src/jalview/io/RnamlFile.java

   1 package jalview.io;
   2
   3
   4
   5
   6
   7 import jalview.datamodel.AlignmentAnnotation;
   8 import jalview.datamodel.Annotation;
   9 import jalview.datamodel.SecondaryStructureAnnotation;
  10 import jalview.datamodel.Sequence;
  11 import jalview.datamodel.SequenceFeature;
  12 import jalview.datamodel.SequenceI;
  13 import jalview.ws.jws1.Annotate3D;
  14
  15 import java.io.BufferedReader;
  16 import java.io.FileNotFoundException;
  17 import java.io.IOException;
  18 import java.io.Reader;
  19 import java.io.FileReader;
  20 import java.lang.reflect.Array;
  21 import java.util.ArrayList;
  22 import java.util.Collections;
  23 import java.util.Hashtable;
  24 import java.util.List;
  25 import java.util.Vector;
  26
  27 import javax.xml.parsers.ParserConfigurationException;
  28 import javax.xml.parsers.SAXParser;
  29 import javax.xml.parsers.SAXParserFactory;
  30
  31 import org.xml.sax.InputSource;
  32 import org.xml.sax.SAXException;
  33
  34 import com.stevesoft.pat.Regex;
  35
  36 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
  37 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
  38 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
  39 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
  40 import fr.orsay.lri.varna.factories.RNAFactory;
  41 import fr.orsay.lri.varna.factories.RNAFactory.RNAFileType;
  42 import fr.orsay.lri.varna.models.rna.RNA;
  43 import fr.orsay.lri.varna.utils.RNAMLParser;
  44
  45
  46
  47
  48 public class RnamlFile extends AlignFile
  49 {
  50          public String id;
  51          protected ArrayList<RNA> result;
  52
  53          public RnamlFile()
  54           {
  55                  super();
  56
  57           }
  58
  59          public RnamlFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
  60           {
  61             super(inFile, type);
  62
  63           }
  64
  65           public RnamlFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
  66           {
  67             super(source);
  68
  69           }
  70
  71 //        public RnamlFile(BufferedReader r) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
  72 //        {
  73 //                      super();
  74 //                  parse(r);
  75 //                  // sets the index of each sequence in the alignment
  76 //                  for( int i=0,c=seqs.size(); i<c; i++ ) {
  77 //                      seqs.get(i).setIndex(i);
  78 //                  }
  79 //
  80 //
  81 //        }
  82
  83         public BufferedReader CreateReader() throws FileNotFoundException
  84         {
  85                  FileReader fr = null;
  86                   fr = new FileReader(inFile);
  87
  88                   BufferedReader r = new BufferedReader (fr);
  89                   return r;
  90         }
  91
  92
  93         @SuppressWarnings("unchecked")
  94         public void parse() throws FileNotFoundException, ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax
  95         {
  96                  result = RNAFactory.loadSecStrRNAML(getReader());
  97
  98                  System.out.println("this is the secondary scructure:" +result.size());
  99                   //System.out.println("this is the secondary scructure:" +result.toString());
 100                   //System.out.println("this is the secondary scructure:" +result.size());
 101                  SequenceI[] seqs = new SequenceI[result.size()];
 102                   System.out.println(type); //the type is "File"
 103                   System.out.println(inFile );//inFile is the path
 104
 105                  for(int i=0;i<result.size();i++)
 106                         {
 107                          RNA current = result.get(i);
 108                   System.out.println(current.getSeq());
 109                   //System.out.println(result.get(i).getStructBPSEQ());
 110                   System.out.println(result.get(i).getStructDBN(true));
 111                   System.out.println(i);
 112                   String rna =current.getStructDBN(true);
 113                   //System.out.println(result.get(0).getAnnotations());
 114                   String seq = current.getSeq();
 115
 116                   int begin=0;
 117                   int end = seq.length()-1;
 118
 119                   id = safeName(getDataName());
 120                   seqs[i] = new Sequence(id, seq, begin, end);
 121                   //System.out.println(seq);
 122                   System.out.println("Rna is still "+rna);
 123                   //SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
 124                   //seqs[i].addSequenceFeature(feat);
 125
 126                   String[] annot=new String[rna.length()] ;
 127                   Annotation[] ann = new Annotation[rna.length()];
 128
 129                   for(int j=0;j<rna.length();j++)
 130                         {
 131                           annot[j] =rna.substring(j,j+1);
 132
 133                         }
 134
 135                   for(int k=0;k<rna.length();k++)
 136                 {
 137                           ann[k] = new Annotation(annot[k], "", jalview.schemes.ResidueProperties.getRNASecStrucState(annot[k]).charAt(0), 0f);
 138
 139                 }
 140                   AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",current.getID(),ann);
 141
 142                   seqs[i].addAlignmentAnnotation(align);
 143                   seqs[i].setRNA(result.get(i));
 144                   this.annotations.addElement(align);
 145                 }
 146           this.setSeqs(seqs);
 147
 148
 149
 150
 151         }
 152
 153
 154           public void parse(BufferedReader r) throws ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax
 155           {
 156                    System.out.println("parse with Buffer (RnamlFile");
 157                   Hashtable seqhash = new Hashtable();
 158                   Vector headers = new Vector();
 159                   //ArrayList<String> seq =new ArrayList();
 160                   //System.out.println(r);
 161
 162                   result = RNAFactory.loadSecStr(r,RNAFileType.FILE_TYPE_RNAML);
 163
 164                   System.out.println("this is the secondary scructure:" +result.toArray());
 165                   System.out.println("this is the secondary scructure:" +result.toString());
 166                   System.out.println("this is the secondary scructure:" +result.size());
 167                         for(int i=0;i<result.size();i++)
 168                         {
 169                   System.out.println(result.get(0).getSeq());
 170                   System.out.println(result.get(0).getStructBPSEQ());
 171                   System.out.println(result.get(0).getStructDBN(true));
 172                   String rna1 =result.get(0).getStructDBN(true);
 173                   System.out.println(result.get(0).getAnnotations());
 174                   String seq = result.get(0).getSeq();
 175                   System.out.println(type); //the type is "File"
 176                   System.out.println(inFile );//inFile is the path
 177                   int begin=0;
 178                   int end = seq.length()-1;
 179                   SequenceI[] seqs = new SequenceI[1];
 180                   id = safeName(getDataName());
 181                   seqs[0] = new Sequence(id, seq, begin, end);
 182                   SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
 183                   seqs[0].addSequenceFeature(feat);
 184                   this.setSeqs(seqs);
 185
 186                   String[] annot=new String[10000] ;
 187                   Annotation[] ann = new Annotation[1000];
 188                   for(int j=0;j<rna1.length();j++)
 189                         {
 190                   annot[j] =rna1.substring(j,j+1);
 191                   //System.out.println(annot[j]);
 192                         }
 193
 194                   for(int k=0;k<rna1.length();k++)
 195                 {
 196                           ann[k] = new Annotation(annot[k], "", ' ', 0f);
 197
 198                           ann[k].secondaryStructure = jalview.schemes.ResidueProperties.getRNASecStrucState(annot[k]).charAt(0);
 199
 200                 }
 201                   AlignmentAnnotation align = new AlignmentAnnotation("Secondary structure","",ann);
 202                   seqs[0].addAlignmentAnnotation(align);
 203                   this.annotations.addElement(align);
 204                 }
 205                 //Annotate3D tintin = new Annotate3D();
 206
 207                 //System.out.println(tintin);
 208
 209
 210
 211
 212
 213
 214
 215
 216 //                                      for(RNAMLParser.RNATmp rnaTmp : RNAMLData.getMolecules())
 217 //                                      {
 218 //                                              // Retrieving parsed data
 219 //                                              seq = rnaTmp.getSequence(); //contient la séquence sous forme de liste
 220 //                                              System.out.println(seq);
 221 //                                              String seqAsStr = "";
 222 //                                              for(String s:seq)
 223 //                                              {
 224 //                                                      // Only consider last character, e.g. in case of modified nucleotide
 225 //                                                      seqAsStr += s.charAt(s.length()-1);
 226 //                                              }
 227 //                                              int begin=0;
 228 //                                              int end = seqAsStr.length()-1;
 229 //                                              SequenceI[] seqs = new SequenceI[1];
 230 //                                              id = safeName(getDataName());
 231 //                                              seqs[0] = new Sequence(id, seqAsStr, begin, end);
 232 //                                              SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
 233 //
 234 //                          seqs[0].addSequenceFeature(feat);
 235 //                                              this.setSeqs(seqs);
 236
 237                                                 //String pos = annot.substring(1, 2);
 238                                                 //System.out.println(annot);
 239                                                 //System.out.println(pos);
 240
 241                                            // ann[1] = new Annotation(pos, "", ' ', 0f);
 242                                            // ann[1].secondaryStructure = 'A';
 243                                             //System.out.println(ann[1]);
 244
 245                                            // toto.annotations=ann;
 246
 247
 248
 249 ////                                             Annotation[] els = new Annotation[seq.size()];
 250 //
 251 //                                              //System.err.println(""+seq.size());
 252 //                                          Vector<RNAMLParser.BPTemp> allbpsTmp = rnaTmp.getStructure();
 253 //                                          String[] annot = new String[10000];
 254 //
 255 //                                              //Annotation[] ann = new Annotation[allbpsTmp.size()];
 256 //                                              for (int i = 0; i < allbpsTmp.size(); i++) {
 257 //                                              RNAMLParser.BPTemp bp = allbpsTmp.get(i);
 258 //                                              //System.err.println("toto ="+bp);
 259 //                                              int bp5 = bp.pos5;
 260 //                                              annot[bp5]= "(";
 261 //                                              //annot[bp5]= '(';
 262 //                                              System.out.println(annot[bp5]);
 263 //                                              //System.out.println("bp5 ="+bp5);
 264 //                                              int bp3 = bp.pos3;
 265 //
 266 //                                              annot[bp3]= ")";
 267 //                                              System.out.println(annot[bp3]);
 268 //                                              //System.out.println(annot.get(bp3));
 269 //
 270 //                                              //String pos1 = annot.substring(bp5, bp5+1);
 271 //                                              //String pos2 = annot.substring(bp3, bp3+1);
 272 //                                              //ann[i] = new Annotation(pos1, "", ' ', 0f);
 273 //                                              //ann[i+1] = new Annotation(pos2, "", ' ', 0f);
 274 //                                              //System.out.println(pos1);
 275 //
 276 //                                              //System.out.println("bp3 ="+bp3);
 277 //                                              //ModeleBP newStyle = bp.createBPStyle(mb, part);
 278 //                                              }
 279 //                                              Annotation[] ann = new Annotation[annot.length+1];
 280 //                                              for(int i=0;i<annot.length;i++)
 281 //                                              {
 282 //                                                      if(annot[i]==null)
 283 //                                                      {
 284 //                                                              annot[i]=".";
 285 //                                                      }
 286 //
 287 //                                                      ann[i] = new Annotation(annot[i], "", ' ', 0f);
 288 //                                              //System.out.print(annot[i]);
 289 //                                              }
 290 //
 291 //                                              AlignmentAnnotation toto = new AlignmentAnnotation("Secondary structure","",ann);
 292 //                                              this.annotations.addElement(toto);
 293
 294                                                 // Creating empty structure of suitable size
 295 //                                              int[] str = new int[seq.size()];
 296 //                                              for (int i=0;i<str.length;i++)
 297 //                                              { str[i] = -1; }
 298 //                                              Vector<RNAMLParser.BPTemp> allbpsTmp = rnaTmp.getStructure();
 299 //                                              for (int i = 0; i < allbpsTmp.size(); i++) {
 300 //                                                      RNAMLParser.BPTemp bp = allbpsTmp.get(i);
 301 //                                                      //System.err.println("toto ="+bp);
 302 //                                                      int bp5 = bp.pos5;
 303 //                                                      //System.out.println("bp5 ="+bp5);
 304 //                                                      int bp3 = bp.pos3;
 305                                                         //System.out.println("bp3 ="+bp3);
 306                                                         //ModeleBP newStyle = bp.createBPStyle(mb, part);
 307 //                                              }
 308                                                 //Annotation ann;
 309                                             //ann = new Annotation(bp5, "", ' ', 0f);
 310
 311                                         //}
 312
 313
 314
 315 //                              return result;
 316
 317 }
 318
 319
 320           public static String print(SequenceI[] s)
 321           {
 322             return "not yet implemented";
 323           }
 324
 325           public String print()
 326           {
 327                 System.out.print("affiche :");
 328             return print(getSeqsAsArray());
 329           }
 330
 331           /**
 332            * make a friendly ID string.
 333            *
 334            * @param dataName
 335            * @return truncated dataName to after last '/'
 336            */
 337           private String safeName(String dataName)
 338           {
 339             int b = 0;
 340             while ((b = dataName.indexOf("/")) > -1 && b < dataName.length() )
 341             {
 342                 dataName = dataName.substring(b + 1).trim();
 343
 344             }
 345             int e = (dataName.length() - dataName.indexOf("."))+1;
 346             dataName = dataName.substring(1,e).trim();
 347             return dataName;
 348           }
 349
 350           public ArrayList getRNA()
 351           {
 352                   return result;
 353           }
 354
 355           public Vector getAnnot()
 356           {
 357                   return annotations;
 358           }
 359 }