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// Author: Mark Chaisson
#include <pbdata/reads/ScanData.hpp>
#include <algorithm>
#include <iostream>
std::string ScanData::BaseMapToStr(const std::map<char, size_t>& baseMap)
{
std::string baseMapStr = " "; //4 dye channels.
for (auto it = baseMap.begin(); it != baseMap.end(); ++it) {
if (it->second < 4) {
baseMapStr[it->second] = it->first;
}
}
std::string tmpBaseMap = baseMapStr;
std::sort(tmpBaseMap.begin(), tmpBaseMap.end());
std::transform(tmpBaseMap.begin(), tmpBaseMap.end(), tmpBaseMap.begin(), ::toupper);
if (tmpBaseMap != "ACGT") {
std::cout << "ERROR, invalid ScanData BaseMap " << baseMapStr << std::endl;
std::exit(EXIT_FAILURE);
}
return baseMapStr;
}
std::map<char, size_t> ScanData::StrToBaseMap(const std::string& baseMapStr)
{
std::map<char, size_t> ret;
for (size_t i = 0; i < baseMapStr.size(); i++) {
ret[baseMapStr[i]] = i;
}
return ret;
}
bool ScanData::IsValidBaseMap(const std::map<char, size_t>& baseMap)
{
const char X = 'x';
std::string v(4, X);
for (const char base : {'A', 'T', 'G', 'C'}) {
size_t index = baseMap.find(base)->second;
if (not(baseMap.find(base) != baseMap.end() and index <= 3))
return false;
else
v[index] = 'o';
}
if (v.find(X) != std::string::npos)
return false;
else
return true;
}
ScanData::ScanData(const AcqParams& acqParams) : acqParams_(acqParams)
{
platformId = NoPlatform;
frameRate = 0.0;
numFrames = 0;
movieName = runCode = whenStarted = "";
baseMap.clear();
}
ScanData& ScanData::SetAcqParams(const AcqParams& acqParams)
{
acqParams_ = acqParams;
return *this;
}
AcqParams ScanData::GetAcqParams(void) const { return acqParams_; }
std::string ScanData::GetMovieName() { return movieName; }
ScanData& ScanData::PlatformID(const PlatformId& id)
{
platformId = id;
return *this;
}
ScanData& ScanData::FrameRate(const float& rate)
{
frameRate = rate;
return *this;
}
ScanData& ScanData::NumFrames(const unsigned int& num)
{
numFrames = num;
return *this;
}
ScanData& ScanData::MovieName(const std::string& name)
{
movieName = name;
return *this;
}
ScanData& ScanData::RunCode(const std::string& code)
{
runCode = code;
return *this;
}
ScanData& ScanData::WhenStarted(const std::string& when)
{
whenStarted = when;
return *this;
}
ScanData& ScanData::BaseMap(const std::map<char, size_t>& bmp)
{
baseMap.clear();
baseMap.insert(bmp.begin(), bmp.end());
return *this;
}
ScanData& ScanData::BaseMap(const std::string& baseMapStr)
{
return this->BaseMap(ScanData::StrToBaseMap(baseMapStr));
}
ScanData& ScanData::SequencingKit(const std::string sequencingKit)
{
sequencingKit_ = sequencingKit;
return *this;
}
ScanData& ScanData::BindingKit(const std::string bindingKit)
{
bindingKit_ = bindingKit;
return *this;
}
PlatformId ScanData::PlatformID(void) const { return platformId; }
float ScanData::FrameRate(void) const { return frameRate; }
unsigned int ScanData::NumFrames(void) const { return numFrames; }
std::string ScanData::MovieName(void) const { return movieName; }
std::string ScanData::RunCode(void) const { return runCode; }
std::string ScanData::WhenStarted(void) const { return whenStarted; }
std::map<char, size_t> ScanData::BaseMap(void) const { return baseMap; }
std::string ScanData::BaseMapStr(void) const { return ScanData::BaseMapToStr(baseMap); }
std::string ScanData::SequencingKit(void) const { return sequencingKit_; }
std::string ScanData::BindingKit(void) const { return bindingKit_; }
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