Examples of RNA

bgu.bio.ds.rna.RNA
@author milon

Examples of bgu.bio.ds.rna.RNA

    ArrayList<RNA> list = RNA.loadFromFile(fileName, true);
    final int amountOfTrees = list.size();
    double sumNodes = 0, sumLength = 0;
    int minNodes = Integer.MAX_VALUE, maxNodes = Integer.MIN_VALUE, minLength = Integer.MAX_VALUE, maxLength = Integer.MIN_VALUE;
    for (int i = 0; i < amountOfTrees; i++) {
      RNA rna = list.get(i);
      rna.fixEmptyHairpins();
      RNASpecificTree tree = new RNASpecificTree(rna.getHeader());
      tree.buildFromViennaFormat(rna.getPrimary().toCharArray(), rna
          .getSecondary().toCharArray(), false, false);
      if (filter != null && filter.shouldPass(tree)) {
        trees.add(tree);
        sumNodes += tree.getNodeNum();
        sumLength += rna.getPrimary().length();
        minLength = Math.min(minLength, rna.getPrimary().length());
        minNodes = Math.min(minNodes, tree.getNodeNum());
        maxLength = Math.max(maxLength, rna.getPrimary().length());
        maxNodes = Math.max(maxNodes, tree.getNodeNum());
      }


    }
    if (printStats) {

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Examples of bgu.bio.ds.rna.RNA

    Random rand = new Random(seed);
    ArrayList<RNASpecificTree> trees = new ArrayList<RNASpecificTree>();
    ArrayList<RNA> list = RNA.loadFromFile(fileName, true);
    final int amountOfTrees = list.size();
    for (int i = 0; i < amountOfTrees; i++) {
      RNA rna = list.get(i);
      rna.fixEmptyHairpins();
      final char[] seq = rna.getPrimary().toCharArray();
      final char[] str = rna.getSecondary().toCharArray();
      RNASpecificTree tree = new RNASpecificTree(rna.getHeader());
      tree.buildFromViennaFormat(seq, str, false, true);
      if (filter != null && filter.shouldPass(tree)) {
        for (int r = 0; r < repeat; r++) {
          Random randTree = new Random(rand.nextLong());
          tree = new RNASpecificTree(rna.getHeader() + "_rand" + r);
          tree.buildFromViennaFormat(seq, str, false, false);
          tree.shuffle(randTree);
          trees.add(tree);
        }
      }

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Examples of bgu.bio.ds.rna.RNA

    System.out.println(NCBIInformation.match(q, database));


    List<String> l = NCBIInformation.search("AACY020322622.1");
    System.out.println("list:" + l);


    RNA r = NCBIInformation.getSequence("157484856", 1, 100, false);
    System.out.println(r.getHeader() + "\n" + r.getPrimary());
  }

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