srcjar/fr/orsay/lri/varna/views/VueListeAnnotations.java

   1 /*
   2  * VARNA is a tool for the automated drawing, visualization and annotation
   3  * of the secondary structure of RNA, designed as a companion software for
   4  * web servers and databases. Copyright (C) 2008 Kevin Darty, Alain Denise
   5  * and Yann Ponty. electronic mail : Yann.Ponty@lri.fr paper mail : LRI, bat
   6  * 490 Université Paris-Sud 91405 Orsay Cedex France
   7  *
   8  * This file is part of VARNA version 3.1. VARNA version 3.1 is free
   9  * software: you can redistribute it and/or modify it under the terms of the
  10  * GNU General Public License as published by the Free Software Foundation,
  11  * either version 3 of the License, or (at your option) any later version.
  12  *
  13  * VARNA version 3.1 is distributed in the hope that it will be useful, but
  14  * WITHOUT ANY WARRANTY; without even the implied warranty of
  15  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
  16  * Public License for more details.
  17  *
  18  * You should have received a copy of the GNU General Public License along
  19  * with VARNA version 3.1. If not, see http://www.gnu.org/licenses.
  20  */
  21 package fr.orsay.lri.varna.views;
  22
  23 import java.awt.BorderLayout;
  24 import java.awt.Dimension;
  25 import java.awt.GridLayout;
  26 import java.awt.event.ActionEvent;
  27 import java.awt.event.ActionListener;
  28 import java.io.BufferedInputStream;
  29 import java.io.BufferedReader;
  30 import java.io.File;
  31 import java.io.FileInputStream;
  32 import java.io.FileNotFoundException;
  33 import java.io.FileReader;
  34 import java.io.IOException;
  35 import java.io.PrintWriter;
  36 import java.util.ArrayList;
  37
  38 import javax.swing.Box;
  39 import javax.swing.BoxLayout;
  40 import javax.swing.JButton;
  41 import javax.swing.JComponent;
  42 import javax.swing.JFileChooser;
  43 import javax.swing.JOptionPane;
  44 import javax.swing.JPanel;
  45 import javax.swing.JScrollPane;
  46 import javax.swing.JTable;
  47 import javax.swing.filechooser.FileFilter;
  48
  49 import fr.orsay.lri.varna.VARNAPanel;
  50 import fr.orsay.lri.varna.components.AnnotationTableModel;
  51 import fr.orsay.lri.varna.controlers.ControleurTableAnnotations;
  52 import fr.orsay.lri.varna.models.annotations.TextAnnotation;
  53 import fr.orsay.lri.varna.models.rna.ModeleColorMap;
  54
  55 /**
  56  * a view for all annoted texts on the VARNAPanel
  57  *
  58  * @author Darty@lri.fr
  59  *
  60  */
  61 public class VueListeAnnotations extends JPanel {
  62         /**
  63          *
  64          */
  65         private static final long serialVersionUID = 1L;
  66
  67         /**
  68          * if this view is for removing annoted texts
  69          */
  70         public static final int REMOVE = 0;
  71         /**
  72          * if this view is for editing annoted texts
  73          */
  74         public static final int EDIT = 1;
  75
  76         private VARNAPanel _vp;
  77         private ArrayList<Object> data;
  78         private JTable table;
  79         private int type;
  80         private AnnotationTableModel specialTableModel;
  81         // BH SwingJS - this is never used in JavaScript
  82         private static JFileChooser fc = new JFileChooser(){
  83             public void approveSelection(){
  84                 File f = getSelectedFile();
  85                 if(f.exists() && getDialogType() == SAVE_DIALOG){
  86                     int result = JOptionPane.showConfirmDialog(this,"The file exists, overwrite?","Existing file",JOptionPane.YES_NO_OPTION);
  87                     switch(result){
  88                         case JOptionPane.YES_OPTION:
  89                             super.approveSelection();
  90                             return;
  91                         case JOptionPane.NO_OPTION:
  92                             return;
  93                         case JOptionPane.CLOSED_OPTION:
  94                             return;
  95                         case JOptionPane.CANCEL_OPTION:
  96                             cancelSelection();
  97                             return;
  98                     }
  99                 }
 100                 super.approveSelection();
 101             }
 102         };
 103
 104
 105         /**
 106          * creates the view
 107          *
 108          * @param vp
 109          * @param type
 110          *            (REMOVE or EDIT)
 111          */
 112         public VueListeAnnotations(VARNAPanel vp, int type) {
 113                 super(new BorderLayout());
 114                 this.type = type;
 115                 _vp = vp;
 116                 data = new ArrayList<Object>();
 117                 data.addAll(_vp.getListeAnnotations());
 118                 data.addAll(_vp.getRNA().getHighlightRegion());
 119                 data.addAll(_vp.getRNA().getChemProbAnnotations());
 120                 createView();
 121         }
 122
 123         private void createView() {
 124                 specialTableModel = new AnnotationTableModel(data);
 125                 table = new JTable(specialTableModel);
 126                 ControleurTableAnnotations ctrl = new ControleurTableAnnotations(table,
 127                                 _vp, type);
 128                 table.addMouseListener(ctrl);
 129                 table.addMouseMotionListener(ctrl);
 130                 // table.setPreferredScrollableViewportSize(new Dimension(500, 100));
 131                 // TODO: Find equivalent in JRE 1.5
 132                 // table.setFillsViewportHeight(true);
 133                 // Create the scroll pane and add the table to it.
 134                 JScrollPane scrollPane = new JScrollPane(table);
 135
 136                 add(scrollPane, BorderLayout.CENTER);
 137
 138                 FileFilter CPAFiles = new FileFilter(){
 139                         public boolean accept(File f) {
 140                                 return f.getName().toLowerCase().endsWith(".cpa") || f.isDirectory();
 141                         }
 142
 143                         public String getDescription() {
 144                                 return "Chemical Probing Annotations (*.cpa) Files";
 145                         }
 146
 147                 };
 148                 fc.addChoosableFileFilter(CPAFiles);
 149                 fc.setFileFilter(CPAFiles);
 150
 151
 152                 JButton loadStyleButton = new JButton("Load");
 153                 loadStyleButton.addActionListener(new ActionListener(){
 154                         public void actionPerformed(ActionEvent e) {
 155                                 if (fc.showOpenDialog(VueListeAnnotations.this)==JFileChooser.APPROVE_OPTION)
 156                                 {
 157                                         File file = fc.getSelectedFile();
 158                                         try {
 159                                                 BufferedReader br = new BufferedReader(new FileReader(file));
 160                                                 String s = br.readLine();
 161                                                 while(s != null)
 162                                                 {
 163                                                         if (s.startsWith(TextAnnotation.HEADER_TEXT))
 164                                                         s = br.readLine();
 165                                                 }
 166                                                 // TODO
 167                                         } catch (FileNotFoundException e1) {
 168                                                 e1.printStackTrace();
 169                                         } catch (IOException e1) {
 170                                                 e1.printStackTrace();
 171                                         }
 172                                 }
 173                         }
 174
 175                 });
 176                 JButton saveStyleButton = new JButton("Save");
 177                 saveStyleButton.addActionListener(new ActionListener(){
 178                         public void actionPerformed(ActionEvent e) {
 179                                 if (fc.showSaveDialog(VueListeAnnotations.this)==JFileChooser.APPROVE_OPTION)
 180                                 {
 181                                         try {
 182                                                 PrintWriter out = new PrintWriter(fc.getSelectedFile());
 183                                                 // TODO out.println(_gp.getColorMap().getParamEncoding());
 184                                                 out.close();
 185                                         } catch (FileNotFoundException e1) {
 186                                                 e1.printStackTrace();
 187                                         } catch (IOException e1) {
 188                                                 e1.printStackTrace();
 189                                         }
 190                                 }
 191                         }
 192
 193                 });
 194                 saveStyleButton.setAlignmentX(CENTER_ALIGNMENT);
 195                 loadStyleButton.setAlignmentX(CENTER_ALIGNMENT);
 196
 197                 JPanel jp2 = new JPanel();
 198                 BoxLayout bl = new BoxLayout(jp2, BoxLayout.X_AXIS);
 199                 jp2.setLayout(bl);
 200                 jp2.setAlignmentX(CENTER_ALIGNMENT);
 201                 jp2.add(loadStyleButton);
 202                 jp2.add(Box.createRigidArea(new Dimension(5,0)));
 203                 jp2.add(saveStyleButton);
 204                 this.add(jp2,BorderLayout.SOUTH);
 205
 206
 207
 208                 UIvueListeAnnotations();
 209         }
 210
 211         /**
 212          * Create the GUI and show it. For thread safety, this method should be
 213          * invoked from the event-dispatching thread.
 214          */
 215         public void UIvueListeAnnotations() {
 216                 JComponent newContentPane = this;
 217                 newContentPane.setOpaque(true);
 218                 JOptionPane.showMessageDialog(_vp, newContentPane,
 219                                 "Annotation edition", JOptionPane.PLAIN_MESSAGE);
 220         }
 221
 222         public ArrayList<Object> getData() {
 223                 return data;
 224         }
 225
 226         public void setData(ArrayList<Object> data) {
 227                 this.data = data;
 228         }
 229
 230         public VARNAPanel get_vp() {
 231                 return _vp;
 232         }
 233
 234         public JTable getTable() {
 235                 return table;
 236         }
 237
 238         public void setTable(JTable table) {
 239                 this.table = table;
 240         }
 241
 242         public AnnotationTableModel getSpecialTableModel() {
 243                 return specialTableModel;
 244         }
 245
 246         public void setSpecialTableModel(AnnotationTableModel specialTableModel) {
 247                 this.specialTableModel = specialTableModel;
 248         }
 249 }