UniqueIdIndexer.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Clemens Groepl $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/UniqueIdInterface.h>
#include <OpenMS/CONCEPT/LogStream.h>
#include <OpenMS/CONCEPT/Exception.h>
 
#ifdef _MSC_VER // disable some BOOST warnings that distract from ours
#   pragma warning( push ) // save warning state
#   pragma warning( disable : 4396 )
#endif
 
#include <boost/unordered_map.hpp>
 
#ifdef _MSC_VER
#   pragma warning( pop )  // restore old warning state
#endif
 
 
namespace OpenMS
{
 
  template <typename RandomAccessContainer>
  class UniqueIdIndexer
  {
public:
 
    typedef boost::unordered_map<UInt64, Size> UniqueIdMap;
 
    Size
    uniqueIdToIndex(UInt64 unique_id) const
    {
      Size index;
      try
      {
        index = uniqueid_to_index_.at(unique_id);
        if (getBase_().at(index).getUniqueId() != unique_id)
        {
          throw std::out_of_range("unique_id_to_index_");
        }
      }
      catch (std::out_of_range &)
      {
        try
        {
          this->updateUniqueIdToIndex();
          index = uniqueid_to_index_.at(unique_id);
        }
        catch (std::out_of_range &)
        {
          index = -1;   // which means: invalid
        }
      }
      return index;
    }
 
    void
    updateUniqueIdToIndex() const
    {
      Size num_valid_unique_id = 0;
      // add or update unique id of existing features
      for (Size index = 0; index < getBase_().size(); ++index)
      {
        UInt64 unique_id = getBase_()[index].getUniqueId();
        if (UniqueIdInterface::isValid(unique_id))
        {
          uniqueid_to_index_[unique_id] = index;
          ++num_valid_unique_id;
        }
      }
      // remove invalid or outdated entries
      uniqueid_to_index_.erase(UniqueIdInterface::INVALID);
      for (UniqueIdMap::iterator iter = uniqueid_to_index_.begin(); iter != uniqueid_to_index_.end(); /* see loop */)
      {
        if (iter->second >= getBase_().size() || getBase_()[iter->second].getUniqueId() != iter->first)
        {
          iter = uniqueid_to_index_.erase(iter);
        }
        else
        {
          ++iter;
        }
      }
      if (uniqueid_to_index_.size() != num_valid_unique_id)
      {
        std::stringstream ss;
        ss << "Duplicate valid unique ids detected!   RandomAccessContainer has size()==" << getBase_().size();
        ss << ", num_valid_unique_id==" << num_valid_unique_id;
        ss << ", uniqueid_to_index_.size()==" << uniqueid_to_index_.size();
        throw Exception::Postcondition(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, ss.str());
      }
      return;
    }
 
    Size
    resolveUniqueIdConflicts()
    {
      Size invalid_uids(0);
      uniqueid_to_index_.clear();
      // add unique id of existing features
      for (Size index = 0; index < getBase_().size(); ++index)
      {
        UInt64 unique_id = getBase_()[index].getUniqueId();
        if (!UniqueIdInterface::isValid(unique_id))
        {
          getBase_()[index].ensureUniqueId();
          unique_id = getBase_()[index].getUniqueId();
        }
 
        // see if UID already present
        while (uniqueid_to_index_.find(unique_id) != uniqueid_to_index_.end()) // double entry!
        {
          getBase_()[index].setUniqueId();
          unique_id = getBase_()[index].getUniqueId();
          ++invalid_uids;
        }
 
        uniqueid_to_index_[unique_id] = index;
 
      }
 
      return invalid_uids;
    }
 
    void
    swap(UniqueIdIndexer & rhs)
    {
      std::swap(uniqueid_to_index_, rhs.uniqueid_to_index_);
      return;
    }
 
protected:
 
    const RandomAccessContainer &
    getBase_() const
    {
      return *static_cast<const RandomAccessContainer *>(this);
    }
 
    RandomAccessContainer &
    getBase_()
    {
      return *static_cast<RandomAccessContainer *>(this);
    }
 
    mutable UniqueIdMap uniqueid_to_index_;
 
  };
 
} //namespace OpenMS