srcjar/fr/orsay/lri/varna/VARNA.java

   1 package fr.orsay.lri.varna;
   2 /*
   3  VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases.
   4  Copyright (C) 2008  Kevin Darty, Alain Denise and Yann Ponty.
   5  electronic mail : Yann.Ponty@lri.fr
   6  paper mail : LRI, bat 490 Université Paris-Sud 91405 Orsay Cedex France
   7
   8  This file is part of VARNA version 3.1.
   9  VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License
  10  as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11
  12  VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
  13  without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
  14  See the GNU General Public License for more details.
  15
  16  You should have received a copy of the GNU General Public License along with VARNA version 3.1.
  17  If not, see http://www.gnu.org/licenses.
  18  */
  19 import java.awt.Component;
  20 import java.awt.GridLayout;
  21 import java.awt.datatransfer.DataFlavor;
  22 import java.awt.datatransfer.Transferable;
  23 import java.awt.dnd.DnDConstants;
  24 import java.awt.dnd.DropTarget;
  25 import java.awt.dnd.DropTargetDragEvent;
  26 import java.awt.dnd.DropTargetDropEvent;
  27 import java.awt.dnd.DropTargetEvent;
  28 import java.awt.dnd.DropTargetListener;
  29 import java.io.File;
  30 import java.io.FileReader;
  31 import java.io.IOException;
  32 import java.util.ArrayList;
  33 import java.util.List;
  34
  35 import javax.swing.JApplet;
  36 import javax.swing.JOptionPane;
  37
  38 import fr.orsay.lri.varna.controlers.ControleurScriptParser;
  39 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
  40 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
  41 import fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError;
  42 import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
  43 import fr.orsay.lri.varna.exceptions.ExceptionParameterError;
  44 import fr.orsay.lri.varna.interfaces.InterfaceParameterLoader;
  45 import fr.orsay.lri.varna.models.VARNAConfigLoader;
  46 import fr.orsay.lri.varna.models.rna.RNA;
  47
  48
  49 // @j2s issues -- see README_SWINGJS.txt
  50
  51 public class VARNA extends JApplet implements InterfaceParameterLoader,DropTargetListener {
  52         ArrayList<VARNAPanel> _vpl = null;
  53         static{
  54                 /**
  55                  *
  56                  * @j2sNative
  57                  *
  58                  *
  59                  * if (!thisApplet.__Info.sequenceDBN) {
  60                  *  thisApplet.__Info.sequenceDBN = "GGGGCCAAUAUGGCCAUCC";
  61                  *  thisApplet.__Info.structureDBN = "((((((.....))))..))";
  62                  *  thisApplet.__Info.title = "Hello RNA world, from SwingJS!";//prompt("Title?","Hello RNA world!");
  63                  * }
  64                  *
  65                  *
  66                  *
  67                  */
  68         }
  69
  70
  71 //      private static final_long serialVersionUID = -2598221520127067670L;
  72
  73         public VARNA() {
  74                 super();
  75         }
  76
  77         public void init() {
  78                 try {
  79                         VARNAConfigLoader VARNAcfg = new VARNAConfigLoader(this);
  80
  81                         try {
  82                                 _vpl = VARNAcfg.createVARNAPanels();
  83                                 for (int i=0;i<_vpl.size();i++)
  84                                 {
  85                                     new DropTarget(_vpl.get(i), this);
  86                                 }
  87                         } catch (IOException e) {
  88                                 JOptionPane.showMessageDialog(this, e.getMessage(),
  89                                                 "VARNA Error", JOptionPane.ERROR_MESSAGE);
  90                         } catch (ExceptionFileFormatOrSyntax e) {
  91                                 JOptionPane.showMessageDialog(this, e.getMessage(),
  92                                                 "VARNA Error", JOptionPane.ERROR_MESSAGE);
  93                         } catch (ExceptionLoadingFailed e) {
  94                                 JOptionPane.showMessageDialog(this, e.getMessage(),
  95                                                 "VARNA Error", JOptionPane.ERROR_MESSAGE);
  96                         }
  97                         setLayout(new GridLayout(VARNAcfg.getNbColumns(), VARNAcfg
  98                                         .getNbRows()));
  99                         for (int i = 0; i < _vpl.size(); i++) {
 100                                 getContentPane().add(_vpl.get(i));
 101                         }
 102                 } catch (ExceptionParameterError e) {
 103                         VARNAPanel.errorDialogStatic(e, this);
 104                 } catch (ExceptionModeleStyleBaseSyntaxError e) {
 105                         VARNAPanel.errorDialogStatic(e, this);
 106                 } catch (ExceptionNonEqualLength e) {
 107                         VARNAPanel.errorDialogStatic(e, this);
 108                 }
 109
 110         }
 111
 112         public void start() {
 113                 //setVisible(true);
 114                 //repaint();
 115                 //getContentPane().setVisible(true);
 116                 //getContentPane().repaint();
 117         }
 118
 119         public void update() {
 120                 System.out.println("update");
 121         }
 122
 123         public String getParameterValue(String key, String def) {
 124                 if (getParameter(key) == null) {
 125                         return def;
 126                 } else {
 127                         return getParameter(key);
 128                 }
 129         }
 130
 131         public String[][] getParameterInfo() {
 132                 return VARNAConfigLoader.getParameterInfo();
 133         }
 134
 135         public ArrayList<VARNAPanel> getPanels()
 136         {
 137                 return _vpl;
 138         }
 139
 140         public String getSelection()
 141         {
 142                 return getSelection(0);
 143         }
 144
 145         public String getSelection(int panel)
 146         {
 147                 String result = "[";
 148                 VARNAPanel v = _vpl.get(panel);
 149                 List<Integer> l = v.getSelectionIndices();
 150                 for(int i=0;i<l.size();i++)
 151                 {
 152                         int n = l.get(i);
 153                         if (i>0)
 154                         {result += ",";}
 155                         result += n;
 156
 157                 }
 158                 result += "]";
 159                 return result;
 160         }
 161
 162         public void runScript(String script)
 163         {
 164                 if (_vpl.size()>0)
 165                 {
 166                         VARNAPanel _vp = _vpl.get(0);
 167                         try {
 168                                 ControleurScriptParser.executeScript(_vp, script);
 169                         } catch (Exception e) {
 170                                 e.printStackTrace();
 171                         }
 172                 }
 173         }
 174
 175
 176         public void setRNA(String seq, String str)
 177         {
 178                 if (_vpl.size()>0)
 179                 {
 180                         try {
 181                                 _vpl.get(0).drawRNA(seq, str);
 182                         } catch (ExceptionNonEqualLength e) {
 183                                 e.printStackTrace();
 184                         }
 185                 }
 186         }
 187
 188         public void setSmoothedRNA(String seq, String str)
 189         {
 190                 if (_vpl.size()>0)
 191                 {
 192                         try {
 193
 194                                   _vpl.get(0).drawRNAInterpolated(seq, str);
 195                                   _vpl.get(0).repaint();
 196                         } catch (ExceptionNonEqualLength e) {
 197                                 // TODO Auto-generated catch block
 198                                 e.printStackTrace();
 199                         }
 200                 }
 201         }
 202
 203         public void dragEnter(DropTargetDragEvent arg0) {
 204         }
 205
 206         public void dragExit(DropTargetEvent arg0) {
 207         }
 208
 209         public void dragOver(DropTargetDragEvent arg0) {
 210         }
 211
 212         public void drop(DropTargetDropEvent dtde)
 213         {
 214           try
 215           {
 216             Transferable tr = dtde.getTransferable();
 217             DataFlavor[] flavors = tr.getTransferDataFlavors();
 218             for (int i = 0; i < flavors.length; i++)
 219             {
 220               if (flavors[i].isFlavorJavaFileListType())
 221               {
 222                   dtde.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
 223                   List list = (List) tr.getTransferData(flavors[i]);
 224                   for (int j = 0; j < list.size(); j++)
 225                   {
 226                           Object o = list.get(j);
 227                           if (dtde.getSource() instanceof DropTarget)
 228                           {
 229                                   DropTarget dt = (DropTarget) dtde.getSource();
 230                                   Component c = dt.getComponent();
 231                                   if (c instanceof VARNAPanel)
 232                                   {
 233                                           VARNAPanel vp = (VARNAPanel) c;
 234                                           // BH -- in JavaScript, the File object has a .bytes
 235                                           // property that we need to maintain.
 236                                           //String path = o.toString();
 237                                           vp.loadFile((File) o,true);
 238                                           //vp.repaint(); BH unnecessary
 239                                   }
 240                           }
 241                   }
 242                   dtde.dropComplete(true);
 243                   return;
 244               }
 245             }
 246         dtde.rejectDrop();
 247          }
 248          catch (Exception e)
 249          {
 250                  e.printStackTrace();
 251              dtde.rejectDrop();
 252           }
 253         }
 254
 255         public void dropActionChanged(DropTargetDragEvent arg0) {
 256         }
 257
 258
 259 }
 260