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#include "MetricField.hpp"
Field::Field(std::string n, FieldType t) {
name = n;
type = t;
}
bool Field::operator==(const Field &another) const {
return (name == another.name &&
type == another.type);
}
FieldsRequirement::FieldsRequirement(const std::string & m) {
metric = m;
if (metric == "QualityValue" || metric == "InsertionQV" ||
metric == "MergeQV" || metric == "DeletionQV" ||
metric == "DeletionTag" || metric == "SubstitutionTag" ||
metric == "SubstitutionQV" || metric == "PreBaseFrames" ||
metric == "PulseIndex" || metric == "Basecall") {
fieldsUseBasFile.push_back(Field (metric , BasField));
} else if (metric == "ClassifierQV") {
fieldsUsePlsFile.push_back(Field (metric , PlsField));
fieldsUsePlsFile.push_back(Field ("NumEvent" , PlsField));
fieldsUsePlsFile.push_back(Field ("PulseIndex" , BasField));
} else if (metric == "StartTimeOffset") {
fieldsUsePlsFile.push_back(Field ("StartFrame" , PlsField));
fieldsUsePlsFile.push_back(Field ("NumEvent" , PlsField));
fieldsUsePlsFile.push_back(Field ("PulseIndex" , BasField));
} else if (metric == "StartFramePulse") {// Compute StartFrame from PulseCalls only
fieldsUsePlsFile.push_back(Field ("StartFrame" , PlsField));
fieldsUsePlsFile.push_back(Field ("NumEvent" , PlsField));
fieldsUsePlsFile.push_back(Field ("PulseIndex" , BasField));
} else if (metric == "StartFrameBase") {// Compute StartFrame from BaseCalls only
fieldsUseBasFile.push_back(Field ("PreBaseFrames", BasField));
fieldsUseBasFile.push_back(Field ("WidthInFrames", BasField));
} else if (metric == "WhenStarted") {
// WhenStarted does not require any field because it only requires an attribute
} else if (metric == "pkmid") {
fieldsUsePlsFile.push_back(Field ("MidSignal" , PlsField));
fieldsUsePlsFile.push_back(Field ("NumEvent" , PlsField));
fieldsUsePlsFile.push_back(Field ("PulseIndex" , BasField));
} else if (metric == "Light") {
fieldsUsePlsFile.push_back(Field ("WidthInFrames", PlsField));
fieldsUsePlsFile.push_back(Field ("MeanSignal" , PlsField));
fieldsUsePlsFile.push_back(Field ("NumEvent" , PlsField));
fieldsUsePlsFile.push_back(Field ("PulseIndex" , BasField));
} else if (metric == "PulseWidth" || metric == "WidthInFrames") {
// Both metrics require a field "WidthInFrames", which can be read from
// either bas.h5 or pls.h5.
fieldsUseBasFile.push_back(Field ("WidthInFrames", BasField));
fieldsUsePlsFile.push_back(Field ("WidthInFrames", PlsField));
fieldsUsePlsFile.push_back(Field ("NumEvent" , PlsField));
fieldsUsePlsFile.push_back(Field ("PulseIndex" , BasField));
} else if (metric == "StartFrame") {
// Compute StartFrame from either PulseCalls or BaseCalls
fieldsUseBasFile.push_back(Field ("PreBaseFrames", BasField));
fieldsUseBasFile.push_back(Field ("WidthInFrames", BasField));
fieldsUsePlsFile.push_back(Field ("StartFrame" , PlsField));
fieldsUsePlsFile.push_back(Field ("NumEvent" , PlsField));
fieldsUsePlsFile.push_back(Field ("PulseIndex" , BasField));
} else if (metric == "IPD") {
// IPD can be obtained from basFile.PreBaseFrames or computed from
// plsFile.WidthInFrames and plsFile.StartFrame. Use the second method if possible
fieldsUseBasFile.push_back(Field ("PreBaseFrames", BasField));
fieldsUsePlsFile.push_back(Field ("StartFrame" , PlsField));
fieldsUsePlsFile.push_back(Field ("WidthInFrames", PlsField));
fieldsUsePlsFile.push_back(Field ("NumEvent" , PlsField));
fieldsUsePlsFile.push_back(Field ("PulseIndex" , BasField));
} else if (metric == "") {
// No metric, no required fields.
} else {
std::cout << "ERROR, metric [" << metric << "] is not supported." << std::endl;
exit(1);
}
}
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