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) {
}
}
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;
}