Example #1
0
  public static void main(String[] args) {
    try {
      ArrayList<String> sequences = new ArrayList<String>();
      ArrayList<String> sequenceNames = new ArrayList<String>();
      RNAFoldingTools.loadFastaSequences(
          new File(
              "/home/michael/Dropbox/RNA and StatAlign/Distance/Datasets2/TestRNAData1_5seqs.dat.fas"),
          sequences,
          sequenceNames);
      RNAalifoldResult res = RNAalifold.fold(sequences, sequenceNames, "-T 10");
      System.out.println(RNAFoldingTools.getDotBracketStringFromPairedSites(res.pairedSites));
      res = RNAalifold.fold(sequences, sequenceNames, "-T 60");
      System.out.println(RNAFoldingTools.getDotBracketStringFromPairedSites(res.pairedSites));
      // RNAalifold.saveClustalW(sequences, sequenceNames, new
      // File("/home/michael/Desktop/temp.clustalw"));
    } catch (Exception ex) {

    }
  }
Example #2
0
  public static boolean checkRNAalifold() {
    try {
      ArrayList<String> sequences = new ArrayList<String>();
      ArrayList<String> sequenceNames = new ArrayList<String>();
      sequences.add(
          "GGGUGCUUGAAGCUGUCUGCUUUAAGUGCUUGCA----UCAGGCUGAGAGUAGGCAGAGAAAAGCCCCGUAUCA-----A----------------UGUUAAUCAAUACGAGGC-CCUCUGUAAUG");
      sequences.add(
          "GGGUGCUUGAGGCUGUCUGCCUCGGG------CAUGCC---ACCGUAAGGCAGACAGAGAAAAGCCCCAGUUAACAUUACGCGUCCUGCAAGACGCCUAACAUUAAUCUGAGGC-CAAUUU-CAUG");
      sequenceNames.add("a");
      sequenceNames.add("b");

      useOldParams = false;
      String newparams = " -T " + 37 + " --cfactor " + 1 + " --nfactor " + 1 + " ";
      RNAalifoldResult res = null;
      try {
        res = RNAalifold.fold(sequences, sequenceNames, newparams);
      } catch (Exception ex) {
        System.err.println("The following error occured with RNAalifold: " + ex.getMessage());
      }
      // System.out.println("HERE " + res);
      if (res != null) {
        return true;
      } else {
        String oldparams = " -T " + 37 + " -cv " + 1 + " -nc " + 1 + " ";
        useOldParams = true;
        res = RNAalifold.fold(sequences, sequenceNames, oldparams);
        return res != null;
      }
    } catch (Exception ex) {
      System.err.println("The following error occured with RNAalifold: " + ex.getMessage());
    }

    useOldParams = false;

    return false;
  }