ap_main.hxx File Reference

#include "ap_main_type.hxx"
#include "ap_tree_nlen.hxx"

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Classes
struct	PARS_commands

Macros
#define	AWAR_ALIGNMENT   "tmp/pars/alignment"
#define	AWAR_FILTER_NAME   "tmp/pars/filter/name"
#define	AWAR_PARSIMONY   "tmp/pars/parsimony"
#define	AWAR_BEST_PARSIMONY   "tmp/pars/best_parsimony"
#define	AWAR_STACKPOINTER   "tmp/pars/stackpointer"
#define	AWAR_PARS_TYPE   "pars/pars_type"
#define	REUSE_EDGES

Enumerations
enum	PARS_pars_type { PARS_WAGNER, PARS_TRANSVERSION }

Functions
AP_tree_nlen *	rootNode ()
AP_tree_edge *	rootEdge ()
AP_tree_edge *	makeEdge (AP_tree_nlen *n1, AP_tree_nlen *n2)
void	destroyEdge (AP_tree_edge *edge)

Variables
AP_main *	ap_main

Macro Definition Documentation

#define AWAR_ALIGNMENT   "tmp/pars/alignment"

Definition at line 22 of file ap_main.hxx.

Referenced by create_pars_init_window(), pars_check_size(), pars_create_all_awars(), pars_generate_aliview(), and pars_start_cb().

#define AWAR_FILTER_NAME   "tmp/pars/filter/name"

Definition at line 23 of file ap_main.hxx.

Referenced by create_pars_init_window(), and pars_create_all_awars().

#define AWAR_PARSIMONY   "tmp/pars/parsimony"

Definition at line 24 of file ap_main.hxx.

Referenced by pars_create_all_awars(), pars_reset_optimal_parsimony(), and pars_start_cb().

#define AWAR_BEST_PARSIMONY   "tmp/pars/best_parsimony"

Definition at line 25 of file ap_main.hxx.

Referenced by pars_create_all_awars(), pars_reset_optimal_parsimony(), and pars_start_cb().

#define AWAR_STACKPOINTER   "tmp/pars/stackpointer"

Definition at line 26 of file ap_main.hxx.

Referenced by AP_user_pop_cb(), AP_user_push_cb(), pars_create_all_awars(), and pars_start_cb().

#define AWAR_PARS_TYPE   "pars/pars_type"

Definition at line 28 of file ap_main.hxx.

Referenced by pars_create_all_awars().

#define REUSE_EDGES

Definition at line 65 of file ap_main.hxx.

Enumeration Type Documentation

enum PARS_pars_type

Enumerator
PARS_WAGNER
PARS_TRANSVERSION

Definition at line 30 of file ap_main.hxx.

Function Documentation

AP_tree_nlen* rootNode ( )

inline

Definition at line 54 of file ap_main.hxx.

Referenced by insert_all_species_into_tree(), insert_species_into_tree(), AP_tree_edge::kl_rec(), PARSIMONY_testenv< SEQTYPE >::load_tree(), AP_tree_edge::nni_mutPerSite(), AP_tree_edge::nni_rec(), nt_add(), nt_add_partial(), ArbParsimony::optimize_tree(), optimizeTree(), pars_start_cb(), randomMixTree(), recursiveNNI(), rootEdge(), and update_undefined_leaf_branchlength().

AP_tree_edge* rootEdge ( )

inline

Definition at line 58 of file ap_main.hxx.

References rootNode().

AP_tree_edge* makeEdge ( AP_tree_nlen *  n1, AP_tree_nlen *  n2  )

inline

Definition at line 117 of file ap_main.hxx.

References AP_main::makeEdge().

void destroyEdge ( AP_tree_edge *  edge )

inline

Definition at line 120 of file ap_main.hxx.

References AP_main::destroyEdge().

Variable Documentation

AP_main* ap_main

Definition at line 65 of file PARS_main.cxx.

Referenced by ArbParsimony::kernighan_optimize_tree(), AP_tree_edge::kl_rec(), PARSIMONY_testenv< SEQTYPE >::load_tree(), AP_tree_edge::nni_mutPerSite(), AP_tree_edge::nni_rec(), pars_exit(), PARS_tree_init(), PARSIMONY_testenv< SEQTYPE >::PARSIMONY_testenv(), push_all_upnode_sequences(), undefine_branchlengths(), update_undefined_leaf_branchlength(), and PARSIMONY_testenv< SEQTYPE >::~PARSIMONY_testenv().