/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-%ModuleCode
-
+%ModuleHeaderCode
+#include <exception>
#include "gromacs/options/basicoptions.h"
-#include "gromacs/utility/gmxassert.h"
+#include "gromacs/options/filenameoption.h"
+#include "gromacs/selection/selectionoption.h"
#include <map>
#include <string>
-#include <exception>
class PyOptionsHolder {
public:
class DuplicateOption : public std::exception {
public:
- virtual const char* what() const noexcept { return "This option is already defined"; }
+ virtual const char* what() const throw();
};
- gmx::DoubleOption doubleOption(const char *name, double def = 0) {
- if (storage.count(name))
- throw DuplicateOption();
-
- double *store = new double;
- *store = def;
- gmx::DoubleOption option(name);
- option.store(store);
- storage[name] = {store, "d"};
-
- return option;
- }
- PyObject* get_value(const char *name) {
- if (!storage.count(name))
- return NULL;
-
- option_value v = storage[name];
- switch (*v.type) {
- case 'd':
- return sipBuildResult(NULL, v.type, *((double*) v.value));
- break;
- }
-
- GMX_ASSERT(false, "Some type is not handled in PyOptionsHolder.get_value");
- return NULL;
- }
- // TODO: destructor (need to handle each type separately)
- // TODO: support for vector options
+ class StringList {
+ public:
+ StringList(const std::vector<std::string>*);
+ StringList(const std::string*, size_t);
+ const char* operator[] (size_t);
+ private:
+ const std::string *list;
+ size_t size;
+ const std::vector<std::string> *vector;
+ };
+ gmx::DoubleOption doubleOption(const char*, size_t = 1, double* = NULL);
+ gmx::IntegerOption integerOption(const char*, size_t = 1, int* = NULL);
+ gmx::StringOption stringOption(const char*, size_t = 1, const char* = NULL);
+ gmx::BooleanOption booleanOption(const char*, size_t = 1, bool = 0);
+ gmx::SelectionOption selectionOption(const char*, size_t = 1);
+ gmx::FileNameOption fileNameOption(const char*, size_t = 1);
+ PyObject* get_value(const char*);
+ ~PyOptionsHolder();
private:
struct option_value {
void *value;
const char *type;
+ int *count;
+ bool vector;
+ const char *name;
};
std::map<std::string, option_value> storage;
+ template<typename T, typename U> U createStorage(const char*, const char*, int, const T* = 0);
+ template<typename T> PyObject* buildValue(const char*, const option_value&, const sipTypeDef* = NULL, size_t = 0);
+ template<typename T> void deleteStorage(const option_value&);
};
+%End
+
+%ModuleCode
+#include "gromacs/utility/gmxassert.h"
+
+const char* PyOptionsHolder::DuplicateOption::what() const throw() {
+ return "This option is already defined";
+}
+
+PyOptionsHolder::StringList::StringList(const std::vector<std::string> *vector) :
+ list(NULL), size(vector->size()), vector(vector)
+{}
+
+PyOptionsHolder::StringList::StringList(const std::string *list, size_t size) :
+ list(list), size(size), vector(NULL)
+{}
+
+const char* PyOptionsHolder::StringList::operator[](size_t i) {
+ if (i >= size)
+ return NULL;
+ return vector ? (*vector)[i].data() : list[i].data();
+}
+
+template<typename T, typename U> U PyOptionsHolder::createStorage(const char *name, const char *type, int count, const T *def) {
+ if (storage.count(name))
+ throw DuplicateOption();
+
+ U option(name);
+
+ option_value value;
+ value.type = type;
+ value.count = new int;
+ value.name = name;
+
+ if (count == 0) { // std::vector of values
+ std::vector<T> *store = new std::vector<T>();
+ option.storeVector(store);
+ option.multiValue();
+ option.storeCount(value.count);
+
+ *value.count = 0;
+ if (def) {
+ store->push_back(*def);
+ *value.count = 1;
+ }
+
+ value.value = store;
+ value.vector = true;
+ } else { // exactly `count` values
+ T *store = new T[count];
+ if (def)
+ store[0] = *def;
+
+ option.store(store);
+ if (count > 1)
+ option.valueCount(count);
+
+ value.value = store;
+ value.vector = false;
+ *value.count = count;
+ }
+ storage[name] = value;
+ return option;
+}
+
+gmx::DoubleOption PyOptionsHolder::doubleOption(const char *name, size_t count, double *def) {
+ gmx::DoubleOption option = createStorage<double, gmx::DoubleOption>(name, "d", count, def);
+
+ return option;
+}
+
+gmx::IntegerOption PyOptionsHolder::integerOption(const char *name, size_t count, int *def) {
+ gmx::IntegerOption option = createStorage<int, gmx::IntegerOption>(name, "i", count, def);
+
+ return option;
+}
+
+gmx::StringOption PyOptionsHolder::stringOption(const char *name, size_t count, const char* def) {
+ std::string *s_def = NULL;
+ if (def)
+ s_def = new std::string(def);
+
+ gmx::StringOption option = createStorage<std::string, gmx::StringOption>(name, "A", count, s_def);
+ delete s_def;
+
+ return option;
+}
+
+// FIXME: Unify with the rest
+gmx::BooleanOption PyOptionsHolder::booleanOption(const char *name, size_t count, bool def) {
+ if (storage.count(name))
+ throw DuplicateOption();
+
+ bool *store = new bool;
+ *store = def;
+ gmx::BooleanOption option(name);
+ option.store(store);
+ option_value value = {store, "b"};
+ storage[name] = value;
+
+ return option;
+}
+
+gmx::SelectionOption PyOptionsHolder::selectionOption(const char *name, size_t count) {
+ gmx::SelectionOption option = createStorage<gmx::Selection, gmx::SelectionOption>(name, "S", count);
+
+ return option;
+}
+
+gmx::FileNameOption PyOptionsHolder::fileNameOption(const char *name, size_t count) {
+ gmx::FileNameOption option = createStorage<std::string, gmx::FileNameOption>(name, "f", count);
+
+ return option;
+}
+
+template<typename T> PyObject* PyOptionsHolder::buildValue(const char *sipType, const PyOptionsHolder::option_value &value, const sipTypeDef *td, size_t size) {
+ int count = *value.count;
+ T *store = !value.vector ? (T*) value.value : ((std::vector<T>*) value.value)->data();
+
+ if (count == 1 && !value.vector) {
+ if (td)
+ return sipConvertFromType(store, td, NULL);
+ else
+ return sipBuildResult(NULL, sipType, *store);
+ } else {
+ if (td)
+ return sipConvertToTypedArray(store, td, NULL, size, count, SIP_READ_ONLY);
+ else
+ return sipConvertToArray(store, sipType, count, SIP_READ_ONLY);
+ }
+}
+
+
+PyObject* PyOptionsHolder::get_value(const char *name) {
+ if (!storage.count(name))
+ return NULL;
+
+ option_value v = storage[name];
+ switch (*v.type) {
+ case 'd': // double
+ return buildValue<double>("d", v);
+ break;
+ case 'i': // int
+ return buildValue<int>("i", v);
+ break;
+ case 'A': // std::string
+ case 'f': // FileNameOption
+ if (v.vector)
+ return sipConvertFromType(new PyOptionsHolder::StringList(((std::vector<std::string>*) v.value)), sipType_PyOptionsHolder_StringList, Py_None);
+ else if (*v.count == 1)
+ return sipBuildResult(NULL, "A", ((std::string*) v.value)->data());
+ else
+ return sipConvertFromType(new PyOptionsHolder::StringList((std::string*) v.value, *v.count), sipType_PyOptionsHolder_StringList, Py_None);
+ break;
+ case 'b': // bool
+ // TODO: support vector bool options
+ return sipBuildResult(NULL, v.type, *((bool*) v.value));
+ break;
+ case 'S': // Selection
+ return buildValue<gmx::Selection>(NULL, v, sipType_Selection, sizeof(gmx::Selection));
+ break;
+ }
+
+ GMX_ASSERT(false, "Some type is not handled in PyOptionsHolder.get_value");
+ return NULL;
+}
+
+template<typename T> void PyOptionsHolder::deleteStorage(const PyOptionsHolder::option_value &value) {
+ if (value.vector)
+ delete (std::vector<T> *) value.value;
+ else
+ delete[] (T*) value.value;
+
+ delete value.count;
+}
+
+PyOptionsHolder::~PyOptionsHolder() {
+ for (std::map<std::string, option_value>::iterator it = storage.begin(); it != storage.end(); it++)
+ switch (*(it->second.type)) {
+ case 'd': // double
+ deleteStorage<double>(it->second);
+ break;
+ case 'i': // int
+ deleteStorage<int>(it->second);
+ break;
+ case 'A': // std::string
+ case 'f': // FileNameOption (the storage type is still std::string)
+ deleteStorage<std::string>(it->second);
+ break;
+ case 'b': // bool
+ delete (bool*) it->second.value;
+ break;
+ case 'S': // Selection
+ deleteStorage<gmx::Selection>(it->second);
+ break;
+ }
+}
%End
%Exception PyOptionsHolder::DuplicateOption {
%End
public:
- DoubleOption doubleOption(const char *name, double def = 0) throw (PyOptionsHolder::DuplicateOption);
+ class StringList /NoDefaultCtors/ {
+ public:
+ const char* operator[] (int);
+ %MethodCode
+ sipRes = (*sipCpp)[a0];
+
+ if (!sipRes) {
+ SIP_BLOCK_THREADS;
+ PyErr_SetString(PyExc_IndexError, "Index out of range");
+ SIP_UNBLOCK_THREADS;
+ sipIsErr = 1;
+ }
+ %End
+ };
+ // These methods are given twice to workaround sip setting 0 for when '*def = NULL' option is not given
+ DoubleOption doubleOption(const char *name /KeepReference/, int count = 1) throw (PyOptionsHolder::DuplicateOption);
+ DoubleOption doubleOption(const char *name /KeepReference/, int count, const double *def) throw (PyOptionsHolder::DuplicateOption);
+
+ IntegerOption integerOption(const char *name /KeepReference/, int count = 1) throw (PyOptionsHolder::DuplicateOption);
+ IntegerOption integerOption(const char *name /KeepReference/, int count, const int *def) throw (PyOptionsHolder::DuplicateOption);
+
+ StringOption stringOption(const char *name /KeepReference/, int count = 1) throw (PyOptionsHolder::DuplicateOption);
+ StringOption stringOption(const char *name /KeepReference/, int count, const char *def) throw (PyOptionsHolder::DuplicateOption);
+
+ BooleanOption booleanOption(const char *name /KeepReference/, int count = 1, bool def = 0) throw (PyOptionsHolder::DuplicateOption);
+
+ SelectionOption selectionOption(const char *name /KeepReference/, int count = 1) throw (PyOptionsHolder::DuplicateOption);
+
+ FileNameOption fileNameOption(const char *name /KeepReference/, int count = 1) throw (PyOptionsHolder::DuplicateOption);
SIP_PYOBJECT __getitem__(const char *name);
%MethodCode
sipRes = sipCpp->get_value(a0);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff