AffxByteArray AffxByteArray::reverseComplement()
{
AffxByteArray ba = *this;
AffxString strComplement = "tvghefcdijmlknopqysaabwxrz";
char by = 0;
int iCount = getSize();
int iIndex = 0;
ba.toLowerCase();
if (((iCount / 2) * 2) != iCount)
{
iIndex = (iCount / 2);
ba.setAt(iIndex, strComplement.getAt(ba.getAt(iIndex) - 'a'));
}
for (int i = 0; (i < (iCount / 2)); i++)
{
iIndex = (iCount - i - 1);
by = ba.getAt(i);
ba.setAt(i, strComplement.getAt(ba.getAt(iIndex) - 'a'));
ba.setAt(iIndex, strComplement.getAt(by - 'a'));
}
return ba;
}
bool AffxByteArray::equals(const AffxString &str) const
{
bool bEqual = false;
int iThisSize = getSize();
int iThatSize = (int)str.length();
if (iThisSize == iThatSize)
{
if ((iThisSize == 0) && (iThatSize == 0)) {bEqual = true;}
else
{
for (int i = 0; (i < iThisSize); i++)
{
if (getAt(i) == str.getAt(i))
bEqual = true;
else
{
bEqual = false;
break;
}
}
}
}
return bEqual;
}
AffxString CNReporter::prepareAscii(const AffxString& str, int iLength)
{
AffxString strPrepared = str;
int iActualLength = (int)strPrepared.length();
strPrepared.padBlanks(iLength);
strPrepared.setAt(iActualLength, 0);
return strPrepared;
}
void CNReporter::loadBuffer(char* pBuffer, int& iIndex, AffxString& str, int iLength)
{
if (iLength == -1) {
iLength = str.length();
}
unsigned int ui = htonl(iLength);
memcpy((void*)(pBuffer + iIndex), (void*)&ui, sizeof(unsigned int));
iIndex += sizeof(unsigned int);
memcpy((void*)(pBuffer + iIndex), str.c_str(), iLength); iIndex += iLength;
}
int AffxByteArray::append(const AffxString& srcIn)
{
AffxString src = srcIn;
int nOldSize = m_nSize;
setSize(m_nSize + (int)src.length());
memcpy(m_pData + nOldSize, src.c_str(), src.length() * sizeof(char));
return nOldSize;
}
void CNReporter::loadParam(const AffxString& strName, PgOpt::PgOptType type, const AffxString& strValue, affymetrix_calvin_parameter::ParameterNameValueType& param)
{
param.SetName(StringUtils::ConvertMBSToWCS(strName));
switch (type) {
case PgOpt::BOOL_OPT: param.SetValueInt8(((strValue == "true") ? (char)1 : (char)0)); break;
case PgOpt::DOUBLE_OPT: param.SetValueFloat((float)::getDouble(strValue)); break;
case PgOpt::INT_OPT: param.SetValueInt32(::getInt(strValue)); break;
case PgOpt::STRING_OPT:
if ((strName.indexOf("command-line") != -1) || (strName.indexOf("analysis") != -1) || (strName.indexOf("program-cvs-id") != -1) || (strName.indexOf("version-to-report") != -1) || (strName.endsWith("-dir"))) {
param.SetValueText(StringUtils::ConvertMBSToWCS(strValue));
} else {
param.SetValueText(StringUtils::ConvertMBSToWCS(Fs::basename(strValue)));
}
break;
default: throw(Except("Cannot find PgOpt type for: " + strName));
}
}
/**
* @brief Return the array name
* @return AffxString - The array name
*/
AffxString CNReporter::getArrayName()
{
AffxString strArrayName;
if (m_pEngine->getOpt("array-name") == "") {
if ((m_pEngine->isOptDefined("cdf-file")) && (m_pEngine->getOpt("cdf-file") != "")) {
strArrayName = Fs::basename(m_pEngine->getOpt("cdf-file"));
int iFindIndex = strArrayName.indexOf(".");
if (iFindIndex != -1) {
strArrayName = strArrayName.substring(0, iFindIndex);
}
} else if ((m_pEngine->isOptDefined("spf-file")) && (m_pEngine->getOpt("spf-file") != "")) {
strArrayName = Fs::basename(m_pEngine->getOpt("spf-file"));
int iFindIndex = strArrayName.indexOf(".");
if (iFindIndex != -1) {
strArrayName = strArrayName.substring(0, iFindIndex);
}
} else {
if (m_pEngine->isOptDefined("annotation-file")) {
strArrayName = Fs::basename(m_pEngine->getOpt("annotation-file"));
int iFindIndex = strArrayName.indexOf(".");
if (iFindIndex != -1) {
strArrayName = strArrayName.substring(0, iFindIndex);
}
}
}
} else {
strArrayName = m_pEngine->getOpt("array-name");
}
return strArrayName;
}
int AffxByteArray::compareTo(const AffxString & that) const
{
int iResult = 0;
int iLength = __minimum(this->m_nSize, (int)that.length());
bool bEqual = true;
for (int iIndex = 0; (iIndex < iLength); iIndex++)
{
if (this->m_pData[iIndex] != that.charAt(iIndex))
{
bEqual = false;
iResult = (this->m_pData[iIndex] - that.charAt(iIndex));
break;
}
}
if (bEqual) {iResult = (this->m_nSize - (int)that.length());}
return iResult;
}
bool AffxByteArray::startsWith(const AffxString& strCompare)
{
bool bStartsWith = false;
int iCompareLength = strCompare.getLength();
if (getSize() >= iCompareLength)
{
bStartsWith = true;
for (int iIndex = 0; (iIndex < iCompareLength); iIndex++)
{
if (getAt(iIndex) != strCompare.getAt(iIndex))
{
bStartsWith = false;
break;
}
}
}
return bStartsWith;
}
bool AffxBinaryFile::open(const AffxString& strFileName, m_enumOpenOptions enumOpenOption)
{
std::fstream fstrm;
switch (enumOpenOption)
{
case LOAD:
fstrm.open(strFileName.c_str(), std::fstream::in | std::fstream::binary);
if (fstrm.is_open()) {fstrm.close();} else {return false;}
m_pistrm = new std::ifstream(strFileName.c_str(), std::ios::in | std::ios::binary);
if (m_pistrm == NULL) {return false;}
break;
case SAVE:
m_postrm = new std::ofstream(strFileName.c_str(), std::ios::out | std::ios::binary);
if (m_postrm == NULL) {return false;}
break;
case APPEND:
m_postrm = new std::ofstream(strFileName.c_str(), std::ios::out | std::ios::binary | std::ios::app);
if (m_postrm == NULL) {return false;}
break;
default:
return false;
}
return true;
}
bool AffxByteArray::equalsIgnoreCase(const AffxString &str)
{
bool bEqual = false;
int iThisSize = getSize();
int iThatSize = (int)str.length();
if (iThisSize == iThatSize)
{
for (int i = 0; (i < iThisSize); i++)
{
if (getAt(i) >= 'A' && getAt(i) <= 'Z')
{
if ((getAt(i) == str.getAt(i)) || (getAt(i) + ' ' == str.getAt(i)))
bEqual = true;
else
{
bEqual = false;
break;
}
}
else if (getAt(i) >= 'a' && getAt(i) <= 'z')
{
if ((getAt(i) == str.getAt(i)) || (getAt(i) - ' ' == str.getAt(i)))
bEqual = true;
else
{
bEqual = false;
break;
}
}
else if (getAt(i) == str.getAt(i))
bEqual = true;
else
{
bEqual = false;
break;
}
}
}
return bEqual;
}