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#815 Replace ObjArray with std::vector. #824

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#815 Replace ObjArray with std::vector. #824

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7c36750
#815 Replace ObjArray with std::vector.
Aug 10, 2022
07a1928
Issue #815 Replace ObjArray with std::vector
Aug 10, 2022
181aad2
Merge branch 'master' into feature/815_obj_array_properties_map
AliaksandrDziarkach Apr 1, 2024
fdb8c40
fix formatin according to clang-format
AliaksandrDziarkach Apr 1, 2024
43b271e
Fix warning
AliaksandrDziarkach Apr 1, 2024
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10 changes: 8 additions & 2 deletions api/c/indigo-renderer/src/indigo_render2d.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -523,7 +523,10 @@ CEXPORT int indigoRenderGrid(int objects, int* refAtoms, int nColumns, int outpu
rp.mols.add(new Molecule());
Array<char>& title = rp.titles.push();
if (objs[i]->getProperties().contains(rp.cnvOpt.titleProp.ptr()))
title.copy(objs[i]->getProperties().valueBuf(rp.cnvOpt.titleProp.ptr()));
{
const auto& val = objs[i]->getProperties().valueBuf(rp.cnvOpt.titleProp.ptr());
title.copy(val.c_str(), val.size() + 1);
}

if (rp.rOpt.mode == DINGO_MODE::MODE_CDXML)
{
Expand Down Expand Up @@ -560,7 +563,10 @@ CEXPORT int indigoRenderGrid(int objects, int* refAtoms, int nColumns, int outpu
rp.rxns.add(new Reaction());
Array<char>& title = rp.titles.push();
if (objs[i]->getProperties().contains(rp.cnvOpt.titleProp.ptr()))
title.copy(objs[i]->getProperties().valueBuf(rp.cnvOpt.titleProp.ptr()));
{
const auto& val = objs[i]->getProperties().valueBuf(rp.cnvOpt.titleProp.ptr());
title.copy(val.c_str(), val.size() + 1);
}

rp.rxns.top()->clone(objs[i]->getBaseReaction(), 0, 0, 0);
rp.rmode = RENDER_RXN;
Expand Down
68 changes: 26 additions & 42 deletions core/indigo-core/common/base_cpp/properties_map.cpp
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Expand Up @@ -17,13 +17,15 @@
***************************************************************************/
#include <string>

#include <algorithm>

#include "base_cpp/properties_map.h"

using namespace indigo;

IMPL_ERROR(PropertiesMap, "properties map");

void PropertiesMap::copy(RedBlackStringObjMap<Array<char>>& other)
void PropertiesMap::copy(const RedBlackStringObjMap<Array<char>>& other)
{
clear();
for (int i = other.begin(); i != other.end(); i = other.next(i))
Expand Down Expand Up @@ -53,53 +55,42 @@ void PropertiesMap::insert(const char* key, const std::string& value)

void PropertiesMap::insert(const char* key, const char* value)
{
if (_properties.find(key))
const auto it = _properties.find(key);
if (it != _properties.end())
{
auto& val = _properties.at(key);
if (value != 0)
val.readString(value, true);
_properties.at(key) = value;
}
else
{
auto& name = _propertyNames.push();
name.readString(key, true);
int k = _properties.insert(key);
if (value != 0)
_properties.value(k).readString(value, true);
auto newIt = _properties.emplace(key, value).first;
_propertiesOrdered.push_back(std::move(newIt));
}
}
Array<char>& PropertiesMap::insert(const char* key)
std::string& PropertiesMap::insert(const char* key)
{
insert(key, 0);
insert(key, "");
return valueBuf(key);
}
const char* PropertiesMap::key(int i)
const char* PropertiesMap::key(int i) const
{
return _propertyNames.at(i).ptr();
return _propertiesOrdered.at(i)->first.c_str();
}

const char* PropertiesMap::value(int i)
const char* PropertiesMap::value(int i) const
{
auto& buf = valueBuf(_propertyNames.at(i).ptr());
if (buf.size() > 0)
{
return buf.ptr();
}
else
{
return "";
}
return _propertiesOrdered.at(i)->second.c_str();
}

Array<char>& PropertiesMap::valueBuf(const char* key)
std::string& PropertiesMap::valueBuf(const char* key)
{
return _properties.at(key);
}

void PropertiesMap::clear()
{
_properties.clear();
_propertyNames.clear();
_propertiesOrdered.clear();
}

bool PropertiesMap::is_empty()
Expand All @@ -109,31 +100,24 @@ bool PropertiesMap::is_empty()

bool PropertiesMap::contains(const char* key) const
{
return _properties.find(key);
return _properties.find(key) != _properties.end();
}

const char* PropertiesMap::at(const char* key) const
{
return _properties.at(key).ptr();
return _properties.at(key).c_str();
}

void PropertiesMap::remove(const char* key)
{
if (_properties.find(key))
const auto it = _properties.find(key);
if (it != _properties.end())
{
_properties.remove(key);
int to_remove = -1;
for (auto i = 0; i < _propertyNames.size(); i++)
_properties.erase(it);
const auto orderedIt = std::find(_propertiesOrdered.begin(), _propertiesOrdered.end(), it);
if (orderedIt != _propertiesOrdered.end())
{
if (strcmp(_propertyNames.at(i).ptr(), key) == 0)
{
to_remove = i;
break;
}
}
if (to_remove >= 0)
{
_propertyNames.remove(to_remove);
_propertiesOrdered.erase(orderedIt);
}
else
{
Expand Down Expand Up @@ -168,5 +152,5 @@ int PropertiesMap::PrAuto::next(int k)
}
PropertiesMap::PrIter PropertiesMap::PrAuto::end()
{
return PropertiesMap::PrIter(_owner, _owner._propertyNames.size());
}
return PropertiesMap::PrIter(_owner, static_cast<int>(_owner._propertiesOrdered.size()));
}
31 changes: 15 additions & 16 deletions core/indigo-core/common/base_cpp/properties_map.h
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Expand Up @@ -24,11 +24,12 @@
#pragma warning(disable : 4251)
#endif

#include "base_cpp/array.h"
#include "base_cpp/auto_iter.h"
#include "base_cpp/exception.h"
#include "base_cpp/obj_array.h"
#include "base_cpp/red_black.h"
#include <map>
#include <string>
#include <vector>

namespace indigo
{
Expand All @@ -41,23 +42,17 @@ namespace indigo
explicit PropertiesMap()
{
}
~PropertiesMap()
{
}
// inline RedBlackStringObjMap< Array<char> >& getProperties() {
// return _properties;
// }
void copy(RedBlackStringObjMap<Array<char>>& properties);

void copy(const RedBlackStringObjMap<Array<char>>& properties);
void copy(PropertiesMap&);
void merge(PropertiesMap&);
void insert(const char* key, const char* value);
void insert(const char* key, const std::string& value);
std::string& insert(const char* key);

Array<char>& insert(const char* key);

const char* key(int);
const char* value(int);
Array<char>& valueBuf(const char* key);
const char* key(int) const;
const char* value(int) const;
std::string& valueBuf(const char* key);

bool contains(const char* key) const;
const char* at(const char* key) const;
Expand Down Expand Up @@ -92,9 +87,13 @@ namespace indigo
PrAuto elements();

private:
// std::less<...> is used to avoid creation of temp string when searching by const char* index
using StorageType = std::map<std::string, std::string, std::less<std::string>>;

PropertiesMap(const PropertiesMap&);
RedBlackStringObjMap<Array<char>> _properties;
ObjArray<Array<char>> _propertyNames;

StorageType _properties;
std::vector<StorageType::iterator> _propertiesOrdered;
};

} // namespace indigo
Expand Down
4 changes: 2 additions & 2 deletions core/indigo-core/molecule/src/multiple_cdx_loader.cpp
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Expand Up @@ -307,10 +307,10 @@ void MultipleCdxLoader::_getObject(int parent_tag)
{
auto& propVal = properties.insert(name.ptr());
if (value.size() > 0)
propVal.readString(value.ptr(), true);
propVal = value.ptr();
else if (_latest_text.size() > 0)
{
propVal.readString(_latest_text.ptr(), true);
propVal = _latest_text.ptr();
_latest_text.clear();
}
}
Expand Down
42 changes: 20 additions & 22 deletions core/indigo-core/molecule/src/rdf_loader.cpp
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Expand Up @@ -164,7 +164,7 @@ void RdfLoader::readNext()
/*
* Current value for property reading
*/
Array<char>* current_datum = 0;
std::string* current_datum = 0;
/*
* Read properties
*/
Expand Down Expand Up @@ -214,7 +214,9 @@ void RdfLoader::readNext()
scanner.skip(6);
scanner.skipSpace();

_readLine(scanner, *current_datum);
Array<char> buffer;
_readLine(scanner, buffer);
*current_datum = buffer.ptr();

continue;
}
Expand All @@ -224,8 +226,8 @@ void RdfLoader::readNext()
*/
if (_innerBuffer.size() && current_datum && current_datum->size())
{
current_datum->appendString("\n", true);
current_datum->appendString(_innerBuffer.ptr(), true);
(*current_datum) += '\n';
(*current_datum) += _innerBuffer.ptr();
}

} while (_readLine(_getScanner(), _innerBuffer));
Expand Down Expand Up @@ -253,30 +255,26 @@ bool RdfLoader::_readIdentifiers(bool from_begin)
word.push(0);
if (strcmp(word.ptr(), "$MIREG") == 0 || strcmp(word.ptr(), "$RIREG") == 0)
{
/*
* Insert new property key
*/
Array<char>& val = properties.insert("internal-regno");
scanner.skipSpace();
/*
* Insert new property value
*/
scanner.readWord(val, 0);
val.push(0);

Array<char> buffer;
scanner.readWord(buffer, 0);
buffer.push(0);

properties.insert("internal-regno", buffer.ptr());

result = true;
}
else if (strcmp(word.ptr(), "$MEREG") == 0 || strcmp(word.ptr(), "$REREG") == 0)
{
/*
* Insert new property key
*/
Array<char>& val = properties.insert("external-regno");
scanner.skipSpace();
/*
* Insert new property value
*/
scanner.readWord(val, 0);
val.push(0);

Array<char> buffer;
scanner.readWord(buffer, 0);
buffer.push(0);

properties.insert("mexternal-regno", buffer.ptr());

result = true;
}
else if (from_begin)
Expand Down
7 changes: 3 additions & 4 deletions core/indigo-core/molecule/src/sdf_loader.cpp
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Expand Up @@ -192,7 +192,7 @@ void SdfLoader::readNext()
auto& propBuf = properties.insert(word.ptr());
// auto& propBuf = properties.valueBuf(word.ptr());
// int idx = properties.findOrInsert(word.ptr());
propBuf.copy(str);
propBuf = str.ptr();
output.writeStringCR(str.ptr());
if (str.size() > 1)
{
Expand All @@ -205,9 +205,8 @@ void SdfLoader::readNext()
output.writeStringCR(str.ptr());
if (str.size() > 1)
{
propBuf.pop(); // Remove string end marker (0)
propBuf.push('\n');
propBuf.appendString(str.ptr(), true);
propBuf += '\n';
propBuf += str.ptr();
}
} while (str.size() > 1);
}
Expand Down
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