private static int readSeqLineP(
PushbackReader in,
int s,
int pos,
int maxPos,
char[][] data,
String[] identifiers,
FormattedInput fi,
int maxLabelLength,
int lineLength)
throws IOException {
if (pos == 0) {
identifiers[s] = fi.readLabel(in, maxLabelLength).toUpperCase();
}
if (s == 0) {
String thisLine = fi.readLine(in, false);
if (thisLine.length() > maxPos - pos) {
lineLength = maxPos - pos;
} else {
lineLength = thisLine.length();
}
for (int i = 0; i < lineLength; i++) {
data[0][pos + i] = thisLine.charAt(i);
if (data[0][pos + i] == '.') {
throw new IllegalArgumentException(
"Copy character (.) in first sequence not allowed (pos. " + (i + pos + 1) + ")");
}
}
} else {
for (int i = 0; i < lineLength; i++) {
data[s][pos + i] = (char) fi.readNextChar(in);
if (data[s][pos + i] == '.') {
data[s][pos + i] = data[0][pos + i];
}
}
fi.nextLine(in);
}
return lineLength;
}
// Read alignment (in PHYLIP 3.4 INTERLEAVED or PHYLIP SEQUENTIAL format)
private static GenotypeTable readPHYLIP(PushbackReader in, int maxLabelLength) {
FormattedInput fi = FormattedInput.getInstance();
TaxaList idGroup;
int numSeqs = 0, numSites = 0, lineLength = 0;
char[][] data = null;
int c, pos = 0, seq = 0;
try {
// Parse PHYLIP header line
numSeqs = fi.readInt(in);
numSites = fi.readInt(in);
String[] identifiers = new String[numSeqs];
data = new char[numSeqs][numSites];
// Determine whether sequences are in INTERLEAVED
// or in sequential format
String header = fi.readLine(in, false);
boolean interleaved = true;
if (header.length() > 0) {
if (header.charAt(0) == 'S') {
interleaved = false;
}
}
if (interleaved) // PHYLIP INTERLEAVED
{
// Reading data
while (pos < numSites) {
// Go to next block
c = fi.readNextChar(in);
in.unread(c);
for (seq = 0; seq < numSeqs; seq++) {
lineLength =
readSeqLineP(
in, seq, pos, numSites, data, identifiers, fi, maxLabelLength, lineLength);
}
pos += lineLength;
}
} else // PHYLIP SEQUENTIAL
{
// System.out.println("PHYLIP SEQUENTIAL");
for (seq = 0; seq < numSeqs; seq++) {
// Go to next block
c = fi.readNextChar(in);
in.unread(c);
// Read label
identifiers[seq] = fi.readLabel(in, maxLabelLength).toUpperCase();
// Read sequences
for (pos = 0; pos < numSites; pos++) {
data[seq][pos] = (char) fi.readNextChar(in);
if (data[0][pos] == '.') {
if (seq == 0) {
throw new IllegalArgumentException(
"Copy character (.) in first sequence not allowed (pos. " + (pos + 1) + ")");
} else {
data[seq][pos] = data[0][pos];
}
}
}
}
}
idGroup = new TaxaListBuilder().addAll(identifiers).build();
} catch (IOException e) {
throw new IllegalArgumentException(
"IO error after pos. " + (pos + 1) + ", seq. " + (seq + 1));
}
String[] s = new String[numSeqs];
for (int i = 0; i < numSeqs; i++) {
s[i] = (new String(data[i])).toUpperCase();
}
// SimpleAlignment saa = SimpleAlignment.getInstance(idGroup, s, new Nucleotides());
String[] sites = new String[numSites];
int[] positions = new int[numSites];
for (int i = 0; i < numSites; i++) {
positions[i] = i;
sites[i] = Integer.toString(i);
}
GenotypeCallTable genotype =
GenotypeCallTableBuilder.getUnphasedNucleotideGenotypeBuilder(numSeqs, numSites)
.setBases(s)
.build();
return GenotypeTableBuilder.getInstance(
genotype, PositionListBuilder.getInstance(numSites), idGroup);
}