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.api.FeatureColourI;
  24 import jalview.datamodel.AlignmentAnnotation;
  25 import jalview.datamodel.SequenceI;
  26 import jalview.io.AnnotationFile;
  27 import jalview.io.FeaturesFile;
  28 import jalview.io.JalviewFileChooser;
  29 import jalview.io.JalviewFileView;
  30 import jalview.util.MessageManager;
  31
  32 import java.awt.BorderLayout;
  33 import java.awt.Color;
  34 import java.awt.FlowLayout;
  35 import java.awt.event.ActionEvent;
  36 import java.awt.event.ActionListener;
  37 import java.util.List;
  38 import java.util.Map;
  39
  40 import javax.swing.BorderFactory;
  41 import javax.swing.ButtonGroup;
  42 import javax.swing.JButton;
  43 import javax.swing.JInternalFrame;
  44 import javax.swing.JLabel;
  45 import javax.swing.JLayeredPane;
  46 import javax.swing.JPanel;
  47 import javax.swing.JRadioButton;
  48 import javax.swing.SwingConstants;
  49
  50 /**
  51  *
  52  * GUI dialog for exporting features or alignment annotations depending upon
  53  * which method is called.
  54  *
  55  * @author AMW
  56  *
  57  */
  58 public class AnnotationExporter extends JPanel
  59 {
  60   JInternalFrame frame;
  61
  62   AlignmentPanel ap;
  63
  64   boolean features = true;
  65
  66   private AlignmentAnnotation[] annotations;
  67
  68   private boolean wholeView;
  69
  70   public AnnotationExporter()
  71   {
  72     try
  73     {
  74       jbInit();
  75     } catch (Exception ex)
  76     {
  77       ex.printStackTrace();
  78     }
  79
  80     frame = new JInternalFrame();
  81     frame.setContentPane(this);
  82     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  83     Desktop.addInternalFrame(frame, "", frame.getPreferredSize().width,
  84             frame.getPreferredSize().height);
  85   }
  86
  87   public void exportFeatures(AlignmentPanel ap)
  88   {
  89     this.ap = ap;
  90     features = true;
  91     CSVFormat.setVisible(false);
  92     frame.setTitle(MessageManager.getString("label.export_features"));
  93   }
  94
  95   public void exportAnnotations(AlignmentPanel ap)
  96   {
  97     this.ap = ap;
  98     annotations = ap.av.isShowAnnotation() ? null
  99             : ap.av.getAlignment().getAlignmentAnnotation();
 100     wholeView = true;
 101     startExportAnnotation();
 102   }
 103
 104   public void exportAnnotations(AlignmentPanel alp,
 105           AlignmentAnnotation[] toExport)
 106   {
 107     ap = alp;
 108     annotations = toExport;
 109     wholeView = false;
 110     startExportAnnotation();
 111   }
 112
 113   private void startExportAnnotation()
 114   {
 115     features = false;
 116     GFFFormat.setVisible(false);
 117     CSVFormat.setVisible(true);
 118     frame.setTitle(MessageManager.getString("label.export_annotations"));
 119   }
 120
 121   public void toFile_actionPerformed(ActionEvent e)
 122   {
 123     JalviewFileChooser chooser = new JalviewFileChooser(
 124             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 125
 126     chooser.setFileView(new JalviewFileView());
 127     chooser.setDialogTitle(features
 128             ? MessageManager.getString("label.save_features_to_file")
 129             : MessageManager.getString("label.save_annotation_to_file"));
 130     chooser.setToolTipText(MessageManager.getString("action.save"));
 131
 132     int value = chooser.showSaveDialog(this);
 133
 134     if (value == JalviewFileChooser.APPROVE_OPTION)
 135     {
 136       String text = getFileContents();
 137
 138       try
 139       {
 140         java.io.PrintWriter out = new java.io.PrintWriter(
 141                 new java.io.FileWriter(chooser.getSelectedFile()));
 142
 143         out.print(text);
 144         out.close();
 145       } catch (Exception ex)
 146       {
 147         ex.printStackTrace();
 148       }
 149     }
 150
 151     close_actionPerformed(null);
 152   }
 153
 154   private String getFileContents()
 155   {
 156     String text = MessageManager
 157             .getString("label.no_features_on_alignment");
 158     if (features)
 159     {
 160       FeaturesFile formatter = new FeaturesFile();
 161       SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
 162       Map<String, FeatureColourI> featureColours = ap.getFeatureRenderer()
 163               .getDisplayedFeatureCols();
 164       List<String> featureGroups = ap.getFeatureRenderer()
 165               .getDisplayedFeatureGroups();
 166       boolean includeNonPositional = ap.av.isShowNPFeats();
 167       if (GFFFormat.isSelected())
 168       {
 169         text = formatter.printGffFormat(sequences, featureColours,
 170                 featureGroups, includeNonPositional);
 171       }
 172       else
 173       {
 174         text = formatter.printJalviewFormat(sequences, featureColours,
 175                 featureGroups, includeNonPositional);
 176       }
 177     }
 178     else
 179     {
 180       if (CSVFormat.isSelected())
 181       {
 182         text = new AnnotationFile().printCSVAnnotations(annotations);
 183       }
 184       else
 185       {
 186         if (wholeView)
 187         {
 188           text = new AnnotationFile().printAnnotationsForView(ap.av);
 189         }
 190         else
 191         {
 192           text = new AnnotationFile().printAnnotations(annotations, null,
 193                   null);
 194         }
 195       }
 196     }
 197     return text;
 198   }
 199
 200   public void toTextbox_actionPerformed(ActionEvent e)
 201   {
 202     CutAndPasteTransfer cap = new CutAndPasteTransfer();
 203
 204     try
 205     {
 206       String text = getFileContents();
 207       cap.setText(text);
 208       Desktop.addInternalFrame(cap, (features ? MessageManager
 209               .formatMessage("label.features_for_params", new String[]
 210               { ap.alignFrame.getTitle() })
 211               : MessageManager.formatMessage("label.annotations_for_params",
 212                       new String[]
 213                       { ap.alignFrame.getTitle() })),
 214               600, 500);
 215     } catch (OutOfMemoryError oom)
 216     {
 217       new OOMWarning((features ? MessageManager.formatMessage(
 218               "label.generating_features_for_params", new String[]
 219               { ap.alignFrame.getTitle() })
 220               : MessageManager.formatMessage(
 221                       "label.generating_annotations_for_params",
 222                       new String[]
 223                       { ap.alignFrame.getTitle() })),
 224               oom);
 225       cap.dispose();
 226     }
 227
 228     close_actionPerformed(null);
 229   }
 230
 231   public void close_actionPerformed(ActionEvent e)
 232   {
 233     try
 234     {
 235       frame.setClosed(true);
 236     } catch (java.beans.PropertyVetoException ex)
 237     {
 238     }
 239   }
 240
 241   private void jbInit() throws Exception
 242   {
 243     this.setLayout(new BorderLayout());
 244
 245     toFile.setText(MessageManager.getString("label.to_file"));
 246     toFile.addActionListener(new ActionListener()
 247     {
 248       @Override
 249       public void actionPerformed(ActionEvent e)
 250       {
 251         toFile_actionPerformed(e);
 252       }
 253     });
 254     toTextbox.setText(MessageManager.getString("label.to_textbox"));
 255     toTextbox.addActionListener(new ActionListener()
 256     {
 257       @Override
 258       public void actionPerformed(ActionEvent e)
 259       {
 260         toTextbox_actionPerformed(e);
 261       }
 262     });
 263     close.setText(MessageManager.getString("action.close"));
 264     close.addActionListener(new ActionListener()
 265     {
 266       @Override
 267       public void actionPerformed(ActionEvent e)
 268       {
 269         close_actionPerformed(e);
 270       }
 271     });
 272     jalviewFormat.setOpaque(false);
 273     jalviewFormat.setSelected(true);
 274     jalviewFormat.setText("Jalview");
 275     GFFFormat.setOpaque(false);
 276     GFFFormat.setText("GFF");
 277     CSVFormat.setOpaque(false);
 278     CSVFormat.setText(MessageManager.getString("label.csv_spreadsheet"));
 279     jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
 280     jLabel1.setText(MessageManager.getString("action.format") + " ");
 281     this.setBackground(Color.white);
 282     jPanel3.setBorder(BorderFactory.createEtchedBorder());
 283     jPanel3.setOpaque(false);
 284     jPanel1.setOpaque(false);
 285     jPanel1.add(toFile);
 286     jPanel1.add(toTextbox);
 287     jPanel1.add(close);
 288     jPanel3.add(jLabel1);
 289     jPanel3.add(jalviewFormat);
 290     jPanel3.add(GFFFormat);
 291     jPanel3.add(CSVFormat);
 292     buttonGroup.add(jalviewFormat);
 293     buttonGroup.add(GFFFormat);
 294     buttonGroup.add(CSVFormat);
 295     this.add(jPanel3, BorderLayout.CENTER);
 296     this.add(jPanel1, BorderLayout.SOUTH);
 297   }
 298
 299   JPanel jPanel1 = new JPanel();
 300
 301   JButton toFile = new JButton();
 302
 303   JButton toTextbox = new JButton();
 304
 305   JButton close = new JButton();
 306
 307   ButtonGroup buttonGroup = new ButtonGroup();
 308
 309   JRadioButton jalviewFormat = new JRadioButton();
 310
 311   JRadioButton GFFFormat = new JRadioButton();
 312
 313   JRadioButton CSVFormat = new JRadioButton();
 314
 315   JLabel jLabel1 = new JLabel();
 316
 317   JPanel jPanel3 = new JPanel();
 318
 319   FlowLayout flowLayout1 = new FlowLayout();
 320 }