std::string ReverseComplement(const std::string& seq) {
std::string output;
output.reserve(seq.length());
for (auto it = seq.crbegin(); it != seq.crend(); ++it) {
auto bp = *it;
switch(bp) {
case 'A':
output.push_back('T');
break;
case 'C':
output.push_back('G');
break;
case 'G':
output.push_back('C');
break;
case 'T':
output.push_back('A');
break;
case '-':
output.push_back('-');
break;
default:
Rcpp::stop("Tried to reverse complement sequence with non ATGC-");
}
}
return output;
}
inline void Parser::getCodeTagAttributes( const std::string &text, std::string &data )
{
auto find_iter = std::find( text.cbegin(), text.cend(), ']' );
if( find_iter != text.cend() && find_iter != text.crend().base() ) {
data = std::string( text.cbegin(), find_iter + 1 );
}
}
bool is_palindrome(std::string word){
if(word.size() % 2) return false;
boost::algorithm::to_lower(word);
std::string reversedWord{word.crbegin(), word.crend()};
return word == reversedWord;
}
/// <summary>
/// Reverses the given std::string.
/// </summary>
/// <param name="original_str">The given std::string</param>
/// <returns>A reverse std::string of the original std::string</returns>
std::string StringFunctions::reverse(const std::string &original_str)
{
std::string working_str = "";
for (std::string::const_reverse_iterator itr = original_str.crbegin(); itr != original_str.crend(); itr++)
{
working_str += *itr;
}
return working_str;
}
string_view_t match(const string_view_t & numview) const {
string_view_t empty_result {numview.str, numview.pos_end, numview.pos_end};
if ( (is_terminal_rule() && !numview.right_aligned())
|| (is_start_rule() && !numview.leftt_aligned()) )
return empty_result;
auto inumber = numview.crbegin();
for (auto ipattern = pattern.crbegin(); ipattern != pattern.crend(); ++ipattern) {
if (::isspace(*ipattern) || *ipattern == '.' || *ipattern == '$') continue;
if (inumber == numview.crend() || (*ipattern == '#' && *inumber == '?')) return empty_result;
if (*ipattern == '#') break;
if (*inumber != *ipattern) return empty_result;
++inumber;
}
if (is_start_rule() && inumber != numview.crend()) return empty_result;
return string_view_t{empty_result}.set_begin(inumber);
}
BigInt::BigInt(std::string s)
: sign(Sign::positive)
{
if (s == "") {
BigInt::BigInt();
return;
}
if (s[0] == '-') { // handle the leading '-' sign
sign = Sign::negative;
s.erase(0, 1); // leave only numbers in the string
}
// need to read number is reverse order since that's how they are stored
for (auto it = s.crbegin(); it != s.crend(); ++it) {
if (isdigit(*it))
digits.push_back((*it) - '0');
}
}
std::string insert_finjector::inject(const std::string& chunk) {
std::string output;
auto out_it = std::back_inserter(output);
auto first = chunk.cbegin();
auto end = chunk.cend();
if (skip_ws_) {
// Find the first and last non ws char
first = std::find_if(first, end, isgraph);
end = std::find_if(chunk.crbegin(), chunk.crend(), isgraph).base();
// Still need to copy all the leading ws to the output
std::copy(chunk.cbegin(), first, out_it);
}
if (position_ & position::begining) {
for (size_t i = 0; i < n_; ++i)
std::copy(insert_.cbegin(), insert_.cend(), out_it);
}
if (position_ & position::middle) {
auto mid = first + (end - first) / 2;
std::copy(first, mid, out_it);
for (size_t i = 0; i < n_; ++i)
std::copy(insert_.cbegin(), insert_.cend(), out_it);
std::copy(mid, end, out_it);
}
else
std::copy(first, end, out_it);
if (position_ & position::end) {
for (size_t i = 0; i < n_; ++i)
std::copy(insert_.cbegin(), insert_.cend(), out_it);
}
// In case there was some ws we skipped at the end, add them last
std::copy(end, chunk.cend(), out_it);
return output;
}
void Number::fromString(const std::string &input)
{
m_decimals = 0;
m_digits.clear();
m_negative = false;
int numbersAdded = 0;
for (auto it = input.crbegin(); it != input.crend(); it++) {
if (*it == '-' || *it == '+') {
if (numbersAdded == 0)
throw Exception("Invalid number: Sign before any digit read");
m_negative = (*it == '-');
break;
}
if (*it == '.' || *it == ',') {
if (m_decimals != 0)
throw Exception("Invalid number: Multiple decimal seperators found");
m_decimals = numbersAdded;
continue;
}
if (*it < '0' || *it > '9')
throw Exception("Invalid number: Unknown character found");
m_digits.push_back(*it - '0');
++numbersAdded;
}
m_trailingZeros = normalize();
m_precision = m_decimals > 9 ? m_decimals : 10;
}
explicit BigNumber(std::string const& num)
{
for(auto c = num.crbegin(); c != num.crend(); ++c)
if(std::isdigit(*c)) push_front(*c - 48);
}
CNum::Counter::Counter(const std::string &s) : value() {
if (s.size() == 0) {
setZero();
return;
}
// Parse the correct base
auto rBegin = s.crbegin();
auto rEnd = s.crend();
Unit base = 10;
if (s.size() >= 2 && s[0] == '0') {
if (s[1] == 'x') {
base = 16;
rEnd -= 2;
} else if (s[1] == 'b') {
base = 2;
rEnd -= 2;
}
}
// rBegin and rEnd is set
if (base == 16) {
// 1 character in hex occupied 4 bits
Index shift = 0;
Unit unit = 0;
for (auto itr = rBegin; itr != rEnd; itr++) {
Unit c = *itr;
if ('0' <= c && c <= '9') {
c -= '0';
} else if ('a' <= c && c <= 'f') {
c = c - 'a' + 10;
} else if ('A' <= c && c <= 'F') {
c = c - 'A' + 10;
} else {
throw;
}
unit |= (c << shift);
shift = (shift + HEX_CHAR_SIZE) % UNIT_BIT_SIZE;
if (shift == 0) {
value.push_back(unit);
unit = 0;
}
}
value.push_back(unit);
} else if (base == 10) {
// Naive algorithm that make use of multiplication and addition
*this = 0;
Counter exp = 1;
for (auto itr = rBegin; itr != rEnd; itr++, exp *= base) {
Unit c = *itr;
if ('0' <= c && c <= '9') {
c -= '0';
} else {
throw;
}
*this += (c * exp);
}
} else {
throw;
}
normalize();
assert(isNormalized());
}
std::string reverse_complement(const std::string& sequence) {
auto rev = std::string{};
rev.reserve(sequence.length());
std::transform(sequence.crbegin(), sequence.crend(), std::back_inserter(rev), complement_base);
return rev;
}
bool oppositeOrder(std::string input)
{
return std::is_sorted(input.crbegin(), input.crend());
}
bool EndsWith(const std::string& strData, const std::string& strSearch, bool bIgnoreCase /* = false */)
{
return StartsWithOrEndsWith(strData.crbegin(), strData.crend(), strSearch.crbegin(), strSearch.crend(), bIgnoreCase);
}
TEST(JsArgumentHelpersTest, args) {
const bool aBool = true;
const int64_t anInt = 17;
const double aDouble = 3.14;
const string aString = "word";
const dynamic anArray = dynamic::array("a", "b", "c");
const dynamic anObject = dynamic::object("k1", "v1")("k2", "v2");
const string aNumericString = to<string>(anInt);
folly::dynamic args = dynamic::array(aBool, anInt, aDouble, aString, anArray, anObject, aNumericString);
ABI22_0_0EXPECT_EQ(jsArgAsBool(args, 0), aBool);
ABI22_0_0EXPECT_EQ(jsArgAsInt(args, 1), anInt);
ABI22_0_0EXPECT_EQ(jsArgAsDouble(args, 2), aDouble);
ABI22_0_0EXPECT_EQ(jsArgAsString(args, 3), aString);
ABI22_0_0EXPECT_EQ(jsArgAsArray(args, 4), anArray);
ABI22_0_0EXPECT_EQ(jsArgAsObject(args, 5), anObject);
// const args
const folly::dynamic& cargs = args;
const folly::dynamic& a4 = jsArgAsArray(cargs, 4);
ABI22_0_0EXPECT_EQ(a4, anArray);
ABI22_0_0EXPECT_EQ(jsArgAsObject(cargs, 5), anObject);
// helpers returning dynamic should return same object without copying
ABI22_0_0EXPECT_EQ(&jsArgAsArray(args, 4), &(args[4]));
ABI22_0_0EXPECT_EQ(&jsArgAsArray(cargs, 4), &(args[4]));
// dynamics returned for mutable args should be mutable. The test is that
// this compiles.
jsArgAsArray(args, 4)[2] = "d";
jsArgAsArray(args, 4)[2] = "c";
// These fail to compile due to constness.
// jsArgAsArray(cargs, 4)[2] = "d";
// jsArgAsArray(cargs, 4)[2] = "c";
// ref-qualified member function tests
ABI22_0_0EXPECT_EQ(jsArgN(args, 3, &folly::dynamic::getString), aString);
ABI22_0_0EXPECT_EQ(jsArg(args[3], &folly::dynamic::getString), aString);
// conversions
ABI22_0_0EXPECT_EQ(jsArgAsDouble(args, 1), anInt * 1.0);
ABI22_0_0EXPECT_EQ(jsArgAsString(args, 1), aNumericString);
ABI22_0_0EXPECT_EQ(jsArgAsInt(args, 6), anInt);
// Test exception messages.
// out_of_range
ABI22_0_0EXPECT_JSAE(jsArgAsBool(args, 7),
"JavaScript provided 7 arguments for C++ method which references at least "
"8 arguments: out of range in dynamic array");
// Conv range_error (invalid value conversion)
const std::string exhead = "Could not convert argument 3 to required type: ";
const std::string extail = ": Invalid leading character: \"word\"";
try {
jsArgAsInt(args, 3);
FAIL() << "Expected JsArgumentException(" << exhead << "..." << extail << ") not thrown";
} catch (const JsArgumentException& ex) {
const std::string exwhat = ex.what();
ABI22_0_0EXPECT_GT(exwhat.size(), exhead.size());
ABI22_0_0EXPECT_GT(exwhat.size(), extail.size());
ABI22_0_0EXPECT_TRUE(std::equal(exhead.cbegin(), exhead.cend(), exwhat.cbegin()))
<< "JsArgumentException('" << exwhat << "') does not begin with '" << exhead << "'";
ABI22_0_0EXPECT_TRUE(std::equal(extail.crbegin(), extail.crend(), exwhat.crbegin()))
<< "JsArgumentException('" << exwhat << "') does not end with '" << extail << "'";
}
// inconvertible types
ABI22_0_0EXPECT_JSAE(jsArgAsArray(args, 2),
"Argument 3 of type double is not required type Array");
ABI22_0_0EXPECT_JSAE(jsArgAsInt(args, 4),
"Error converting javascript arg 4 to C++: "
"TypeError: expected dynamic type `int/double/bool/string', but had type `array'");
// type predicate failure
ABI22_0_0EXPECT_JSAE(jsArgAsObject(args, 4),
"Argument 5 of type array is not required type Object");
}