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libcifpp
Commit f4506438 by Maarten L. Hekkelman
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Added remove column

parent fc14a655
Showing with 179 additions and 114 deletions
include/cif++/category.hpp
......@@ -31,22 +31,22 @@
#include "cif++/condition.hpp"
#include "cif++/iterator.hpp"
#include "cif++/row.hpp"
#include "cif++/validate.hpp"
#include "cif++/text.hpp"
#include "cif++/validate.hpp"
#include <array>
/** \file category.hpp
* Documentation for the cif::category class
*
* The category class should meet the requirements of Container and
* SequenceContainer.
*
* TODO: implement all of:
* https://en.cppreference.com/w/cpp/named_req/Container
* https://en.cppreference.com/w/cpp/named_req/SequenceContainer
* and more?
*/
* Documentation for the cif::category class
*
* The category class should meet the requirements of Container and
* SequenceContainer.
*
* TODO: implement all of:
* https://en.cppreference.com/w/cpp/named_req/Container
* https://en.cppreference.com/w/cpp/named_req/SequenceContainer
* and more?
*/
namespace cif
{
......@@ -61,9 +61,9 @@ namespace cif
class duplicate_key_error : public std::runtime_error
{
public:
/**
* @brief Construct a new duplicate key error object
*/
/**
* @brief Construct a new duplicate key error object
*/
duplicate_key_error(const std::string &msg)
: std::runtime_error(msg)
{
......@@ -75,9 +75,9 @@ class duplicate_key_error : public std::runtime_error
class missing_key_error : public std::runtime_error
{
public:
/**
* @brief Construct a new duplicate key error object
*/
/**
* @brief Construct a new duplicate key error object
*/
missing_key_error(const std::string &msg, const std::string &key)
: std::runtime_error(msg)
, m_key(key)
......@@ -95,9 +95,9 @@ class missing_key_error : public std::runtime_error
class multiple_results_error : public std::runtime_error
{
public:
/**
* @brief Construct a new multiple results error object
*/
/**
* @brief Construct a new multiple results error object
*/
multiple_results_error()
: std::runtime_error("query should have returned exactly one row")
{
......@@ -156,8 +156,8 @@ class category
// --------------------------------------------------------------------
const std::string &name() const { return m_name; } ///< Returns the name of the category
iset key_fields() const; ///< Returns the cif::iset of key field names. Retrieved from the @ref category_validator for this category
std::set<uint16_t> key_field_indices() const; ///< Returns a set of indices for the key fields.
iset key_fields() const; ///< Returns the cif::iset of key field names. Retrieved from the @ref category_validator for this category
std::set<uint16_t> key_field_indices() const; ///< Returns a set of indices for the key fields.
/// @brief Set the validator for this category to @a v
/// @param v The category_validator to assign. A nullptr value is allowed.
......@@ -182,7 +182,7 @@ class category
/// @brief Validate links, that means, values in this category should have an
/// accompanying value in parent categories.
///
///
/// @note
/// The code makes one exception when validating missing links and that's between
/// *atom_site* and a parent *pdbx_poly_seq_scheme* or *entity_poly_seq*.
......@@ -285,7 +285,7 @@ class category
/// Return the theoretical maximum number or rows that can be stored
size_t max_size() const
{
return std::numeric_limits<size_t>::max(); // this is a bit optimistic, I guess
return std::numeric_limits<size_t>::max(); // this is a bit optimistic, I guess
}
/// Return true if the category is empty
......@@ -321,7 +321,7 @@ class category
/// @code{.cpp}
/// for (const auto &[name, value] : cat.rows<std::string,int>("item_name", "item_value"))
/// std::cout << name << ": " << value << '\n';
/// @endcode
/// @endcode
///
/// @tparam Ts The types for the columns requested
/// @param names The names for the columns requested
......@@ -344,7 +344,7 @@ class category
///
/// for (int id : cat.rows<int>("id"))
/// std::cout << id << '\n';
/// @endcode
/// @endcode
///
/// @tparam Ts The types for the columns requested
/// @param names The names for the columns requested
......@@ -363,7 +363,7 @@ class category
/// @code{.cpp}
/// for (row_handle rh : cat.find(cif::key("first_name") == "John" and cif::key("last_name") == "Doe"))
/// .. // do something with rh
/// @endcode
/// @endcode
///
/// @param cond The condition for the query
/// @return A special iterator that loops over all elements that match. The iterator can be dereferenced
......@@ -417,7 +417,7 @@ class category
/// @code{.cpp}
/// for (const auto &[name, value] : cat.find<std::string,int>(cif::key("item_value") > 10, "item_name", "item_value"))
/// std::cout << name << ": " << value << '\n';
/// @endcode
/// @endcode
///
/// @param cond The condition for the query
/// @tparam Ts The types for the columns requested
......@@ -776,8 +776,7 @@ class category
/// @brief Return whether a row exists that matches condition @a cond
/// @param cond The condition to match
/// @return True if a row exists
[[deprecated("Use contains instead")]]
bool exists(condition &&cond) const
[[deprecated("Use contains instead")]] bool exists(condition &&cond) const
{
return contains(std::move(cond));
}
......@@ -875,7 +874,7 @@ class category
// insert_impl(pos, std::move(row));
// }
/// Erase the row pointed to by @a pos and return the iterator to the
/// Erase the row pointed to by @a pos and return the iterator to the
/// row following pos.
iterator erase(iterator pos);
......@@ -941,7 +940,6 @@ class category
/// result is unique in the context of this category
std::string get_unique_id(std::function<std::string(int)> generator = cif::cif_id_for_number);
/// @brief Generate a new, unique ID based on a string prefix followed by a number
/// @param prefix The string prefix
/// @return a new unique ID
......@@ -1038,6 +1036,11 @@ class category
return result;
}
/** @brief Remove column name @a colum_name
* @param column_name The column to be removed
*/
void remove_column(std::string_view column_name);
/// @brief Return whether a column with name @a name exists in this category
/// @param name The name of the column
/// @return True if the column exists
......@@ -1082,11 +1085,10 @@ class category
void write(std::ostream &os, const std::vector<uint16_t> &order, bool includeEmptyColumns) const;
public:
/// friend function to make it possible to do:
/// @code {.cpp}
/// std::cout << my_category;
/// @endcode
/// @endcode
friend std::ostream &operator<<(std::ostream &os, const category &cat)
{
cat.write(os);
......
src/datablock.cpp
......@@ -374,6 +374,10 @@ void datablock::write(std::ostream &os, const std::vector<std::string> &tag_orde
bool datablock::operator==(const datablock &rhs) const
{
// shortcut
if (this == &rhs)
return true;
auto &dbA = *this;
auto &dbB = rhs;
......
src/pdb/reconstruct.cpp
......@@ -117,8 +117,8 @@ void fixNegativeSeqID(category &atom_site)
const auto &[auth_seq_id, label_seq_id] = poly_seq.front();
for (auto row : atom_site.find(key("label_asym_id") == asym_id and
key("auth_seq_id") == auth_seq_id and
key("label_seq_id") == label_seq_id))
key("auth_seq_id") == auth_seq_id and
key("label_seq_id") == label_seq_id))
{
row.assign("label_seq_id", ".", false, false);
}
......@@ -236,20 +236,19 @@ void checkAtomRecords(datablock &db)
{ "auth_seq_id", auth_seq_id.value_or(std::to_string(*label_seq_id)) },
{ "auth_comp_id", auth_comp_id.value_or(*label_comp_id) },
{ "auth_atom_id", auth_atom_id.value_or(*label_atom_id) } });
// Rewrite the coordinates and other fields that look better in a fixed format
// Be careful not to nuke invalidly formatted data here
for (auto [tag, prec] : std::vector<std::tuple<std::string_view,std::string::size_type>>{
{ "cartn_x", 3 },
{ "cartn_y", 3 },
{ "cartn_z", 3 },
{ "occupancy", 2 },
{ "b_iso_or_equiv", 2 }
})
for (auto [tag, prec] : std::vector<std::tuple<std::string_view, std::string::size_type>>{
{ "cartn_x", 3 },
{ "cartn_y", 3 },
{ "cartn_z", 3 },
{ "occupancy", 2 },
{ "b_iso_or_equiv", 2 } })
{
if (row[tag].empty())
continue;
float v;
auto s = row.get<std::string>(tag);
if (auto [ptr, ec] = cif::from_chars(s.data(), s.data() + s.length(), v); ec != std::errc())
......@@ -260,8 +259,30 @@ void checkAtomRecords(datablock &db)
char b[12];
if (auto [ptr, ec] = cif::to_chars(b, b + sizeof(b), v, cif::chars_format::fixed, prec); ec == std::errc())
row.assign(tag, {b, static_cast<std::string::size_type>(ptr - b)}, false, false);
row.assign(tag, { b, static_cast<std::string::size_type>(ptr - b) }, false, false);
}
}
}
auto *cv = atom_site.get_cat_validator();
if (cv)
{
// See if there are columns that are no longer known
for (auto tag : atom_site.get_columns())
{
if (cv->get_validator_for_item(tag) != nullptr)
continue;
auto r = atom_site.find_first(key(tag) != null);
if (not r)
{
if (cif::VERBOSE > 0)
std::clog << "Dropping unknown column " << tag << '\n';
atom_site.remove_column(tag);
}
else if (cif::VERBOSE > 0)
std::clog << "Keeping unknown column " << std::quoted(tag) << " in atom_site since it is not empty\n";
}
}
}
......@@ -607,14 +628,14 @@ void comparePolySeqSchemes(datablock &db)
if (i == asym_ids_ndb.end() or *i != asym_id)
asym_ids_ndb.insert(i, asym_id);
}
for (auto asym_id : pdbx_poly_seq_scheme.rows<std::string>("asym_id"))
{
auto i = std::lower_bound(asym_ids_pdbx.begin(), asym_ids_pdbx.end(), asym_id);
if (i == asym_ids_pdbx.end() or *i != asym_id)
asym_ids_pdbx.insert(i, asym_id);
}
// If we have different Asym ID's assume the ndb is invalid.
if (asym_ids_ndb != asym_ids_pdbx)
{
......@@ -632,7 +653,7 @@ void comparePolySeqSchemes(datablock &db)
auto pdbx_range = pdbx_poly_seq_scheme.find(key("asym_id") == asym_id);
for (auto ndb_i = ndb_range.begin(), pdbx_i = pdbx_range.begin();
ndb_i != ndb_range.end() or pdbx_i != pdbx_range.end(); ++ndb_i, ++pdbx_i)
ndb_i != ndb_range.end() or pdbx_i != pdbx_range.end(); ++ndb_i, ++pdbx_i)
{
if (ndb_i == ndb_range.end() or pdbx_i == pdbx_range.end())
{
......@@ -662,6 +683,9 @@ void comparePolySeqSchemes(datablock &db)
}
}
}
if (ndb_poly_seq_scheme.empty())
db.erase(std::remove(db.begin(), db.end(), ndb_poly_seq_scheme), db.end());
}
void reconstruct_pdbx(file &file, std::string_view dictionary)
......
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