Split lines with many copyright years

[gromacs.git] / src / gromacs / selection / selectionoptionmanager.cpp

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
 * Copyright (c) 2019,2020, 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.
 *
 * GROMACS is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 *
 * GROMACS is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with GROMACS; if not, see
 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
 *
 * If you want to redistribute modifications to GROMACS, please
 * consider that scientific software is very special. Version
 * control is crucial - bugs must be traceable. We will be happy to
 * consider code for inclusion in the official distribution, but
 * derived work must not be called official GROMACS. Details are found
 * in the README & COPYING files - if they are missing, get the
 * official version at http://www.gromacs.org.
 *
 * To help us fund GROMACS development, we humbly ask that you cite
 * the research papers on the package. Check out http://www.gromacs.org.
 */
/*! \internal \file
 * \brief
 * Implements gmx::SelectionOptionManager.
 *
 * \author Teemu Murtola <teemu.murtola@gmail.com>
 * \ingroup module_selection
 */
#include "gmxpre.h"

#include "selectionoptionmanager.h"

#include <cstdio>

#include "gromacs/selection/selection.h"
#include "gromacs/selection/selectioncollection.h"
#include "gromacs/selection/selectionoption.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/stringutil.h"

#include "selectionoptionstorage.h"

namespace gmx
{

/********************************************************************
 * SelectionOptionManager::Impl
 */

/*! \internal \brief
 * Private implemention class for SelectionOptionManager.
 *
 * \ingroup module_selection
 */
class SelectionOptionManager::Impl
{
public:
    /*! \brief
     * Request for postponed parsing of selections.
     */
    struct SelectionRequest
    {
        //! Initializes a request for the given option.
        explicit SelectionRequest(SelectionOptionStorage* storage) : storage_(storage) {}

        //! Returns name of the requested selection optin.
        const std::string& name() const { return storage_->name(); }
        //! Returns description for the requested selection option.
        const std::string& description() const { return storage_->description(); }
        /*! \brief
         * Returns the number of selections requested in this request.
         *
         * -1 indicates no upper limit.
         */
        int count() const { return storage_->maxValueCount(); }

        //! Storage object to which the selections will be added.
        SelectionOptionStorage* storage_;
    };

    //! Collection for a list of selection requests.
    typedef std::vector<SelectionRequest> RequestList;
    //! Collection for list of option storage objects.
    typedef std::vector<SelectionOptionStorage*> OptionList;

    /*! \brief
     * Helper class that clears a request list on scope exit.
     *
     * Methods in this class do not throw.
     */
    class RequestsClearer
    {
    public:
        //! Constructs an object that clears given list on scope exit.
        explicit RequestsClearer(RequestList* requests) : requests_(requests) {}
        //! Clears the request list given to the constructor.
        ~RequestsClearer() { requests_->clear(); }

    private:
        RequestList* requests_;
    };

    /*! \brief
     * Creates a new selection collection.
     *
     * \throws  std::bad_alloc if out of memory.
     */
    explicit Impl(SelectionCollection* collection);

    /*! \brief
     * Assign selections from a list to pending requests.
     *
     * \param[in] selections  List of selections to assign.
     * \throws    std::bad_alloc if out of memory.
     * \throws    InvalidInputError if the assignment cannot be done
     *      (see parseRequestedFromFile() for documented conditions).
     *
     * Loops through \p selections and the pending requests lists in order,
     * and for each requests, assigns the first yet unassigned selections
     * from the list.
     */
    void placeSelectionsInRequests(const SelectionList& selections);
    /*! \brief
     * Adds a request for each required option that is not yet set.
     *
     * \throws    std::bad_alloc if out of memory.
     */
    void requestUnsetRequiredOptions();

    //! Selection collection to which selections are stored.
    SelectionCollection& collection_;
    //! List of selection options (storage objects) this manager manages.
    OptionList options_;
    //! List of selections requested for later parsing.
    RequestList requests_;
};

SelectionOptionManager::Impl::Impl(SelectionCollection* collection) : collection_(*collection) {}

void SelectionOptionManager::Impl::placeSelectionsInRequests(const SelectionList& selections)
{
    if (requests_.empty())
    {
        requestUnsetRequiredOptions();
    }

    RequestsClearer clearRequestsOnExit(&requests_);

    SelectionList::const_iterator first = selections.begin();
    SelectionList::const_iterator last  = first;
    RequestList::const_iterator   i;
    for (i = requests_.begin(); i != requests_.end(); ++i)
    {
        const SelectionRequest& request = *i;
        if (request.count() > 0)
        {
            int remaining = selections.end() - first;
            if (remaining < request.count())
            {
                int assigned = first - selections.begin();
                GMX_THROW(InvalidInputError(
                        formatString("Too few selections provided for '%s': "
                                     "Expected %d selections, but only %d left "
                                     "after assigning the first %d to other selections.",
                                     request.name().c_str(), request.count(), remaining, assigned)));
            }
            last = first + request.count();
        }
        else
        {
            RequestList::const_iterator nextRequest = i;
            ++nextRequest;
            if (nextRequest != requests_.end())
            {
                const char* name         = request.name().c_str();
                const char* conflictName = nextRequest->name().c_str();
                GMX_THROW(InvalidInputError(
                        formatString("Ambiguous selections for '%s' and '%s': "
                                     "Any number of selections is acceptable for "
                                     "'%s', but you have requested subsequent "
                                     "selections to be assigned to '%s'. "
                                     "Resolution for such cases is not implemented, "
                                     "and may be impossible.",
                                     name, conflictName, name, conflictName)));
            }
            last = selections.end();
        }
        SelectionList curr(first, last);
        request.storage_->addSelections(curr, true);
        first = last;
    }
    if (last != selections.end())
    {
        int count     = selections.end() - selections.begin();
        int remaining = selections.end() - last;
        int assigned  = last - selections.begin();
        GMX_THROW(InvalidInputError(
                formatString("Too many selections provided: "
                             "Expected %d selections, but %d provided. "
                             "Last %d selections could not be assigned to any option.",
                             assigned, count, remaining)));
    }
}

void SelectionOptionManager::Impl::requestUnsetRequiredOptions()
{
    OptionList::const_iterator i;
    for (i = options_.begin(); i != options_.end(); ++i)
    {
        SelectionOptionStorage& storage = **i;
        if (storage.isRequired() && !storage.isSet())
        {
            requests_.emplace_back(&storage);
        }
    }
}


/********************************************************************
 * SelectionOptionManager
 */

SelectionOptionManager::SelectionOptionManager(SelectionCollection* collection) :
    impl_(new Impl(collection))
{
}

SelectionOptionManager::~SelectionOptionManager() {}

void SelectionOptionManager::registerOption(SelectionOptionStorage* storage)
{
    impl_->requests_.reserve(impl_->options_.size() + 1);
    impl_->options_.push_back(storage);
}

void SelectionOptionManager::convertOptionValue(SelectionOptionStorage* storage,
                                                const std::string&      value,
                                                bool                    bFullValue)
{
    SelectionList selections = impl_->collection_.parseFromString(value);
    storage->addSelections(selections, bFullValue);
}

void SelectionOptionManager::requestOptionDelayedParsing(SelectionOptionStorage* storage)
{
    impl_->requests_.emplace_back(storage);
}

bool SelectionOptionManager::hasRequestedSelections() const
{
    return !impl_->requests_.empty();
}

void SelectionOptionManager::initOptions(IOptionsContainer* options)
{
    bool                             allowOnlyAtomOutput = true;
    Impl::OptionList::const_iterator iter;
    for (iter = impl_->options_.begin(); iter != impl_->options_.end(); ++iter)
    {
        if (!(*iter)->allowsOnlyAtoms())
        {
            allowOnlyAtomOutput = false;
        }
    }

    SelectionCollection::SelectionTypeOption typeOption =
            allowOnlyAtomOutput ? SelectionCollection::AlwaysAtomSelections
                                : SelectionCollection::IncludeSelectionTypeOption;
    impl_->collection_.initOptions(options, typeOption);
}

void SelectionOptionManager::parseRequestedFromStdin(bool bInteractive)
{
    Impl::RequestsClearer clearRequestsOnExit(&impl_->requests_);

    Impl::RequestList::const_iterator i;
    for (i = impl_->requests_.begin(); i != impl_->requests_.end(); ++i)
    {
        const Impl::SelectionRequest& request = *i;
        std::string   context = formatString("for option '%s'\n(%s)", request.name().c_str(),
                                           request.description().c_str());
        SelectionList selections =
                impl_->collection_.parseFromStdin(request.count(), bInteractive, context);
        request.storage_->addSelections(selections, true);
    }
}

void SelectionOptionManager::parseRequestedFromFile(const std::string& filename)
{
    SelectionList selections = impl_->collection_.parseFromFile(filename);
    try
    {
        impl_->placeSelectionsInRequests(selections);
    }
    catch (GromacsException& ex)
    {
        ex.prependContext(formatString("Error in adding selections from file '%s'", filename.c_str()));
        throw;
    }
}

void SelectionOptionManager::parseRequestedFromString(const std::string& str)
{
    SelectionList selections = impl_->collection_.parseFromString(str);
    impl_->placeSelectionsInRequests(selections);
}

} // namespace gmx