/**
* Converts the fasta sequences into phylip format: <number of sequences> <length of aligned
* sequences> <id - exactly ten-space character padded><sequence for id> ...
*
* @param fasta_aligned_sequences
* @return the phylip formatted result
*/
protected String fasta2phylip(String fasta_aligned_sequences) throws IOException {
StringBuffer seq = new StringBuffer();
int count = 0;
int length = 0;
boolean prev = false;
BufferedReader rdr = new BufferedReader(new StringReader(fasta_aligned_sequences));
String line;
String cur_id = null;
StringBuffer tmp = new StringBuffer();
while ((line = rdr.readLine()) != null) {
// System.err.println(cur_id+" "+line);
if (line.startsWith(">")) {
count++;
if (prev) {
seq.append(fasta_accession2phylip(cur_id) + tmp + "\n");
cur_id = line.trim().substring(1);
length = tmp.length();
tmp = new StringBuffer();
} else {
prev = true;
cur_id = line.trim().substring(1);
}
} else {
tmp.append(line.trim());
}
}
// dont forget the last sequence
if (tmp.length() > 0) {
seq.append(fasta_accession2phylip(cur_id) + tmp + "\n");
}
return " " + count + " " + length + "\n" + seq.toString();
}
