char U2AssemblyReadIterator::nextLetter() {
assert(hasNext());
skip();
SAFE_POINT(offsetInCigar < cigar.size(), "CIGAR out of range", 0);
if(offsetInToken != cigar.at(offsetInCigar).count) { //staying in the current token
offsetInToken++;
} else { //current token is finished
advanceToNextToken();
offsetInToken = 1;
}
bool del = isDeletion();
char c = del ? '-' : read.at(offsetInRead); //TODO: hardcoded '-'
offsetInRead += !del; //adjust offsetInRead only when going through match token
return c;
}
U2AssemblyReadIterator::U2AssemblyReadIterator(const QByteArray & read_, QList<U2CigarToken> cigar_, int startPos /* = 0*/) :
offsetInRead(0), read(read_), offsetInToken(0), offsetInCigar(0), cigar(cigar_)
{
for(int i = 0; i < startPos && hasNext();) {
skip();
U2CigarToken t = cigar.at(offsetInCigar);
if(i + t.count <= startPos) { //we are going to skip the current token
if(isMatch()) {
offsetInRead += t.count;
}
i += t.count;
offsetInToken += t.count;
if(!hasNext()) break;
advanceToNextToken();
} else {
//landing in the current token
offsetInToken = startPos - i;
if(isMatch()) {
offsetInRead += offsetInToken;
}
break;
}
}
}
static void
getToken(xmlrpc_env * const envP,
Tokenizer * const tokP) {
/* The token starts where the last one left off */
tokP->begin = tokP->end;
advanceToNextToken(tokP);
if (*tokP->begin == '\0') {
/* End of document */
tokP->end = tokP->begin;
tokP->type = typeEof;
tokP->size = tokP->end - tokP->begin;
} else {
tokP->end = tokP->begin; /* initial value */
if (*tokP->begin == '{') {
finishDelimiterToken(tokP);
tokP->type = typeOpenBrace;
} else if (*tokP->begin == '}') {
finishDelimiterToken(tokP);
tokP->type = typeCloseBrace;
} else if (*tokP->begin == '[') {
finishDelimiterToken(tokP);
tokP->type = typeOpenBracket;
} else if (*tokP->begin == ']') {
finishDelimiterToken(tokP);
tokP->type = typeCloseBracket;
} else if (*tokP->begin == ':') {
finishDelimiterToken(tokP);
tokP->type = typeColon;
} else if (*tokP->begin == ',') {
finishDelimiterToken(tokP);
tokP->type = typeComma;
} else if (*tokP->begin == '"') {
finishStringToken(envP, tokP);
if (!envP->fault_occurred)
tokP->type = typeString;
} else {
if (isWordChar(*tokP->begin)) {
finishAlphanumericWordToken(tokP);
if (isInteger(tokP->begin, tokP->size))
tokP->type = typeInteger;
else if (isFloat(tokP->begin, tokP->size))
tokP->type = typeFloat;
else if (xmlrpc_strneq(tokP->begin, "null", tokP->size))
tokP->type = typeNull;
else if (xmlrpc_strneq(tokP->begin, "undefined", tokP->size))
tokP->type = typeUndefined;
else if(xmlrpc_strneq(tokP->begin, "false", tokP->size))
tokP->type = typeFalse;
else if(xmlrpc_strneq(tokP->begin, "true", tokP->size))
tokP->type = typeTrue;
else
setParseErr(envP, tokP, "Invalid word token -- "
"Not a valid integer, floating point "
"number, 'null', 'true', or 'false'");
} else {
setParseErr(envP, tokP,
"Not a valid token -- starts with '%c'; "
"a valid token starts with "
"one of []{}:,\"-. or digit or letter",
*tokP->begin);
}
}
}
}
