void CProfileInfo::SetProfileInfo()
{
CProfileIterator* it = CProfileManager::Get_Iterator();
float fTotal = 0.0f;
while( !it->Is_Done() )
{
fTotal += it->Get_Current_Total_Time();
it->Next();
}
it->First();
Clear();
m_vecstrProfileInfo.push_back( "Root" );
char szTab[64], szTemp[4096];
while( !it->Is_Done() )
{
memset( szTab, 0, sizeof(szTab) );
for( DWORD i=0; i<it->GetPreOrderDepth(); i++ )
strcat( szTab, PROFILE_TAB_STR );
sprintf( szTemp, "%s---> %.2f%% %s, <%.3f ms>, <%d calls>, <%f ms/call>", szTab, (it->Get_Current_Total_Time() / fTotal) * 100,
it->Get_Current_Name(), it->Get_Current_Total_Time() * 1000, it->Get_Current_Total_Calls(),
(it->Get_Current_Total_Time() * 1000) / (it->Get_Current_Total_Calls() ? it->Get_Current_Total_Calls() : 1));
m_vecstrProfileInfo.push_back( szTemp );
it->NextPreOrder();
}
CProfileManager::Release_Iterator( it );
Reset();
if( fTotal * 1000 > SEC( 1 ) ) // 1초이상 지연되면 로그 남김
FileOut( "..\\profile.txt" );
}
int TemplateCommand :: Execute( ALib::CommandLine & cmd ) {
GetSkipOptions( cmd );
ReadTemplate( cmd );
if ( cmd.HasFlag( FLAG_FNAMES ) ) {
mFileTemplate = cmd.GetValue( FLAG_FNAMES );
}
IOManager io( cmd );
CSVRow row;
while( io.ReadCSV( row ) ) {
if ( Skip( row ) ) {
continue;
}
if ( mFileTemplate.empty() ) {
io.Out() << ReplaceColumns( mTemplate, row );
}
else {
FileOut( row );
}
}
return 0;
}
void TDimension::WriteDimensionFile(TString FileName)
{
std::ofstream FileOut(FileName);
if(!FileOut.is_open())
{
std::cout<<"Error opening "<<FileName<<std::endl;
}
std::cout<<" Writing parameters to file: "<<FileName<<std::endl;
FileOut<<"Thickness Gem_Radius Gem_Pitch Pitch Gain ElectronADC"<<std::endl;
double Thickness;
Thickness=Z_Drift-Z_Gem;
FileOut << Thickness<<" "<<Gem_Radius<<" "<<Gem_Pitch<<" "<<Pitch<<" "<<Gain<<" "<<ElectronADC<<" "<<Pressure<<std::endl;
FileOut.close();
}
void CMSPeak::CullChargeAndWhich(const CMSSearchSettings& Settings)
{
int iCharges;
for(iCharges = 0; iCharges < GetNumCharges(); iCharges++){
int TempLen(0);
CMZI *Temp = new CMZI [GetPeakLists()[eMSPeakListOriginal]->GetNum()]; // temporary holder
copy(SetPeakLists()[eMSPeakListOriginal]->GetMZI(),
SetPeakLists()[eMSPeakListOriginal]->GetMZI() +
GetPeakLists()[eMSPeakListOriginal]->GetNum(), Temp);
TempLen = GetPeakLists()[eMSPeakListOriginal]->GetNum();
bool ConsiderMultProduct(false);
CullPrecursor(Temp,
TempLen,
CalcPrecursorMass(GetCharges()[iCharges]),
GetCharges()[iCharges],
Settings.GetPrecursorcull() != 0,
Settings.GetChargehandling().GetNegative());
//#define DEBUG_PEAKS1
#ifdef DEBUG_PEAKS1
{
sort(Temp, Temp+TempLen , CMZICompare());
ofstream FileOut("afterprecurse.dta");
xWrite(FileOut, Temp, TempLen);
sort(Temp, Temp+TempLen , CMZICompareIntensity());
}
#endif
if(GetCharges()[iCharges] >= ConsiderMult) ConsiderMultProduct = true;
SmartCull(Settings,
Temp, TempLen, ConsiderMultProduct);
// make the array of culled peaks
EMSPeakListTypes Which = GetWhich(GetCharges()[iCharges]);
SetPeakLists()[Which]->CreateLists(TempLen);
copy(Temp, Temp+TempLen, SetPeakLists()[Which]->GetMZI());
SetPeakLists()[Which]->Sort(eMSPeakListSortIntensity);
SetPeakLists()[Which]->Rank();
SetPeakLists()[Which]->Sort(eMSPeakListSortMZ);
delete [] Temp;
}
}
// recursively culls the peaks
void CMSPeak::SmartCull(const CMSSearchSettings& Settings,
CMZI *Temp,
int& TempLen,
const bool ConsiderMultProduct)
{
int iMZI = 0; // starting point
// prep the data
CullBaseLine(Settings.GetCutlo(), Temp, TempLen);
#ifdef DEBUG_PEAKS1
{
sort(Temp, Temp+TempLen , CMZICompare());
ofstream FileOut("afterbase.dta");
xWrite(FileOut, Temp, TempLen);
sort(Temp, Temp+TempLen , CMZICompareIntensity());
}
#endif
CullIsotope(Temp, TempLen);
#ifdef DEBUG_PEAKS1
{
sort(Temp, Temp+TempLen , CMZICompare());
ofstream FileOut("afteriso.dta");
xWrite(FileOut, Temp, TempLen);
sort(Temp, Temp+TempLen , CMZICompareIntensity());
}
#endif
// h20 and nh3 loss ignored until this cut can be studied
#if 0
sort(Temp, Temp + TempLen, CMZICompareHigh());
CullH20NH3(Temp, TempLen);
sort(Temp, Temp + TempLen, CMZICompareIntensity());
#endif
// now do the recursion
int iTemp(0), jMZI;
set <int> Deleted;
map <int, int> MajorPeak; // maps a peak to it's "major peak"
int HitsAllowed; // the number of hits allowed in a window
int Window; // the m/z range used to limit the number of peaks
int HitCount; // number of nearby peaks
// scan for isotopes, starting at highest peak
for(iMZI = 0; iMZI < TempLen - 1; iMZI++) {
if(Deleted.count(iMZI) != 0) continue;
HitCount = 0;
if(!ConsiderMultProduct ||
Temp[iMZI].GetMZ() >
Precursormz) {
// if charge 1 region, allow fewer peaks
Window = Settings.GetSinglewin(); //27;
HitsAllowed = Settings.GetSinglenum();
}
else {
// otherwise allow a greater number
Window = Settings.GetDoublewin(); //14;
HitsAllowed = Settings.GetDoublenum();
}
// go over smaller peaks
set <int> Considered;
for(jMZI = iMZI + 1; jMZI < TempLen; jMZI++) {
if(Temp[jMZI].GetMZ() < Temp[iMZI].GetMZ() + MSSCALE2INT(Window) + tol &&
Temp[jMZI].GetMZ() > Temp[iMZI].GetMZ() - MSSCALE2INT(Window) - tol &&
Deleted.find(jMZI) == Deleted.end()) {
if(IsMajorPeak(Temp[iMZI].GetMZ(), Temp[jMZI].GetMZ(), tol)) {
// link little peak to big peak
MajorPeak[jMZI] = iMZI;
// ignore for deletion
continue;
}
// if linked to a major peak, skip
if(MajorPeak.find(jMZI) != MajorPeak.end()) {
if(Considered.find(jMZI) != Considered.end())
continue;
Considered.insert(jMZI);
HitCount++;
if(HitCount <= HitsAllowed) continue;
}
// if the first peak, skip
HitCount++;
if(HitCount <= HitsAllowed) continue;
Deleted.insert(jMZI);
}
}
}
// delete the culled peaks
for(iMZI = 0; iMZI < TempLen; iMZI++) {
if(Deleted.count(iMZI) == 0) {
Temp[iTemp] = Temp[iMZI];
iTemp++;
}
}
TempLen = iTemp;
#ifdef DEBUG_PEAKS1
{
sort(Temp, Temp+TempLen , CMZICompare());
ofstream FileOut("aftercull.dta");
xWrite(FileOut, Temp, TempLen);
sort(Temp, Temp+TempLen , CMZICompareIntensity());
}
#endif
}
