/** @param args the command line arguments */
public static void main(String[] args) {
// args=tests();
try {
setOptions(args);
} catch (Exception e) {
help();
}
String os = System.getProperty("os.name").toLowerCase();
if (!os.contains("win") && rnafoldlinux.isEmpty()) {
System.out.println(
"You must submit the RNAfold program path (option -r). See help with -help option");
} else {
// check Vienna tools
if (!Vienna.checkViennaTools()) {
System.err.println("Vienna tools cannot be executed");
} else if (predictMiRNAFromPrec) {
mirdupExecutionPredictor();
} else {
miRdupExecutionEMBL();
}
}
}
/**
* Get probabilities for each pairs stored in the ps file
*
* @param aBdot5ps
*/
private void getBasePairsProbabilities(String aBdot5ps) {
boolean finalProbs = false;
int nucleotide5p = 0;
try {
BufferedReader br = new BufferedReader(new FileReader(aBdot5ps));
String line = br.readLine();
while (!line.startsWith("%data")) {
line = br.readLine();
}
line = br.readLine();
while (!line.startsWith("showpage")) {
String tab[] = line.split(" ");
int actual5pnt = Integer.valueOf(tab[0]) - 1;
int nucleotide3p = Integer.valueOf(tab[1]) - 1;
double score = Double.valueOf(tab[2]);
Double content[] = {Double.valueOf(actual5pnt), Double.valueOf(nucleotide3p), score};
if (actual5pnt < nucleotide5p) {
finalProbs = true;
}
nucleotide5p = actual5pnt;
// System.out.println(line);
assignBasePairsProbability(
bothmirnas.charAt(actual5pnt), bothmirnas.charAt(nucleotide3p), score);
BPprobGlobal += score;
if (finalProbs) {
BPprobFinalStructure += score;
alBPprobFinalStructure.add(content);
} else {
BPprobTmpStructure += score;
hmBPprobTmpStructure.put(actual5pnt, content);
ComplexBoltzmannProbability += -Math.exp(-score / (8.3144621 * 37));
}
line = br.readLine();
}
br.close();
// ensemblized bulges at +4 and -4
int numberOfUnpairedBases = 0;
double SumUnpairedBasesAroundBulges = 0;
for (int i = 0; i < alBPprobFinalStructure.size(); i++) {
if (alBPprobFinalStructure.get(i)[0] != i) {
numberOfUnpairedBases++;
for (int j = i - 4; j <= i + 4; j++) {
try {
SumUnpairedBasesAroundBulges += hmBPprobTmpStructure.get(j)[2];
} catch (Exception e) {
}
}
}
}
BPprobEnsemblizedBulges = SumUnpairedBasesAroundBulges / numberOfUnpairedBases;
// ComplexBoltzmannProbability
if (calculateConstraint) {
String constraint = "";
if (mirna5p.length() == mirna3p.length()) {
for (int i = 0; i < mirna5p.length(); i++) {
constraint += "(";
}
constraint += "&";
for (int i = 0; i < mirna3p.length(); i++) {
constraint += ")";
}
} else if (mirna5p.length() < mirna3p.length()) {
for (int i = 0; i < mirna5p.length(); i++) {
constraint += "(";
}
constraint += "&";
for (int i = 0; i < mirna5p.length(); i++) {
constraint += ")";
}
for (int i = 0; i < mirna5p.length() - mirna5p.length(); i++) {
constraint += ".";
}
} else {
for (int i = 0; i < mirna5p.length() - mirna3p.length(); i++) {
constraint += ".";
}
for (int i = 0; i < mirna3p.length(); i++) {
constraint += "(";
}
constraint += "&";
for (int i = 0; i < mirna3p.length(); i++) {
constraint += ")";
}
}
double Q =
Vienna.GetInfosDuplexRNAcofoldConstraint(mirna5p, mirna3p, constraint)
.ComplexBoltzmannProbability;
ComplexBoltzmannProbability = ComplexBoltzmannProbability / Q;
}
} catch (Exception e) {
e.printStackTrace();
}
}