A template for a class that reads an AGI (Admixture Graph Input) file. The file provides the following information: A set of branch length variable names, a set of admixture proportion parameter names, a component size (K), and K*(K-1)/2 number of expressions representing C matrix entries. More...

#include <jade.agi_reader.hpp>

Collaboration diagram for jade::basic_agi_reader< TValue >:

Public Types
typedef TValue	value_type
	The value type. More...

typedef jade::basic_shunting_yard< value_type >	shunting_yard_type
	The shunting yard algorithm used to parse and evaluate expressions. More...

typedef shunting_yard_type::args_type	args_type
	The arguments used to evaluate the shunting yard algorithm. More...

Public Member Functions
	basic_agi_reader (std::istream &in)
	Initializes a new instance of the class by reading and parsing the specified input stream. More...

	basic_agi_reader (const std::string &path)
	Initializes a new instance of the class by reading and parsing the file with the specified path. More...

const args_type &	get_args () const
	Returns a table of arguments that maps variables to values. The table reference returned has all values set to zero. The table can be used to evaluate all expression entries. More...

const std::vector< std::string > &	get_branch_names () const
	Returns the vector of branch names. More...

const std::vector< std::string > &	get_proportion_names () const
	Returns the vector of proportion names. More...

std::size_t	get_k () const
	Returns the number of components. More...

const std::vector< shunting_yard_type > &	get_entries () const
	Returns the vector of expressions for the C matrix entries. More...

Detailed Description

template<typename TValue>
class jade::basic_agi_reader< TValue >

A template for a class that reads an AGI (Admixture Graph Input) file. The file provides the following information: A set of branch length variable names, a set of admixture proportion parameter names, a component size (K), and K*(K-1)/2 number of expressions representing C matrix entries.

An example of the file format is as follows:

# Branch length parameters, range: [0, inf)
a b c d e f g

# Admixture proportion parameters, range: [0, 1]
p

# K value
3

# Matrix entries, total number should be: K*(K-1)/2
# They map to a C matrix, e.g. K=3 maps to:
#   0 1
#   1 2
(1 - p) * (b + e + g + f + a) + p * (b + d + a)
p * a + (1 - p) * (g + f + a)
c + g + f + a

Definition at line 42 of file jade.agi_reader.hpp.

Member Typedef Documentation

◆ args_type

template<typename TValue >

typedef shunting_yard_type::args_type jade::basic_agi_reader< TValue >::args_type

The arguments used to evaluate the shunting yard algorithm.

Definition at line 58 of file jade.agi_reader.hpp.

◆ shunting_yard_type

template<typename TValue >

typedef jade::basic_shunting_yard<value_type> jade::basic_agi_reader< TValue >::shunting_yard_type

The shunting yard algorithm used to parse and evaluate expressions.

Definition at line 53 of file jade.agi_reader.hpp.

◆ value_type

template<typename TValue >

typedef TValue jade::basic_agi_reader< TValue >::value_type

The value type.

Definition at line 48 of file jade.agi_reader.hpp.

Constructor & Destructor Documentation

◆ basic_agi_reader() [1/2]

template<typename TValue >

jade::basic_agi_reader< TValue >::basic_agi_reader ( std::istream & in )

inlineexplicit

Initializes a new instance of the class by reading and parsing the specified input stream.

Parameters

in	The input stream.

Definition at line 65 of file jade.agi_reader.hpp.

             : _args             ()
             , _branch_names     (_read_names(in))
             , _proportion_names (_read_names(in))
             , _k                (_read_size(in))
             , _entries          (_read_entries(in, _k))
         {
             std::string token;
             if (!!(in >> token))
                 throw jade::error() << "unexpected token: " << token;
  
             //
             // Require that all variable names across both sets are unique. In
             // doing so, build a set of all defined variable names.
             //
             std::set<std::string> defined;
             const auto vectors = { &_branch_names, &_proportion_names };
             for (const auto vector : vectors)
                 for (const auto & name : *vector)
                     if (!defined.insert(name).second)
                         throw jade::error()
                             << "duplicate variable name '" << name << "'";
  
             //
             // Require that all variables defined in the expressions are found
             // in the set of defined variable names.
             //
             for (const auto & entry : _entries)
                 for (const auto & pair : entry.get_args())
                     if (defined.insert(pair.first).second)
                         throw jade::error()
                             << "undefined variable name '"
                             << pair.first << "' in expression";
  
             //
             // Create a set of the variables used in the expressions.
             //
             std::set<std::string> used;
             for (const auto & entry : _entries)
                 for (const auto & pair : entry.get_args())
                     used.insert(pair.first);
  
             //
             // Remove unused variables from the branch and proportion sets.
             //
             {
                 const auto remove = [&used](std::vector<std::string> & names)
                 {
                     const auto end = std::remove_if(
                         names.begin(),
                         names.end(),
                         [&used](const std::string & name)
                         {
                             return used.find(name) == used.end();
                         });
  
                     names.erase(end, names.end());
                 };
  
                 remove(_branch_names);
                 remove(_proportion_names);
             }
  
             //
             // Now that it is verified that all names are unique and that all
             // variables in the expressions are defined as either branch or
             // proportions, initialize the set of default arguments based on
             // the variables used in the expressions.
             //
             for (const auto & name : used)
                 _args[name] = value_type(0);
         }

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◆ basic_agi_reader() [2/2]

template<typename TValue >

jade::basic_agi_reader< TValue >::basic_agi_reader ( const std::string & path )

inlineexplicit

Initializes a new instance of the class by reading and parsing the file with the specified path.

Parameters

path	The path to the file to read and parse.

Definition at line 143 of file jade.agi_reader.hpp.

             : _args             ()
             , _branch_names     ()
             , _proportion_names ()
             , _k                (0)
             , _entries          ()
         {
             try
             {
                 std::ifstream in (path);
                 *this = basic_agi_reader(in);
             }
             catch (const std::exception & e)
             {
                 throw jade::error()
                         << "error reading admixture graph input from file '"
                         << path
                         << "': "
                         << e.what();
             }
         }

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Member Function Documentation

◆ get_args()

template<typename TValue >

const args_type& jade::basic_agi_reader< TValue >::get_args ( ) const

inline

Returns a table of arguments that maps variables to values. The table reference returned has all values set to zero. The table can be used to evaluate all expression entries.

Returns: A table mapping variables to values.

Definition at line 171 of file jade.agi_reader.hpp.

         {
             return _args;
         }

◆ get_branch_names()

template<typename TValue >

const std::vector<std::string>& jade::basic_agi_reader< TValue >::get_branch_names ( ) const

inline

Returns the vector of branch names.

Returns: The vector of branch names.

Definition at line 180 of file jade.agi_reader.hpp.

         {
             return _branch_names;
         }

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◆ get_entries()

template<typename TValue >

const std::vector<shunting_yard_type>& jade::basic_agi_reader< TValue >::get_entries ( ) const

inline

Returns the vector of expressions for the C matrix entries.

Returns: The vector of expressions for the C matrix entries.

Definition at line 207 of file jade.agi_reader.hpp.

         {
             return _entries;
         }

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◆ get_k()

template<typename TValue >

std::size_t jade::basic_agi_reader< TValue >::get_k ( ) const

inline

Returns the number of components.

Returns: The number of components.

Definition at line 198 of file jade.agi_reader.hpp.

         {
             return _k;
         }

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◆ get_proportion_names()

template<typename TValue >

const std::vector<std::string>& jade::basic_agi_reader< TValue >::get_proportion_names ( ) const

inline

Returns the vector of proportion names.

Returns: The vector of proportion names.

Definition at line 189 of file jade.agi_reader.hpp.

         {
             return _proportion_names;
         }

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The documentation for this class was generated from the following file:

jade.agi_reader.hpp

Public Types

Public Member Functions

Detailed Description

template<typename TValue> class jade::basic_agi_reader< TValue >

Member Typedef Documentation

◆ args_type

◆ shunting_yard_type

◆ value_type

Constructor & Destructor Documentation

◆ basic_agi_reader() [1/2]

◆ basic_agi_reader() [2/2]

Member Function Documentation

◆ get_args()

◆ get_branch_names()

◆ get_entries()

◆ get_k()

◆ get_proportion_names()

template<typename TValue>
class jade::basic_agi_reader< TValue >