPanel3.add(GFFFormat);
 275     jPanel3.add(CSVFormat);
 276     buttonGroup.add(jalviewFormat);
 277     buttonGroup.add(GFFFormat);
 278     buttonGroup.add(CSVFormat);
 279     this.add(jPanel3, BorderLayout.CENTER);
 280     this.add(jPanel1, BorderLayout.SOUTH);
 281   }
 282
 283   JPanel jPanel1 = new JPanel();
 284
 285   JButton toFile = new JButton();
 286
 287   JButton toTextbox = new JButton();
 288
 289   JButton close = new JButton();
 290
 291   ButtonGroup buttonGroup = new ButtonGroup();
 292
 293   JRadioButton jalviewFormat = new JRadioButton();
 294
 295   JRadioButton GFFFormat = new JRadioButton();
 296
 297   JRadioButton CSVFormat = new JRadioButton();
 298
 299   JLabel jLabel1 = new JLabel();
 300
 301   JPanel jPanel3 = new JPanel();
 302
 303   FlowLayout flowLayout1 = new FlowLayout();
 304
 305 }