src2/fr/orsay/lri/varna/utils/VARNASessionParser.java

   1 /*
   2  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.
   3  Copyright (C) 2008  Kevin Darty, Alain Denise and Yann Ponty.
   4  electronic mail : Yann.Ponty@lri.fr
   5  paper mail : LRI, bat 490 Universit� Paris-Sud 91405 Orsay Cedex France
   6
   7  This file is part of VARNA version 3.1.
   8  VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License
   9  as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10
  11  VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
  12  without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
  13  See the GNU General Public License for more details.
  14
  15  You should have received a copy of the GNU General Public License along with VARNA version 3.1.
  16  If not, see http://www.gnu.org/licenses.
  17  */
  18 package fr.orsay.lri.varna.utils;
  19
  20 import java.awt.Color;
  21 import java.awt.Font;
  22 import java.awt.Point;
  23 import java.awt.geom.Point2D;
  24 import java.io.InputStream;
  25 import java.io.InputStreamReader;
  26 import java.io.StringReader;
  27 import java.net.URL;
  28 import java.net.URLConnection;
  29 import java.text.DecimalFormat;
  30 import java.text.NumberFormat;
  31 import java.util.ArrayList;
  32 import java.util.Collections;
  33 import java.util.Hashtable;
  34 import java.util.List;
  35 import java.util.Stack;
  36 import java.util.TreeSet;
  37 import java.util.Vector;
  38
  39 import org.xml.sax.Attributes;
  40 import org.xml.sax.InputSource;
  41 import org.xml.sax.SAXException;
  42 import org.xml.sax.helpers.DefaultHandler;
  43
  44 import fr.orsay.lri.varna.VARNAPanel;
  45 import fr.orsay.lri.varna.models.VARNAConfig;
  46 import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation;
  47 import fr.orsay.lri.varna.models.annotations.ChemProbAnnotation.ChemProbAnnotationType;
  48 import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
  49 import fr.orsay.lri.varna.models.annotations.TextAnnotation;
  50 import fr.orsay.lri.varna.models.annotations.TextAnnotation.AnchorType;
  51 import fr.orsay.lri.varna.models.rna.ModeleBP;
  52 import fr.orsay.lri.varna.models.rna.ModeleBP.Edge;
  53 import fr.orsay.lri.varna.models.rna.ModeleBP.Stericity;
  54 import fr.orsay.lri.varna.models.rna.ModeleBPStyle;
  55 import fr.orsay.lri.varna.models.rna.ModeleBackbone;
  56 import fr.orsay.lri.varna.models.rna.ModeleBackboneElement;
  57 import fr.orsay.lri.varna.models.rna.ModeleBase;
  58 import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide;
  59 import fr.orsay.lri.varna.models.rna.ModeleBasesComparison;
  60 import fr.orsay.lri.varna.models.rna.ModelBaseStyle;
  61 import fr.orsay.lri.varna.models.rna.RNA;
  62 import fr.orsay.lri.varna.models.rna.VARNAPoint;
  63
  64 public class VARNASessionParser extends DefaultHandler {
  65
  66         StringBuffer _buffer = null;
  67         ModeleBaseNucleotide mbn = null;
  68         ModeleBasesComparison mbc = null;
  69         ModeleBP mbp = null;
  70         ModeleBPStyle mbps = null;
  71         ModelBaseStyle msb = null;
  72         TextAnnotation ta = null;
  73         ModeleBackbone backbone = null;
  74         HighlightRegionAnnotation hra = null;
  75         RNA rna = null;
  76         Font f = null;
  77         VARNAConfig config = null;
  78
  79     public VARNASessionParser() {
  80                 super();
  81         }
  82
  83         public InputSource createSourceFromURL(String path)
  84         {
  85                 URL url = null;
  86                 try {
  87                         url = new URL(path);
  88                         URLConnection connexion = url.openConnection();
  89                         connexion.setUseCaches(false);
  90                         InputStream r = connexion.getInputStream();
  91                         InputStreamReader inr = new InputStreamReader(r);
  92                         return new InputSource(inr);
  93                 }
  94                 catch(Exception e)
  95                 {
  96                         e.printStackTrace();
  97                 }
  98                 return new InputSource(new StringReader(""));
  99         }
 100
 101         public InputSource resolveEntity(String publicId, String systemId) {
 102                         return new InputSource(new StringReader(""));
 103         }
 104
 105
 106         private TreeSet<String> _context = new TreeSet<String>();
 107
 108         private void addToContext(String s)
 109         {
 110                 _context.add(s);
 111         }
 112
 113         private void removeFromContext(String s)
 114         {
 115                 _context.remove(s);
 116         }
 117
 118         private boolean contextContains(String s)
 119         {
 120                 return _context.contains(s);
 121         }
 122
 123         public void startElement(String uri, String localName, String qName, Attributes attributes) throws SAXException {
 124                 if (qName.equals(VARNAPanel.XML_ELEMENT_NAME)) {
 125                 }
 126                 else if (qName.equals(VARNAConfig.XML_ELEMENT_NAME)){
 127                         config = new VARNAConfig();
 128                         config.loadFromXMLAttributes(attributes);
 129                 }
 130                 else if (qName.equals(RNA.XML_ELEMENT_NAME)){
 131                         rna = new RNA();
 132                         int mode = Integer.parseInt(attributes.getValue(RNA.XML_VAR_DRAWN_MODE_NAME));
 133                         rna.setDrawMode(mode);
 134                 }
 135                 else if (qName.equals(ModeleBackbone.XML_ELEMENT_NAME)){
 136                         backbone = new ModeleBackbone();
 137                         rna.setBackbone(backbone);
 138                 }
 139                 else if (qName.equals(ModeleBackboneElement.XML_ELEMENT_NAME)){
 140                         if (backbone!=null){
 141                                 int index = Integer.parseInt(attributes.getValue(ModeleBackboneElement.XML_VAR_INDEX_NAME));
 142                                 ModeleBackboneElement.BackboneType type = ModeleBackboneElement.BackboneType.getType(
 143                                                 (attributes.getValue(ModeleBackboneElement.XML_VAR_TYPE_NAME)));
 144                                 Color c = null;
 145                                 if (type == ModeleBackboneElement.BackboneType.CUSTOM_COLOR)
 146                                 {
 147                                         c = Color.decode(attributes.getValue(TextAnnotation.XML_VAR_COLOR_NAME));
 148                                         backbone.addElement(new ModeleBackboneElement(index, c));
 149                                 }
 150                                 else
 151                                 {
 152                                         backbone.addElement(new ModeleBackboneElement(index, type));
 153                                 }
 154                         }
 155                 }
 156                 else if (qName.equals(ModeleBackbone.XML_ELEMENT_NAME)){
 157                         backbone = new ModeleBackbone();
 158                 }
 159                 else if (qName.equals(ModeleBaseNucleotide.XML_ELEMENT_NAME)){
 160                         if (rna!=null){
 161                                 mbn = new ModeleBaseNucleotide(rna.getSize());
 162                                 if (mbn.getIndex()!=Integer.parseInt(attributes.getValue(ModeleBase.XML_VAR_INDEX_NAME)))
 163                                         throw new SAXException("Index mismatch for Base");
 164                                 mbn.setBaseNumber(Integer.parseInt(attributes.getValue(ModeleBase.XML_VAR_NUMBER_NAME)));
 165                                 mbn.setLabel(attributes.getValue(ModeleBase.XML_VAR_LABEL_NAME));
 166                                 mbn.setColorie(Boolean.parseBoolean(attributes.getValue(ModeleBase.XML_VAR_CUSTOM_DRAWN_NAME)));
 167                                 mbn.setValue(Double.parseDouble(attributes.getValue(ModeleBase.XML_VAR_VALUE_NAME)));
 168                                 rna.addBase(mbn);
 169                         }
 170                 }
 171                 else if (qName.equals(XMLUtils.XML_FONT_ELEMENT_NAME)){
 172                         f = XMLUtils.getFont(qName,attributes);
 173                         if (contextContains(TextAnnotation.XML_ELEMENT_NAME))
 174                         {
 175                                 ta.setFont(f);
 176                                 f=null;
 177                         }
 178                         else if (contextContains(VARNAConfig.XML_ELEMENT_NAME))
 179                         {
 180                                 String role = attributes.getValue(XMLUtils.XML_ROLE_NAME);
 181                                 if (role.equals(VARNAConfig.XML_VAR_TITLE_FONT))
 182                                 {
 183                                         config._titleFont = XMLUtils.getFont(qName, attributes);
 184                                 }
 185                                 else if (role.equals(VARNAConfig.XML_VAR_NUMBERS_FONT))
 186                                 {
 187                                         config._numbersFont = XMLUtils.getFont(qName, attributes);
 188                                 }
 189                                 else if (role.equals(VARNAConfig.XML_VAR_FONT_BASES))
 190                                 {
 191                                         config._fontBasesGeneral = XMLUtils.getFont(qName, attributes);
 192                                 }
 193                         }
 194                 }
 195                 else if (qName.equals(ModeleBaseNucleotide.XML_VAR_CONTENT_NAME)){
 196                         _buffer = new StringBuffer();
 197                 }
 198                 else if (qName.equals(ModeleBasesComparison.XML_VAR_FIRST_CONTENT_NAME)){
 199                         _buffer = new StringBuffer();
 200                 }
 201                 else if (qName.equals(ModeleBasesComparison.XML_VAR_SECOND_CONTENT_NAME)){
 202                         _buffer = new StringBuffer();
 203                 }
 204                 else if (qName.equals(ModeleBasesComparison.XML_ELEMENT_NAME)){
 205                         if (rna!=null){
 206                                 mbc = new ModeleBasesComparison(rna.getSize());
 207                                 if (mbc.getIndex()!=Integer.parseInt(attributes.getValue(ModeleBase.XML_VAR_INDEX_NAME)))
 208                                         throw new SAXException("Index mismatch for Base");
 209                                 mbc.setBaseNumber(Integer.parseInt(attributes.getValue(ModeleBase.XML_VAR_NUMBER_NAME)));
 210                                 mbc.setLabel(attributes.getValue(ModeleBase.XML_VAR_LABEL_NAME));
 211                                 mbc.set_appartenance(Integer.parseInt(attributes.getValue(ModeleBasesComparison.XML_VAR_MEMBERSHIP_NAME)));
 212                                 mbc.setColorie(Boolean.parseBoolean(attributes.getValue(ModeleBase.XML_VAR_CUSTOM_DRAWN_NAME)));
 213                                 mbc.setValue(Double.parseDouble(attributes.getValue(ModeleBase.XML_VAR_VALUE_NAME)));
 214                                 rna.addBase(mbc);
 215                         }
 216                 }
 217                 else if (qName.equals(RNA.XML_VAR_NAME_NAME))
 218                 {
 219                         if (rna!=null){
 220                                 _buffer = new StringBuffer();
 221                         }
 222                 }
 223                 else if (qName.equals(ModeleBP.XML_ELEMENT_NAME))
 224                 {
 225                         Edge e5 = Edge.valueOf(attributes.getValue(ModeleBP.XML_VAR_EDGE5_NAME));
 226                         Edge e3 = Edge.valueOf(attributes.getValue(ModeleBP.XML_VAR_EDGE3_NAME));
 227                         Stericity s = Stericity.valueOf(attributes.getValue(ModeleBP.XML_VAR_STERICITY_NAME));
 228                         int i5 = Integer.parseInt(attributes.getValue(ModeleBP.XML_VAR_PARTNER5_NAME));
 229                         int i3 = Integer.parseInt(attributes.getValue(ModeleBP.XML_VAR_PARTNER3_NAME));
 230                         boolean inSecStr = Boolean.parseBoolean(attributes.getValue(ModeleBP.XML_VAR_SEC_STR_NAME));
 231                         mbp = new ModeleBP(rna.getBaseAt(i5),rna.getBaseAt(i3),e5,e3,s);
 232                         if (inSecStr)
 233                                 rna.addBP(i5,i3,mbp);
 234                         else
 235                                 rna.addBPAux(i5,i3,mbp);
 236                 }
 237                 else if (qName.equals(ChemProbAnnotation.XML_ELEMENT_NAME))
 238                 {
 239                         int i5 = Integer.parseInt(attributes.getValue(ChemProbAnnotation.XML_VAR_INDEX5_NAME));
 240                         int i3 = Integer.parseInt(attributes.getValue(ChemProbAnnotation.XML_VAR_INDEX3_NAME));
 241                         ChemProbAnnotation cpa = new ChemProbAnnotation(rna.getBaseAt(i5),rna.getBaseAt(i3));
 242                         cpa.setColor(Color.decode(attributes.getValue(ChemProbAnnotation.XML_VAR_COLOR_NAME)));
 243                         cpa.setIntensity(Double.parseDouble(attributes.getValue(ChemProbAnnotation.XML_VAR_INTENSITY_NAME)));
 244                         cpa.setType(ChemProbAnnotationType.valueOf(attributes.getValue(ChemProbAnnotation.XML_VAR_TYPE_NAME)));
 245                         cpa.setOut(Boolean.parseBoolean(attributes.getValue(ChemProbAnnotation.XML_VAR_OUTWARD_NAME)));
 246                         rna.addChemProbAnnotation(cpa);
 247                 }
 248                 else if (qName.equals(TextAnnotation.XML_VAR_TEXT_NAME)){
 249                         _buffer = new StringBuffer();
 250                 }
 251                 else if (qName.equals(VARNAConfig.XML_VAR_TITLE)){
 252                         _buffer = new StringBuffer();
 253                 }
 254                 else if (qName.equals(VARNAConfig.XML_VAR_CM_CAPTION)){
 255                         _buffer = new StringBuffer();
 256                 }
 257                 else if (qName.equals(TextAnnotation.XML_ELEMENT_NAME))
 258                 {
 259                         AnchorType t = AnchorType.valueOf(attributes.getValue(TextAnnotation.XML_VAR_TYPE_NAME));
 260                         ta = new TextAnnotation("");
 261                         ta.setColor(Color.decode(attributes.getValue(TextAnnotation.XML_VAR_COLOR_NAME)));
 262                         ta.setAngleInDegres(Double.parseDouble(attributes.getValue(TextAnnotation.XML_VAR_ANGLE_NAME)));
 263                         ta.setType(t);
 264                 }
 265                 else if (qName.equals(HighlightRegionAnnotation.XML_ELEMENT_NAME))
 266                 {
 267                         hra = new HighlightRegionAnnotation();
 268                         rna.addHighlightRegion(hra);
 269                         hra.setOutlineColor(Color.decode(attributes.getValue(HighlightRegionAnnotation.XML_VAR_OUTLINE_NAME)));
 270                         hra.setFillColor(Color.decode(attributes.getValue(HighlightRegionAnnotation.XML_VAR_FILL_NAME)));
 271                         hra.setRadius(Double.parseDouble(attributes.getValue(HighlightRegionAnnotation.XML_VAR_RADIUS_NAME)));
 272                 }
 273                 else if (qName.equals(XMLUtils.XML_BASELIST_ELEMENT_NAME))
 274                 {
 275                         _buffer = new StringBuffer();
 276                 }
 277                 else if (qName.equals(VARNAPoint.XML_ELEMENT_NAME))
 278                 {
 279                         Point2D.Double vp = new Point2D.Double();
 280                         vp.x = Double.parseDouble(attributes.getValue(VARNAPoint.XML_VAR_X_NAME));
 281                         vp.y = Double.parseDouble(attributes.getValue(VARNAPoint.XML_VAR_Y_NAME));
 282                         String role = attributes.getValue(VARNAPoint.XML_VAR_ROLE_NAME);
 283                         if (contextContains(ModeleBaseNucleotide.XML_ELEMENT_NAME))
 284                         {
 285                                 if (role != null)
 286                                 {
 287                                         if (role.equals(ModeleBase.XML_VAR_POSITION_NAME))
 288                                         {
 289                                                 if (mbn!=null)
 290                                                 {  mbn.setCoords(vp);  }
 291                                                 else throw new SAXException("No Base model for this position Point");
 292                                         }
 293                                         else if (role.equals(ModeleBase.XML_VAR_CENTER_NAME))
 294                                         {
 295                                                 if (mbn!=null)
 296                                                 {  mbn.setCenter(vp);  }
 297                                                 else throw new SAXException("No Base model for this center Point");
 298                                         }
 299
 300                                 }
 301                         }
 302                         if (contextContains(ModeleBasesComparison.XML_ELEMENT_NAME))
 303                         {
 304                                 if (role != null)
 305                                 {
 306                                         if (role.equals(ModeleBase.XML_VAR_POSITION_NAME))
 307                                         {
 308                                                 if (mbc!=null)
 309                                                 {  mbc.setCoords(vp);  }
 310                                                 else throw new SAXException("No Base model for this position Point");
 311                                         }
 312                                         else if (role.equals(ModeleBase.XML_VAR_CENTER_NAME))
 313                                         {
 314                                                 if (mbc!=null)
 315                                                 {  mbc.setCenter(vp);  }
 316                                                 else throw new SAXException("No Base model for this center Point");
 317                                         }
 318                                 }
 319                         }
 320                         if (contextContains(TextAnnotation.XML_ELEMENT_NAME))
 321                         {
 322                                 if (ta!=null)
 323                                 ta.setAncrage(vp.x,vp.y);
 324                                 else throw new SAXException("No TextAnnotation model for this Point");
 325                         }
 326                 }
 327                 else if (qName.equals(ModelBaseStyle.XML_ELEMENT_NAME))
 328                 {
 329                         msb = new ModelBaseStyle();
 330                         msb.setBaseOutlineColor(Color.decode(attributes.getValue(ModelBaseStyle.XML_VAR_OUTLINE_NAME)));
 331                         msb.setBaseInnerColor(Color.decode(attributes.getValue(ModelBaseStyle.XML_VAR_INNER_NAME)));
 332                         msb.setBaseNameColor(Color.decode(attributes.getValue(ModelBaseStyle.XML_VAR_NAME_NAME)));
 333                         msb.setBaseNumberColor(Color.decode(attributes.getValue(ModelBaseStyle.XML_VAR_NUMBER_NAME)));
 334                         if (mbn!=null)
 335                         {  mbn.setStyleBase(msb);  }
 336                         else if (mbc!=null)
 337                         {  mbc.setStyleBase(msb);  }
 338                         msb = null;
 339                 }
 340                 else if (qName.equals(ModeleBPStyle.XML_ELEMENT_NAME))
 341                 {
 342                         mbps = new ModeleBPStyle();
 343                         boolean customColor = Boolean.parseBoolean(attributes.getValue(ModeleBPStyle.XML_VAR_CUSTOM_STYLED_NAME));
 344                         if (customColor)
 345                                 mbps.setCustomColor(Color.decode(attributes.getValue(ModeleBPStyle.XML_VAR_COLOR_NAME)));
 346                         mbps.setThickness(Double.parseDouble(attributes.getValue(ModeleBPStyle.XML_VAR_THICKNESS_NAME)));
 347                         mbps.setBent(Double.parseDouble(attributes.getValue(ModeleBPStyle.XML_VAR_BENT_NAME)));
 348                         if (mbp!=null)
 349                         {  mbp.setStyle(mbps);  }
 350                         mbps = null;
 351                 }
 352                 addToContext(qName);
 353         }
 354
 355
 356
 357         public void endElement(String uri, String localName, String qName)
 358                         throws SAXException {
 359                 if (qName.equals(ModeleBaseNucleotide.XML_VAR_CONTENT_NAME)){
 360                         if (_buffer==null){
 361                                 throw new SAXException("Invalid location for tag "+ModeleBaseNucleotide.XML_VAR_CONTENT_NAME);
 362                         }
 363                         if (mbn==null){
 364                                 throw new SAXException("Invalid location for tag "+ModeleBaseNucleotide.XML_VAR_CONTENT_NAME);
 365                         }
 366                         String val = _buffer.toString();
 367                         mbn.setContent(val);
 368                 }
 369                 else if (qName.equals(ModeleBasesComparison.XML_VAR_FIRST_CONTENT_NAME)){
 370                         if (_buffer==null){
 371                                 throw new SAXException("Invalid location for tag "+ModeleBaseNucleotide.XML_VAR_CONTENT_NAME);
 372                         }
 373                         if (mbc==null){
 374                                 throw new SAXException("Invalid location for tag "+ModeleBaseNucleotide.XML_VAR_CONTENT_NAME);
 375                         }
 376                         String val = _buffer.toString();
 377                         mbc.setBase1(val.trim().charAt(0));
 378                 }
 379                 else if (qName.equals(ModeleBasesComparison.XML_VAR_SECOND_CONTENT_NAME)){
 380                         if (_buffer==null){
 381                                 throw new SAXException("Invalid location for tag "+ModeleBaseNucleotide.XML_VAR_CONTENT_NAME);
 382                         }
 383                         if (mbc==null){
 384                                 throw new SAXException("Invalid location for tag "+ModeleBaseNucleotide.XML_VAR_CONTENT_NAME);
 385                         }
 386                         String val = _buffer.toString();
 387                         mbc.setBase2(val.trim().charAt(0));
 388                 }
 389                 else if (qName.equals(ModeleBaseNucleotide.XML_ELEMENT_NAME)){
 390                         mbn = null;
 391                 }
 392                 else if (qName.equals(ModeleBP.XML_ELEMENT_NAME))
 393                 {
 394                         mbp = null;
 395                 }
 396                 else if (qName.equals(HighlightRegionAnnotation.XML_ELEMENT_NAME))
 397                 {
 398                         hra = null;
 399                 }
 400                 else if (qName.equals(TextAnnotation.XML_VAR_TEXT_NAME))
 401                 {
 402                         String text = _buffer.toString();
 403                         ta.setText(text);
 404                         _buffer = null;
 405                 }
 406                 else if (qName.equals(RNA.XML_VAR_NAME_NAME))
 407                 {
 408                         if (rna!=null){
 409                                 rna.setName(_buffer.toString());
 410                                 _buffer = null;
 411                         }
 412                 }
 413                 else if (qName.equals(VARNAConfig.XML_VAR_CM_CAPTION)){
 414                         config._colorMapCaption = _buffer.toString();
 415                         _buffer = null;
 416                 }
 417
 418                 else if (qName.equals(TextAnnotation.XML_ELEMENT_NAME))
 419                 {
 420                         rna.addAnnotation(ta);
 421                         ta = null;
 422                 }
 423                 else if (qName.equals(XMLUtils.XML_BASELIST_ELEMENT_NAME))
 424                 {
 425                         String result = _buffer.toString();
 426                         ArrayList<ModeleBase> al = XMLUtils.toModeleBaseArray(result, rna);
 427                         if (contextContains(TextAnnotation.XML_ELEMENT_NAME))
 428                         {
 429                                 switch(ta.getType())
 430                                 {
 431                                 case POSITION:
 432                                         break;
 433                                 case BASE:
 434                                         ta.setAncrage(al.get(0));
 435                                         break;
 436                                 case HELIX:
 437                                 case LOOP:
 438                                         try {
 439                                                 ta.setAncrage(al, ta.getType());
 440                                         } catch (Exception e) {
 441                                                 // TODO Auto-generated catch block
 442                                                 e.printStackTrace();
 443                                         }
 444                                         break;
 445                                 default:
 446                                 }
 447                         }
 448                         if (contextContains(HighlightRegionAnnotation.XML_ELEMENT_NAME))
 449                         {
 450                           hra.setBases(al);
 451                         }
 452                         _buffer = null;
 453                 }
 454
 455                 removeFromContext(qName);
 456         }
 457
 458         public void characters(char[] ch, int start, int length)
 459                         throws SAXException {
 460                 String lecture = new String(ch, start, length);
 461                 if (_buffer != null)
 462                         _buffer.append(lecture);
 463         }
 464
 465         public void startDocument() throws SAXException {
 466         }
 467
 468         public void endDocument() throws SAXException {
 469         }
 470
 471         public RNA getRNA()
 472         {
 473                 return rna;
 474         }
 475
 476         public VARNAConfig getVARNAConfig()
 477         {
 478                 return config;
 479         }
 480
 481 }