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.datamodel.SequenceI;
  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 import java.util.Map;
  37
  38 import javax.swing.BorderFactory;
  39 import javax.swing.ButtonGroup;
  40 import javax.swing.JButton;
  41 import javax.swing.JInternalFrame;
  42 import javax.swing.JLabel;
  43 import javax.swing.JLayeredPane;
  44 import javax.swing.JPanel;
  45 import javax.swing.JRadioButton;
  46 import javax.swing.SwingConstants;
  47
  48 /**
  49  *
  50  * GUI dialog for exporting features or alignment annotations depending upon
  51  * which method is called.
  52  *
  53  * @author AMW
  54  *
  55  */
  56 public class AnnotationExporter extends JPanel
  57 {
  58   JInternalFrame frame;
  59
  60   AlignmentPanel ap;
  61
  62   boolean features = true;
  63
  64   private AlignmentAnnotation[] annotations;
  65
  66   private boolean wholeView;
  67
  68   public AnnotationExporter()
  69   {
  70     try
  71     {
  72       jbInit();
  73     } catch (Exception ex)
  74     {
  75       ex.printStackTrace();
  76     }
  77
  78     frame = new JInternalFrame();
  79     frame.setContentPane(this);
  80     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  81     Desktop.addInternalFrame(frame, "", frame.getPreferredSize().width,
  82             frame.getPreferredSize().height);
  83   }
  84
  85   public void exportFeatures(AlignmentPanel ap)
  86   {
  87     this.ap = ap;
  88     features = true;
  89     CSVFormat.setVisible(false);
  90     frame.setTitle(MessageManager.getString("label.export_features"));
  91   }
  92
  93   public void exportAnnotations(AlignmentPanel ap)
  94   {
  95     this.ap = ap;
  96     annotations = ap.av.isShowAnnotation() ? null : ap.av.getAlignment()
  97             .getAlignmentAnnotation();
  98     wholeView = true;
  99     startExportAnnotation();
 100   }
 101
 102   public void exportAnnotations(AlignmentPanel alp,
 103           AlignmentAnnotation[] toExport)
 104   {
 105     ap = alp;
 106     annotations = toExport;
 107     wholeView = false;
 108     startExportAnnotation();
 109   }
 110
 111   private void startExportAnnotation()
 112   {
 113     features = false;
 114     GFFFormat.setVisible(false);
 115     CSVFormat.setVisible(true);
 116     frame.setTitle(MessageManager.getString("label.export_annotations"));
 117   }
 118
 119   public void toFile_actionPerformed(ActionEvent e)
 120   {
 121     JalviewFileChooser chooser = new JalviewFileChooser(
 122             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 123
 124     chooser.setFileView(new JalviewFileView());
 125     chooser.setDialogTitle(features ? MessageManager
 126             .getString("label.save_features_to_file") : MessageManager
 127             .getString("label.save_annotation_to_file"));
 128     chooser.setToolTipText(MessageManager.getString("action.save"));
 129
 130     int value = chooser.showSaveDialog(this);
 131
 132     if (value == JalviewFileChooser.APPROVE_OPTION)
 133     {
 134       String text = getFileContents();
 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   private String getFileContents()
 153   {
 154     String text = MessageManager
 155             .getString("label.no_features_on_alignment");
 156     if (features)
 157     {
 158       FeaturesFile formatter = new FeaturesFile();
 159       SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
 160       Map<String, Object> featureColours = ap.getFeatureRenderer()
 161               .getDisplayedFeatureCols();
 162       boolean includeNonPositional = ap.av.isShowNPFeats();
 163       if (GFFFormat.isSelected())
 164       {
 165         text = formatter.printGffFormat(sequences, featureColours, true,
 166                 includeNonPositional);
 167       }
 168       else
 169       {
 170         text = formatter.printJalviewFormat(sequences, featureColours,
 171                 true, includeNonPositional);
 172       }
 173     }
 174     else
 175     {
 176       if (CSVFormat.isSelected())
 177       {
 178         text = new AnnotationFile().printCSVAnnotations(annotations);
 179       }
 180       else
 181       {
 182         if (wholeView)
 183         {
 184           text = new AnnotationFile().printAnnotationsForView(ap.av);
 185         }
 186         else
 187         {
 188           text = new AnnotationFile().printAnnotations(annotations, null,
 189                   null);
 190         }
 191       }
 192     }
 193     return text;
 194   }
 195
 196   public void toTextbox_actionPerformed(ActionEvent e)
 197   {
 198     CutAndPasteTransfer cap = new CutAndPasteTransfer();
 199
 200     try
 201     {
 202       String text = getFileContents();
 203       cap.setText(text);
 204       Desktop.addInternalFrame(
 205               cap,
 206               (features ? MessageManager.formatMessage(
 207                       "label.features_for_params",
 208                       new String[] { ap.alignFrame.getTitle() })
 209                       : MessageManager.formatMessage(
 210                               "label.annotations_for_params",
 211                               new String[] { ap.alignFrame.getTitle() })),
 212               600, 500);
 213     } catch (OutOfMemoryError oom)
 214     {
 215       new OOMWarning((features ? MessageManager.formatMessage(
 216               "label.generating_features_for_params",
 217               new String[] { ap.alignFrame.getTitle() })
 218               : MessageManager.formatMessage(
 219                       "label.generating_annotations_for_params",
 220                       new String[] { ap.alignFrame.getTitle() })), oom);
 221       cap.dispose();
 222     }
 223
 224     close_actionPerformed(null);
 225   }
 226
 227   public void close_actionPerformed(ActionEvent e)
 228   {
 229     try
 230     {
 231       frame.setClosed(true);
 232     } catch (java.beans.PropertyVetoException ex)
 233     {
 234     }
 235   }
 236
 237   private void jbInit() throws Exception
 238   {
 239     this.setLayout(new BorderLayout());
 240
 241     toFile.setText(MessageManager.getString("label.to_file"));
 242     toFile.addActionListener(new ActionListener()
 243     {
 244       @Override
 245       public void actionPerformed(ActionEvent e)
 246       {
 247         toFile_actionPerformed(e);
 248       }
 249     });
 250     toTextbox.setText(MessageManager.getString("label.to_textbox"));
 251     toTextbox.addActionListener(new ActionListener()
 252     {
 253       @Override
 254       public void actionPerformed(ActionEvent e)
 255       {
 256         toTextbox_actionPerformed(e);
 257       }
 258     });
 259     close.setText(MessageManager.getString("action.close"));
 260     close.addActionListener(new ActionListener()
 261     {
 262       @Override
 263       public void actionPerformed(ActionEvent e)
 264       {
 265         close_actionPerformed(e);
 266       }
 267     });
 268     jalviewFormat.setOpaque(false);
 269     jalviewFormat.setSelected(true);
 270     jalviewFormat.setText("Jalview");
 271     GFFFormat.setOpaque(false);
 272     GFFFormat.setText("GFF");
 273     CSVFormat.setOpaque(false);
 274     CSVFormat.setText(MessageManager.getString("label.csv_spreadsheet"));
 275     jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
 276     jLabel1.setText(MessageManager.getString("action.format") + " ");
 277     this.setBackground(Color.white);
 278     jPanel3.setBorder(BorderFactory.createEtchedBorder());
 279     jPanel3.setOpaque(false);
 280     jPanel1.setOpaque(false);
 281     jPanel1.add(toFile);
 282     jPanel1.add(toTextbox);
 283     jPanel1.add(close);
 284     jPanel3.add(jLabel1);
 285     jPanel3.add(jalviewFormat);
 286     jPanel3.add(GFFFormat);
 287     jPanel3.add(CSVFormat);
 288     buttonGroup.add(jalviewFormat);
 289     buttonGroup.add(GFFFormat);
 290     buttonGroup.add(CSVFormat);
 291     this.add(jPanel3, BorderLayout.CENTER);
 292     this.add(jPanel1, BorderLayout.SOUTH);
 293   }
 294
 295   JPanel jPanel1 = new JPanel();
 296
 297   JButton toFile = new JButton();
 298
 299   JButton toTextbox = new JButton();
 300
 301   JButton close = new JButton();
 302
 303   ButtonGroup buttonGroup = new ButtonGroup();
 304
 305   JRadioButton jalviewFormat = new JRadioButton();
 306
 307   JRadioButton GFFFormat = new JRadioButton();
 308
 309   JRadioButton CSVFormat = new JRadioButton();
 310
 311   JLabel jLabel1 = new JLabel();
 312
 313   JPanel jPanel3 = new JPanel();
 314
 315   FlowLayout flowLayout1 = new FlowLayout();
 316 }