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- Committer: Package Import Robot
- Author(s): Julien Dutheil
- Date: 2013-03-07 10:51:00 UTC
- mfrom: (1.1.2)
- Revision ID: package-import@ubuntu.com-20130307105100-7ij3w7iyab9t2mbt
Tags: 2.1.0-1
Bug fixed and warnings removed.
- files added:
- .pc
- files removed:
- PopGen.spec
- files modified:
- CMakeLists.txt
added
removed
src/Bpp/PopGen/PolymorphismSequenceContainer.h
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//
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/*
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Copyright or © or Copr. CNRS, (November 17, 2004)
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Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
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This software is a computer program whose purpose is to provide classes
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for population genetics analysis.
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The fact that you are presently reading this means that you have had
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knowledge of the CeCILL license and that you accept its terms.
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*/
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*/
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#ifndef _POLYMORPHISMSEQUENCECONTAINER_H_
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#define _POLYMORPHISMSEQUENCECONTAINER_H_
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* The PopGenLib library provides classes for population genetics analysis.
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* It makes intensive use of the SeqLib library, and adds a dedicated container
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* named bpp::PolymorphismSequenceContainer, which associates frequencies to the
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* sequences in the set. The bpp::PolymorphismSequenceContainerTools and
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* sequences in the set. The bpp::PolymorphismSequenceContainerTools and
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* bpp::SequenceStatistics static classes provide several tools for data analysis,
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* including diversity indices and positive selection tests.
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*
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namespace bpp
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{
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/**
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* @brief The PolymorphismSequenceContainer class.
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*
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* This is a VectorSiteContainer with effectif for each sequence.
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* It also has flag for ingroup and outgroup.
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*
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* @author Sylvain Gaillard
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*/
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class PolymorphismSequenceContainer:
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public VectorSiteContainer
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/**
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* @brief The PolymorphismSequenceContainer class.
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*
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* This is a VectorSiteContainer with effectif for each sequence.
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* It also has flag for ingroup and outgroup.
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*
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* @author Sylvain Gaillard
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*/
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class PolymorphismSequenceContainer :
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public VectorSiteContainer
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{
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private:
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std::vector<bool> ingroup_;
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std::vector<size_t> count_;
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std::vector<size_t> group_;
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public:
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// Constructors and destructor
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/**
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* @brief Build a new empty PolymorphismSequenceContainer.
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*/
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PolymorphismSequenceContainer(const Alphabet* alpha);
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/**
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* @brief Build a new empty PolymorphismSequenceContainer of given size.
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*/
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PolymorphismSequenceContainer(size_t size, const Alphabet* alpha);
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/**
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* @brief Build a PolymorphismSequenceContainer by copying data from an OrderedSequenceContainer.
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*/
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PolymorphismSequenceContainer(const OrderedSequenceContainer& sc);
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/**
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* @brief Build a PolymorphismSequenceContainer by copying data from a SiteContainer.
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*/
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PolymorphismSequenceContainer(const SiteContainer& sc);
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/**
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* @brief Copy constructor.
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*/
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PolymorphismSequenceContainer(const PolymorphismSequenceContainer& psc);
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/**
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* @brief Operator= : copy operator.
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*/
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PolymorphismSequenceContainer& operator=(const PolymorphismSequenceContainer& psc);
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/**
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* @brief Destroy a PolymorphismSequenceContainer.
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*/
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virtual ~PolymorphismSequenceContainer();
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/**
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* @brief Clone a PolymorphismSequenceContainer.
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*/
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PolymorphismSequenceContainer* clone() const
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{
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private:
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std::vector<bool> ingroup_;
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std::vector<unsigned int> count_;
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std::vector<unsigned int> group_;
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public: // Constructors and destructor
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/**
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* @brief Build a new empty PolymorphismSequenceContainer.
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*/
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PolymorphismSequenceContainer(const Alphabet* alpha);
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/**
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* @brief Build a new empty PolymorphismSequenceContainer of given size.
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*/
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PolymorphismSequenceContainer(unsigned int size, const Alphabet* alpha);
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/**
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* @brief Build a PolymorphismSequenceContainer by copying data from an OrderedSequenceContainer.
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*/
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PolymorphismSequenceContainer(const OrderedSequenceContainer& sc);
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/**
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* @brief Build a PolymorphismSequenceContainer by copying data from a SiteContainer.
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*/
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PolymorphismSequenceContainer(const SiteContainer& sc);
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/**
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* @brief Copy constructor.
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*/
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PolymorphismSequenceContainer(const PolymorphismSequenceContainer& psc);
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/**
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* @brief Operator= : copy operator.
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*/
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PolymorphismSequenceContainer& operator=(const PolymorphismSequenceContainer& psc);
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/**
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* @brief Destroy a PolymorphismSequenceContainer.
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*/
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virtual ~PolymorphismSequenceContainer();
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/**
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* @brief Clone a PolymorphismSequenceContainer.
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*/
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PolymorphismSequenceContainer* clone() const
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{
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return new PolymorphismSequenceContainer(*this);
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}
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public: // Other methods
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/**
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* @brief Remove a sequence by index and return a pointer to this removed sequence.
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*
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* @throw IndexOutOfBoundsException if index excedes the number of sequences.
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*/
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Sequence * removeSequence(unsigned int index) throw (IndexOutOfBoundsException);
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/**
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* @brief Remove a sequence by name and return a pointer to this removed sequence.
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*
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* @throw SequenceNotFoundException if name is not found among the sequences' names.
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*/
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Sequence * removeSequence(const std::string &name) throw (SequenceNotFoundException);
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/**
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* @brief Delete a sequence by index.
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*
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* @throw IndexOutOfBoundsException if index excedes the number of sequences.
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*/
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void deleteSequence(unsigned int index) throw (IndexOutOfBoundsException);
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/**
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* @brief Delete a sequence by name.
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*
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* @throw SequenceNotFoundException if name is not found among the sequences' names.
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*/
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void deleteSequence(const std::string &name) throw (SequenceNotFoundException);
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/**
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* @brief Add a sequence to the container.
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*
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* @throw AlphabetMismatchException if the sequence's alphabet doesn't match the container's alphabet.
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* @throw SequenceException if the sequence's size doesn't match the sequence's size of the container.
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* @throw SequenceException if the sequence's name already exists in the container.
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*/
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void addSequence(const Sequence &sequence,unsigned int effectif=1, bool checkNames=true) throw (Exception);
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/**
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* @brief Clear the container of all its sequences.
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*/
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void clear();
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/**
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* @brief Get the group identifier of the sequence.
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*
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* @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
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*/
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unsigned int getGroupId(unsigned int index) const throw (IndexOutOfBoundsException);
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/**
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* @brief Get the group identifier of a sequence.
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*
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* @throw SequenceNotFoundException if name is not found among the sequences' names.
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*/
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unsigned int getGroupId(const std::string & name) const throw (SequenceNotFoundException);
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/**
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* @brief Get all the groups identifiers.
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*/
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std::set<unsigned int> getAllGroupsIds() const;
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/**
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* @brief Set the group identifier of a sequence.
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*
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* @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
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*/
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void setGroupId(unsigned int index, unsigned int group_id) throw (IndexOutOfBoundsException);
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/**
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* @brief Set the group identifier of a sequence.
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*
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* @throw SequenceNotFoundException if name is not found among the sequences' names.
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*/
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void setGroupId(const std::string & name, unsigned int group_id) throw (SequenceNotFoundException);
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/**
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* @brief Get the number of groups.
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*/
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unsigned int getNumberOfGroups() const;
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/**
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* @brief Tell if the sequence is ingroup by index.
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*
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* @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
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*/
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bool isIngroupMember(unsigned int index) const throw (IndexOutOfBoundsException);
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/**
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* @brief Tell if a sequence is ingroup by name.
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*
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* @throw SequenceNotFoundException if name is not found among the sequences' names.
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*/
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bool isIngroupMember(const std::string &name) const throw (SequenceNotFoundException);
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/**
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* @brief Set a sequence as ingroup member by index.
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*
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* @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
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*/
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void setAsIngroupMember(unsigned int index) throw (IndexOutOfBoundsException);
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/**
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* @brief Set a sequence as ingroup member by name.
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*
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* @throw SequenceNotFoundException if name is not found among the sequences' names.
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*/
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void setAsIngroupMember(const std::string &name) throw (SequenceNotFoundException);
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/**
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* @brief Set a sequence as outgroup member by index.
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*
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* @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
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*/
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void setAsOutgroupMember(unsigned int index) throw (IndexOutOfBoundsException);
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/**
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* @brief Set a sequence as outgroup member by name.
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*
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* @throw SequenceNotFoundException if name is not found among the sequences' names.
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*/
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void setAsOutgroupMember(const std::string &name) throw (SequenceNotFoundException);
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/**
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* @brief Set the count of a sequence by index.
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*
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* @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
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* @throw BadIntegerException if count < 1 ... use deleteSequence instead of setting the count to 0.
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*/
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void setSequenceCount(unsigned int index, unsigned int count) throw (Exception);
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/**
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* @brief Set the count of a sequence by name.
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*
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* @throw throw SequenceNotFoundException if name is not found among the sequences' names.
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* @throw BadIntegerException if count < 1 ... use deleteSequence instead of setting the count to 0.
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*/
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void setSequenceCount(const std::string &name, unsigned int count) throw (Exception);
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/**
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* @brief Add 1 to the sequence count.
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*
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* @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
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*/
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void incrementSequenceCount(unsigned int index) throw (IndexOutOfBoundsException);
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/**
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* @brief Add 1 to the sequence count.
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*
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* @throw throw SequenceNotFoundException if name is not found among the sequences' names.
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*/
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void incrementSequenceCount(const std::string &name) throw (SequenceNotFoundException);
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/**
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* @brief Remove 1 to the sequence count.
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*
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* @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
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* @throw BadIntegerException if count < 1 ... use deleteSequence instead of setting the count to 0.
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*/
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void decrementSequenceCount(unsigned int index) throw (Exception);
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/**
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* @brief Remove 1 to the sequence count.
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*
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* @throw throw SequenceNotFoundException if name is not found among the sequences' names.
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* @throw BadIntegerException if count < 1 ... use deleteSequence instead of setting the count to 0.
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*/
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void decrementSequenceCount(const std::string & name) throw (Exception);
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/**
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* @brief Get the count of a sequence by index.
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*
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* @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
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*/
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unsigned int getSequenceCount(unsigned int index) const throw (IndexOutOfBoundsException);
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/**
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* @brief Get the count of a sequence by name.
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*
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* @throw SequenceNotFoundException if name is not found among the sequences' names.
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*/
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unsigned int getSequenceCount(const std::string &name) const throw (SequenceNotFoundException);
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};
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} //end of namespace bpp;
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#endif //_POLYMORPHISMSEQUENCECONTAINER_H_
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return new PolymorphismSequenceContainer(*this);
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}
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public:
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// Other methods
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/**
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* @brief Remove a sequence by index and return a pointer to this removed sequence.
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*
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* @throw IndexOutOfBoundsException if index excedes the number of sequences.
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*/
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Sequence* removeSequence(size_t index) throw (IndexOutOfBoundsException);
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/**
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* @brief Remove a sequence by name and return a pointer to this removed sequence.
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*
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* @throw SequenceNotFoundException if name is not found among the sequences' names.
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*/
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Sequence* removeSequence(const std::string& name) throw (SequenceNotFoundException);
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/**
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* @brief Delete a sequence by index.
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*
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* @throw IndexOutOfBoundsException if index excedes the number of sequences.
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*/
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void deleteSequence(size_t index) throw (IndexOutOfBoundsException);
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/**
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* @brief Delete a sequence by name.
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*
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* @throw SequenceNotFoundException if name is not found among the sequences' names.
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*/
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void deleteSequence(const std::string& name) throw (SequenceNotFoundException);
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/**
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* @brief Add a sequence to the container.
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*
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* @throw AlphabetMismatchException if the sequence's alphabet doesn't match the container's alphabet.
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* @throw SequenceException if the sequence's size doesn't match the sequence's size of the container.
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* @throw SequenceException if the sequence's name already exists in the container.
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*/
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void addSequence(const Sequence& sequence, size_t effectif = 1, bool checkNames = true) throw (Exception);
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/**
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* @brief Clear the container of all its sequences.
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*/
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void clear();
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/**
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* @brief Get the group identifier of the sequence.
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*
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* @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
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*/
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size_t getGroupId(size_t index) const throw (IndexOutOfBoundsException);
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/**
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* @brief Get the group identifier of a sequence.
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*
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* @throw SequenceNotFoundException if name is not found among the sequences' names.
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*/
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size_t getGroupId(const std::string& name) const throw (SequenceNotFoundException);
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/**
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* @brief Get all the groups identifiers.
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*/
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std::set<size_t> getAllGroupsIds() const;
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/**
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* @brief Set the group identifier of a sequence.
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*
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* @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
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*/
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void setGroupId(size_t index, size_t group_id) throw (IndexOutOfBoundsException);
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/**
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* @brief Set the group identifier of a sequence.
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*
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* @throw SequenceNotFoundException if name is not found among the sequences' names.
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*/
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void setGroupId(const std::string& name, size_t group_id) throw (SequenceNotFoundException);
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/**
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* @brief Get the number of groups.
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*/
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size_t getNumberOfGroups() const;
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/**
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* @brief Tell if the sequence is ingroup by index.
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*
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* @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
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*/
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bool isIngroupMember(size_t index) const throw (IndexOutOfBoundsException);
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/**
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* @brief Tell if a sequence is ingroup by name.
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*
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* @throw SequenceNotFoundException if name is not found among the sequences' names.
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*/
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bool isIngroupMember(const std::string& name) const throw (SequenceNotFoundException);
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/**
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* @brief Set a sequence as ingroup member by index.
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*
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* @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
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*/
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void setAsIngroupMember(size_t index) throw (IndexOutOfBoundsException);
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/**
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* @brief Set a sequence as ingroup member by name.
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*
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* @throw SequenceNotFoundException if name is not found among the sequences' names.
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*/
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void setAsIngroupMember(const std::string& name) throw (SequenceNotFoundException);
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/**
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* @brief Set a sequence as outgroup member by index.
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*
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* @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
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*/
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void setAsOutgroupMember(size_t index) throw (IndexOutOfBoundsException);
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/**
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* @brief Set a sequence as outgroup member by name.
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*
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* @throw SequenceNotFoundException if name is not found among the sequences' names.
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*/
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void setAsOutgroupMember(const std::string& name) throw (SequenceNotFoundException);
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/**
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* @brief Set the count of a sequence by index.
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*
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* @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
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* @throw BadIntegerException if count < 1 ... use deleteSequence instead of setting the count to 0.
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*/
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void setSequenceCount(size_t index, size_t count) throw (Exception);
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/**
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* @brief Set the count of a sequence by name.
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*
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* @throw throw SequenceNotFoundException if name is not found among the sequences' names.
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* @throw BadIntegerException if count < 1 ... use deleteSequence instead of setting the count to 0.
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*/
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void setSequenceCount(const std::string& name, size_t count) throw (Exception);
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/**
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* @brief Add 1 to the sequence count.
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*
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* @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
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*/
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void incrementSequenceCount(size_t index) throw (IndexOutOfBoundsException);
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/**
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* @brief Add 1 to the sequence count.
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*
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* @throw throw SequenceNotFoundException if name is not found among the sequences' names.
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*/
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void incrementSequenceCount(const std::string& name) throw (SequenceNotFoundException);
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/**
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* @brief Remove 1 to the sequence count.
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*
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* @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
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* @throw BadIntegerException if count < 1 ... use deleteSequence instead of setting the count to 0.
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*/
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void decrementSequenceCount(size_t index) throw (Exception);
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/**
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* @brief Remove 1 to the sequence count.
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*
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* @throw throw SequenceNotFoundException if name is not found among the sequences' names.
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* @throw BadIntegerException if count < 1 ... use deleteSequence instead of setting the count to 0.
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*/
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void decrementSequenceCount(const std::string& name) throw (Exception);
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/**
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* @brief Get the count of a sequence by index.
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*
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* @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
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*/
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size_t getSequenceCount(size_t index) const throw (IndexOutOfBoundsException);
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/**
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* @brief Get the count of a sequence by name.
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*
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* @throw SequenceNotFoundException if name is not found among the sequences' names.
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*/
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size_t getSequenceCount(const std::string& name) const throw (SequenceNotFoundException);
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};
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} // end of namespace bpp;
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#endif // _POLYMORPHISMSEQUENCECONTAINER_H_
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