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// Author: Mark Chaisson
// Modified by: Yuan Li
#include <pbdata/reads/RegionTable.hpp>
#include <algorithm>
#include <iostream>
#include <ostream>
RegionTable& RegionTable::Reset()
{
map_.clear();
columnNames.clear();
regionTypes.clear();
regionDescriptions.clear();
regionSources.clear();
regionTypeEnums.clear();
return *this;
}
std::vector<RegionType> RegionTable::RegionTypeEnums(void) const { return regionTypeEnums; }
std::vector<std::string> RegionTable::RegionTypes(void) const { return regionTypes; }
std::vector<std::string> RegionTable::ColumnNames(void) const { return columnNames; }
std::vector<std::string> RegionTable::RegionDescriptions(void) const { return regionDescriptions; }
std::vector<std::string> RegionTable::RegionSources(void) const { return regionSources; }
RegionTable& RegionTable::ConstructTable(std::vector<RegionAnnotation>& table,
const std::vector<std::string>& regionTypeStrs)
{
RegionTypes(regionTypeStrs); //< Set both regionTypes and regionTypeEnums.
// Must sort region annotations by HoleNumber, RegionTypeIndex, Start, End, and Score
std::sort(table.begin(), table.end(), compare_region_annotation_by_type);
// Construct map_<holeNumber, RegionAnnotations>
if (table.size() > 0) {
UInt pre_hn = table[0].GetHoleNumber();
auto itBegin = table.begin();
for (auto it = table.begin(); it != table.end(); it++) {
// Discrepency between data type of Regions/HoleNumber and ZMW/HoleNumber
if (it->GetHoleNumber() > static_cast<int>(pre_hn)) {
map_.insert(std::pair<UInt, RegionAnnotations>(
pre_hn, RegionAnnotations(pre_hn, std::vector<RegionAnnotation>(itBegin, it),
regionTypeEnums)));
pre_hn = it->GetHoleNumber();
itBegin = it;
}
}
map_.insert(std::pair<UInt, RegionAnnotations>(
pre_hn, RegionAnnotations(pre_hn, std::vector<RegionAnnotation>(itBegin, table.end()),
regionTypeEnums)));
}
return *this;
}
std::vector<RegionType> RegionTable::DefaultRegionTypes(void)
{
std::vector<RegionType> ret;
for (std::string regionTypeString : PacBio::AttributeValues::Regions::regiontypes) {
ret.push_back(RegionTypeMap::ToRegionType(regionTypeString));
}
return ret;
}
RegionTable& RegionTable::RegionTypes(const std::vector<std::string>& regionTypeStrs)
{
regionTypes = regionTypeStrs;
for (std::string regionTypeString : regionTypeStrs) {
regionTypeEnums.push_back(RegionTypeMap::ToRegionType(regionTypeString));
}
return *this;
}
RegionTable& RegionTable::ColumnNames(const std::vector<std::string>& in)
{
columnNames = in;
return *this;
}
RegionTable& RegionTable::RegionDescriptions(const std::vector<std::string>& in)
{
regionDescriptions = in;
return *this;
}
RegionTable& RegionTable::RegionSources(const std::vector<std::string>& in)
{
regionSources = in;
return *this;
}
bool RegionTable::HasHoleNumber(const UInt holeNumber) const
{
return (map_.find(holeNumber) != map_.end());
}
RegionAnnotations RegionTable::operator[](const UInt holeNumber) const
{
// Must check whether a zmw exists or not first.
assert(HasHoleNumber(holeNumber) && "Could not find zmw in region table.");
return map_.find(holeNumber)->second;
}
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