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.factories.RNAFactory;
  40 import fr.orsay.lri.varna.factories.RNAFactory.RNAFileType;
  41 import fr.orsay.lri.varna.models.rna.RNA;
  42 import fr.orsay.lri.varna.utils.RNAMLParser;
  43
  44
  45
  46
  47 public class RnamlFile extends AlignFile
  48 {
  49          public String id;
  50          protected ArrayList<RNA> result;
  51
  52          public RnamlFile()
  53           {
  54                  super();
  55
  56           }
  57
  58          public RnamlFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
  59           {
  60             super(inFile, type);
  61
  62           }
  63
  64           public RnamlFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
  65           {
  66             super(source);
  67
  68           }
  69
  70 //        public RnamlFile(BufferedReader r) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
  71 //        {
  72 //                      super();
  73 //                  parse(r);
  74 //                  // sets the index of each sequence in the alignment
  75 //                  for( int i=0,c=seqs.size(); i<c; i++ ) {
  76 //                      seqs.get(i).setIndex(i);
  77 //                  }
  78 //
  79 //
  80 //        }
  81
  82         public BufferedReader CreateReader() throws FileNotFoundException
  83         {
  84                  FileReader fr = null;
  85                   fr = new FileReader(inFile);
  86
  87                   BufferedReader r = new BufferedReader (fr);
  88                   return r;
  89         }
  90
  91
  92         public void parse() throws FileNotFoundException, ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax
  93         {
  94                  FileReader fr = null;
  95                   fr = new FileReader(inFile);
  96
  97                   BufferedReader r = new BufferedReader (fr);
  98                  Hashtable seqhash = new Hashtable();
  99                   Vector headers = new Vector();
 100                   //ArrayList<String> seq =new ArrayList();
 101                   //System.out.println(r);
 102
 103
 104                  result = RNAFactory.loadSecStrRNAML(r);
 105
 106                  System.out.println("this is the secondary scructure:" +result.toArray());
 107                   //System.out.println("this is the secondary scructure:" +result.toString());
 108                   //System.out.println("this is the secondary scructure:" +result.size());
 109                         for(int i=0;i<result.size();i++)
 110                         {
 111                   //System.out.println(result.get(0).getSeq());
 112                   //System.out.println(result.get(0).getStructBPSEQ());
 113                   //System.out.println(result.get(0).getStructDBN(true));
 114                   String rna1 =result.get(0).getStructDBN(true);
 115                   //System.out.println(result.get(0).getAnnotations());
 116                   String seq = result.get(0).getSeq();
 117                   System.out.println(type); //the type is "File"
 118                   System.out.println(inFile );//inFile is the path
 119                   int begin=0;
 120                   int end = seq.length()-1;
 121                   SequenceI[] seqs = new SequenceI[1];
 122                   id = safeName(getDataName());
 123                   seqs[0] = new Sequence(id, seq, begin, end);
 124                   SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
 125                   seqs[0].addSequenceFeature(feat);
 126                   this.setSeqs(seqs);
 127
 128                   String[] annot=new String[10000] ;
 129                   Annotation[] ann = new Annotation[1000];
 130                   for(int j=0;j<rna1.length();j++)
 131                         {
 132                   annot[j] =rna1.substring(j,j+1);
 133                   System.out.println(annot[j]);
 134                         }
 135
 136                   for(int k=0;k<rna1.length();k++)
 137                 {
 138                           ann[k] = new Annotation(annot[k], "", ' ', 0f);
 139
 140                           ann[k].secondaryStructure = jalview.schemes.ResidueProperties.getRNASecStrucState(annot[k]).charAt(0);
 141
 142                 }
 143                   AlignmentAnnotation align = new AlignmentAnnotation("Secondary structure","",ann);
 144                   seqs[0].addAlignmentAnnotation(align);
 145                   seqs[0].setRNA(result.get(begin));
 146                   this.annotations.addElement(align);
 147
 148
 149                 }
 150
 151                 //Annotate3D tintin = new Annotate3D();
 152
 153                 //System.out.println(tintin);
 154         }
 155
 156
 157           public void parse(BufferedReader r) throws ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax
 158           {
 159                    System.out.println("parse with Buffer (RnamlFile");
 160                   Hashtable seqhash = new Hashtable();
 161                   Vector headers = new Vector();
 162                   //ArrayList<String> seq =new ArrayList();
 163                   //System.out.println(r);
 164
 165                   result = RNAFactory.loadSecStr(r,RNAFileType.FILE_TYPE_RNAML);
 166
 167                   System.out.println("this is the secondary scructure:" +result.toArray());
 168                   System.out.println("this is the secondary scructure:" +result.toString());
 169                   System.out.println("this is the secondary scructure:" +result.size());
 170                         for(int i=0;i<result.size();i++)
 171                         {
 172                   System.out.println(result.get(0).getSeq());
 173                   System.out.println(result.get(0).getStructBPSEQ());
 174                   System.out.println(result.get(0).getStructDBN(true));
 175                   String rna1 =result.get(0).getStructDBN(true);
 176                   System.out.println(result.get(0).getAnnotations());
 177                   String seq = result.get(0).getSeq();
 178                   System.out.println(type); //the type is "File"
 179                   System.out.println(inFile );//inFile is the path
 180                   int begin=0;
 181                   int end = seq.length()-1;
 182                   SequenceI[] seqs = new SequenceI[1];
 183                   id = safeName(getDataName());
 184                   seqs[0] = new Sequence(id, seq, begin, end);
 185                   SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
 186                   seqs[0].addSequenceFeature(feat);
 187                   this.setSeqs(seqs);
 188
 189                   String[] annot=new String[10000] ;
 190                   Annotation[] ann = new Annotation[1000];
 191                   for(int j=0;j<rna1.length();j++)
 192                         {
 193                   annot[j] =rna1.substring(j,j+1);
 194                   //System.out.println(annot[j]);
 195                         }
 196
 197                   for(int k=0;k<rna1.length();k++)
 198                 {
 199                           ann[k] = new Annotation(annot[k], "", ' ', 0f);
 200
 201                           ann[k].secondaryStructure = jalview.schemes.ResidueProperties.getRNASecStrucState(annot[k]).charAt(0);
 202
 203                 }
 204                   AlignmentAnnotation align = new AlignmentAnnotation("Secondary structure","",ann);
 205                   seqs[0].addAlignmentAnnotation(align);
 206                   this.annotations.addElement(align);
 207                 }
 208                 //Annotate3D tintin = new Annotate3D();
 209
 210                 //System.out.println(tintin);
 211
 212
 213
 214
 215
 216
 217
 218
 219 //                                      for(RNAMLParser.RNATmp rnaTmp : RNAMLData.getMolecules())
 220 //                                      {
 221 //                                              // Retrieving parsed data
 222 //                                              seq = rnaTmp.getSequence(); //contient la séquence sous forme de liste
 223 //                                              System.out.println(seq);
 224 //                                              String seqAsStr = "";
 225 //                                              for(String s:seq)
 226 //                                              {
 227 //                                                      // Only consider last character, e.g. in case of modified nucleotide
 228 //                                                      seqAsStr += s.charAt(s.length()-1);
 229 //                                              }
 230 //                                              int begin=0;
 231 //                                              int end = seqAsStr.length()-1;
 232 //                                              SequenceI[] seqs = new SequenceI[1];
 233 //                                              id = safeName(getDataName());
 234 //                                              seqs[0] = new Sequence(id, seqAsStr, begin, end);
 235 //                                              SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
 236 //
 237 //                          seqs[0].addSequenceFeature(feat);
 238 //                                              this.setSeqs(seqs);
 239
 240                                                 //String pos = annot.substring(1, 2);
 241                                                 //System.out.println(annot);
 242                                                 //System.out.println(pos);
 243
 244                                            // ann[1] = new Annotation(pos, "", ' ', 0f);
 245                                            // ann[1].secondaryStructure = 'A';
 246                                             //System.out.println(ann[1]);
 247
 248                                            // toto.annotations=ann;
 249
 250
 251
 252 ////                                             Annotation[] els = new Annotation[seq.size()];
 253 //
 254 //                                              //System.err.println(""+seq.size());
 255 //                                          Vector<RNAMLParser.BPTemp> allbpsTmp = rnaTmp.getStructure();
 256 //                                          String[] annot = new String[10000];
 257 //
 258 //                                              //Annotation[] ann = new Annotation[allbpsTmp.size()];
 259 //                                              for (int i = 0; i < allbpsTmp.size(); i++) {
 260 //                                              RNAMLParser.BPTemp bp = allbpsTmp.get(i);
 261 //                                              //System.err.println("toto ="+bp);
 262 //                                              int bp5 = bp.pos5;
 263 //                                              annot[bp5]= "(";
 264 //                                              //annot[bp5]= '(';
 265 //                                              System.out.println(annot[bp5]);
 266 //                                              //System.out.println("bp5 ="+bp5);
 267 //                                              int bp3 = bp.pos3;
 268 //
 269 //                                              annot[bp3]= ")";
 270 //                                              System.out.println(annot[bp3]);
 271 //                                              //System.out.println(annot.get(bp3));
 272 //
 273 //                                              //String pos1 = annot.substring(bp5, bp5+1);
 274 //                                              //String pos2 = annot.substring(bp3, bp3+1);
 275 //                                              //ann[i] = new Annotation(pos1, "", ' ', 0f);
 276 //                                              //ann[i+1] = new Annotation(pos2, "", ' ', 0f);
 277 //                                              //System.out.println(pos1);
 278 //
 279 //                                              //System.out.println("bp3 ="+bp3);
 280 //                                              //ModeleBP newStyle = bp.createBPStyle(mb, part);
 281 //                                              }
 282 //                                              Annotation[] ann = new Annotation[annot.length+1];
 283 //                                              for(int i=0;i<annot.length;i++)
 284 //                                              {
 285 //                                                      if(annot[i]==null)
 286 //                                                      {
 287 //                                                              annot[i]=".";
 288 //                                                      }
 289 //
 290 //                                                      ann[i] = new Annotation(annot[i], "", ' ', 0f);
 291 //                                              //System.out.print(annot[i]);
 292 //                                              }
 293 //
 294 //                                              AlignmentAnnotation toto = new AlignmentAnnotation("Secondary structure","",ann);
 295 //                                              this.annotations.addElement(toto);
 296
 297                                                 // Creating empty structure of suitable size
 298 //                                              int[] str = new int[seq.size()];
 299 //                                              for (int i=0;i<str.length;i++)
 300 //                                              { str[i] = -1; }
 301 //                                              Vector<RNAMLParser.BPTemp> allbpsTmp = rnaTmp.getStructure();
 302 //                                              for (int i = 0; i < allbpsTmp.size(); i++) {
 303 //                                                      RNAMLParser.BPTemp bp = allbpsTmp.get(i);
 304 //                                                      //System.err.println("toto ="+bp);
 305 //                                                      int bp5 = bp.pos5;
 306 //                                                      //System.out.println("bp5 ="+bp5);
 307 //                                                      int bp3 = bp.pos3;
 308                                                         //System.out.println("bp3 ="+bp3);
 309                                                         //ModeleBP newStyle = bp.createBPStyle(mb, part);
 310 //                                              }
 311                                                 //Annotation ann;
 312                                             //ann = new Annotation(bp5, "", ' ', 0f);
 313
 314                                         //}
 315
 316
 317
 318 //                              return result;
 319
 320 }
 321
 322
 323           public static String print(SequenceI[] s)
 324           {
 325             return "not yet implemented";
 326           }
 327
 328           public String print()
 329           {
 330                 System.out.print("affiche :");
 331             return print(getSeqsAsArray());
 332           }
 333
 334           /**
 335            * make a friendly ID string.
 336            *
 337            * @param dataName
 338            * @return truncated dataName to after last '/'
 339            */
 340           private String safeName(String dataName)
 341           {
 342             int b = 0;
 343             while ((b = dataName.indexOf("/")) > -1 && b < dataName.length() )
 344             {
 345                 dataName = dataName.substring(b + 1).trim();
 346
 347             }
 348             int e = (dataName.length() - dataName.indexOf("."))+1;
 349             dataName = dataName.substring(1,e).trim();
 350             return dataName;
 351           }
 352
 353           public ArrayList getRNA()
 354           {
 355                   return result;
 356           }
 357
 358           public Vector getAnnot()
 359           {
 360                   return annotations;
 361           }
 362 }
 363