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ProFormaWriter.cpp
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ProFormaWriter.cpp
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#include "ProFormaWriter.h" // Include the header for ProFormaWriter class
#include "ProFormaParseException.h" // Include the header for ProFormaParseException class
namespace TopDownProteomics {
namespace ProForma {
std::string ProFormaWriter::WriteString(const ProFormaTerm& term) const {
auto WriteTagOrGroup = [&](const ObjectVariant& obj, std::string& sb, bool displayValue, double weight) {
if (std::holds_alternative<ProFormaTag>(obj)) {
const ProFormaTag& tag = std::get<ProFormaTag>(obj);
if (!tag.Descriptors.empty())
sb += "[" + CreateDescriptorsText(tag.Descriptors) + "]";
} else if (std::holds_alternative<ProFormaTagGroup>(obj)) {
const ProFormaTagGroup& group = std::get<ProFormaTagGroup>(obj);
if (displayValue)
sb += "[" + CreateDescriptorText(group) + "#" + group.Name;
else
sb += "[#" + group.Name;
if (weight > 0.0)
sb += "(" + std::to_string(weight) + ")]";
else
sb += "]";
}
};
std::string sb;
// Check global modifications
if (term.GlobalModifications) {
for (const auto& globalMod : *term.GlobalModifications) {
if (globalMod.TargetAminoAcids)
sb += "<[" + CreateDescriptorsText(globalMod.Descriptors) + "]@" +
StringJoin(*globalMod.TargetAminoAcids, ",") + ">";
else
sb += "<" + CreateDescriptorsText(globalMod.Descriptors) + ">";
}
}
// Check labile modifications
if (term.LabileDescriptors) {
sb += "{" + CreateDescriptorsText(*term.LabileDescriptors) + "}";
}
// Check unlocalized modifications
if (term.UnlocalizedTags && !term.UnlocalizedTags->empty()) {
for (const auto& tag : *term.UnlocalizedTags) {
if (!tag.Descriptors.empty())
sb += "[" + CreateDescriptorsText(tag.Descriptors) + "]";
if (tag.Count != 1)
sb += "^" + std::to_string(tag.Count);
}
// Only write out a single question mark
sb += '?';
}
// Check N-terminal modifications
if (term.NTerminalDescriptors && !term.NTerminalDescriptors->empty()) {
sb += "[" + CreateDescriptorsText(*term.NTerminalDescriptors) + "]-";
}
std::vector<std::tuple<ObjectVariant, int, int, bool, double>> tagsAndGroups;
if (term.Tags) {
for (const auto& tag : *term.Tags) {
tagsAndGroups.emplace_back(tag, tag.ZeroBasedStartIndex, tag.ZeroBasedEndIndex, true, 0.0);
}
}
if (term.TagGroups) {
for (const auto& group : *term.TagGroups) {
for (const auto& member : group.Members) {
tagsAndGroups.emplace_back(group, member.ZeroBasedStartIndex, member.ZeroBasedEndIndex, member == group.Members[group.PreferredLocation], member.Weight);
}
}
}
// Check indexed modifications
if (!tagsAndGroups.empty()) {
// Sort by start index
std::sort(tagsAndGroups.begin(), tagsAndGroups.end(), [](const auto& lhs, const auto& rhs) {
return std::get<1>(lhs) < std::get<1>(rhs);
});
int currentIndex = 0;
for (const auto& [obj, startIndex, endIndex, displayValue, weight] : tagsAndGroups) {
bool hasAmbiguousSequence = std::holds_alternative<ProFormaTag>(obj) && std::get<ProFormaTag>(obj).HasAmbiguousSequence;
if (startIndex == endIndex && !hasAmbiguousSequence) {
// Write sequence up to tag
sb += term.Sequence.substr(currentIndex, startIndex - currentIndex + 1);
currentIndex = startIndex + 1;
} else { // Handle ambiguity range
// Write sequence up to range (checking for internal tags)
sb += term.Sequence.substr(currentIndex, startIndex - currentIndex);
currentIndex = startIndex;
// Start sequence in range
sb += "(";
if (hasAmbiguousSequence)
sb += '?';
// Check for other tags that might be inside this range
int j = 0;
while (j < tagsAndGroups.size() && std::get<1>(tagsAndGroups[j]) <= endIndex) {
const auto& [internalTagObj, internalStartIndex, internalEndIndex, internalDisplayValue, internalWeight] = tagsAndGroups[j];
if (internalStartIndex != internalEndIndex)
throw ProFormaParseException("Can't nest ranges within each other.");
sb += term.Sequence.substr(currentIndex, internalStartIndex - currentIndex + 1);
currentIndex = internalEndIndex + 1;
WriteTagOrGroup(internalTagObj, sb, internalDisplayValue, internalWeight);
j++;
}
sb += term.Sequence.substr(currentIndex, endIndex - currentIndex + 1) + ")";
currentIndex = endIndex + 1;
}
WriteTagOrGroup(obj, sb, displayValue, weight);
}
// Write the rest of the sequence
sb += term.Sequence.substr(currentIndex);
} else {
sb += term.Sequence;
}
// Check C-terminal modifications
if (term.CTerminalDescriptors && !term.CTerminalDescriptors->empty()) {
sb += "-[" + CreateDescriptorsText(*term.CTerminalDescriptors) + "]";
}
return sb;
}
std::string ProFormaWriter::CreateDescriptorsText(const std::vector<ProFormaDescriptor>& descriptors) const {
std::string sb;
for (size_t i = 0; i < descriptors.size(); i++) {
sb += CreateDescriptorText(descriptors[i]);
if (i < descriptors.size() - 1)
sb += '|';
}
return sb;
}
std::string ProFormaWriter::CreateDescriptorText(const IProFormaDescriptor& descriptor) const {
switch (descriptor.Key()) {
case ProFormaKey::Formula:
return "Formula:" + descriptor.Value();
case ProFormaKey::Glycan:
return "Glycan:" + descriptor.Value();
case ProFormaKey::Info:
return "Info:" + descriptor.Value();
case ProFormaKey::Name:
case ProFormaKey::Mass:
switch (descriptor.EvidenceType()) {
case ProFormaEvidenceType::None:
return descriptor.Value(); // We assume the name is enough
case ProFormaEvidenceType::Observed:
return "Obs:" + descriptor.Value();
case ProFormaEvidenceType::Unimod:
return "U:" + descriptor.Value();
case ProFormaEvidenceType::Resid:
return "R:" + descriptor.Value();
case ProFormaEvidenceType::PsiMod:
return "M:" + descriptor.Value();
case ProFormaEvidenceType::XlMod:
return "X:" + descriptor.Value();
case ProFormaEvidenceType::Gno:
return "G:" + descriptor.Value();
case ProFormaEvidenceType::Brno:
return "B:" + descriptor.Value();
default:
throw std::runtime_error("Can't handle " + std::to_string(static_cast<int>(descriptor.Key())) + " with evidence type: " + std::to_string(static_cast<int>(descriptor.EvidenceType())));
}
case ProFormaKey::Identifier:
switch (descriptor.EvidenceType()) {
case ProFormaEvidenceType::Observed:
return "Obs:" + descriptor.Value();
case ProFormaEvidenceType::Unimod:
return descriptor.Value();
default:
return descriptor.Value();
}
default:
return descriptor.Value();
}
}
} // namespace ProForma
} // namespace TopDownProteomics