Package bgu.bio.adt.rna

Examples of bgu.bio.adt.rna.RNASpecificTree.toDotFile()

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            .toCharArray(),
        "((..(......)(((.....)))...(((((.......)))))))...."
            .toCharArray());
    sR.shuffle(rand);
    sR.toFASTAFile("sR.fasta");
    sR.toDotFile("sR.dot", false);
    s.toDotFile("s.dot", false);
    t.toDotFile("t.dot", false);
    prune2.calculateCost(t);
    prune2.calculateCost(s);
    prune2.calculateCost(sR);
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    prune.calculateCost(t);
    smooth.calculateCost(t);
   
    try {
      t.toDotFile("/home/milon/tmp/1.dot", true);
    } catch (IOException e) {
      // TODO Auto-generated catch block
      e.printStackTrace();
    }
 
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    tree.buildFromViennaFormat(
        "CGACAGGAAACUGACAAACCCUUUCAUCUUAA".toCharArray(),
        "...((((...))...(((...)))..))....".toCharArray());
    tree.groupByStructure();
    try {
      tree.toDotFile("/home/milon/tmp/1.dot", true);
    } catch (IOException e) {
      e.printStackTrace();
    }

    for (int t = 0; t < tree.getNodeNum(); t++) {
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