sniplay: egglib/egglib-2.1.5/include/egglib-cpp/Arg.hpp comparison

comparison egglib/egglib-2.1.5/include/egglib-cpp/Arg.hpp @ 9:98c37a5d67f4 draft

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author	dereeper
date	Wed, 07 Feb 2018 22:08:47 -0500
parents	420b57c3c185
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+:98c37a5d67f4
+/*
+Copyright 2009-2010 Stéphane De Mita, Mathieu Siol
+This file is part of the EggLib library.
+EggLib is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+EggLib 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 General Public License for more details.
+You should have received a copy of the GNU General Public License
+along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
+*/
+#ifndef EGGLIB_ARG_HPP
+#define EGGLIB_ARG_HPP
+#include "Current.hpp"
+#include "Edge.hpp"
+#include <string>
+/** \defgroup coalesce coalesce
+*
+* \brief Coalescent simulator
+*
+* The set of classes implements a three-scale coalescent simulator with
+* recombination, and a flexible mutation model. The main classes are
+* Controller (the starting point for generating genealogies), ParamSet
+* (that centralizes parameter specification), the Change hierarchy
+* (that implements demographic change specifications), Arg (ancestral
+* recombination graph; the result of generation a genealogy) and
+* Mutator (that generates genotype data from an ARG).
+*
+*/
+namespace egglib {
+class Random;
+/** \brief Ancestral recombination graph
+*
+* \ingroup coalesce
+*
+* This class stores the ARG (genealogical information). It is
+* progressively built by appropriate (especially regarding to the
+* timing) calls to coal() and recomb() methods. Then it can be
+* used by a mutator class to generates data, or it can also
+* generate newick trees (one tree by non-recombining segment).
+*
+*/
+class Arg {
+public:
+/** \brief Default constructor
+*
+* Creates a null, useless, object.
+*
+*/
+Arg();
+/** \brief Object initialization
+*
+* \param current address of the Current instance used by
+* the simulator.
+*
+* \param numberOfSegments number of recombining segments.
+*
+*/
+void set(Current* current, unsigned int numberOfSegments);
+/** \brief Object reset method
+*
+* This method doesn't reset all parameters (the number of
+* segments and associated tables are retained, as well as
+* the Edge object pool).
+*
+* \param current address of the Current instance used by
+* the simulator.
+*
+*/
+void reset(Current* current);
+/** \brief Standard constructor
+*
+* \param current address of the Current instance used by
+* the simulator.
+*
+* \param numberOfSegments number of recombining segments
+*
+*/
+Arg(Current* current, unsigned int numberOfSegments);
+/** \brief Destructor
+*
+* Clears all Edge instances referenced in the object.
+*
+*/
+virtual ~Arg();
+/** \brief Gets the current value of the time counter
+*
+*/
+double time() const;
+/** \brief Increments the time counter
+*
+*/
+void addTime(double increment);
+/** \brief Performs a coalescence event
+*
+* For this version, the two lineages to coalesce are
+* predefined.
+*
+* \param incr increment of the time counter.
+* \param pop index of the population.
+* \param index1 first lineage to coalesce.
+* \param index2 second lineage to coalesce.
+*
+*/
+void coalescence(double incr, unsigned int pop, unsigned int index1, unsigned int index2);
+/** \brief Performs a coalescence event
+*
+* For this version, the two lineages to coalesce are
+* randomly picked in the given population
+*
+* \param incr increment of the time counter.
+* \param pop index of the population.
+* \param random pointer to simulator's random generator
+* instance.
+*
+*/
+void coalescence(double incr, unsigned int pop, Random* random);
+/** \brief Performs a recombination event
+*
+* \param incr increment of the time counter.
+* \param random pointer to simulator's random generator
+* instance.
+*
+*/
+void recombination(double incr, Random* random);
+/** \brief Places a mutation
+*
+* \param segment index of the segment affected.
+*
+* \param treePosition a random number placed on the
+* interval defined by the tree length at this position.
+*
+* \return the concerned Edge's address.
+*
+* \todo why this is not encapsulated?
+*
+* Another nerve-taking point: calling this method assume
+* that all Edge of have previously undergone a call of
+* branchLength(position) with intervalPosition - what
+* should be done by the called (that is, Mutator) through
+* my (Arg's) treeLength of something. BEWARE WHEN MODIFYING
+* (enhancements should be directed to Edge in my view)
+*
+*/
+Edge* mute(unsigned int segment, double treePosition);
+/** \brief Age of the uMRCA
+*
+* The uMRCA is the ultimate Most Recent Common Ancestor,
+* that is the point where the last segment finds its most
+* recent common ancestor. This member will have a meaningful
+* value only if the coalescent process is completed.
+*
+*/
+inline double ageUltimateMRCA() const {
+return _time;
+}
+/** \brief Age of the MRCA for a given segment
+*
+* The MRCA is the Most Recent Common Ancestor, that is the
+* point where the coalescent process is over (all lineages
+* have coalesced). This member will have a meaningful
+* value only if the coalescent process is completed.
+*
+* Note that the value is cached; it is computed only one
+* upon first call and no again, even if the Arg is modified<
+*
+*/
+inline double ageMRCA(unsigned int segmentIndex) {
+return _MRCA[segmentIndex]->bottom;
+}
+/** \brief  MRCA for each segment
+*
+* The MRCA is the Most Recent Common Ancestor, that is the
+* point where the coalescent process is over (all lineages
+* have coalesced). This member will have a meaningful
+* value only if the coalescent process is completed.
+*
+* Note that the value is cached; it is computed only one
+* upon first call and no again, even if the Arg is modified
+*
+*/
+inline const Edge* MRCA(unsigned int segmentIndex) {
+return _MRCA[segmentIndex];
+}
+/// Ultimate MRCA
+inline const Edge* uMRCA() {
+return edges[numberOfEdges-1];
+}
+/// the number of recombining segments
+unsigned int numberOfSegments;
+/** \brief Formats the newick-formatted tree for a segment
+*
+*/
+std::string newick(unsigned int segment);
+/// Number of initial lineages
+unsigned int numberOfSamples;
+/** \brief Total tree length (summed over all segments)
+*
+*/
+double totalLength;
+/** \brief Segment-specific tree length
+*
+*/
+double* segmentLengths;
+/// Current number of Edges in the tree (including the MRCA node)
+unsigned int numberOfEdges;
+/// Total number of recombination events that occurred
+unsigned int numberOfRecombinationEvents;
+/// Set the number of actual sites in all branches
+void set_actualNumberOfSites(unsigned int actualNumberOfSites);
+private:
+/// Copy constructor not available
+Arg(const Arg&) { }
+/// Assignment operator not available
+Arg& operator=(const Arg&) { return *this; }
+void init_stable_parameters();
+void init_variable_parameters();
+void clear();
+void addEdge(Edge*);
+std::string rnewick(Edge* edge, unsigned int segment, double cache);
+Current* current;
+double _time;
+Edge** edges;
+void findMRCA(unsigned int segmentIndex);
+void computeTotalLength();
+void computeSegmentLength(unsigned int segmentIndex);
+unsigned int* numberOfEdgesPerSegment;
+Edge** _MRCA;
+EdgePool edgePool;
+};
+}
+#endif

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comparison egglib/egglib-2.1.5/include/egglib-cpp/Arg.hpp @ 9:98c37a5d67f4 draft