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libcifpp
Commit b0ac33c1 by Maarten L. Hekkelman
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optimisation in query 

fix memory problem in cif::item, making it safer
parent 82e73a95
Showing with 302 additions and 141 deletions
.gitignore
...@@ -13,5 +13,4 @@ msvc/ ...@@ -13,5 +13,4 @@ msvc/
Testing/ Testing/
rsrc/feature-request.txt rsrc/feature-request.txt
test/test-create_sugar_?.cif test/test-create_sugar_?.cif
test/oprofile_data/abi test/oprofile_data/
test/oprofile_data/samples/operf.log
include/cif++/category.hpp
...@@ -550,6 +550,14 @@ class category ...@@ -550,6 +550,14 @@ class category
return create_item(ix, i.value()); return create_item(ix, i.value());
} }
item_value *create_item(const std::tuple<std::string_view,std::string> &i)
{
const auto &[name, value] = i;
uint16_t ix = add_column(name);
return create_item(ix, value);
}
void delete_item(item_value *iv) void delete_item(item_value *iv)
{ {
if (iv->m_length >= item_value::kBufferSize) if (iv->m_length >= item_value::kBufferSize)
......
include/cif++/condition.hpp
...@@ -30,6 +30,7 @@ ...@@ -30,6 +30,7 @@
#include <functional> #include <functional>
#include <iostream> #include <iostream>
#include <regex> #include <regex>
#include <utility>
#include <cif++/row.hpp> #include <cif++/row.hpp>
...@@ -52,7 +53,7 @@ namespace detail ...@@ -52,7 +53,7 @@ namespace detail
{ {
virtual ~condition_impl() {} virtual ~condition_impl() {}
virtual void prepare(const category &c) {} virtual condition_impl *prepare(const category &c) { return this; }
virtual bool test(row_handle r) const = 0; virtual bool test(row_handle r) const = 0;
virtual void str(std::ostream &os) const = 0; virtual void str(std::ostream &os) const = 0;
virtual std::optional<row_handle> single() const { return {}; }; virtual std::optional<row_handle> single() const { return {}; };
...@@ -106,12 +107,7 @@ class condition ...@@ -106,12 +107,7 @@ class condition
m_impl = nullptr; m_impl = nullptr;
} }
void prepare(const category &c) void prepare(const category &c);
{
if (m_impl)
m_impl->prepare(c);
m_prepared = true;
}
bool operator()(row_handle r) const bool operator()(row_handle r) const
{ {
...@@ -149,6 +145,9 @@ class condition ...@@ -149,6 +145,9 @@ class condition
} }
private: private:
void optimise(condition_impl *&impl);
condition_impl *m_impl; condition_impl *m_impl;
bool m_prepared = false; bool m_prepared = false;
}; };
...@@ -162,9 +161,10 @@ namespace detail ...@@ -162,9 +161,10 @@ namespace detail
{ {
} }
void prepare(const category &c) override condition_impl *prepare(const category &c) override
{ {
m_item_ix = get_column_ix(c, m_item_tag); m_item_ix = get_column_ix(c, m_item_tag);
return this;
} }
bool test(row_handle r) const override bool test(row_handle r) const override
...@@ -181,15 +181,15 @@ namespace detail ...@@ -181,15 +181,15 @@ namespace detail
size_t m_item_ix = 0; size_t m_item_ix = 0;
}; };
struct key_is_condition_impl : public condition_impl struct key_equals_condition_impl : public condition_impl
{ {
key_is_condition_impl(item &&i) key_equals_condition_impl(item &&i)
: m_item_tag(i.name()) : m_item_tag(i.name())
, m_value(i.value()) , m_value(i.value())
{ {
} }
void prepare(const category &c) override; condition_impl *prepare(const category &c) override;
bool test(row_handle r) const override bool test(row_handle r) const override
{ {
...@@ -215,6 +215,51 @@ namespace detail ...@@ -215,6 +215,51 @@ namespace detail
std::optional<row_handle> m_single_hit; std::optional<row_handle> m_single_hit;
}; };
struct key_equals_or_empty_condition_impl : public condition_impl
{
key_equals_or_empty_condition_impl(key_equals_condition_impl *equals, key_is_empty_condition_impl *empty)
: m_item_tag(equals->m_item_tag)
, m_value(equals->m_value)
, m_icase(equals->m_icase)
, m_single_hit(equals->m_single_hit)
{
assert(empty->m_item_ix == equals->m_item_ix);
}
condition_impl *prepare(const category &c) override
{
m_item_ix = get_column_ix(c, m_item_tag);
m_icase = is_column_type_uchar(c, m_item_tag);
return this;
}
bool test(row_handle r) const override
{
bool result = false;
if (m_single_hit.has_value())
result = *m_single_hit == r;
else
result = r[m_item_ix].empty() or r[m_item_ix].compare(m_value, m_icase) == 0;
return result;
}
void str(std::ostream &os) const override
{
os << m_item_tag << (m_icase ? "^ " : " ") << " == " << m_value << " OR " << m_item_tag << " IS NULL";
}
virtual std::optional<row_handle> single() const override
{
return m_single_hit;
}
std::string m_item_tag;
size_t m_item_ix = 0;
bool m_icase = false;
std::string m_value;
std::optional<row_handle> m_single_hit;
};
struct key_compare_condition_impl : public condition_impl struct key_compare_condition_impl : public condition_impl
{ {
template <typename COMP> template <typename COMP>
...@@ -225,10 +270,11 @@ namespace detail ...@@ -225,10 +270,11 @@ namespace detail
{ {
} }
void prepare(const category &c) override condition_impl *prepare(const category &c) override
{ {
m_item_ix = get_column_ix(c, m_item_tag); m_item_ix = get_column_ix(c, m_item_tag);
m_icase = is_column_type_uchar(c, m_item_tag); m_icase = is_column_type_uchar(c, m_item_tag);
return this;
} }
bool test(row_handle r) const override bool test(row_handle r) const override
...@@ -257,9 +303,10 @@ namespace detail ...@@ -257,9 +303,10 @@ namespace detail
{ {
} }
void prepare(const category &c) override condition_impl *prepare(const category &c) override
{ {
m_item_ix = get_column_ix(c, m_item_tag); m_item_ix = get_column_ix(c, m_item_tag);
return this;
} }
bool test(row_handle r) const override bool test(row_handle r) const override
...@@ -364,48 +411,78 @@ namespace detail ...@@ -364,48 +411,78 @@ namespace detail
struct and_condition_impl : public condition_impl struct and_condition_impl : public condition_impl
{ {
and_condition_impl(condition &&a, condition &&b) and_condition_impl(condition &&a, condition &&b)
: mA(nullptr)
, mB(nullptr)
{ {
std::swap(mA, a.m_impl); mSub.emplace_back(std::exchange(a.m_impl, nullptr));
std::swap(mB, b.m_impl); mSub.emplace_back(std::exchange(b.m_impl, nullptr));
} }
~and_condition_impl() ~and_condition_impl()
{ {
delete mA; for (auto sub : mSub)
delete mB; delete sub;
} }
void prepare(const category &c) override condition_impl *prepare(const category &c) override;
{
mA->prepare(c);
mB->prepare(c);
}
bool test(row_handle r) const override bool test(row_handle r) const override
{ {
return mA->test(r) and mB->test(r); bool result = true;
for (auto sub : mSub)
{
if (sub->test(r))
continue;
result = false;
break;
}
return result;
} }
void str(std::ostream &os) const override void str(std::ostream &os) const override
{ {
os << '('; os << '(';
mA->str(os);
os << ") AND ("; bool first = true;
mB->str(os); for (auto sub : mSub)
{
if (first)
first = false;
else
os << " AND ";
sub->str(os);
}
os << ')'; os << ')';
} }
virtual std::optional<row_handle> single() const override virtual std::optional<row_handle> single() const override
{ {
auto sa = mA->single(); std::optional<row_handle> result;
auto sb = mB->single();
return sa == sb ? sa : std::optional<row_handle>(); for (auto sub : mSub)
{
auto s = sub->single();
if (not result.has_value())
{
result = s;
continue;
} }
condition_impl *mA; if (s == result)
condition_impl *mB; continue;
result.reset();
break;
}
return result;
}
std::vector<condition_impl *> mSub;
}; };
struct or_condition_impl : public condition_impl struct or_condition_impl : public condition_impl
...@@ -424,11 +501,7 @@ namespace detail ...@@ -424,11 +501,7 @@ namespace detail
delete mB; delete mB;
} }
void prepare(const category &c) override condition_impl *prepare(const category &c) override;
{
mA->prepare(c);
mB->prepare(c);
}
bool test(row_handle r) const override bool test(row_handle r) const override
{ {
...@@ -474,9 +547,10 @@ namespace detail ...@@ -474,9 +547,10 @@ namespace detail
delete mA; delete mA;
} }
void prepare(const category &c) override condition_impl *prepare(const category &c) override
{ {
mA->prepare(c); mA = mA->prepare(c);
return this;
} }
bool test(row_handle r) const override bool test(row_handle r) const override
...@@ -543,13 +617,13 @@ struct key ...@@ -543,13 +617,13 @@ struct key
template <typename T> template <typename T>
condition operator==(const key &key, const T &v) condition operator==(const key &key, const T &v)
{ {
return condition(new detail::key_is_condition_impl({ key.m_item_tag, v })); return condition(new detail::key_equals_condition_impl({ key.m_item_tag, v }));
} }
inline condition operator==(const key &key, const char *value) inline condition operator==(const key &key, const char *value)
{ {
if (value != nullptr and *value != 0) if (value != nullptr and *value != 0)
return condition(new detail::key_is_condition_impl({ key.m_item_tag, value })); return condition(new detail::key_equals_condition_impl({ key.m_item_tag, value }));
else else
return condition(new detail::key_is_empty_condition_impl(key.m_item_tag)); return condition(new detail::key_is_empty_condition_impl(key.m_item_tag));
} }
......
include/cif++/item.hpp
...@@ -59,10 +59,8 @@ class item ...@@ -59,10 +59,8 @@ class item
/// content a single character string with content \a value /// content a single character string with content \a value
item(std::string_view name, char value) item(std::string_view name, char value)
: m_name(name) : m_name(name)
, m_value(m_buffer, 1) , m_value({ value })
{ {
m_buffer[0] = value;
m_buffer[1] = 0;
} }
/// \brief constructor for an item with name \a name and as /// \brief constructor for an item with name \a name and as
...@@ -75,13 +73,15 @@ class item ...@@ -75,13 +73,15 @@ class item
using namespace std; using namespace std;
using namespace cif; using namespace cif;
auto r = to_chars(m_buffer, m_buffer + sizeof(m_buffer) - 1, value, chars_format::fixed, precision); char buffer[32];
auto r = to_chars(buffer, buffer + sizeof(buffer) - 1, value, chars_format::fixed, precision);
if (r.ec != std::errc()) if (r.ec != std::errc())
throw std::runtime_error("Could not format number"); throw std::runtime_error("Could not format number");
assert(r.ptr >= m_buffer and r.ptr < m_buffer + sizeof(m_buffer)); assert(r.ptr >= buffer and r.ptr < buffer + sizeof(buffer));
*r.ptr = 0; *r.ptr = 0;
m_value = std::string_view(m_buffer, r.ptr - m_buffer); m_value.assign(buffer, r.ptr - buffer);
} }
/// \brief constructor for an item with name \a name and as /// \brief constructor for an item with name \a name and as
...@@ -94,13 +94,15 @@ class item ...@@ -94,13 +94,15 @@ class item
using namespace std; using namespace std;
using namespace cif; using namespace cif;
auto r = to_chars(m_buffer, m_buffer + sizeof(m_buffer) - 1, value, chars_format::general); char buffer[32];
auto r = to_chars(buffer, buffer + sizeof(buffer) - 1, value, chars_format::general);
if (r.ec != std::errc()) if (r.ec != std::errc())
throw std::runtime_error("Could not format number"); throw std::runtime_error("Could not format number");
assert(r.ptr >= m_buffer and r.ptr < m_buffer + sizeof(m_buffer)); assert(r.ptr >= buffer and r.ptr < buffer + sizeof(buffer));
*r.ptr = 0; *r.ptr = 0;
m_value = std::string_view(m_buffer, r.ptr - m_buffer); m_value.assign(buffer, r.ptr - buffer);
} }
/// \brief constructor for an item with name \a name and as /// \brief constructor for an item with name \a name and as
...@@ -109,13 +111,15 @@ class item ...@@ -109,13 +111,15 @@ class item
item(const std::string_view name, const T &value) item(const std::string_view name, const T &value)
: m_name(name) : m_name(name)
{ {
auto r = std::to_chars(m_buffer, m_buffer + sizeof(m_buffer) - 1, value); char buffer[32];
auto r = std::to_chars(buffer, buffer + sizeof(buffer) - 1, value);
if (r.ec != std::errc()) if (r.ec != std::errc())
throw std::runtime_error("Could not format number"); throw std::runtime_error("Could not format number");
assert(r.ptr >= m_buffer and r.ptr < m_buffer + sizeof(m_buffer)); assert(r.ptr >= buffer and r.ptr < buffer + sizeof(buffer));
*r.ptr = 0; *r.ptr = 0;
m_value = std::string_view(m_buffer, r.ptr - m_buffer); m_value.assign(buffer, r.ptr - buffer);
} }
/// \brief constructor for an item with name \a name and as /// \brief constructor for an item with name \a name and as
...@@ -152,10 +156,17 @@ class item ...@@ -152,10 +156,17 @@ class item
/// \brief the length of the value string /// \brief the length of the value string
size_t length() const { return m_value.length(); } size_t length() const { return m_value.length(); }
/// \brief support for structured binding
template<size_t N>
decltype(auto) get() const
{
if constexpr (N == 0) return name();
else if constexpr (N == 1) return value();
}
private: private:
std::string_view m_name; std::string_view m_name;
std::string_view m_value; std::string m_value;
char m_buffer[64]; // TODO: optimize this magic number, might be too large
}; };
// -------------------------------------------------------------------- // --------------------------------------------------------------------
...@@ -193,7 +204,7 @@ struct item_value ...@@ -193,7 +204,7 @@ struct item_value
// By using std::string_view instead of c_str we obain a // By using std::string_view instead of c_str we obain a
// nice performance gain since we avoid many calls to strlen. // nice performance gain since we avoid many calls to strlen.
std::string_view text() const constexpr inline std::string_view text() const
{ {
return { m_length >= kBufferSize ? m_data : m_local_data, m_length }; return { m_length >= kBufferSize ? m_data : m_local_data, m_length };
} }
...@@ -289,9 +300,6 @@ struct item_handle ...@@ -289,9 +300,6 @@ struct item_handle
std::string_view text() const; std::string_view text() const;
// bool operator!=(const std::string &s) const { return s != c_str(); }
// bool operator==(const std::string &s) const { return s == c_str(); }
item_handle(uint16_t column, row_handle &row) item_handle(uint16_t column, row_handle &row)
: m_column(column) : m_column(column)
, m_row_handle(row) , m_row_handle(row)
...@@ -491,3 +499,21 @@ struct item_handle::item_value_as<T, std::enable_if_t<std::is_same_v<T, std::str ...@@ -491,3 +499,21 @@ struct item_handle::item_value_as<T, std::enable_if_t<std::is_same_v<T, std::str
}; };
} // namespace cif } // namespace cif
namespace std
{
template<> struct tuple_size<::cif::item>
: public std::integral_constant<std::size_t, 2> {};
template<> struct tuple_element<0, ::cif::item>
{
using type = decltype(std::declval<::cif::item>().name());
};
template<> struct tuple_element<1, ::cif::item>
{
using type = decltype(std::declval<::cif::item>().value());
};
}
\ No newline at end of file
include/cif++/row.hpp
...@@ -307,13 +307,13 @@ class row_initializer : public std::vector<item> ...@@ -307,13 +307,13 @@ class row_initializer : public std::vector<item>
row_initializer(row_handle rh); row_initializer(row_handle rh);
void set_value(std::string_view name, std::string_view value); void set_value(std::string_view name, std::string_view value);
void set_value(item &&i) void set_value(const item &i)
{ {
set_value(i.name(), i.value()); set_value(i.name(), i.value());
} }
void set_value_if_empty(std::string_view name, std::string_view value); void set_value_if_empty(std::string_view name, std::string_view value);
void set_value_if_empty(item &&i) void set_value_if_empty(const item &i)
{ {
set_value_if_empty(i.name(), i.value()); set_value_if_empty(i.name(), i.value());
} }
......
src/category.cpp
...@@ -367,7 +367,7 @@ row *category_index::find_by_value(row_initializer k) const ...@@ -367,7 +367,7 @@ row *category_index::find_by_value(row_initializer k) const
{ {
auto fld = m_category.get_column_name(f); auto fld = m_category.get_column_name(f);
auto ki = find_if(k.begin(), k.end(), [&fld](item &i) { return i.name() == fld; }); auto ki = find_if(k.begin(), k.end(), [&fld](auto &i) { return i.name() == fld; });
if (ki == k.end()) if (ki == k.end())
k2.emplace_back(fld, ""); k2.emplace_back(fld, "");
else else
...@@ -1715,54 +1715,54 @@ category::iterator category::insert_impl(const_iterator pos, row *n) ...@@ -1715,54 +1715,54 @@ category::iterator category::insert_impl(const_iterator pos, row *n)
// #endif // #endif
} }
category::iterator category::erase_impl(const_iterator pos) // category::iterator category::erase_impl(const_iterator pos)
{ // {
if (pos == cend()) // if (pos == cend())
return end(); // return end();
assert(false); // assert(false);
// TODO: implement // // TODO: implement
// row *n = const_cast<row *>(pos.row()); // // row *n = const_cast<row *>(pos.row());
// row *cur; // // row *cur;
// if (m_head == n) // // if (m_head == n)
// { // // {
// m_head = static_cast<row *>(m_head->m_next); // // m_head = static_cast<row *>(m_head->m_next);
// if (m_head == nullptr) // // if (m_head == nullptr)
// m_tail = nullptr; // // m_tail = nullptr;
// n->m_next = nullptr; // // n->m_next = nullptr;
// delete_row(n); // // delete_row(n);
// cur = m_head; // // cur = m_head;
// } // // }
// else // // else
// { // // {
// cur = static_cast<row *>(n->m_next); // // cur = static_cast<row *>(n->m_next);
// if (m_tail == n) // // if (m_tail == n)
// m_tail = static_cast<row *>(n->m_prev); // // m_tail = static_cast<row *>(n->m_prev);
// row *p = m_head; // // row *p = m_head;
// while (p != nullptr and p->m_next != n) // // while (p != nullptr and p->m_next != n)
// p = p->m_next; // // p = p->m_next;
// if (p != nullptr and p->m_next == n) // // if (p != nullptr and p->m_next == n)
// { // // {
// p->m_next = n->m_next; // // p->m_next = n->m_next;
// if (p->m_next != nullptr) // // if (p->m_next != nullptr)
// p->m_next->m_prev = p; // // p->m_next->m_prev = p;
// n->m_next = nullptr; // // n->m_next = nullptr;
// } // // }
// else // // else
// throw std::runtime_error("remove for a row not found in the list"); // // throw std::runtime_error("remove for a row not found in the list");
// delete_row(n); // // delete_row(n);
// } // // }
// return iterator(*this, cur); // // return iterator(*this, cur);
} // }
void category::swap_item(size_t column_ix, row_handle &a, row_handle &b) void category::swap_item(size_t column_ix, row_handle &a, row_handle &b)
{ {
......
src/condition.cpp
...@@ -61,7 +61,7 @@ bool is_column_type_uchar(const category &cat, std::string_view col) ...@@ -61,7 +61,7 @@ bool is_column_type_uchar(const category &cat, std::string_view col)
namespace detail namespace detail
{ {
void key_is_condition_impl::prepare(const category &c) condition_impl *key_equals_condition_impl::prepare(const category &c)
{ {
m_item_ix = get_column_ix(c, m_item_tag); m_item_ix = get_column_ix(c, m_item_tag);
m_icase = is_column_type_uchar(c, m_item_tag); m_icase = is_column_type_uchar(c, m_item_tag);
...@@ -72,8 +72,67 @@ namespace detail ...@@ -72,8 +72,67 @@ namespace detail
{ {
m_single_hit = c[{ { m_item_tag, m_value } }]; m_single_hit = c[{ { m_item_tag, m_value } }];
} }
return this;
}
condition_impl *and_condition_impl::prepare(const category &c)
{
for (auto &sub : mSub)
sub = sub->prepare(c);
for (;;)
{
auto si = find_if(mSub.begin(), mSub.end(), [](condition_impl *sub) { return dynamic_cast<and_condition_impl *>(sub) != nullptr; });
if (si == mSub.end())
break;
and_condition_impl *sub_and = static_cast<and_condition_impl *>(*si);
mSub.erase(si);
mSub.insert(mSub.end(), sub_and->mSub.begin(), sub_and->mSub.end());
sub_and->mSub.clear();
delete sub_and;
}
return this;
}
condition_impl *or_condition_impl::prepare(const category &c)
{
condition_impl *result = this;
mA = mA->prepare(c);
mB = mB->prepare(c);
key_equals_condition_impl *equals = dynamic_cast<key_equals_condition_impl*>(mA);
key_is_empty_condition_impl *empty = dynamic_cast<key_is_empty_condition_impl*>(mB);
if (equals == nullptr and empty == nullptr)
{
equals = dynamic_cast<key_equals_condition_impl*>(mB);
empty = dynamic_cast<key_is_empty_condition_impl*>(mA);
}
if (equals != nullptr and empty != nullptr)
{
result = new detail::key_equals_or_empty_condition_impl(equals, empty);
result = result->prepare(c);
delete this;
}
return result;
} }
} // namespace detail } // namespace detail
void condition::prepare(const category &c)
{
if (m_impl)
m_impl = m_impl->prepare(c);
m_prepared = true;
}
} // namespace cif } // namespace cif
src/file.cpp
...@@ -206,8 +206,8 @@ void file::save(const std::filesystem::path &p) const ...@@ -206,8 +206,8 @@ void file::save(const std::filesystem::path &p) const
void file::save(std::ostream &os) const void file::save(std::ostream &os) const
{ {
if (not is_valid()) // if (not is_valid())
std::cout << "File is not valid!" << std::endl; // std::cout << "File is not valid!" << std::endl;
for (auto &db : *this) for (auto &db : *this)
db.write(os); db.write(os);
......
src/model.cpp
...@@ -99,7 +99,10 @@ float atom::atom_impl::get_property_float(std::string_view name) const ...@@ -99,7 +99,10 @@ float atom::atom_impl::get_property_float(std::string_view name) const
void atom::atom_impl::set_property(const std::string_view name, const std::string &value) void atom::atom_impl::set_property(const std::string_view name, const std::string &value)
{ {
row().assign(name, value, true, true); auto r = row();
if (not r)
throw std::runtime_error("Trying to modify a row that does not exist");
r.assign(name, value, true, true);
} }
// int atom::atom_impl::compare(const atom_impl &b) const // int atom::atom_impl::compare(const atom_impl &b) const
...@@ -2231,9 +2234,9 @@ branch &structure::create_branch(std::vector<row_initializer> atoms) ...@@ -2231,9 +2234,9 @@ branch &structure::create_branch(std::vector<row_initializer> atoms)
// sanity check // sanity check
for (auto &nag_atom : atoms) for (auto &nag_atom : atoms)
{ {
for (auto info : nag_atom) for (const auto &[name, value] : nag_atom)
{ {
if (info.name() == "label_comp_id" and info.value() != "NAG") if (name == "label_comp_id" and value != "NAG")
throw std::logic_error("The first sugar in a branch should be a NAG"); throw std::logic_error("The first sugar in a branch should be a NAG");
} }
} }
...@@ -2316,14 +2319,14 @@ branch &structure::extend_branch(const std::string &asym_id, std::vector<row_ini ...@@ -2316,14 +2319,14 @@ branch &structure::extend_branch(const std::string &asym_id, std::vector<row_ini
for (auto &atom : atom_info) for (auto &atom : atom_info)
{ {
for (auto info : atom) for (const auto &[name, value] : atom)
{ {
if (info.name() != "label_comp_id") if (name != "label_comp_id")
continue; continue;
if (compoundID.empty()) if (compoundID.empty())
compoundID = info.value(); compoundID = value;
else if (info.value() != compoundID) else if (value != compoundID)
throw std::logic_error("All atoms should be of the same type"); throw std::logic_error("All atoms should be of the same type");
} }
} }
......
src/row.cpp
...@@ -88,7 +88,7 @@ void row_initializer::set_value(std::string_view name, std::string_view value) ...@@ -88,7 +88,7 @@ void row_initializer::set_value(std::string_view name, std::string_view value)
void row_initializer::set_value_if_empty(std::string_view name, std::string_view value) void row_initializer::set_value_if_empty(std::string_view name, std::string_view value)
{ {
if (find_if(begin(), end(), [name](item &i) { return i.name() == name; }) == end()) if (find_if(begin(), end(), [name](auto &i) { return i.name() == name; }) == end())
emplace_back(name, value); emplace_back(name, value);
} }
......
test/sugar-test.cpp
...@@ -118,14 +118,8 @@ BOOST_AUTO_TEST_CASE(create_sugar_1) ...@@ -118,14 +118,8 @@ BOOST_AUTO_TEST_CASE(create_sugar_1)
// NOTE, row_initializer does not actually hold the data, so copy it first // NOTE, row_initializer does not actually hold the data, so copy it first
// before it gets destroyed by remove_residue // before it gets destroyed by remove_residue
std::list<std::string> storage;
for (auto r : as.find("label_asym_id"_key == "L")) for (auto r : as.find("label_asym_id"_key == "L"))
{
auto &ri = ai.emplace_back(r); auto &ri = ai.emplace_back(r);
for (auto &rii : ri)
rii.value(storage.emplace_back(rii.value()));
}
s.remove_residue(NAG); s.remove_residue(NAG);
...@@ -156,7 +150,6 @@ BOOST_AUTO_TEST_CASE(create_sugar_2) ...@@ -156,7 +150,6 @@ BOOST_AUTO_TEST_CASE(create_sugar_2)
BOOST_CHECK_EQUAL(bH.size(), 2); BOOST_CHECK_EQUAL(bH.size(), 2);
std::list<std::string> storage;
std::vector<cif::row_initializer> ai[2]; std::vector<cif::row_initializer> ai[2];
auto &db = s.get_datablock(); auto &db = s.get_datablock();
...@@ -165,17 +158,11 @@ BOOST_AUTO_TEST_CASE(create_sugar_2) ...@@ -165,17 +158,11 @@ BOOST_AUTO_TEST_CASE(create_sugar_2)
for (size_t i = 0; i < 2; ++i) for (size_t i = 0; i < 2; ++i)
{ {
for (auto r : as.find("label_asym_id"_key == "H" and "auth_seq_id"_key == i + 1)) for (auto r : as.find("label_asym_id"_key == "H" and "auth_seq_id"_key == i + 1))
{
auto &ri = ai[i].emplace_back(r); auto &ri = ai[i].emplace_back(r);
for (auto &rii : ri)
rii.value(storage.emplace_back(rii.value()));
}
} }
s.remove_branch(bH); s.remove_branch(bH);
file.save(gTestDir / "test-create_sugar_2-0.cif");
BOOST_CHECK(file.is_valid()); BOOST_CHECK(file.is_valid());
auto &bN = s.create_branch(ai[0]); auto &bN = s.create_branch(ai[0]);
...@@ -217,7 +204,7 @@ BOOST_AUTO_TEST_CASE(delete_sugar_1) ...@@ -217,7 +204,7 @@ BOOST_AUTO_TEST_CASE(delete_sugar_1)
BOOST_CHECK(file.is_valid()); BOOST_CHECK(file.is_valid());
file.save(gTestDir / "test-create_sugar_3.cif"); // file.save(gTestDir / "test-create_sugar_3.cif");
BOOST_CHECK_NO_THROW(cif::mm::structure s2(file)); BOOST_CHECK_NO_THROW(cif::mm::structure s2(file));
} }
test/unit-v2-test.cpp
...@@ -142,13 +142,17 @@ BOOST_AUTO_TEST_CASE(item_1) ...@@ -142,13 +142,17 @@ BOOST_AUTO_TEST_CASE(item_1)
BOOST_CHECK_EQUAL(i2.value(), ci2.value()); BOOST_CHECK_EQUAL(i2.value(), ci2.value());
BOOST_CHECK_EQUAL(i3.value(), ci3.value()); BOOST_CHECK_EQUAL(i3.value(), ci3.value());
item mi1(std::move(i1)); item mi1(std::move(ci1));
item mi2(std::move(i2)); item mi2(std::move(ci2));
item mi3(std::move(i3)); item mi3(std::move(ci3));
BOOST_CHECK_EQUAL(i1.value(), mi1.value()); BOOST_CHECK_EQUAL(i1.value(), mi1.value());
BOOST_CHECK_EQUAL(i2.value(), mi2.value()); BOOST_CHECK_EQUAL(i2.value(), mi2.value());
BOOST_CHECK_EQUAL(i3.value(), mi3.value()); BOOST_CHECK_EQUAL(i3.value(), mi3.value());
BOOST_CHECK(ci1.empty());
BOOST_CHECK(ci2.empty());
BOOST_CHECK(ci3.empty());
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
......
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