-// for(RNAMLParser.RNATmp rnaTmp : RNAMLData.getMolecules())
-// {
-// // Retrieving parsed data
-// seq = rnaTmp.getSequence(); //contient la séquence sous forme de liste
-// System.out.println(seq);
-// String seqAsStr = "";
-// for(String s:seq)
-// {
-// // Only consider last character, e.g. in case of modified nucleotide
-// seqAsStr += s.charAt(s.length()-1);
-// }
-// int begin=0;
-// int end = seqAsStr.length()-1;
-// SequenceI[] seqs = new SequenceI[1];
-// id = safeName(getDataName());
-// seqs[0] = new Sequence(id, seqAsStr, begin, end);
-// SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
-//
-// seqs[0].addSequenceFeature(feat);
-// this.setSeqs(seqs);
-
- //String pos = annot.substring(1, 2);
- //System.out.println(annot);
- //System.out.println(pos);
-
- // ann[1] = new Annotation(pos, "", ' ', 0f);
- // ann[1].secondaryStructure = 'A';
- //System.out.println(ann[1]);
-
- // toto.annotations=ann;
-
-
-
-//// Annotation[] els = new Annotation[seq.size()];
-//
-// //System.err.println(""+seq.size());
-// Vector<RNAMLParser.BPTemp> allbpsTmp = rnaTmp.getStructure();
-// String[] annot = new String[10000];
-//
-// //Annotation[] ann = new Annotation[allbpsTmp.size()];
-// for (int i = 0; i < allbpsTmp.size(); i++) {
-// RNAMLParser.BPTemp bp = allbpsTmp.get(i);
-// //System.err.println("toto ="+bp);
-// int bp5 = bp.pos5;
-// annot[bp5]= "(";
-// //annot[bp5]= '(';
-// System.out.println(annot[bp5]);
-// //System.out.println("bp5 ="+bp5);
-// int bp3 = bp.pos3;
-//
-// annot[bp3]= ")";
-// System.out.println(annot[bp3]);
-// //System.out.println(annot.get(bp3));
-//
-// //String pos1 = annot.substring(bp5, bp5+1);
-// //String pos2 = annot.substring(bp3, bp3+1);
-// //ann[i] = new Annotation(pos1, "", ' ', 0f);
-// //ann[i+1] = new Annotation(pos2, "", ' ', 0f);
-// //System.out.println(pos1);
-//
-// //System.out.println("bp3 ="+bp3);
-// //ModeleBP newStyle = bp.createBPStyle(mb, part);
-// }
-// Annotation[] ann = new Annotation[annot.length+1];
-// for(int i=0;i<annot.length;i++)
-// {
-// if(annot[i]==null)
-// {
-// annot[i]=".";
-// }
-//
-// ann[i] = new Annotation(annot[i], "", ' ', 0f);
-// //System.out.print(annot[i]);
-// }
-//
-// AlignmentAnnotation toto = new AlignmentAnnotation("Secondary structure","",ann);
-// this.annotations.addElement(toto);
-
- // Creating empty structure of suitable size
-// int[] str = new int[seq.size()];
-// for (int i=0;i<str.length;i++)
-// { str[i] = -1; }
-// Vector<RNAMLParser.BPTemp> allbpsTmp = rnaTmp.getStructure();
-// for (int i = 0; i < allbpsTmp.size(); i++) {
-// RNAMLParser.BPTemp bp = allbpsTmp.get(i);
-// //System.err.println("toto ="+bp);
-// int bp5 = bp.pos5;
-// //System.out.println("bp5 ="+bp5);
-// int bp3 = bp.pos3;
- //System.out.println("bp3 ="+bp3);
- //ModeleBP newStyle = bp.createBPStyle(mb, part);
-// }
- //Annotation ann;
- //ann = new Annotation(bp5, "", ' ', 0f);
-
- //}