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.datamodel.AlignmentAnnotation;
  24 import jalview.io.AnnotationFile;
  25 import jalview.io.FeaturesFile;
  26 import jalview.io.JalviewFileChooser;
  27 import jalview.io.JalviewFileView;
  28 import jalview.util.MessageManager;
  29
  30 import java.awt.BorderLayout;
  31 import java.awt.Color;
  32 import java.awt.FlowLayout;
  33 import java.awt.event.ActionEvent;
  34 import java.awt.event.ActionListener;
  35
  36 import javax.swing.BorderFactory;
  37 import javax.swing.ButtonGroup;
  38 import javax.swing.JButton;
  39 import javax.swing.JInternalFrame;
  40 import javax.swing.JLabel;
  41 import javax.swing.JLayeredPane;
  42 import javax.swing.JPanel;
  43 import javax.swing.JRadioButton;
  44 import javax.swing.SwingConstants;
  45
  46 /**
  47  *
  48  * GUI dialog for exporting features or alignment annotations depending upon
  49  * which method is called.
  50  *
  51  * @author AMW
  52  *
  53  */
  54 public class AnnotationExporter extends JPanel
  55 {
  56   JInternalFrame frame;
  57
  58   AlignmentPanel ap;
  59
  60   boolean features = true;
  61
  62   private AlignmentAnnotation[] annotations;
  63
  64   private boolean wholeView;
  65
  66   public AnnotationExporter()
  67   {
  68     try
  69     {
  70       jbInit();
  71     } catch (Exception ex)
  72     {
  73       ex.printStackTrace();
  74     }
  75
  76     frame = new JInternalFrame();
  77     frame.setContentPane(this);
  78     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  79     Desktop.addInternalFrame(frame, "", frame.getPreferredSize().width,
  80             frame.getPreferredSize().height);
  81   }
  82
  83   public void exportFeatures(AlignmentPanel ap)
  84   {
  85     this.ap = ap;
  86     features = true;
  87     CSVFormat.setVisible(false);
  88     frame.setTitle(MessageManager.getString("label.export_features"));
  89   }
  90
  91   public void exportAnnotations(AlignmentPanel ap)
  92   {
  93     this.ap = ap;
  94     annotations = ap.av.isShowAnnotation() ? null : ap.av.getAlignment()
  95             .getAlignmentAnnotation();
  96     wholeView = true;
  97     startExportAnnotation();
  98   }
  99
 100   public void exportAnnotations(AlignmentPanel alp,
 101           AlignmentAnnotation[] toExport)
 102   {
 103     ap = alp;
 104     annotations = toExport;
 105     wholeView = false;
 106     startExportAnnotation();
 107   }
 108
 109   private void startExportAnnotation()
 110   {
 111     features = false;
 112     GFFFormat.setVisible(false);
 113     CSVFormat.setVisible(true);
 114     frame.setTitle(MessageManager.getString("label.export_annotations"));
 115   }
 116
 117   public void toFile_actionPerformed(ActionEvent e)
 118   {
 119     JalviewFileChooser chooser = new JalviewFileChooser(
 120             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 121
 122     chooser.setFileView(new JalviewFileView());
 123     chooser.setDialogTitle(features ? MessageManager.getString("label.save_features_to_file")
 124             : MessageManager.getString("label.save_annotation_to_file"));
 125     chooser.setToolTipText(MessageManager.getString("action.save"));
 126
 127     int value = chooser.showSaveDialog(this);
 128
 129     if (value == JalviewFileChooser.APPROVE_OPTION)
 130     {
 131       String text = getFileContents();
 132
 133       try
 134       {
 135         java.io.PrintWriter out = new java.io.PrintWriter(
 136                 new java.io.FileWriter(chooser.getSelectedFile()));
 137
 138         out.print(text);
 139         out.close();
 140       } catch (Exception ex)
 141       {
 142         ex.printStackTrace();
 143       }
 144     }
 145
 146     close_actionPerformed(null);
 147   }
 148
 149   private String getFileContents()
 150   {
 151     String text = MessageManager
 152             .getString("label.no_features_on_alignment");
 153     if (features)
 154     {
 155       if (GFFFormat.isSelected())
 156       {
 157         text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
 158                 .getDataset().getSequencesArray(), ap.getFeatureRenderer()
 159                 .getDisplayedFeatureCols(), true, ap.av.isShowNPFeats());// ap.av.featuresDisplayed//);
 160       }
 161       else
 162       {
 163         text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
 164                 .getDataset().getSequencesArray(), ap.getFeatureRenderer()
 165                 .getDisplayedFeatureCols(), true, ap.av.isShowNPFeats()); // ap.av.featuresDisplayed);
 166       }
 167     }
 168     else
 169     {
 170       if (CSVFormat.isSelected())
 171       {
 172         text = new AnnotationFile().printCSVAnnotations(annotations);
 173       }
 174       else
 175       {
 176         if (wholeView)
 177         {
 178           text = new AnnotationFile().printAnnotationsForView(ap.av);
 179         }
 180         else
 181         {
 182           text = new AnnotationFile().printAnnotations(annotations, null,
 183                   null);
 184         }
 185       }
 186     }
 187     return text;
 188   }
 189   public void toTextbox_actionPerformed(ActionEvent e)
 190   {
 191     CutAndPasteTransfer cap = new CutAndPasteTransfer();
 192
 193     try
 194     {
 195       String text = getFileContents();
 196       cap.setText(text);
 197       Desktop.addInternalFrame(
 198               cap,
 199               (features ? MessageManager.formatMessage(
 200                       "label.features_for_params", new String[]
 201                       { ap.alignFrame.getTitle() }) : MessageManager
 202                       .formatMessage("label.annotations_for_params",
 203                               new String[]
 204                               { ap.alignFrame.getTitle() })), 600, 500);
 205     } catch (OutOfMemoryError oom)
 206     {
 207       new OOMWarning((features ? MessageManager.formatMessage(
 208               "label.generating_features_for_params", new String[]
 209               { ap.alignFrame.getTitle() }) : MessageManager.formatMessage(
 210               "label.generating_annotations_for_params", new String[]
 211               { ap.alignFrame.getTitle() })), oom);
 212       cap.dispose();
 213     }
 214
 215     close_actionPerformed(null);
 216   }
 217   public void close_actionPerformed(ActionEvent e)
 218   {
 219     try
 220     {
 221       frame.setClosed(true);
 222     } catch (java.beans.PropertyVetoException ex)
 223     {
 224     }
 225   }
 226
 227   private void jbInit() throws Exception
 228   {
 229     this.setLayout(new BorderLayout());
 230
 231     toFile.setText(MessageManager.getString("label.to_file"));
 232     toFile.addActionListener(new ActionListener()
 233     {
 234       public void actionPerformed(ActionEvent e)
 235       {
 236         toFile_actionPerformed(e);
 237       }
 238     });
 239     toTextbox.setText(MessageManager.getString("label.to_textbox"));
 240     toTextbox.addActionListener(new ActionListener()
 241     {
 242       public void actionPerformed(ActionEvent e)
 243       {
 244         toTextbox_actionPerformed(e);
 245       }
 246     });
 247     close.setText(MessageManager.getString("action.close"));
 248     close.addActionListener(new ActionListener()
 249     {
 250       public void actionPerformed(ActionEvent e)
 251       {
 252         close_actionPerformed(e);
 253       }
 254     });
 255     jalviewFormat.setOpaque(false);
 256     jalviewFormat.setSelected(true);
 257     jalviewFormat.setText("Jalview");
 258     GFFFormat.setOpaque(false);
 259     GFFFormat.setText("GFF");
 260     CSVFormat.setOpaque(false);
 261     CSVFormat.setText(MessageManager.getString("label.csv_spreadsheet"));
 262     jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
 263     jLabel1.setText(MessageManager.getString("action.format") + " ");
 264     this.setBackground(Color.white);
 265     jPanel3.setBorder(BorderFactory.createEtchedBorder());
 266     jPanel3.setOpaque(false);
 267     jPanel1.setOpaque(false);
 268     jPanel1.add(toFile);
 269     jPanel1.add(toTextbox);
 270     jPanel1.add(close);
 271     jPanel3.add(jLabel1);
 272     jPanel3.add(jalviewFormat);
 273     jPanel3.add(GFFFormat);
 274     jPanel3.add(CSVFormat);
 275     buttonGroup.add(jalviewFormat);
 276     buttonGroup.add(GFFFormat);
 277     buttonGroup.add(CSVFormat);
 278     this.add(jPanel3, BorderLayout.CENTER);
 279     this.add(jPanel1, BorderLayout.SOUTH);
 280   }
 281
 282   JPanel jPanel1 = new JPanel();
 283
 284   JButton toFile = new JButton();
 285
 286   JButton toTextbox = new JButton();
 287
 288   JButton close = new JButton();
 289
 290   ButtonGroup buttonGroup = new ButtonGroup();
 291
 292   JRadioButton jalviewFormat = new JRadioButton();
 293
 294   JRadioButton GFFFormat = new JRadioButton();
 295
 296   JRadioButton CSVFormat = new JRadioButton();
 297
 298   JLabel jLabel1 = new JLabel();
 299
 300   JPanel jPanel3 = new JPanel();
 301
 302   FlowLayout flowLayout1 = new FlowLayout();
 303 }