/**
* Changes the sequence itself. BaseSequence doesn't care what sequence you try feeding in here.
*/
public void changeSequence(String seq) throws SequenceException {
StringBuffer buff = new StringBuffer();
// important step: is this sequence actually 'valid' (are all the brackets closed?)
//
// Also: convert round brackets into 'system-standard' (i.e. TaxonDNA specific) square brackets.
//
int count = 0;
int length = 0;
for (int x = 0; x < seq.length(); x++) {
char ch = seq.charAt(x);
// convert round brackets to square
if (ch == '(') ch = '[';
else if (ch == ')') ch = ']';
// count the brackets!
if (ch == '[') count++;
if (ch == ']') count--;
// this way, we delete this *once*
if (count == 0) length++;
buff.append(ch);
}
if (count != 0)
throw new SequenceException(
getFullName(),
"This sequence cannot be changed to the specified sequence, as the brackets are not properly closed. Please ensure that all brackets are closed, and try again.");
seq = buff.toString(); // hey, if we _can_ ...
synchronized (this) {
this.id = new UUID();
this.seq = seq.toCharArray();
this.len = length;
}
}
/**
* Returns a subsequence of this sequence. If the subsequence is completely 'valid', we might
* return a Sequence! Otherwise, we return a BaseSequence.
*/
public Sequence getSubsequence(int from, int to) throws SequenceException {
// make sure we're not being fed garbage
if (from < 1
|| // the first char is index = 1
to > getLength() // the 'to' field must not be greater than the length of the sequence
)
throw new SequenceException(
this.getFullName(),
"There is no subsequence at (" + from + ", " + to + ") in sequence " + this);
if (to < from) {
throw new SequenceException(
this.getFullName(),
"I cannot generate the reverse-complement of this sequence, since I do not understand what sort of data it is.");
}
// so, now we have a 'from' and a 'to'.
// Let's get cracking!
java.io.StringReader r = new java.io.StringReader(getSequence());
StringBuffer output = new StringBuffer();
// System.err.println("Base.cut: from: " + from + " to: " + to);
boolean writing = false;
int char_at = 0;
try {
while (r.ready()) {
int x = r.read();
if (x == -1) throw new java.io.EOFException();
if (char_at == from - 1) // off by one, here
writing = true;
if (char_at == to) // off by one, here too, but for a slightly different reason
writing = false;
if (x == '(' || x == '[') {
int initial_char = x;
int final_char = ' ';
if (x == '(') final_char = ')';
else final_char = ']';
// convert brackets to the Real Thing
if (writing) output.append('[');
while (x != ']') {
x = r.read();
if (x == final_char) x = ']';
if (x == -1) throw new java.io.EOFException();
if (writing) output.append((char) x);
}
} else {
if (writing) output.append((char) x);
}
char_at++;
}
} catch (java.io.EOFException e) {
// okay, done.
// did you know that
} catch (java.io.IOException e) {
throw new RuntimeException("Why is reading from a string causing an IOException?! " + e);
}
String seq_str = output.toString();
// System.err.println("What've we got: " + seq_str);
Sequence seq =
BaseSequence.createSequence(
getFullName() + " (segment:" + from + "-" + to + ":inclusive)", seq_str);
// System.err.println("Ended up with: " + seq);
return seq;
}
