// TODO: This should be streaming instead of creating an entire collection
public LineFile print(PackageFileSystem<A> fs) {
LineFile lines = new LineFile();
Tree<PackageFileSystemObject<A>> tree = fs.prettify().getTree();
lines.add(".");
print(1, lines, tree.subForest()._1());
return lines;
}
private void print(int i, LineFile lines, Stream<Tree<PackageFileSystemObject<A>>> children) {
String indent = StringUtils.repeat(" ", i);
i++;
for (Tree<PackageFileSystemObject<A>> child : children) {
// UnixFsObject unixFsObject = child.root().getUnixFsObject();
// lines.add( indent + unixFsObject.path.name() + ", filters=" +
// unixFsObject.filters );
lines.add(indent + child.root().getUnixFsObject().path.name());
print(i, lines, child.subForest()._1());
}
}
/* Read in DNA or Peptide FA record in mixed case. Allow any upper or lower case
* letter, or the dash character in.
*
* boolean faMixedSpeedReadNext(struct lineFile *lf, DNA **retDna, int *retSize, char **retName)
* */
public boolean faMixedSpeedReadNext(LineFile f, DnaSeq seq)
throws IOException, FaFormatException {
char c;
int bufIx = 0;
String name = null; // the name of teh fa sequence.
int lineSize, i;
String line;
// this could be necesary
// dnaUtilOpen();
/* Read first line, make sure it starts with '>', and read first word
* as name of sequence. */
if ((line = f.lineFileNext()) == null) { // f, &line, &lineSize
// *retDna = NULL;
// *retSize = 0;
return false;
}
if (line.charAt(0) == '>') {
name = line.substring(1).split(" ")[0]; // .substring(1).replaceAll(" ", "");
if (line.equals("")) {
System.err.println("Expecting sequence name after '>' " + f.getFile().getName());
throw new FaFormatException();
}
} else {
System.err.println("Expecting '>' line " + f.getFile().getName());
throw new FaFormatException();
}
/* Read until next '>' */
for (; ; ) {
if ((line = f.lineFileNext()) == null) // !lineFileNext(lf, &line, &lineSize)
break;
if (line.charAt(0) == '>') {
f.lineFileReuse(line);
break;
}
for (char m : line.toCharArray()) {
if (Character.isLetter(m) || m == '-') {
buff.put(m);
}
}
}
// if (bufIx >= faFastBufSize)
// expandFaFastBuf(bufIx, 0);
// faFastBuf[bufIx] = 0;
// *retDna = faFastBuf;
// *retSize = bufIx;
char[] dna = new char[buff.position()];
char[] c_buff = buff.array();
for (int k = 0; k < dna.length; k++) {
dna[k] = c_buff[k];
}
seq.setName(name);
seq.setDna(dna);
// if (bufIx == 0){
// System.err.println("Invalid fasta format: sequence size == 0 for element " + name);
// }
buff.clear();
return true;
}
