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#ifndef TAKANE_HEIGHT_HPP
#define TAKANE_HEIGHT_HPP
#include <functional>
#include <string>
#include <stdexcept>
#include <filesystem>
#include "utils_public.hpp"
#include "atomic_vector.hpp"
#include "string_factor.hpp"
#include "simple_list.hpp"
#include "data_frame.hpp"
#include "data_frame_factor.hpp"
#include "genomic_ranges.hpp"
#include "atomic_vector_list.hpp"
#include "data_frame_list.hpp"
#include "genomic_ranges_list.hpp"
#include "dense_array.hpp"
#include "compressed_sparse_matrix.hpp"
#include "summarized_experiment.hpp"
#include "sequence_string_set.hpp"
#include "bumpy_atomic_array.hpp"
#include "bumpy_data_frame_array.hpp"
#include "vcf_experiment.hpp"
/**
* @file _height.hpp
* @brief Dispatch to functions for the object's height.
*/
namespace takane {
/**
* @cond
*/
namespace internal_height {
inline auto default_registry() {
std::unordered_map<std::string, std::function<size_t(const std::filesystem::path&, const ObjectMetadata& m, Options& os)> > registry;
registry["atomic_vector"] = [](const std::filesystem::path& p, const ObjectMetadata& m, Options& o) -> size_t { return atomic_vector::height(p, m, o); };
registry["string_factor"] = [](const std::filesystem::path& p, const ObjectMetadata& m, Options& o) -> size_t { return string_factor::height(p, m, o); };
registry["simple_list"] = [](const std::filesystem::path& p, const ObjectMetadata& m, Options& o) -> size_t { return simple_list::height(p, m, o); };
registry["data_frame"] = [](const std::filesystem::path& p, const ObjectMetadata& m, Options& o) -> size_t { return data_frame::height(p, m, o); };
registry["data_frame_factor"] = [](const std::filesystem::path& p, const ObjectMetadata& m, Options& o) -> size_t { return data_frame_factor::height(p, m, o); };
registry["genomic_ranges"] = [](const std::filesystem::path& p, const ObjectMetadata& m, Options& o) -> size_t { return genomic_ranges::height(p, m, o); };
registry["atomic_vector_list"] = [](const std::filesystem::path& p, const ObjectMetadata& m, Options& o) -> size_t { return atomic_vector_list::height(p, m, o); };
registry["data_frame_list"] = [](const std::filesystem::path& p, const ObjectMetadata& m, Options& o) -> size_t { return data_frame_list::height(p, m, o); };
registry["genomic_ranges_list"] = [](const std::filesystem::path& p, const ObjectMetadata& m, Options& o) -> size_t { return genomic_ranges_list::height(p, m, o); };
registry["dense_array"] = [](const std::filesystem::path& p, const ObjectMetadata& m, Options& o) -> size_t { return dense_array::height(p, m, o); };
registry["compressed_sparse_matrix"] = [](const std::filesystem::path& p, const ObjectMetadata& m, Options& o) -> size_t { return compressed_sparse_matrix::height(p, m, o); };
// Subclasses of the SE, so we just re-use its methods here.
registry["summarized_experiment"] = [](const std::filesystem::path& p, const ObjectMetadata& m, Options& o) -> size_t { return summarized_experiment::height(p, m, o); };
registry["ranged_summarized_experiment"] = [](const std::filesystem::path& p, const ObjectMetadata& m, Options& o) -> size_t { return summarized_experiment::height(p, m, o); };
registry["single_cell_experiment"] = [](const std::filesystem::path& p, const ObjectMetadata& m, Options& o) -> size_t { return summarized_experiment::height(p, m, o); };
registry["spatial_experiment"] = [](const std::filesystem::path& p, const ObjectMetadata& m, Options& o) -> size_t { return summarized_experiment::height(p, m, o); };
registry["sequence_string_set"] = [](const std::filesystem::path& p, const ObjectMetadata& m, Options& o) -> size_t { return sequence_string_set::height(p, m, o); };
registry["bumpy_atomic_array"] = [](const std::filesystem::path& p, const ObjectMetadata& m, Options& o) -> size_t { return bumpy_atomic_array::height(p, m, o); };
registry["bumpy_data_frame_array"] = [](const std::filesystem::path& p, const ObjectMetadata& m, Options& o) -> size_t { return bumpy_data_frame_array::height(p, m, o); };
registry["vcf_experiment"] = [](const std::filesystem::path& p, const ObjectMetadata& m, Options& o) -> size_t { return vcf_experiment::height(p, m, o); };
registry["delayed_array"] = [](const std::filesystem::path& p, const ObjectMetadata& m, Options& o) -> size_t { return delayed_array::height(p, m, o); };
return registry;
}
}
/**
* @endcond
*/
/**
* Get the height of an object in a subdirectory, based on the supplied object type.
*
* `height()` is used to check the shape of objects stored in vertical containers, e.g., columns of a `data_frame`.
* For vectors or other 1-dimensional objects, the height is usually just the length of the object (for some object-specific definition of "length").
* For higher-dimensional objects, the height is usually the extent of the first dimension.
*
* Applications can supply custom height functions for a given type via `Options::custom_height`.
* If available, the supplied custom function will be used instead of the default.
*
* @param path Path to a directory representing an object.
* @param metadata Metadata for the object, typically determined from its `OBJECT` file.
* @param options Validation options.
*
* @return The object's height.
*/
inline size_t height(const std::filesystem::path& path, const ObjectMetadata& metadata, Options& options) {
auto cIt = options.custom_height.find(metadata.type);
if (cIt != options.custom_height.end()) {
return (cIt->second)(path, metadata, options);
}
static const auto height_registry = internal_height::default_registry();
auto vrIt = height_registry.find(metadata.type);
if (vrIt == height_registry.end()) {
throw std::runtime_error("no registered 'height' function for object type '" + metadata.type + "' at '" + path.string() + "'");
}
return (vrIt->second)(path, metadata, options);
}
/**
* Get the height of an object in a subdirectory, using its `OBJECT` file to automatically determine the type.
*
* @param path Path to a directory containing an object.
* @param options Validation options.
* @return The object's height.
*/
inline size_t height(const std::filesystem::path& path, Options& options) {
return height(path, read_object_metadata(path), options);
}
/**
* Overload of `height()` with default settings.
*
* @param path Path to a directory containing an object.
* @return The object's height.
*/
inline size_t height(const std::filesystem::path& path) {
Options options;
return height(path, options);
}
}
#endif
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