src/jalview/gui/AnnotationExporter.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
   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 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  * The Jalview Authors are detailed in the 'AUTHORS' file.
  18  */
  19 package jalview.gui;
  20
  21 import java.util.*;
  22 import java.util.List;
  23
  24 import java.awt.*;
  25 import java.awt.event.*;
  26 import javax.swing.*;
  27
  28 import jalview.datamodel.*;
  29 import jalview.io.*;
  30 import jalview.util.MessageManager;
  31
  32 /**
  33  *
  34  * GUI dialog for exporting features or alignment annotations depending upon
  35  * which method is called.
  36  *
  37  * @author AMW
  38  *
  39  */
  40 public class AnnotationExporter extends JPanel
  41 {
  42   JInternalFrame frame;
  43
  44   AlignmentPanel ap;
  45
  46   boolean features = true;
  47
  48   AlignmentAnnotation[] annotations;
  49
  50   List<SequenceGroup> sequenceGroups;
  51
  52   Hashtable alignmentProperties;
  53
  54   public AnnotationExporter()
  55   {
  56     try
  57     {
  58       jbInit();
  59     } catch (Exception ex)
  60     {
  61       ex.printStackTrace();
  62     }
  63
  64     frame = new JInternalFrame();
  65     frame.setContentPane(this);
  66     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  67     Desktop.addInternalFrame(frame, "", frame.getPreferredSize().width,
  68             frame.getPreferredSize().height);
  69   }
  70
  71   public void exportFeatures(AlignmentPanel ap)
  72   {
  73     this.ap = ap;
  74     features = true;
  75     CSVFormat.setVisible(false);
  76     frame.setTitle("Export Features");
  77   }
  78
  79   public void exportAnnotations(AlignmentPanel ap,
  80           AlignmentAnnotation[] annotations, List<SequenceGroup> list,
  81           Hashtable alProperties)
  82   {
  83     this.ap = ap;
  84     features = false;
  85     GFFFormat.setVisible(false);
  86     CSVFormat.setVisible(true);
  87     this.annotations = annotations;
  88     this.sequenceGroups = list;
  89     this.alignmentProperties = alProperties;
  90     frame.setTitle("Export Annotations");
  91   }
  92
  93   public void toFile_actionPerformed(ActionEvent e)
  94   {
  95     JalviewFileChooser chooser = new JalviewFileChooser(
  96             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
  97
  98     chooser.setFileView(new JalviewFileView());
  99     chooser.setDialogTitle(features ? "Save Features to File"
 100             : "Save Annotation to File");
 101     chooser.setToolTipText(MessageManager.getString("action.save"));
 102
 103     int value = chooser.showSaveDialog(this);
 104
 105     if (value == JalviewFileChooser.APPROVE_OPTION)
 106     {
 107       String text = "No features found on alignment";
 108       if (features)
 109       {
 110         if (GFFFormat.isSelected())
 111         {
 112           text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
 113                   .getDataset().getSequencesArray(),
 114                   getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);
 115         }
 116         else
 117         {
 118           text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
 119                   .getDataset().getSequencesArray(),
 120                   getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);
 121         }
 122       }
 123       else
 124       {
 125         if (CSVFormat.isSelected())
 126         {
 127           text = new AnnotationFile().printCSVAnnotations(annotations);
 128         }
 129         else
 130         {
 131           text = new AnnotationFile().printAnnotations(annotations,
 132                   sequenceGroups, alignmentProperties);
 133         }
 134       }
 135
 136       try
 137       {
 138         java.io.PrintWriter out = new java.io.PrintWriter(
 139                 new java.io.FileWriter(chooser.getSelectedFile()));
 140
 141         out.print(text);
 142         out.close();
 143       } catch (Exception ex)
 144       {
 145         ex.printStackTrace();
 146       }
 147     }
 148
 149     close_actionPerformed(null);
 150   }
 151
 152   public void toTextbox_actionPerformed(ActionEvent e)
 153   {
 154     String text = "No features found on alignment";
 155     if (features)
 156     {
 157       if (GFFFormat.isSelected())
 158       {
 159         text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
 160                 .getDataset().getSequencesArray(),
 161                 getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
 162       }
 163       else
 164       {
 165         text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
 166                 .getDataset().getSequencesArray(),
 167                 getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
 168       }
 169     }
 170     else if (!features)
 171     {
 172       if (CSVFormat.isSelected())
 173       {
 174         text = new AnnotationFile().printCSVAnnotations(annotations);
 175       }
 176       else
 177       {
 178         text = new AnnotationFile().printAnnotations(annotations,
 179                 sequenceGroups, alignmentProperties);
 180       }
 181     }
 182
 183     CutAndPasteTransfer cap = new CutAndPasteTransfer();
 184     try
 185     {
 186       cap.setText(text);
 187       Desktop.addInternalFrame(cap, (features ? MessageManager.formatMessage("label.features_for_params", new String[]{ap.alignFrame.getTitle()})
 188               : MessageManager.formatMessage("label.annotations_for_params", new String[]{ap.alignFrame.getTitle()})), 600, 500);
 189     } catch (OutOfMemoryError oom)
 190     {
 191       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()}))
 192               , oom);
 193       cap.dispose();
 194     }
 195
 196     close_actionPerformed(null);
 197   }
 198
 199   private Hashtable getDisplayedFeatureCols()
 200   {
 201     Hashtable fcols = new Hashtable();
 202     if (ap.av.featuresDisplayed == null)
 203     {
 204       return fcols;
 205     }
 206     Enumeration en = ap.av.featuresDisplayed.keys();
 207     FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider
 208                                                                      // higher
 209                                                                      // level
 210                                                                      // method ?
 211     while (en.hasMoreElements())
 212     {
 213       Object col = en.nextElement();
 214       fcols.put(col, fr.featureColours.get(col));
 215     }
 216     return fcols;
 217   }
 218
 219   public void close_actionPerformed(ActionEvent e)
 220   {
 221     try
 222     {
 223       frame.setClosed(true);
 224     } catch (java.beans.PropertyVetoException ex)
 225     {
 226     }
 227   }
 228
 229   private void jbInit() throws Exception
 230   {
 231     this.setLayout(new BorderLayout());
 232
 233     toFile.setText(MessageManager.getString("label.to_file"));
 234     toFile.addActionListener(new ActionListener()
 235     {
 236       public void actionPerformed(ActionEvent e)
 237       {
 238         toFile_actionPerformed(e);
 239       }
 240     });
 241     toTextbox.setText(MessageManager.getString("label.to_textbox"));
 242     toTextbox.addActionListener(new ActionListener()
 243     {
 244       public void actionPerformed(ActionEvent e)
 245       {
 246         toTextbox_actionPerformed(e);
 247       }
 248     });
 249     close.setText(MessageManager.getString("action.close"));
 250     close.addActionListener(new ActionListener()
 251     {
 252       public void actionPerformed(ActionEvent e)
 253       {
 254         close_actionPerformed(e);
 255       }
 256     });
 257     jalviewFormat.setOpaque(false);
 258     jalviewFormat.setSelected(true);
 259     jalviewFormat.setText("Jalview");
 260     GFFFormat.setOpaque(false);
 261     GFFFormat.setText("GFF");
 262     CSVFormat.setOpaque(false);
 263     CSVFormat.setText(MessageManager.getString("label.csv_spreadsheet"));
 264     jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
 265     jLabel1.setText(MessageManager.getString("action.format") + " ");
 266     this.setBackground(Color.white);
 267     jPanel3.setBorder(BorderFactory.createEtchedBorder());
 268     jPanel3.setOpaque(false);
 269     jPanel1.setOpaque(false);
 270     jPanel1.add(toFile);
 271     jPanel1.add(toTextbox);
 272     jPanel1.add(close);
 273     jPanel3.add(jLabel1);
 274     jPanel3.add(jalviewFormat);
 275     jPanel3.add(GFFFormat);
 276     jPanel3.add(CSVFormat);
 277     buttonGroup.add(jalviewFormat);
 278     buttonGroup.add(GFFFormat);
 279     buttonGroup.add(CSVFormat);
 280     this.add(jPanel3, BorderLayout.CENTER);
 281     this.add(jPanel1, BorderLayout.SOUTH);
 282   }
 283
 284   JPanel jPanel1 = new JPanel();
 285
 286   JButton toFile = new JButton();
 287
 288   JButton toTextbox = new JButton();
 289
 290   JButton close = new JButton();
 291
 292   ButtonGroup buttonGroup = new ButtonGroup();
 293
 294   JRadioButton jalviewFormat = new JRadioButton();
 295
 296   JRadioButton GFFFormat = new JRadioButton();
 297
 298   JRadioButton CSVFormat = new JRadioButton();
 299
 300   JLabel jLabel1 = new JLabel();
 301
 302   JPanel jPanel3 = new JPanel();
 303
 304   FlowLayout flowLayout1 = new FlowLayout();
 305
 306 }