Examples of fixEmptyHairpins()

Examples of bgu.bio.ds.rna.RNA.fixEmptyHairpins()

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    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);
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Examples of bgu.bio.ds.rna.RNA.fixEmptyHairpins()

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    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)) {
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