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.bin.Cache;
  24 import jalview.datamodel.AlignmentAnnotation;
  25 import jalview.io.AnnotationFile;
  26 import jalview.io.FeaturesFile;
  27 import jalview.io.JalviewFileChooser;
  28 import jalview.io.JalviewFileView;
  29 import jalview.util.MessageManager;
  30
  31 import java.awt.BorderLayout;
  32 import java.awt.Color;
  33 import java.awt.FlowLayout;
  34 import java.awt.event.ActionEvent;
  35 import java.awt.event.ActionListener;
  36
  37 import javax.swing.BorderFactory;
  38 import javax.swing.ButtonGroup;
  39 import javax.swing.JButton;
  40 import javax.swing.JInternalFrame;
  41 import javax.swing.JLabel;
  42 import javax.swing.JLayeredPane;
  43 import javax.swing.JPanel;
  44 import javax.swing.JRadioButton;
  45 import javax.swing.SwingConstants;
  46
  47 /**
  48  *
  49  * GUI dialog for exporting features or alignment annotations depending upon
  50  * which method is called.
  51  *
  52  * @author AMW
  53  *
  54  */
  55 public class AnnotationExporter extends JPanel
  56 {
  57   JInternalFrame frame;
  58
  59   AlignmentPanel ap;
  60
  61   boolean features = true;
  62
  63   private AlignmentAnnotation[] annotations;
  64
  65   private boolean wholeView;
  66
  67   public AnnotationExporter()
  68   {
  69     try
  70     {
  71       jbInit();
  72     } catch (Exception ex)
  73     {
  74       ex.printStackTrace();
  75     }
  76
  77     frame = new JInternalFrame();
  78     frame.setContentPane(this);
  79     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  80     Desktop.addInternalFrame(frame, "", frame.getPreferredSize().width,
  81             frame.getPreferredSize().height);
  82   }
  83
  84   public void exportFeatures(AlignmentPanel ap)
  85   {
  86     this.ap = ap;
  87     features = true;
  88     CSVFormat.setVisible(false);
  89     frame.setTitle(MessageManager.getString("label.export_features"));
  90   }
  91
  92   public void exportAnnotations(AlignmentPanel ap)
  93   {
  94     this.ap = ap;
  95     annotations = ap.av.isShowAnnotation() ? null : ap.av.getAlignment()
  96             .getAlignmentAnnotation();
  97     wholeView = true;
  98     startExportAnnotation();
  99   }
 100
 101   public void exportAnnotations(AlignmentPanel alp,
 102           AlignmentAnnotation[] toExport)
 103   {
 104     ap = alp;
 105     annotations = toExport;
 106     wholeView = false;
 107     startExportAnnotation();
 108   }
 109
 110   private void startExportAnnotation()
 111   {
 112     features = false;
 113     GFFFormat.setVisible(false);
 114     CSVFormat.setVisible(true);
 115     frame.setTitle(MessageManager.getString("label.export_annotations"));
 116   }
 117
 118   public void toFile_actionPerformed(ActionEvent e)
 119   {
 120     JalviewFileChooser chooser = new JalviewFileChooser(
 121             Cache.getProperty("LAST_DIRECTORY"));
 122
 123     chooser.setFileView(new JalviewFileView());
 124     chooser.setDialogTitle(features ? MessageManager.getString("label.save_features_to_file")
 125             : MessageManager.getString("label.save_annotation_to_file"));
 126     chooser.setToolTipText(MessageManager.getString("action.save"));
 127
 128     int value = chooser.showSaveDialog(this);
 129
 130     if (value == JalviewFileChooser.APPROVE_OPTION)
 131     {
 132       String text = getFileContents();
 133
 134       try
 135       {
 136         java.io.PrintWriter out = new java.io.PrintWriter(
 137                 new java.io.FileWriter(chooser.getSelectedFile()));
 138
 139         out.print(text);
 140         out.close();
 141       } catch (Exception ex)
 142       {
 143         ex.printStackTrace();
 144       }
 145     }
 146
 147     close_actionPerformed(null);
 148   }
 149
 150   private String getFileContents()
 151   {
 152     String text = MessageManager
 153             .getString("label.no_features_on_alignment");
 154     if (features)
 155     {
 156       if (GFFFormat.isSelected())
 157       {
 158         text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
 159                 .getDataset().getSequencesArray(), ap.getFeatureRenderer()
 160                 .getDisplayedFeatureCols(), true, ap.av.isShowNPFeats());// ap.av.featuresDisplayed//);
 161       }
 162       else
 163       {
 164         text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
 165                 .getDataset().getSequencesArray(), ap.getFeatureRenderer()
 166                 .getDisplayedFeatureCols(), true, ap.av.isShowNPFeats()); // ap.av.featuresDisplayed);
 167       }
 168     }
 169     else
 170     {
 171       if (CSVFormat.isSelected())
 172       {
 173         text = new AnnotationFile().printCSVAnnotations(annotations);
 174       }
 175       else
 176       {
 177         if (wholeView)
 178         {
 179           text = new AnnotationFile().printAnnotationsForView(ap.av);
 180         }
 181         else
 182         {
 183           text = new AnnotationFile().printAnnotations(annotations, null,
 184                   null);
 185         }
 186       }
 187     }
 188     return text;
 189   }
 190   public void toTextbox_actionPerformed(ActionEvent e)
 191   {
 192     CutAndPasteTransfer cap = new CutAndPasteTransfer();
 193
 194     try
 195     {
 196       String text = getFileContents();
 197       cap.setText(text);
 198       Desktop.addInternalFrame(
 199               cap,
 200               (features ? MessageManager.formatMessage(
 201                       "label.features_for_params", new String[]
 202                       { ap.alignFrame.getTitle() }) : MessageManager
 203                       .formatMessage("label.annotations_for_params",
 204                               new String[]
 205                               { ap.alignFrame.getTitle() })), 600, 500);
 206     } catch (OutOfMemoryError oom)
 207     {
 208       new OOMWarning((features ? MessageManager.formatMessage(
 209               "label.generating_features_for_params", new String[]
 210               { ap.alignFrame.getTitle() }) : MessageManager.formatMessage(
 211               "label.generating_annotations_for_params", new String[]
 212               { ap.alignFrame.getTitle() })), oom);
 213       cap.dispose();
 214     }
 215
 216     close_actionPerformed(null);
 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 }