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
 124             .getString("label.save_features_to_file") : MessageManager
 125             .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
 191   public void toTextbox_actionPerformed(ActionEvent e)
 192   {
 193     CutAndPasteTransfer cap = new CutAndPasteTransfer();
 194
 195     try
 196     {
 197       String text = getFileContents();
 198       cap.setText(text);
 199       Desktop.addInternalFrame(
 200               cap,
 201               (features ? MessageManager.formatMessage(
 202                       "label.features_for_params",
 203                       new String[] { ap.alignFrame.getTitle() })
 204                       : MessageManager.formatMessage(
 205                               "label.annotations_for_params",
 206                               new String[] { ap.alignFrame.getTitle() })),
 207               600, 500);
 208     } catch (OutOfMemoryError oom)
 209     {
 210       new OOMWarning((features ? MessageManager.formatMessage(
 211               "label.generating_features_for_params",
 212               new String[] { ap.alignFrame.getTitle() })
 213               : MessageManager.formatMessage(
 214                       "label.generating_annotations_for_params",
 215                       new String[] { ap.alignFrame.getTitle() })), oom);
 216       cap.dispose();
 217     }
 218
 219     close_actionPerformed(null);
 220   }
 221
 222   public void close_actionPerformed(ActionEvent e)
 223   {
 224     try
 225     {
 226       frame.setClosed(true);
 227     } catch (java.beans.PropertyVetoException ex)
 228     {
 229     }
 230   }
 231
 232   private void jbInit() throws Exception
 233   {
 234     this.setLayout(new BorderLayout());
 235
 236     toFile.setText(MessageManager.getString("label.to_file"));
 237     toFile.addActionListener(new ActionListener()
 238     {
 239       public void actionPerformed(ActionEvent e)
 240       {
 241         toFile_actionPerformed(e);
 242       }
 243     });
 244     toTextbox.setText(MessageManager.getString("label.to_textbox"));
 245     toTextbox.addActionListener(new ActionListener()
 246     {
 247       public void actionPerformed(ActionEvent e)
 248       {
 249         toTextbox_actionPerformed(e);
 250       }
 251     });
 252     close.setText(MessageManager.getString("action.close"));
 253     close.addActionListener(new ActionListener()
 254     {
 255       public void actionPerformed(ActionEvent e)
 256       {
 257         close_actionPerformed(e);
 258       }
 259     });
 260     jalviewFormat.setOpaque(false);
 261     jalviewFormat.setSelected(true);
 262     jalviewFormat.setText("Jalview");
 263     GFFFormat.setOpaque(false);
 264     GFFFormat.setText("GFF");
 265     CSVFormat.setOpaque(false);
 266     CSVFormat.setText(MessageManager.getString("label.csv_spreadsheet"));
 267     jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
 268     jLabel1.setText(MessageManager.getString("action.format") + " ");
 269     this.setBackground(Color.white);
 270     jPanel3.setBorder(BorderFactory.createEtchedBorder());
 271     jPanel3.setOpaque(false);
 272     jPanel1.setOpaque(false);
 273     jPanel1.add(toFile);
 274     jPanel1.add(toTextbox);
 275     jPanel1.add(close);
 276     jPanel3.add(jLabel1);
 277     jPanel3.add(jalviewFormat);
 278     jPanel3.add(GFFFormat);
 279     jPanel3.add(CSVFormat);
 280     buttonGroup.add(jalviewFormat);
 281     buttonGroup.add(GFFFormat);
 282     buttonGroup.add(CSVFormat);
 283     this.add(jPanel3, BorderLayout.CENTER);
 284     this.add(jPanel1, BorderLayout.SOUTH);
 285   }
 286
 287   JPanel jPanel1 = new JPanel();
 288
 289   JButton toFile = new JButton();
 290
 291   JButton toTextbox = new JButton();
 292
 293   JButton close = new JButton();
 294
 295   ButtonGroup buttonGroup = new ButtonGroup();
 296
 297   JRadioButton jalviewFormat = new JRadioButton();
 298
 299   JRadioButton GFFFormat = new JRadioButton();
 300
 301   JRadioButton CSVFormat = new JRadioButton();
 302
 303   JLabel jLabel1 = new JLabel();
 304
 305   JPanel jPanel3 = new JPanel();
 306
 307   FlowLayout flowLayout1 = new FlowLayout();
 308 }