public static void main(String[] args) throws IOException {
// Sequence[] s1 = readDatabase(new File("N:/temp/lean-dataset/imp_struct.fasta"), 1);
//
// System.out.println(Arrays.toString(s1));
//
// Sequence[] s2 = readDatabase(new File("N:/temp/lean-dataset/sol.fasta"), 1);
//
// System.out.println(Arrays.toString(s2));
Sequence[] s3 = readDatabase(new File(args[0]), 1);
System.out.println(Arrays.toString(s3));
for (Sequence s : s3) System.out.println(s.getId() + "\n" + s.getSequence() + "\n");
}
public final String printAA(String prefix, Sequence seq) {
StringBuilder sb = new StringBuilder(prefix);
for (SequencePosition sp : seq.getSequence()) {
sb.append(sp.getAminoAcid().toString());
}
return sb.toString();
}
public final String printHPalgebraicSign(String prefix, Sequence seq) {
StringBuilder sb = new StringBuilder(prefix);
for (SequencePosition sp : seq.getSequence()) {
if (sp.getHydrophobicity() > 0) {
sb.append("+");
} else {
sb.append("-");
}
}
return sb.toString();
}
public final String printSSE(String prefix, Sequence seq) {
StringBuilder sb = new StringBuilder(prefix);
for (SequencePosition sp : seq.getSequence()) {
String sse = sp.getSecondaryStructure().toString().toLowerCase();
if (sse.equals("helix")) {
sb.append("H");
} else if (sse.equals("coil")) {
sb.append("c");
} else {
sb.append("_");
}
}
return sb.toString();
}
public final String printHPvalues(String prefix, Sequence seq) {
NumberFormat nf = NumberFormat.getIntegerInstance(Locale.ENGLISH);
nf.setMaximumFractionDigits(0);
nf.setMinimumFractionDigits(0);
nf.setMaximumIntegerDigits(1);
nf.setMinimumIntegerDigits(1);
StringBuilder sb = new StringBuilder(prefix);
for (SequencePosition sp : seq.getSequence()) {
double hp = sp.getHydrophobicity();
String out = nf.format(hp);
if (out.contains("-")) {
sb.append(out.substring(1, 2));
} else {
sb.append(out);
}
}
return sb.toString();
}