static int stringToParent(const String& argsmode)
{
if(!argsmode.size()) return Object::DISABLE_PARENT;
//normalize
String smode=argsmode.toUpper();
smode.replace(" ","");
//split
std::vector<String> listMode;
smode.split("|",listMode);
//mode out:
int mode=Object::DISABLE_PARENT;
//for each mode
for(auto& astr:listMode)
{
if(astr=="ALL")
return Object::ENABLE_ALL;
else if(astr=="POSITION")
mode|=Object::ENABLE_POSITION;
else if(astr=="ROTATION")
mode|=Object::ENABLE_ROTATION;
else if(astr=="SCALE")
mode|=Object::ENABLE_SCALE;
if(mode==Object::ENABLE_ALL)
return Object::ENABLE_ALL;
}
return mode;
}
bool isExtensionManaged(const YString& file)
{
// Check whether it is a valid jpg file
String extension;
IO::ExtractExtension(extension, file, false, false);
// Only JPG files managed at the moment
return (extension.toUpper() == "JPG");
}
bool SystemFile::saveFile(LPCSTR fileName,INT pid)
{
String name = SQLSTRING(fileName);
String sql;
SQRes res;
sql.printf("SELECT file_id,file_lname FROM tb_file2 WHERE file_pid=%d and file_name='%s';", pid, name.c_str());
res = m_db->exec(sql);
if (res->getRows())
{
LPCSTR lfile = res->getColumn(1);
if (lfile[0] == 0)
return false;
removeFile(atoi(res->getColumn(0)));
}
LPCSTR data = Method::POST();
INT length = Method::getPostLength();
std::string hash;
MD5::Data(hash, data,length);
String localName;
localName.printf("%s.dat", hash.c_str());
String saveName;
saveName.printf("%s%s", m_dataDir.c_str(), localName.c_str());
FILE* file = fopen(saveName,"wb");
if (file)
{
fwrite(data, length, 1, file);
fclose(file);
}
String type;
String comment;
String date;
LPCSTR d = strrchr(SQLSTRING(fileName), '.');
if (d)
{
type = d + 1;
type.toUpper();
}
Time::getDateTime(date);
sql.printf("INSERT INTO tb_file2 values(null,%d,0,'%s','%s','%s',%d,'%s','%s','');",
pid, name.c_str(), localName.c_str(), type.c_str(), length,
date.c_str(), hash.c_str());
res = m_db->exec(sql);
return !res->isError();
}
bool MrcpRtpHandler::received(Message& msg)
{
String trans = msg.getValue("transport");
trans.toUpper();
bool tls = false;
if (trans == "TCP/TLS/MRCPV2")
tls = true;
else if (trans != "TCP/MRCPV2")
return false;
Debug(&plugin,DebugAll,"RTP message received, TLS: %s",String::boolText(tls));
return true;
}
FileId::Md5Hash FileId::hash(String path)
{
// Ensure we've a normalized path.
if(QDir::isRelativePath(path))
{
path = App_BasePath() / path;
}
#if defined(WIN32) || defined(MACOSX)
// This is a case insensitive operation.
path = path.toUpper();
#endif
return QCryptographicHash::hash(path.toUtf8(), QCryptographicHash::Md5);
}
bool SystemFile::saveFile(const MethodFile* file,INT pid)
{
if(!file || !*file->getName())
return false;
String sql;
SQRes res;
sql.printf("SELECT file_id,file_lname FROM tb_file2 WHERE file_pid=%d and file_name='%s';",pid,file->getName());
res = m_db->exec(sql);
if(res->getRows())
{
LPCSTR lfile = res->getColumn(1);
if(lfile[0] == 0)
return false;
removeFile(atoi(res->getColumn(0)));
}
std::string hash;
MD5::File(hash,file->getFile());
String localName;
localName.printf("%s.dat",hash.c_str());
String saveName;
saveName.printf("%s%s",m_dataDir.c_str(),localName.c_str());
if(!file->save(saveName))
return false;
String name;
String type;
String comment;
String date;
name = SQLSTRING(file->getName());
LPCSTR d = strrchr(SQLSTRING(file->getName()),'.');
if(d)
{
type = d + 1;
type.toUpper();
}
Time::getDateTime(date);
sql.printf("INSERT INTO tb_file2 values(null,%d,0,'%s','%s','%s',%d,'%s','%s','');",
pid,name.c_str(),localName.c_str(),type.c_str(),file->getSize(),
date.c_str(),hash.c_str());
res = m_db->exec(sql);
return !res->isError();
}
bool MolecularFileDialog::canHandle(const String& fileformat) const
{
String formats = getSupportedFileFormats();
vector<String> fields;
formats.split(fields, "*. ");
for (Position p = 0; p < fields.size(); p++)
{
String s = fields[p];
if (s == fileformat) return true;
s.toUpper();
if (s == fileformat) return true;
}
return false;
}
FileTypes::Type FileTypes::nameToType(const String& name)
{
String tmp = name;
tmp.toUpper();
String tmp2;
for (int i = 0; i < FileTypes::SIZE_OF_TYPE; ++i)
{
tmp2 = FileTypes::typeToName((FileTypes::Type)i);
tmp2.toUpper();
if (tmp == tmp2)
{
return (FileTypes::Type)i;
}
}
return FileTypes::UNKNOWN;
}
int RenderContext::stringToBlendContant(String fun, int vlDefault)
{
//normalize
fun.replaceAll(" ","");
fun=fun.toUpper();
//
if(fun=="ONE") return GL_ONE;
if(fun=="ZERO") return GL_ZERO;
//
if(fun=="ONE::MINUS::DST::COLOR") return GL_ONE_MINUS_DST_COLOR;
if(fun=="ONE::MINUS::DST::ALPHA") return GL_ONE_MINUS_DST_ALPHA;
if(fun=="ONE::MINUS::SRC::COLOR") return GL_ONE_MINUS_SRC_COLOR;
if(fun=="ONE::MINUS::SRC::ALPHA") return GL_ONE_MINUS_SRC_ALPHA;
//
if(fun=="DST::COLOR") return GL_DST_COLOR;
if(fun=="DST::ALPHA") return GL_DST_ALPHA;
//
if(fun=="SRC::COLOR") return GL_SRC_COLOR;
if(fun=="SRC::ALPHA") return GL_SRC_ALPHA;
if(fun=="SRC::ALPHA::SATURATE") return GL_SRC_ALPHA_SATURATE;
return vlDefault;
}
bool Search::setParameter(String param, int value) {
#if defined(CLOP) || defined(DEBUG_MODE)
param.toUpper();
bool res = true;
if (param == "FUTIL_MARGIN") {
FUTIL_MARGIN = value;
} else if (param == "EXT_FUTILY_MARGIN") {
EXT_FUTILY_MARGIN = value;
} else if (param == "RAZOR_MARGIN") {
RAZOR_MARGIN = value;
} else if (param == "ATTACK_KING") {
ATTACK_KING = value;
} else if (param == "BACKWARD_PAWN") {
BACKWARD_PAWN = value;
} else if (param == "BISHOP_ON_QUEEN") {
BISHOP_ON_QUEEN = value;
} else if (param == "BONUS2BISHOP") {
BONUS2BISHOP = value;
} else if (param == "CONNECTED_ROOKS") {
CONNECTED_ROOKS = value;
} else if (param == "DOUBLED_ISOLATED_PAWNS") {
DOUBLED_ISOLATED_PAWNS = value;
} else if (param == "DOUBLED_PAWNS") {
DOUBLED_PAWNS = value;
} else if (param == "END_OPENING") {
END_OPENING = value;
} else if (param == "ENEMY_NEAR_KING") {
ENEMY_NEAR_KING = value;
} else if (param == "FRIEND_NEAR_KING") {
FRIEND_NEAR_KING = value;
} else if (param == "HALF_OPEN_FILE_Q") {
HALF_OPEN_FILE_Q = value;
} else if (param == "OPEN_FILE") {
OPEN_FILE = value;
} else if (param == "OPEN_FILE_Q") {
OPEN_FILE_Q = value;
} else if (param == "PAWN_IN_7TH") {
PAWN_IN_7TH = value;
} else if (param == "PAWN_CENTER") {
PAWN_CENTER = value;
} else if (param == "PAWN_IN_8TH") {
PAWN_IN_8TH = value;
} else if (param == "PAWN_ISOLATED") {
PAWN_ISOLATED = value;
} else if (param == "PAWN_NEAR_KING") {
PAWN_NEAR_KING = value;
} else if (param == "PAWN_BLOCKED") {
PAWN_BLOCKED = value;
} else if (param == "ROOK_7TH_RANK") {
ROOK_7TH_RANK = value;
} else if (param == "ROOK_BLOCKED") {
ROOK_BLOCKED = value;
} else if (param == "ROOK_TRAPPED") {
ROOK_TRAPPED = value;
} else if (param == "UNDEVELOPED_KNIGHT") {
UNDEVELOPED_KNIGHT = value;
} else if (param == "UNDEVELOPED_BISHOP") {
UNDEVELOPED_BISHOP = value;
} else if (param == "VAL_WINDOW") {
VAL_WINDOW = value;
} else if (param == "UNPROTECTED_PAWNS") {
UNPROTECTED_PAWNS = value;
} else {
res = false;
}
return res;
#else
cout << param << " " << value << endl;
return false;
#endif
}
int test(char** argv)
{
verbose = getenv("PEGASUS_TEST_VERBOSE") ? true : false;
String s1 = "Hello World";
String s2 = s1;
String s3(s2);
PEGASUS_TEST_ASSERT(String::equal(s1, s3));
// Test append characters to String
String s4 = "Hello";
s4.append(Char16(0x0000));
s4.append(Char16(0x1234));
s4.append(Char16(0x5678));
s4.append(Char16(0x9cde));
s4.append(Char16(0xffff));
{
#ifdef HAVE_SSTREAM
stringstream os;
#endif
#ifdef HAVE_STRSTREAM
ostrstream os;
#endif
os << s4;
#ifdef HAVE_STRSTREAM
os.put('\0');
#endif
#ifndef PEGASUS_HAS_ICU
const char EXPECTED[] = "Hello\\x0000\\x1234\\x5678\\x9CDE\\xFFFF";
#else
CString cstr = s4.getCString();
const char * EXPECTED = (const char *)cstr;
#endif
#ifdef HAVE_SSTREAM
string os_str = os.str();
const char* tmp = os_str.c_str();
#endif
#ifdef HAVE_STRSTREAM
char *tmp = os.str();
#endif
PEGASUS_TEST_ASSERT(strcmp(EXPECTED, tmp) == 0);
#ifdef PEGASUS_PLATFORM_AIX_RS_IBMCXX
os.freeze(false);
#else
#ifdef HAVE_STRSTREAM
delete tmp;
#endif
#endif
}
{
// Test getCString
const char STR0[] = "one two three four";
String s = STR0;
PEGASUS_TEST_ASSERT(strcmp(s.getCString(), STR0) == 0);
}
{
// Test remove
String s = "abcdefg";
s.remove(3, 3);
PEGASUS_TEST_ASSERT(String::equal(s, "abcg"));
PEGASUS_TEST_ASSERT(s.size() == 4);
s = "abcdefg";
s.remove(3, 4);
PEGASUS_TEST_ASSERT(String::equal(s, "abc"));
PEGASUS_TEST_ASSERT(s.size() == 3);
s = "abcdefg";
s.remove(3);
PEGASUS_TEST_ASSERT(String::equal(s, "abc"));
PEGASUS_TEST_ASSERT(s.size() == 3);
s = "abc";
s.remove(3);
PEGASUS_TEST_ASSERT(String::equal(s, "abc"));
PEGASUS_TEST_ASSERT(s.size() == 3);
s = "abc";
s.remove(0);
PEGASUS_TEST_ASSERT(String::equal(s, ""));
PEGASUS_TEST_ASSERT(s.size() == 0);
s = "abc";
s.remove(0, 1);
PEGASUS_TEST_ASSERT(String::equal(s, "bc"));
PEGASUS_TEST_ASSERT(s.size() == 2);
String t1 = "HELLO";
String t2 = t1;
t2.toLower();
PEGASUS_TEST_ASSERT(String::equal(t1, "HELLO"));
PEGASUS_TEST_ASSERT(String::equal(t2, "hello"));
}
{
// another test of the append method
String t1 = "one";
t1.append(" two");
PEGASUS_TEST_ASSERT(String::equal(t1, "one two"));
t1.append(' ');
t1.append('t');
t1.append('h');
t1.append('r');
t1.append("ee");
PEGASUS_TEST_ASSERT(String::equal(t1,"one two three"));
// used as example in Doc.
String test = "abc";
test.append("def");
PEGASUS_TEST_ASSERT(test == "abcdef");
}
// Test of the different overload operators
{
// Test the == overload operator
String t1 = "one";
String t2 = "one";
PEGASUS_TEST_ASSERT(t1 == "one");
PEGASUS_TEST_ASSERT("one" == t1);
PEGASUS_TEST_ASSERT(t1 == t2);
PEGASUS_TEST_ASSERT(t2 == t1);
PEGASUS_TEST_ASSERT(String("one") == "one");
const char STR0[] = "one two three four";
String s = STR0;
CString tmp = s.getCString();
PEGASUS_TEST_ASSERT(tmp == s);
PEGASUS_TEST_ASSERT(s == tmp);
}
{
// Tests of the + Overload operator
String t1 = "abc";
String t2 = t1 + t1;
PEGASUS_TEST_ASSERT(t2 == "abcabc");
t1 = "abc";
t2 = t1 + "def";
PEGASUS_TEST_ASSERT(t2 == "abcdef");
t1 = "ghi";
PEGASUS_TEST_ASSERT(t1 == "ghi");
// ATTN: the following fails because there
// is no single character overload operator
// KS: Apr 2001
// t2 = t1 + 'k' + 'l' + 'm' + "nop";
t2 = t1 + "k" + "l" + "m" + "nop";
PEGASUS_TEST_ASSERT(t2 == "ghiklmnop");
PEGASUS_TEST_ASSERT(String::equal(t2,"ghiklmnop"));
// add tests for != operator.
t1 = "abc";
PEGASUS_TEST_ASSERT(t1 != "ghi");
PEGASUS_TEST_ASSERT(t1 != t2);
// add tests for other compare operators
// Operater <
t1 = "ab";
t2 = "cde";
PEGASUS_TEST_ASSERT(t1 < t2);
PEGASUS_TEST_ASSERT(t1 <= t2);
PEGASUS_TEST_ASSERT(t2 > t1);
PEGASUS_TEST_ASSERT(t2 >=t1);
PEGASUS_TEST_ASSERT(String::compare(t1,t2) < 0);
PEGASUS_TEST_ASSERT(String::compare(t2,t1) > 0);
PEGASUS_TEST_ASSERT(String::compare(t1, t2, 1) < 0);
PEGASUS_TEST_ASSERT(String::compare(t2, t1, 1) > 0);
PEGASUS_TEST_ASSERT(String::compare(t1, t2, 10) < 0);
PEGASUS_TEST_ASSERT(String::compare(t2, t1, 10) > 0);
PEGASUS_TEST_ASSERT(String::compare(t1, t2, 0) == 0);
t2 = t1;
PEGASUS_TEST_ASSERT(t1 <= t2);
PEGASUS_TEST_ASSERT(t1 >= t2);
PEGASUS_TEST_ASSERT(String::compare(t1, t2) == 0);
PEGASUS_TEST_ASSERT(String::compare(t1, t2, 0) == 0);
PEGASUS_TEST_ASSERT(String::compare(t1, t2, 1) == 0);
PEGASUS_TEST_ASSERT(String::compare(t1, t2, 10) == 0);
// Tests for compare with same length
t1 = "abc";
t2 = "def";
PEGASUS_TEST_ASSERT(t1 < t2);
PEGASUS_TEST_ASSERT(String::compare(t1, t2) < 0);
PEGASUS_TEST_ASSERT(String::compare(t2, t1) > 0);
PEGASUS_TEST_ASSERT(String::compare(t1, t2, 10) < 0);
PEGASUS_TEST_ASSERT(String::compare(t1, t2, 0) == 0);
t1 = "abc";
t2 = "ABC";
PEGASUS_TEST_ASSERT(String::equalNoCase(t1,t2));
PEGASUS_TEST_ASSERT(!String::equal(t1,t2));
PEGASUS_TEST_ASSERT(String::compareNoCase(t1,t2) == 0);
t1.toUpper();
t2.toLower();
PEGASUS_TEST_ASSERT(String::equal(t1, "ABC"));
PEGASUS_TEST_ASSERT(String::equal(t2, "abc"));
t1 = "1000";
t2 = "1001";
PEGASUS_TEST_ASSERT(String::compareNoCase(t1,t2) < 0);
PEGASUS_TEST_ASSERT(String::compare(t1, t2) < 0);
PEGASUS_TEST_ASSERT(String::compare(t1, t2, 3) == 0);
PEGASUS_TEST_ASSERT(String::compare(t1, t2, 4) < 0);
#ifdef PEGASUS_HAS_ICU
//
// Strings used to test non-ascii case mappings
// Tests context sensitve mappings (eg. greek)
// Tests expansion after mapping (eg german)
//
// Lower case german and greek
// --latin small letter sharp s (german) (2 of these to cause
// ICU overflow error inside of String)
// --greek small letter sigma (followed by another letter)
// --latin small a
// --greek small letter sigma (NOT followed by another letter)
const Char16 lowermap[] = {
0xdf,
0xdf,
0x3c3,
'a',
0x3c2,
0x00};
String degkLow(lowermap);
// Needed because the german char does not round trip
// after an uppercase followed by lower case.
// --latin small letters 's' 's' (4 of these due to expansion)
// --greek small letter sigma (followed by another letter)
// --latin small a
// --greek small letter sigma (NOT followed by another letter)
const Char16 lowermap2[] = {
's', 's', 's', 's',
0x3c3,
'a',
0x3c2,
0x00};
String degkLow2(lowermap2);
// Upper case greek and german
// latin cap letter sharp s (german) (4 of these due to expansion)
// greek cap letter sigma (followed by another letter)
// latin cap A
// greek cap letter sigma (NOT followed by another letter)
const Char16 uppermap[] = {
'S', 'S', 'S', 'S',
0x3a3,
'A',
0x3a3,
0x00};
String degkUp(uppermap);
PEGASUS_TEST_ASSERT(String::compareNoCase(degkLow,degkUp) == 0);
// does a binary compare, so lower > upper
PEGASUS_TEST_ASSERT(String::compare(degkLow,degkUp) > 0);
PEGASUS_TEST_ASSERT(String::equalNoCase(degkLow,degkUp));
String mapTest(degkLow);
mapTest.toUpper();
PEGASUS_TEST_ASSERT(String::equal(mapTest, degkUp));
// Note that the German char does not round trip
mapTest.toLower();
PEGASUS_TEST_ASSERT(String::equal(mapTest, degkLow2));
#endif
}
{
// Test of the [] operator
String t1 = "abc";
Char16 c = t1[1];
// note c is Char16
PEGASUS_TEST_ASSERT(c == 'b');
//ATTN: test for outofbounds exception
try
{
c = t1[200];
}
catch (IndexOutOfBoundsException&)
{
PEGASUS_TEST_ASSERT(true);
}
}
{
// Test the find function
String t1 = "abcdef";
String t2 = "cde";
String t3 = "xyz";
String t4 = "abc";
String t5 = "abd";
String t6 = "defg";
PEGASUS_TEST_ASSERT(t1.find('c') == 2);
PEGASUS_TEST_ASSERT(t1.find(t2)==2);
PEGASUS_TEST_ASSERT(t1.find(t3)==PEG_NOT_FOUND);
PEGASUS_TEST_ASSERT(t1.find(t4)==0);
PEGASUS_TEST_ASSERT(t1.find(t5)==PEG_NOT_FOUND);
PEGASUS_TEST_ASSERT(t1.find(t6)==PEG_NOT_FOUND);
PEGASUS_TEST_ASSERT(t1.find("cde")==2);
PEGASUS_TEST_ASSERT(t1.find("def")==3);
PEGASUS_TEST_ASSERT(t1.find("xyz")==PEG_NOT_FOUND);
PEGASUS_TEST_ASSERT(t1.find("a") ==0);
// test for the case where string
// partly occurs and then later
// completely occurs
String s = "this is an apple";
PEGASUS_TEST_ASSERT(s.find("apple")==11);
PEGASUS_TEST_ASSERT(s.find("appld")==PEG_NOT_FOUND);
PEGASUS_TEST_ASSERT(s.find("this")==0);
PEGASUS_TEST_ASSERT(s.find("t")==0);
PEGASUS_TEST_ASSERT(s.find("e")==15);
s = "a";
PEGASUS_TEST_ASSERT(s.find("b")==PEG_NOT_FOUND);
PEGASUS_TEST_ASSERT(s.find("a")==0);
PEGASUS_TEST_ASSERT(s.find(s)==0);
s = "aaaapple";
PEGASUS_TEST_ASSERT(s.find("apple")==3);
// 20020715-RK This method was removed from the String class
//{
// String nameSpace = "a#b#c";
// nameSpace.translate('#', '/');
// PEGASUS_TEST_ASSERT(nameSpace == "a/b/c");
//}
}
{
//
// Test String unicode enablement
//
char utf8chr[] = {
'\xCE', '\x99', '\xCE', '\xBF', '\xCF', '\x8D',
'\xCE', '\xBD', '\xCE', '\xB9', '\xCE', '\xBA',
'\xCE', '\xBF', '\xCE', '\xBD', '\xCF', '\x84',
'\0'
}; // utf8 string with mutliple byte characters
Char16 utf16chr[] = {
0x0399,0x03BF,0x03CD,0x03BD,0x03B9,
0x03BA,0x03BF,0x03BD,0x03C4,0x00
}; // utf16 representation of the utf8 string
String utf16string(utf16chr);
String utf8string(utf8chr);
String utf16merge(utf8string.getChar16Data());
CString temp = utf8string.getCString();
CString temp2 = utf16string.getCString();
PEGASUS_TEST_ASSERT(utf16string == utf8string);
PEGASUS_TEST_ASSERT(utf16string == utf16merge);
PEGASUS_TEST_ASSERT(utf16string == utf16chr);
PEGASUS_TEST_ASSERT(utf8string == utf16chr);
PEGASUS_TEST_ASSERT(memcmp(utf8string.getChar16Data(),
utf16string.getChar16Data(),sizeof(utf16chr)) == 0);
PEGASUS_TEST_ASSERT(strcmp(utf8string.getCString(),utf8chr) == 0);
PEGASUS_TEST_ASSERT(strcmp(utf16string.getCString(),utf8chr) == 0);
PEGASUS_TEST_ASSERT(strcmp(temp,utf8chr) == 0);
PEGASUS_TEST_ASSERT(strcmp(temp2,utf8chr) == 0);
Uint32 count = 0;
Uint32 size = sizeof(utf8chr);
while(count<size)
{
PEGASUS_TEST_ASSERT(isUTF8(&utf8chr[count]) == true);
UTF8_NEXT(utf8chr,count);
}
// utf8 string with mutliple byte characters
char utf8bad[] =
{
'\xFF','\xFF', '\xFF', '\0', '\0', '\0'
};
count = 0;
size = 3;
while(count<size)
{
PEGASUS_TEST_ASSERT(isUTF8(&utf8bad[count]) == false);
UTF8_NEXT(utf8bad,count);
}
Char16 utf16Chars[] =
{
0x6A19, 0x6E96, 0x842C, 0x570B, 0x78BC,
0x042E, 0x043D, 0x0438, 0x043A, 0x043E, 0x0434,
0x110B, 0x1172, 0x1102, 0x1165, 0x110F, 0x1169, 0x11AE,
0x10E3, 0x10DC, 0x10D8, 0x10D9, 0x10DD, 0x10D3, 0x10D8,
0xdbc0, 0xdc01,
0x05D9, 0x05D5, 0x05E0, 0x05D9, 0x05E7, 0x05D0, 0x05B8, 0x05D3,
0x064A, 0x0648, 0x0646, 0x0650, 0x0643, 0x0648, 0x062F,
0x092F, 0x0942, 0x0928, 0x093F, 0x0915, 0x094B, 0x0921,
0x016A, 0x006E, 0x012D, 0x0063, 0x014D, 0x0064, 0x0065, 0x033D,
0x00E0, 0x248B, 0x0061, 0x2173, 0x0062, 0x1EA6, 0xFF21, 0x00AA,
0x0325, 0x2173, 0x249C, 0x0063,
0x02C8, 0x006A, 0x0075, 0x006E, 0x026A, 0x02CC, 0x006B, 0x006F,
0x02D0, 0x0064,
0x30E6, 0x30CB, 0x30B3, 0x30FC, 0x30C9,
0xFF95, 0xFF86, 0xFF7A, 0xFF70, 0xFF84, 0xFF9E,
0xC720, 0xB2C8, 0xCF5B, 0x7D71, 0x4E00, 0x78BC,
0xdbc0, 0xdc01,
0x00};
String ugly(utf16Chars);
PEGASUS_TEST_ASSERT(ugly == utf16Chars);
//
// Test passing bad utf-8 into String
//
// A utf-8 sequence with a byte zeroed out in a bad spot
char utf8bad1[] = {
'\xCE', '\x99', '\xCE', '\xBF', '\xCF', '\x8D',
'\xCE', '\xBD', '\xCE', '\0', '\xCE', '\xBA',
'\xCE', '\xBF', '\xCE', '\xBD', '\xCF', '\x84',
'\0'
}; // utf8 string with mutliple byte characters
// Test String(char *)
try
{
// the first terminator causes invalid utf-8
String tmp(utf8bad1);
PEGASUS_TEST_ASSERT(false);
}
catch (Exception &)
{
// expect an error
}
// Test String(char *, Uint32)
try
{
// bogus utf-8 char in the middle
String tmp(utf8bad1, sizeof(utf8bad1)-1);
PEGASUS_TEST_ASSERT(false);
}
catch (Exception &)
{
// expect an error
}
// Test String(char *, Uint32)
try
{
// good, but the last utf-8 char extends past the last byte
String tmp(utf8chr, sizeof(utf8chr) - 2);
PEGASUS_TEST_ASSERT(false);
}
catch (Exception &)
{
// expect an error
}
// Test String::assign(char *)
String assigntest(utf8chr); // good so far
try
{
// the first terminator causes invalid utf-8
assigntest.assign(utf8bad1); // bad
PEGASUS_TEST_ASSERT(false);
}
catch (Exception &)
{
// expect an error
}
// Test String::assign(char *, Uint32)
try
{
// bogus utf-8 char in the middle
assigntest.assign(utf8bad1, sizeof(utf8bad1) - 1); // bad
PEGASUS_TEST_ASSERT(false);
}
catch (Exception &)
{
// expect an error
}
// Test String::assign(char *, Uint32)
try
{
// good, but the last utf-8 char extends past the end
assigntest.assign(utf8chr, sizeof(utf8chr) - 2); // bad
PEGASUS_TEST_ASSERT(false);
}
catch (Exception &)
{
// expect an error
}
//
// Test passing in good utf-8 with an embedded terminator
//
// A utf-8 sequence with a byte zeroed out in an ok spot
char utf8good1[] = {
'\xCE', '\x99', '\xCE', '\xBF', '\xCF', '\x8D',
'\xCE', '\xBD', 'A', '\0', '\xCE', '\xBA',
'\xCE', '\xBF', '\xCE', '\xBD', '\xCF', '\x84',
'\0'
}; // utf8 string with mutliple byte characters
// Test String(char *)
try
{
// terminator after 5 chars
String tmp(utf8good1);
PEGASUS_TEST_ASSERT (tmp.size() == 5);
}
catch (Exception &)
{
// didn't see that one coming
PEGASUS_TEST_ASSERT(false);
}
// Test String(char *, Uint32)
try
{
// embedded terminator counts as 1 char
String tmp(utf8good1, sizeof(utf8good1) - 1);
PEGASUS_TEST_ASSERT (tmp.size() == 10);
}
catch (Exception &)
{
// didn't see that one coming
PEGASUS_TEST_ASSERT(false);
}
assigntest.clear();
// Test String::assign(char *)
try
{
// terminator after 5 chars
assigntest.assign(utf8good1);
PEGASUS_TEST_ASSERT (assigntest.size() == 5);
}
catch (Exception &)
{
// didn't see that one coming
PEGASUS_TEST_ASSERT(false);
}
assigntest.clear();
// Test String::assign(char *, Uint32)
try
{
// embedded terminator counts as 1 char
assigntest.assign(utf8good1, sizeof(utf8good1) - 1);
PEGASUS_TEST_ASSERT (assigntest.size() == 10);
}
catch (Exception &)
{
// didn't see that one coming
PEGASUS_TEST_ASSERT(false);
}
//
// Casing tests
//
String little("the quick brown fox jumped over the lazy dog");
String big("THE QUICK BROWN FOX JUMPED OVER THE LAZY DOG");
String tmpBig = big;
String tmpLittle = little;
tmpBig.toLower();
PEGASUS_TEST_ASSERT(tmpBig == little);
tmpBig.toUpper();
PEGASUS_TEST_ASSERT(tmpBig == big);
}
#if 0
// The match code has been removed from the String class
// Test the string match functions
{
String abc = "abc";
String ABC = "ABC";
PEGASUS_TEST_ASSERT(String::match(abc, "abc"));
PEGASUS_TEST_ASSERT(String::match(ABC, "ABC"));
PEGASUS_TEST_ASSERT(!String::match(abc, "ABC"));
PEGASUS_TEST_ASSERT(!String::match(ABC, "abc"));
PEGASUS_TEST_ASSERT(String::matchNoCase(abc, "abc"));
PEGASUS_TEST_ASSERT(String::matchNoCase(ABC, "abc"));
PEGASUS_TEST_ASSERT(String::matchNoCase(abc, "ABC"));
PEGASUS_TEST_ASSERT(String::matchNoCase(ABC, "ABc"));
PEGASUS_TEST_ASSERT(String::match(abc, "???"));
PEGASUS_TEST_ASSERT(String::match(ABC, "???"));
PEGASUS_TEST_ASSERT(String::match(abc, "*"));
PEGASUS_TEST_ASSERT(String::match(ABC, "*"));
PEGASUS_TEST_ASSERT(String::match(abc, "?bc"));
PEGASUS_TEST_ASSERT(String::match(abc, "?b?"));
PEGASUS_TEST_ASSERT(String::match(abc, "??c"));
PEGASUS_TEST_ASSERT(String::matchNoCase(ABC, "?bc"));
PEGASUS_TEST_ASSERT(String::matchNoCase(ABC, "?b?"));
PEGASUS_TEST_ASSERT(String::matchNoCase(ABC, "??c"));
PEGASUS_TEST_ASSERT(String::match(abc, "*bc"));
PEGASUS_TEST_ASSERT(String::match(abc, "a*c"));
PEGASUS_TEST_ASSERT(String::match(abc, "ab*"));
PEGASUS_TEST_ASSERT(String::match(abc, "a*"));
// ATTN-RK-P3-20020603: This match code is broken
//PEGASUS_TEST_ASSERT(String::match(abc, "[axy]bc"));
PEGASUS_TEST_ASSERT(!String::match(abc, "[xyz]bc"));
PEGASUS_TEST_ASSERT(!String::match(abc, "def"));
PEGASUS_TEST_ASSERT(!String::match(abc, "[de]bc"));
// ATTN-RK-P3-20020603: This match code is broken
//PEGASUS_TEST_ASSERT(String::match(abc, "a[a-c]c"));
PEGASUS_TEST_ASSERT(!String::match(abc, "a[d-x]c"));
// ATTN-RK-P3-20020603: This match code does not yet handle escape chars
//PEGASUS_TEST_ASSERT(String::match("*test", "\\*test"));
PEGASUS_TEST_ASSERT(String::match("abcdef123", "*[0-9]"));
PEGASUS_TEST_ASSERT(String::match("This is a test", "*is*"));
PEGASUS_TEST_ASSERT(String::matchNoCase("This is a test", "*IS*"));
PEGASUS_TEST_ASSERT(String::match("Hello", "Hello"));
PEGASUS_TEST_ASSERT(String::matchNoCase("HELLO", "hello"));
PEGASUS_TEST_ASSERT(String::match("This is a test", "This is *"));
PEGASUS_TEST_ASSERT(String::match("This is a test", "* is a test"));
PEGASUS_TEST_ASSERT(!String::match("Hello", "Goodbye"));
String tPattern =
"When in the * of human*e??nts it be?ome[sS] [0-9] nec*";
try
{
String x(reinterpret_cast<const char *>(0));
cerr <<
"Error: Exception not thrown on NULL passed to"
" constructor(const char *)"
<< endl;
}
catch ( const NullPointer & )
{
// This is the exception that should be thrown.
}
catch ( ... )
{
cerr <<
"Error: Wrong exception thrown on NULL passed to"
" constructor(const char *)"
<< endl;
}
try
{
String x(reinterpret_cast<const Char16 *>(0));
cerr <<
"Error: Exception not thrown on NULL passed to"
" constructor(const Char16 *)"
<< endl;
}
catch ( const NullPointer & )
{
// This is the exception that should be thrown.
}
catch ( ... )
{
cerr <<
"Error: Wrong exception thrown on NULL passed to"
" constructor(const Char16 *)"
<< endl;
}
try
{
String x;
x.assign(reinterpret_cast<const char *>(0));
cerr <<
"Error: Exception not thrown on NULL passed to"
" assign(const char *)"
<< endl;
}
catch ( const NullPointer & )
{
// This is the exception that should be thrown.
}
catch ( ... )
{
cerr <<
"Error: Wrong exception thrown on NULL passed to"
" assign(const char *)"
<< endl;
}
try
{
String x;
x.assign(reinterpret_cast<const Char16 *>(0));
cerr <<
"Error: Exception not thrown on NULL passed to"
" assign(const Char16 *)"
<< endl;
}
catch ( const NullPointer & )
{
// This is the exception that should be thrown.
}
catch ( ... )
{
cerr <<
"Error: Wrong exception thrown on NULL passed to"
" assign(const Char16 *)"
<< endl;
}
try
{
String x;
x.append(reinterpret_cast<const char *>(0));
cerr <<
"Error: Exception not thrown on NULL passed to"
" append(const char *)"
<< endl;
}
catch ( const NullPointer & )
{
// This is the exception that should be thrown.
}
catch ( ... )
{
cerr <<
"Error: Wrong exception thrown on NULL passed to"
" append(const char *)"
<< endl;
}
try
{
String x;
x.append(reinterpret_cast<const Char16 *>(0));
cerr <<
"Error: Exception not thrown on NULL passed to"
" append(const Char16 *)"
<< endl;
}
catch ( const NullPointer & )
{
// This is the exception that should be thrown.
}
catch ( ... )
{
cerr <<
"Error: Wrong exception thrown on NULL passed"
" to append(const Char16 *)"
<< endl;
}
// ATTN-RK-P3-20020603: This match code is broken
//PEGASUS_TEST_ASSERT(String::match(
// "When in the course of human events it becomes 0 necessary",
// tPattern));
//PEGASUS_TEST_ASSERT(String::match(
// "When in the xyz of human events it becomes 9 necessary",
// tPattern));
//PEGASUS_TEST_ASSERT(String::match(
// "When in the of human events it becomes 3 necessary",
// tPattern));
}
#endif
// string()
{
String s;
PEGASUS_TEST_ASSERT(s.size() == 0);
PEGASUS_TEST_ASSERT(s[0] == '\0');
}
// String(const String& s)
{
const String s("hello");
const String t = s;
PEGASUS_TEST_ASSERT(s.size() == strlen("hello"));
PEGASUS_TEST_ASSERT(s == "hello");
PEGASUS_TEST_ASSERT(t.size() == strlen("hello"));
PEGASUS_TEST_ASSERT(t == "hello");
}
// String(const char*)
{
const String s("hello");
PEGASUS_TEST_ASSERT(s.size() == strlen("hello"));
PEGASUS_TEST_ASSERT(s == "hello");
}
// reserve()
{
String s;
s.reserveCapacity(100);
PEGASUS_TEST_ASSERT(s.size() == 0);
// PEGASUS_TEST_ASSERT(s.getCapacity() >= 100);
String t("hello world");
PEGASUS_TEST_ASSERT(t.size() == strlen("hello world"));
t.reserveCapacity(500);
PEGASUS_TEST_ASSERT(t.size() == strlen("hello world"));
PEGASUS_TEST_ASSERT(t == "hello world");
}
// assign(const String&)
{
String s("this is a test");
String t;
t = s;
PEGASUS_TEST_ASSERT(s.size() == strlen("this is a test"));
PEGASUS_TEST_ASSERT(s == "this is a test");
PEGASUS_TEST_ASSERT(t.size() == strlen("this is a test"));
PEGASUS_TEST_ASSERT(t == "this is a test");
s = t;
PEGASUS_TEST_ASSERT(s.size() == strlen("this is a test"));
PEGASUS_TEST_ASSERT(s == "this is a test");
PEGASUS_TEST_ASSERT(t.size() == strlen("this is a test"));
PEGASUS_TEST_ASSERT(t == "this is a test");
}
// assign(const char*, size_t)
{
const char MESSAGE[] = "x";
const size_t LENGTH = sizeof(MESSAGE) - 1;
String s;
s.assign(MESSAGE, LENGTH);
PEGASUS_TEST_ASSERT(s.size() == LENGTH);
PEGASUS_TEST_ASSERT(s == MESSAGE);
String t("dummy", 5);
t.assign(MESSAGE, LENGTH);
PEGASUS_TEST_ASSERT(t.size() == LENGTH);
PEGASUS_TEST_ASSERT(t == MESSAGE);
}
// assign(const char*)
{
const char MESSAGE[] = "x";
const size_t LENGTH = sizeof(MESSAGE) - 1;
String s;
s.assign(MESSAGE);
PEGASUS_TEST_ASSERT(s.size() == LENGTH);
PEGASUS_TEST_ASSERT(s == MESSAGE);
String t("dummy", 5);
t.assign(MESSAGE);
PEGASUS_TEST_ASSERT(t.size() == LENGTH);
PEGASUS_TEST_ASSERT(t == MESSAGE);
}
// append(const String&)
{
String s;
s.append(String("xxx"));
PEGASUS_TEST_ASSERT(s.size() == 3);
PEGASUS_TEST_ASSERT(s == "xxx");
s.append(String("yyy"));
PEGASUS_TEST_ASSERT(s.size() == 6);
PEGASUS_TEST_ASSERT(s == "xxxyyy");
s.append(String("zzz"));
PEGASUS_TEST_ASSERT(s.size() == 9);
PEGASUS_TEST_ASSERT(s == "xxxyyyzzz");
}
// append(const char*)
{
String s;
s.append("xxx");
PEGASUS_TEST_ASSERT(s.size() == 3);
PEGASUS_TEST_ASSERT(s == "xxx");
s.append("yyy");
PEGASUS_TEST_ASSERT(s.size() == 6);
PEGASUS_TEST_ASSERT(s == "xxxyyy");
s.append("zzz");
PEGASUS_TEST_ASSERT(s.size() == 9);
PEGASUS_TEST_ASSERT(s == "xxxyyyzzz");
}
// append(const char*)
{
String s;
s.append("xxx");
PEGASUS_TEST_ASSERT(s.size() == 3);
PEGASUS_TEST_ASSERT(s == "xxx");
s.append("yyy");
PEGASUS_TEST_ASSERT(s.size() == 6);
PEGASUS_TEST_ASSERT(s == "xxxyyy");
s.append("zzz");
PEGASUS_TEST_ASSERT(s.size() == 9);
PEGASUS_TEST_ASSERT(s == "xxxyyyzzz");
}
// append(char)
{
String s;
for (int i = 'a'; i <= 'z'; i++)
{
Char16 c = i;
s.append(c);
}
PEGASUS_TEST_ASSERT(s.size() == 26);
PEGASUS_TEST_ASSERT(s == "abcdefghijklmnopqrstuvwxyz");
}
// clear()
{
String s("abc");
String t = s;
String u = s;
s.clear();
PEGASUS_TEST_ASSERT(t.size() == 3);
PEGASUS_TEST_ASSERT(t == "abc");
PEGASUS_TEST_ASSERT(t[0] == 'a');
PEGASUS_TEST_ASSERT(u.size() == 3);
PEGASUS_TEST_ASSERT(u == "abc");
PEGASUS_TEST_ASSERT(u[0] == 'a');
PEGASUS_TEST_ASSERT(s.size() == 0);
PEGASUS_TEST_ASSERT(s[0] == '\0');
t.clear();
PEGASUS_TEST_ASSERT(t.size() == 0);
PEGASUS_TEST_ASSERT(t[0] == '\0');
PEGASUS_TEST_ASSERT(t == "");
PEGASUS_TEST_ASSERT(u.size() == 3);
PEGASUS_TEST_ASSERT(u == "abc");
PEGASUS_TEST_ASSERT(u[0] == 'a');
PEGASUS_TEST_ASSERT(s.size() == 0);
PEGASUS_TEST_ASSERT(s == "");
PEGASUS_TEST_ASSERT(s[0] == '\0');
u.clear();
PEGASUS_TEST_ASSERT(t.size() == 0);
PEGASUS_TEST_ASSERT(t == "");
PEGASUS_TEST_ASSERT(t[0] == '\0');
PEGASUS_TEST_ASSERT(u.size() == 0);
PEGASUS_TEST_ASSERT(u == "");
PEGASUS_TEST_ASSERT(u[0] == '\0');
PEGASUS_TEST_ASSERT(s.size() == 0);
PEGASUS_TEST_ASSERT(s == "");
PEGASUS_TEST_ASSERT(s[0] == '\0');
}
// c_str()
{
String s("abc");
String t("abc");
String u("def");
String v;
String w("");
PEGASUS_TEST_ASSERT(s == "abc");
PEGASUS_TEST_ASSERT(t == "abc");
PEGASUS_TEST_ASSERT(u == "def");
PEGASUS_TEST_ASSERT(s == t);
PEGASUS_TEST_ASSERT(s != u);
PEGASUS_TEST_ASSERT(v == "");
PEGASUS_TEST_ASSERT(v[0] == '\0');
PEGASUS_TEST_ASSERT(v[0] == '\0');
PEGASUS_TEST_ASSERT(w.size() == 0);
PEGASUS_TEST_ASSERT(w[0] == '\0');
PEGASUS_TEST_ASSERT(w[0] == '\0');
}
// set(size_t, char)
{
String s("abcdefghijklmnopqrstuvwxyz");
for (int i = 0; i < 26; i++)
s[i] = toupper(s[i]);
PEGASUS_TEST_ASSERT(s == "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
}
// equal(const String&)
{
String t("abc");
String u("abc");
String v("def");
String w("defg");
String x("");
String y("");
PEGASUS_TEST_ASSERT(String::equal(t, t));
PEGASUS_TEST_ASSERT(String::equal(u, u));
PEGASUS_TEST_ASSERT(String::equal(v, v));
PEGASUS_TEST_ASSERT(String::equal(w, w));
PEGASUS_TEST_ASSERT(String::equal(x, x));
PEGASUS_TEST_ASSERT(String::equal(y, y));
PEGASUS_TEST_ASSERT(String::equal(t, u));
PEGASUS_TEST_ASSERT(String::equal(u, t));
PEGASUS_TEST_ASSERT(!String::equal(t, v));
PEGASUS_TEST_ASSERT(!String::equal(t, w));
PEGASUS_TEST_ASSERT(!String::equal(t, x));
PEGASUS_TEST_ASSERT(!String::equal(t, y));
PEGASUS_TEST_ASSERT(!String::equal(v, t));
PEGASUS_TEST_ASSERT(!String::equal(w, t));
PEGASUS_TEST_ASSERT(!String::equal(x, t));
PEGASUS_TEST_ASSERT(!String::equal(y, t));
PEGASUS_TEST_ASSERT(!String::equal(v, w));
PEGASUS_TEST_ASSERT(!String::equal(w, v));
PEGASUS_TEST_ASSERT(String::equal(x, y));
PEGASUS_TEST_ASSERT(String::equal(y, x));
}
// equal(const char*)
{
String t("abc");
String u("abc");
String v("def");
String w("defg");
String x("");
String y("");
PEGASUS_TEST_ASSERT(String::equal(t, "abc"));
PEGASUS_TEST_ASSERT(String::equal(u, "abc"));
PEGASUS_TEST_ASSERT(String::equal(v, "def"));
PEGASUS_TEST_ASSERT(String::equal(w, "defg"));
PEGASUS_TEST_ASSERT(String::equal(x, ""));
PEGASUS_TEST_ASSERT(String::equal(y, ""));
PEGASUS_TEST_ASSERT(String::equal(t, "abc"));
PEGASUS_TEST_ASSERT(String::equal(u, "abc"));
PEGASUS_TEST_ASSERT(!String::equal(t, "def"));
PEGASUS_TEST_ASSERT(!String::equal(t, "defg"));
PEGASUS_TEST_ASSERT(!String::equal(t, ""));
PEGASUS_TEST_ASSERT(!String::equal(t, ""));
PEGASUS_TEST_ASSERT(!String::equal(v, "abc"));
PEGASUS_TEST_ASSERT(!String::equal(w, "abc"));
PEGASUS_TEST_ASSERT(!String::equal(x, "abc"));
PEGASUS_TEST_ASSERT(!String::equal(y, "abc"));
PEGASUS_TEST_ASSERT(!String::equal(v, "defg"));
PEGASUS_TEST_ASSERT(!String::equal(w, "def"));
PEGASUS_TEST_ASSERT(String::equal(x, ""));
PEGASUS_TEST_ASSERT(String::equal(y, ""));
}
// equali()
{
String s("abc");
String t("abC");
String u("ABC");
String v("xyz");
String w("");
String x("");
PEGASUS_TEST_ASSERT(String::equalNoCase(s, t));
PEGASUS_TEST_ASSERT(String::equalNoCase(s, u));
PEGASUS_TEST_ASSERT(!String::equalNoCase(s, v));
PEGASUS_TEST_ASSERT(String::equalNoCase(w, x));
PEGASUS_TEST_ASSERT(!String::equalNoCase(w, s));
PEGASUS_TEST_ASSERT(!String::equalNoCase(w, t));
PEGASUS_TEST_ASSERT(!String::equalNoCase(w, v));
}
{
String t;
const char MESSAGE[] = "hello";
const size_t LENGTH = sizeof(MESSAGE) - 1;
String s = String(MESSAGE);
t = s;
String u = String(t);
PEGASUS_TEST_ASSERT(t.size() == LENGTH);
PEGASUS_TEST_ASSERT(t == MESSAGE);
PEGASUS_TEST_ASSERT(s.size() == LENGTH);
PEGASUS_TEST_ASSERT(s == MESSAGE);
PEGASUS_TEST_ASSERT(u.size() == LENGTH);
PEGASUS_TEST_ASSERT(u == MESSAGE);
PEGASUS_TEST_ASSERT(t[0] == 'h');
PEGASUS_TEST_ASSERT(t[1] == 'e');
PEGASUS_TEST_ASSERT(t[2] == 'l');
PEGASUS_TEST_ASSERT(t[3] == 'l');
PEGASUS_TEST_ASSERT(t[4] == 'o');
PEGASUS_TEST_ASSERT(t[5] == '\0');
t.append(" world");
PEGASUS_TEST_ASSERT(t.size() == strlen("hello world"));
PEGASUS_TEST_ASSERT(t == "hello world");
PEGASUS_TEST_ASSERT(s != "hello world");
PEGASUS_TEST_ASSERT(s == "hello");
PEGASUS_TEST_ASSERT(s.size() == strlen("hello"));
t[0] = 'x';
PEGASUS_TEST_ASSERT(t == "xello world");
}
// remove()
{
String s("abcXYZdefLMNOP");
s.remove(0,0);
PEGASUS_TEST_ASSERT(s.size() == 14);
PEGASUS_TEST_ASSERT(s == "abcXYZdefLMNOP");
s.remove(0, 3);
PEGASUS_TEST_ASSERT(s.size() == 11);
PEGASUS_TEST_ASSERT(s == "XYZdefLMNOP");
s.remove(3, 3);
PEGASUS_TEST_ASSERT(s.size() == 8);
PEGASUS_TEST_ASSERT(s == "XYZLMNOP");
s.remove(7, 1);
PEGASUS_TEST_ASSERT(s.size() == 7);
PEGASUS_TEST_ASSERT(s == "XYZLMNO");
s.remove(0, 1);
PEGASUS_TEST_ASSERT(s.size() == 6);
PEGASUS_TEST_ASSERT(s == "YZLMNO");
s.remove(2, PEG_NOT_FOUND);
PEGASUS_TEST_ASSERT(s.size() == 2);
PEGASUS_TEST_ASSERT(s == "YZ");
s.remove(2, 0);
PEGASUS_TEST_ASSERT(s.size() == 2);
PEGASUS_TEST_ASSERT(s == "YZ");
s.remove(1, 1);
PEGASUS_TEST_ASSERT(s.size() == 1);
PEGASUS_TEST_ASSERT(s == "Y");
s.remove(0, 1);
PEGASUS_TEST_ASSERT(s.size() == 0);
PEGASUS_TEST_ASSERT(s == "");
PEGASUS_TEST_ASSERT(s[0] == '\0');
s.remove(0,0);
PEGASUS_TEST_ASSERT(s.size() == 0);
PEGASUS_TEST_ASSERT(s == "");
PEGASUS_TEST_ASSERT(s[0] == '\0');
}
// subString()
{
String s("one two three");
PEGASUS_TEST_ASSERT(s.subString(0) == "one two three");
PEGASUS_TEST_ASSERT(s.subString(0, 3) == "one");
PEGASUS_TEST_ASSERT(s.subString(4, 3) == "two");
PEGASUS_TEST_ASSERT(s.subString(8, 5) == "three");
PEGASUS_TEST_ASSERT(s.subString(0, 0) == "");
PEGASUS_TEST_ASSERT(s.subString(13, 0) == "");
}
// Overflow
bool caught_bad_alloc = false;
try
{
String s("junk", Uint32(0xFFFFFFFF));
}
catch(...)
{
caught_bad_alloc = true;
}
PEGASUS_TEST_ASSERT(caught_bad_alloc);
// Added to test funtionality of String(const String& str, Uint32 n)
// for memory overflow.
Boolean caughtBadAlloc = false;
try
{
String s("abc", 0xFFFF0000); //to check for alloc
}
catch(const PEGASUS_STD(bad_alloc)&)
{
caughtBadAlloc = true;
}
// Added to test funtionality of
// void reserveCapacity(Uint32 capacity) for memory overflow.
caughtBadAlloc = false;
try
{
String s;
s.reserveCapacity(0xFFFF0000); //to check for _reserve
}
catch (const PEGASUS_STD(bad_alloc)&)
{
caughtBadAlloc = true;
}
PEGASUS_TEST_ASSERT(caughtBadAlloc);
// Added to test funtionality of
// String& append(const char* str, Uint32 size) for memory overflow.
caughtBadAlloc = false;
try
{
String s;
s.append("xxx", 0xFFFF0000); //to check for _reserve
}
catch (const PEGASUS_STD(bad_alloc)&)
{
caughtBadAlloc = true;
}
PEGASUS_TEST_ASSERT(caughtBadAlloc);
// Added to test funtionality of
// String& append(const Char16* str, Uint32 n) for memory overflow.
caughtBadAlloc = false;
try
{
String s;
s.append((Char16 *)"xxx", 0xFFFF0000); //to check for _reserve
}
catch (const PEGASUS_STD(bad_alloc)&)
{
caughtBadAlloc = true;
}
PEGASUS_TEST_ASSERT(caughtBadAlloc);
// Added to test funtionality of
// String& assign(const char* str, Uint32 n) for memory overflow.
caughtBadAlloc = false;
try
{
String s;
s.assign("xxx", 0xFFFF0000); //to check for alloc
}
catch (const PEGASUS_STD(bad_alloc)&)
{
caughtBadAlloc = true;
}
PEGASUS_TEST_ASSERT(caughtBadAlloc);
// Added to test funtionality of
// String& assign(const Char16* str, Uint32 n) for memory overflow.
caughtBadAlloc = false;
try
{
String s;
s.assign((Char16 *)"xxx", 0xFFFF0000); //to check for alloc
}
catch (const PEGASUS_STD(bad_alloc)&)
{
caughtBadAlloc = true;
}
PEGASUS_TEST_ASSERT(caughtBadAlloc);
// Tests for the dump of a bad strings.
// 40 good chars, bad char, 10 trailing chars.
// Testing the full range of printed data.
caughtBadAlloc = false;
try
{
String s1("1234567890123456789012345678901234567890""\xFF""1234567890");
}
catch ( Exception& ex )
{
caughtBadAlloc = true;
PEGASUS_TEST_ASSERT(
strstr((const char*)ex.getMessage().getCString(),
": 1234567890123456789012345678901234567890"
" 0xFF 0x31 0x32 0x33 0x34 0x35 0x36 0x37 0x38 0x39 0x30")
!= 0);
}
PEGASUS_TEST_ASSERT(caughtBadAlloc);
// 7 good chars, bad char, 7 trailing chars.
// Testing reduced number of chars arround the bad char.
caughtBadAlloc = false;
try
{
String s1("0123456""\xAA""0123456");
}
catch ( Exception& ex )
{
caughtBadAlloc = true;
PEGASUS_TEST_ASSERT(
strstr((const char*)ex.getMessage().getCString(),
": 0123456 0xAA 0x30 0x31 0x32 0x33 0x34 0x35 0x36")
!= 0);
}
PEGASUS_TEST_ASSERT(caughtBadAlloc);
// No good chars, bad char , 20 trailing chars
// Testing no good chars, bad char at beginning,
// more trailing chars available then printed.
caughtBadAlloc = false;
try
{
String s1("\xDD""0123456789012345679");
}
catch ( Exception& ex )
{
caughtBadAlloc = true;
PEGASUS_TEST_ASSERT(
strstr((const char*)ex.getMessage().getCString(),
": 0xDD 0x30 0x31 0x32 0x33 0x34 0x35 0x36 0x37 0x38 0x39")
!= 0);
}
PEGASUS_TEST_ASSERT(caughtBadAlloc);
// 50 good chars ( more the printed ), bad char as last char,
// no trailing chars.
caughtBadAlloc = false;
try
{
String s1("AAAAAAAAAA0123456789012345678901234567890123456789""\xBB");
}
catch ( Exception& ex )
{
caughtBadAlloc = true;
PEGASUS_TEST_ASSERT(
strstr((const char*)ex.getMessage().getCString(),
": 0123456789012345678901234567890123456789 0xBB")
!= 0);
}
PEGASUS_TEST_ASSERT(caughtBadAlloc);
// no good chars, bad char as the only char, no trailing chars.
caughtBadAlloc = false;
try
{
String s1("\x80");
}
catch ( Exception& ex )
{
caughtBadAlloc = true;
PEGASUS_TEST_ASSERT(
strstr((const char*)ex.getMessage().getCString(),": 0x80") != 0);
}
PEGASUS_TEST_ASSERT(caughtBadAlloc);
cout << argv[0] << " +++++ passed all tests" << endl;
char* p = (char*)operator new(88888);
operator delete(p);
return 0;
}
String PepNovoInfile::handlePTMs_(const String& modification, const bool variable)
{
String locations, key, type;
ResidueModification::TermSpecificity ts = ModificationsDB::getInstance()->getModification(modification).getTermSpecificity();
String origin = ModificationsDB::getInstance()->getModification(modification).getOrigin();
double mass = ModificationsDB::getInstance()->getModification(modification).getDiffMonoMass();
String full_name = ModificationsDB::getInstance()->getModification(modification).getFullName();
String full_id = ModificationsDB::getInstance()->getModification(modification).getFullId();
if (variable)
{
type = "OPTIONAL";
}
else
{
type = "FIXED";
}
switch (ts)
{
case ResidueModification::C_TERM: locations = "C_TERM";
break;
case ResidueModification::N_TERM: locations = "N_TERM";
break;
case ResidueModification::ANYWHERE: locations = "ALL";
break;
default: throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Invalid term specificity", String(ts));
}
if (ts == ResidueModification::C_TERM)
{
key = "$";
}
else if (ts == ResidueModification::N_TERM)
{
key = "^";
}
//cout<<"origin: "<<origin<<" loc: "<<locations<<endl;
if ((ts == ResidueModification::C_TERM) && (origin == "X"))
{
origin = "C_TERM";
}
else if ((ts == ResidueModification::N_TERM) && (origin == "X"))
{
origin = "N_TERM";
}
else
{
key = origin;
}
if (mass >= 0)
{
key += "+" + String(Math::round(mass));
}
else
{
key += String(Math::round(mass));
}
String line = "";
line += origin.toUpper();
line += "\t";
line += mass;
line += "\t";
line += type;
line += "\t";
line += locations;
line += "\t";
line += key;
line += "\t";
line += full_name;
mods_and_keys_[key] = full_id;
return line;
}
ExitCodes main_(int, const char**)
{
//-------------------------------------------------------------
// parsing parameters
//-------------------------------------------------------------
String inputfile_name = getStringOption_("in");
String outputfile_name = getStringOption_("out");
Param fit_algorithm = getParam_().copy("fit_algorithm:", true);
fit_algorithm.setValue("out_plot", getStringOption_("out_plot")); // re-assemble full param (was moved to top-level)
bool split_charge = getFlag_("split_charge");
bool top_hits_only = getFlag_("top_hits_only");
double fdr_for_targets_smaller = getDoubleOption_("fdr_for_targets_smaller");
bool target_decoy_available = false;
bool ignore_bad_data = getFlag_("ignore_bad_data");
bool prob_correct = getFlag_("prob_correct");
// Set fixed e-value threshold
smallest_e_value_ = numeric_limits<double>::denorm_min();
//-------------------------------------------------------------
// reading input
//-------------------------------------------------------------
IdXMLFile file;
vector<ProteinIdentification> protein_ids;
vector<PeptideIdentification> peptide_ids;
file.load(inputfile_name, protein_ids, peptide_ids);
vector<double> scores;
vector<double> decoy;
vector<double> target;
set<Int> charges;
PosteriorErrorProbabilityModel PEP_model;
PEP_model.setParameters(fit_algorithm);
StringList search_engines = ListUtils::create<String>("XTandem,OMSSA,MASCOT,SpectraST,MyriMatch,SimTandem,MSGFPlus,MS-GF+,Comet");
//-------------------------------------------------------------
// calculations
//-------------------------------------------------------------
if (split_charge)
{
for (vector<PeptideIdentification>::iterator pep_it = peptide_ids.begin(); pep_it != peptide_ids.end(); ++pep_it)
{
vector<PeptideHit>& hits = pep_it->getHits();
for (std::vector<PeptideHit>::iterator hit_it = hits.begin(); hit_it != hits.end(); ++hit_it)
{
charges.insert(hit_it->getCharge());
}
}
if (charges.empty())
{
throw Exception::ElementNotFound(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "no charges found!");
}
}
for (vector<PeptideIdentification>::iterator pep_it = peptide_ids.begin(); pep_it != peptide_ids.end(); ++pep_it)
{
if (!pep_it->getHits().empty())
{
target_decoy_available = ((pep_it->getScoreType() == "q-value") && pep_it->getHits()[0].metaValueExists("target_decoy"));
break;
}
}
set<Int>::iterator charge_it = charges.begin(); // charges can be empty, no problem if split_charge is not set
if (split_charge && charges.empty())
{
throw Exception::Precondition(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "'split_charge' is set, but the list of charge states is empty");
}
map<String, vector<vector<double> > > all_scores;
char splitter = ','; // to split the engine from the charge state later on
do
{
for (StringList::iterator engine_it = search_engines.begin(); engine_it != search_engines.end(); ++engine_it)
{
for (vector<ProteinIdentification>::iterator prot_it = protein_ids.begin(); prot_it != protein_ids.end(); ++prot_it)
{
String searchengine = prot_it->getSearchEngine();
if ((*engine_it == searchengine) || (*engine_it == searchengine.toUpper()))
{
for (vector<PeptideIdentification>::iterator pep_it = peptide_ids.begin(); pep_it != peptide_ids.end(); ++pep_it)
{
if (prot_it->getIdentifier() == pep_it->getIdentifier())
{
vector<PeptideHit>& hits = pep_it->getHits();
if (top_hits_only)
{
pep_it->sort();
if (!hits.empty() && (!split_charge || hits[0].getCharge() == *charge_it))
{
double score = getScore_(*engine_it, hits[0]);
if (!boost::math::isnan(score)) // issue #740: ignore scores with 0 values, otherwise you will get the error "unable to fit data"
{
scores.push_back(score);
if (target_decoy_available)
{
if (hits[0].getScore() < fdr_for_targets_smaller)
{
target.push_back(score);
}
else
{
decoy.push_back(score);
}
}
}
}
}
else
{
for (std::vector<PeptideHit>::iterator hit_it = hits.begin(); hit_it != hits.end(); ++hit_it)
{
if (!split_charge || (hit_it->getCharge() == *charge_it))
{
double score = getScore_(*engine_it, *hit_it);
if (!boost::math::isnan(score)) // issue #740: ignore scores with 0 values, otherwise you will get the error "unable to fit data"
{
scores.push_back(score);
}
}
}
}
}
}
}
}
if (scores.size() > 2)
{
vector<vector<double> > tmp;
tmp.push_back(scores);
tmp.push_back(target);
tmp.push_back(decoy);
if (split_charge)
{
String engine_with_charge_state = *engine_it + String(splitter) + String(*charge_it);
all_scores.insert(make_pair(engine_with_charge_state, tmp));
}
else
{
all_scores.insert(make_pair(*engine_it, tmp));
}
}
scores.clear();
target.clear();
decoy.clear();
}
if (split_charge) ++charge_it;
}
while (charge_it != charges.end());
if (all_scores.empty())
{
writeLog_("No data collected. Check whether search engine is supported.");
if (!ignore_bad_data) return INPUT_FILE_EMPTY;
}
String out_plot = fit_algorithm.getValue("out_plot").toString().trim();
for (map<String, vector<vector<double> > >::iterator score_it = all_scores.begin(); score_it != all_scores.end(); ++score_it)
{
vector<String> engine_info;
score_it->first.split(splitter, engine_info);
String engine = engine_info[0];
Int charge = -1;
if (engine_info.size() == 2)
{
charge = engine_info[1].toInt();
}
if (split_charge)
{
// only adapt plot output if plot is requested (this badly violates the output rules and needs to change!)
// one way to fix this: plot charges into a single file (no renaming of output file needed) - but this requires major code restructuring
if (!out_plot.empty()) fit_algorithm.setValue("out_plot", out_plot + "_charge_" + String(charge));
PEP_model.setParameters(fit_algorithm);
}
const bool return_value = PEP_model.fit(score_it->second[0]);
if (!return_value) writeLog_("Unable to fit data. Algorithm did not run through for the following search engine: " + engine);
if (!return_value && !ignore_bad_data) return UNEXPECTED_RESULT;
if (return_value)
{
// plot target_decoy
if (!out_plot.empty() && top_hits_only && target_decoy_available && (score_it->second[0].size() > 0))
{
PEP_model.plotTargetDecoyEstimation(score_it->second[1], score_it->second[2]); //target, decoy
}
bool unable_to_fit_data = true;
bool data_might_not_be_well_fit = true;
for (vector<ProteinIdentification>::iterator prot_it = protein_ids.begin(); prot_it != protein_ids.end(); ++prot_it)
{
String searchengine = prot_it->getSearchEngine();
if ((engine == searchengine) || (engine == searchengine.toUpper()))
{
for (vector<PeptideIdentification>::iterator pep_it = peptide_ids.begin(); pep_it != peptide_ids.end(); ++pep_it)
{
if (prot_it->getIdentifier() == pep_it->getIdentifier())
{
String score_type = pep_it->getScoreType() + "_score";
vector<PeptideHit> hits = pep_it->getHits();
for (std::vector<PeptideHit>::iterator hit_it = hits.begin(); hit_it != hits.end(); ++hit_it)
{
if (!split_charge || (hit_it->getCharge() == charge))
{
double score;
hit_it->setMetaValue(score_type, hit_it->getScore());
score = getScore_(engine, *hit_it);
if (boost::math::isnan(score)) // issue #740: ignore scores with 0 values, otherwise you will get the error "unable to fit data"
{
score = 1.0;
}
else
{
score = PEP_model.computeProbability(score);
if ((score > 0.0) && (score < 1.0)) unable_to_fit_data = false; // only if all it->second[0] are 0 or 1 unable_to_fit_data stays true
if ((score > 0.2) && (score < 0.8)) data_might_not_be_well_fit = false; //same as above
}
hit_it->setScore(score);
if (prob_correct)
{
hit_it->setScore(1.0 - score);
}
else
{
hit_it->setScore(score);
}
}
}
pep_it->setHits(hits);
}
if (prob_correct)
{
pep_it->setScoreType("Posterior Probability");
pep_it->setHigherScoreBetter(true);
}
else
{
pep_it->setScoreType("Posterior Error Probability");
pep_it->setHigherScoreBetter(false);
}
}
}
}
if (unable_to_fit_data) writeLog_(String("Unable to fit data for search engine: ") + engine);
if (unable_to_fit_data && !ignore_bad_data) return UNEXPECTED_RESULT;
if (data_might_not_be_well_fit) writeLog_(String("Data might not be well fitted for search engine: ") + engine);
}
}
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
file.store(outputfile_name, protein_ids, peptide_ids);
return EXECUTION_OK;
}
int
main(int argc, char** argv)
{
String a;
a = "Testing...";
cout << a << endl;
cout << "length: " << a.length() << endl;
cout << "capacity: " << a.capacity() << endl;
a = a + "one two three";
cout << a << endl;
cout << "length: " << a.length() << endl;
cout << "capacity: " << a.capacity() << endl;
a = "stuff on the front:" + a;
cout << a << endl;
cout << "length: " << a.length() << endl;
cout << "capacity: " << a.capacity() << endl;
long intval = 0;
if (String("32").parseInt(intval))
cout << "Converting '32' to int: " << intval << endl;
else
cout << "Error converting string to int.\n";
double doubleval = 0.0;
String("3.141592654").parseDouble(doubleval);
cout << "Converting 3.141592654 to double: " << doubleval << endl;
long hexval = 0;
if (String("0x34ab").parseHex(hexval))
cout << "Converting 0x34ab to " << hexval << " (Should be 13483)" << endl;
else
cout << "Hex conversion failed.\n";
String tflag("true");
String fflag("false");
bool boolval;
tflag.parseBool(boolval);
if (boolval)
cout << "This should have been true (and was)" << endl;
else
cout << "tflag was false and should have been true." << endl;
fflag.parseBool(boolval);
if (boolval)
cout << "fflag should have been false and wasn't." << endl;
else
cout << "fflag was false and should have been." << endl;
char c;
a.charAt(3, c);
cout << "\nCharacter at position 3: '" << c << "' \n";
String b("cat");
String d = "cat";
if (b == d)
cout << "Yup, equal.\n";
else
cout << "Nope, not equal.\n";
if (b == "fark")
cout << b << " is less than fark\n";
cout << a.toLower() << endl;
cout << a.toUpper() << endl;
cout << "Substring..." << endl;
String substr_test = "this is a weird string. Much odd.";
cout << substr_test.substring(4, 4) << endl;
cout << "Regular Expressions\n";
String astring = "This is a test.";
if (astring.matches("is a"))
cout << " Matched!\n";
else
cout << " Didn't match.\n";
String csvstuff = "3.1415 2.71828 42 testing";
ArrayList<String> fields = csvstuff.split(" +");
}
ExitCodes main_(int, const char **)
{
//----------------------------------------------------------------
// load data
//----------------------------------------------------------------
String in = getStringOption_("in");
String in_featureXML = getStringOption_("in_featureXML");
String out = getStringOption_("out");
String format = getStringOption_("out_type");
if (format.trim() == "") // get from filename
{
try
{
format = out.suffix('.');
}
catch (Exception::ElementNotFound & /*e*/)
{
format = "nosuffix";
}
StringListUtils::toUpper(out_formats_);
if (!ListUtils::contains(out_formats_, format.toUpper()))
{
LOG_ERROR << "No explicit image output format was provided via 'out_type', and the suffix ('" << format << "') does not resemble a valid type. Please fix one of them." << std::endl;
return ILLEGAL_PARAMETERS;
}
}
MSExperiment<> exp;
MzMLFile f;
f.setLogType(log_type_);
f.load(in, exp);
exp.updateRanges(1);
SignedSize rows = getIntOption_("height");
if (rows == 0)
{
rows = exp.size();
}
if (rows <= 0)
{
writeLog_("Error: Zero rows is not possible.");
return ILLEGAL_PARAMETERS;
}
SignedSize cols = getIntOption_("width");
if (cols == 0)
{
cols = UInt(ceil(exp.getMaxMZ() - exp.getMinMZ()));
}
if (cols <= 0)
{
writeLog_("Error: Zero columns is not possible.");
return ILLEGAL_PARAMETERS;
}
//----------------------------------------------------------------
//Do the actual resampling
BilinearInterpolation<double, double> bilip;
bilip.getData().resize(rows, cols);
if (!getFlag_("transpose"))
{
// scans run bottom-up:
bilip.setMapping_0(0, exp.getMaxRT(), rows - 1, exp.getMinRT());
// peaks run left-right:
bilip.setMapping_1(0, exp.getMinMZ(), cols - 1, exp.getMaxMZ());
for (MSExperiment<>::Iterator spec_iter = exp.begin();
spec_iter != exp.end(); ++spec_iter)
{
if (spec_iter->getMSLevel() != 1) continue;
for (MSExperiment<>::SpectrumType::ConstIterator peak1_iter =
spec_iter->begin(); peak1_iter != spec_iter->end();
++peak1_iter)
{
bilip.addValue(spec_iter->getRT(), peak1_iter->getMZ(),
peak1_iter->getIntensity());
}
}
}
else // transpose
{
// spectra run bottom-up:
bilip.setMapping_0(0, exp.getMaxMZ(), rows - 1, exp.getMinMZ());
// scans run left-right:
bilip.setMapping_1(0, exp.getMinRT(), cols - 1, exp.getMaxRT());
for (MSExperiment<>::Iterator spec_iter = exp.begin();
spec_iter != exp.end(); ++spec_iter)
{
if (spec_iter->getMSLevel() != 1) continue;
for (MSExperiment<>::SpectrumType::ConstIterator peak1_iter =
spec_iter->begin(); peak1_iter != spec_iter->end();
++peak1_iter)
{
bilip.addValue(peak1_iter->getMZ(), spec_iter->getRT(),
peak1_iter->getIntensity());
}
}
}
//----------------------------------------------------------------
//create and store image
int scans = (int) bilip.getData().sizePair().first;
int peaks = (int) bilip.getData().sizePair().second;
MultiGradient gradient;
String gradient_str = getStringOption_("gradient");
if (gradient_str != "")
{
gradient.fromString(String("Linear|") + gradient_str);
}
else
{
gradient.fromString("Linear|0,#FFFFFF;2,#FFFF00;11,#FFAA00;32,#FF0000;55,#AA00FF;78,#5500FF;100,#000000");
}
bool use_log = getFlag_("log_intensity");
writeDebug_("log_intensity: " + String(use_log), 1);
QImage image(peaks, scans, QImage::Format_RGB32);
string s = getStringOption_("background_color");
QColor background_color(s.c_str());
string feature_color_string = getStringOption_("feature_color");
QColor feature_color(feature_color_string.c_str());
QPainter * painter = new QPainter(&image);
painter->setPen(background_color);
painter->fillRect(0, 0, peaks, scans, Qt::SolidPattern);
delete painter;
double factor = getDoubleOption_("max_intensity");
if (factor == 0)
{
factor = (*std::max_element(bilip.getData().begin(), bilip.getData().end()));
}
// logarithmize max. intensity as well:
if (use_log) factor = std::log(factor);
factor /= 100.0;
for (int i = 0; i < scans; ++i)
{
for (int j = 0; j < peaks; ++j)
{
double value = bilip.getData().getValue(i, j);
if (use_log) value = std::log(value);
if (value > 1e-4)
{
image.setPixel(j, i, gradient.interpolatedColorAt(value / factor).rgb());
}
else
{
image.setPixel(j, i, background_color.rgb());
}
}
}
if (getFlag_("precursors"))
{
markMS2Locations_(exp, image, getFlag_("transpose"),
getStringOption_("precursor_color").toQString(),
Size(getIntOption_("precursor_size")));
}
if (!in_featureXML.empty())
{
FeatureMap feature_map;
FeatureXMLFile ff;
ff.load(in_featureXML, feature_map);
markFeatureLocations_(feature_map, exp, image, getFlag_("transpose"), feature_color);
}
if (image.save(out.toQString(), format.c_str())) return EXECUTION_OK;
else return CANNOT_WRITE_OUTPUT_FILE;
}
Protein* PeptideBuilder::construct()
{
if (fragment_db_ == 0)
{
Log.warn() << "PeptideBuilder::construct(): no FragmengDB given!" << std::endl;
return 0;
}
if (sequence_.empty())
{
Log.warn() << "PeptideBuilder::construct(): no amino acid sequence specified." << std::endl;
return 0;
}
int id = 1;
Protein *protein = new Protein(proteinname_);
Chain *chain = new Chain(chainname_);
// create the first residue
Residue* residue = createResidue_(sequence_[0].getType(), id);
chain->insert(*residue);
Residue* residueold = residue;
std::vector<AminoAcidDescriptor>::iterator i = sequence_.begin();
++id;
// consistency check for empty sequences and sequences of length < 2!!
// loop for the remaining residues ;
for (++i; i != sequence_.end(); ++i)
{
// We have to take care of two special cases:
// - the residue we are looking at is proline
// - the last residue was proline
String type = (i-1)->getType();
type.toUpper();
// special case: residue is a proline
type = i->getType();
type.toUpper();
is_proline_ = (type == "PRO") ? true : false;
Residue* residue2 = createResidue_(i->getType(), id);
insert_(*residue2, *residueold);
chain->insert(*residue2);
// set the torsion angle
transform_(i->getPhi(), (i-1)->getPsi(),*residueold, *residue2);
peptide_(*residueold,*residue2);
// set the peptide bond angle omega
setOmega_(*residueold, *residue2, i->getOmega());
residueold=residue2;
++id;
}
protein->insert(*chain);
// read the names for a unique nomenclature
protein->apply(fragment_db_->normalize_names);
// add missing bonds and atoms (including side chains!)
ReconstructFragmentProcessor rfp(*fragment_db_);
protein->apply(rfp);
protein->apply(fragment_db_->build_bonds);
return protein;
}