ARB

#include <ap_tree_nlen.hxx>
Public Member Functions  
AP_tree_edge (AP_tree_nlen *node1, AP_tree_nlen *node2)  
bool  isConnectedTo (const AP_tree_nlen *n) const 
int  indexOf (const AP_tree_nlen *n) const 
AP_tree_nlen *  otherNode (const AP_tree_nlen *n) const 
AP_tree_nlen *  sonNode () const 
AP_tree_nlen *  notSonNode () const 
long  Age () const 
bool  is_root_edge () const 
bool  is_leaf_edge () const 
bool  next_to_folded_group () const 
bool  has_marked () const 
void  set_root () 
Mutations  nni_rec (EdgeSpec whichEdges, AP_BL_MODE mode, AP_tree_nlen *skipNode, bool includeStartEdge) 
bool  kl_rec (const KL_params &KL, const int rec_depth, Mutations pars_best) 
Mutations  calc_branchlengths () 
Mutations  nni_mutPerSite (Mutations pars_one, AP_BL_MODE mode, MutationsPerSite *mps) 
void  mixTree (int repeat, int percent, EdgeSpec whichEdges) 
void  set_visited (bool vis) 
Static Public Member Functions  
static void  initialize (AP_tree_nlen *root) 
static void  destroy (AP_tree_nlen *root) 
Protected Member Functions  
~AP_tree_edge ()  
void  relink (AP_tree_nlen *node1, AP_tree_nlen *node2) 
AP_tree_edge *  unlink () 
Friends  
class  AP_tree_nlen 
class  EdgeChain 
std::ostream &  operator<< (std::ostream &, const AP_tree_edge *) 
AP_tree_edge *  StackFrameData::makeEdge (AP_tree_nlen *n1, AP_tree_nlen *n2) 
void  AP_main::destroyEdge (AP_tree_edge *edge) 
void  ResourceStack::destroy_edges () 
Definition at line 260 of file ap_tree_nlen.hxx.

protected 
Definition at line 35 of file AP_tree_edge.cxx.
References unlink().
AP_tree_edge::AP_tree_edge  (  AP_tree_nlen *  node1, 
AP_tree_nlen *  node2  
) 
Definition at line 25 of file AP_tree_edge.cxx.
References NULp, and relink().
Referenced by initialize().

protected 
Definition at line 101 of file AP_tree_edge.cxx.
References ap_assert.
Referenced by AP_tree_edge(), and StackFrameData::makeEdge().

protected 
Definition at line 88 of file AP_tree_edge.cxx.
References ap_assert, and NULp.
Referenced by ~AP_tree_edge().

static 
Builds all edges in the whole tree. The root node is skipped  instead his two sons are connected with an edge
Definition at line 57 of file AP_tree_edge.cxx.
References AP_tree_edge(), and buildSonEdges().
Referenced by PARSIMONY_testenv< SEQTYPE >::load_tree(), and pars_start_cb().

static 
Destroys all edges in the whole tree
Definition at line 71 of file AP_tree_edge.cxx.
References ANY_EDGE, ap_assert, and NULp.
Referenced by PARSIMONY_testenv< SEQTYPE >::~PARSIMONY_testenv().

inline 
Definition at line 312 of file ap_tree_nlen.hxx.
Referenced by indexOf(), and insert_species_into_tree().

inline 
Definition at line 313 of file ap_tree_nlen.hxx.
References ap_assert, and isConnectedTo().
Referenced by otherNode().

inline 
Definition at line 314 of file ap_tree_nlen.hxx.
References indexOf().
Referenced by EdgeChain::EdgeChain(), insert_species_into_tree(), ArbParsimony::kernighan_optimize_tree(), and notSonNode().

inline 
Definition at line 315 of file ap_tree_nlen.hxx.
Referenced by EdgeChain::EdgeChain(), has_marked(), insert_species_into_tree(), kl_rec(), nni_mutPerSite(), nni_rec(), notSonNode(), and set_root().

inline 
Definition at line 316 of file ap_tree_nlen.hxx.
References otherNode(), and sonNode().
Referenced by insert_species_into_tree().

inline 
Definition at line 318 of file ap_tree_nlen.hxx.

inline 
Definition at line 322 of file ap_tree_nlen.hxx.
Referenced by EdgeChain::EdgeChain(), and has_marked().

inline 
Definition at line 323 of file ap_tree_nlen.hxx.
Referenced by insert_species_into_tree(), ArbParsimony::kernighan_optimize_tree(), kl_rec(), nni_mutPerSite(), and nni_rec().

inline 
Definition at line 324 of file ap_tree_nlen.hxx.
Referenced by ArbParsimony::kernighan_optimize_tree(), and kl_rec().

inline 
Definition at line 325 of file ap_tree_nlen.hxx.
References is_root_edge(), and sonNode().

inline 
Definition at line 333 of file ap_tree_nlen.hxx.
References sonNode().
Referenced by insert_all_species_into_tree(), insert_species_into_tree(), and nni_rec().
Mutations AP_tree_edge::nni_rec  (  EdgeSpec  whichEdges, 
AP_BL_MODE  mode,  
AP_tree_nlen *  skipNode,  
bool  includeStartEdge  
) 
Definition at line 438 of file AP_tree_edge.cxx.
References allBranchlengthsAreDefined(), ANY_EDGE, ap_assert, AP_BL_BL_ONLY, AP_BL_BOOTSTRAP_LIMIT, ap_calc_bootstrap_remark(), ap_main, AP_tree_nlen, implicated, is_leaf(), is_leaf_edge(), nni_mutPerSite(), NULp, AP_main::push_node(), EdgeChain::restart(), rootEdge(), rootNode(), set_root(), EdgeChain::size(), SKIP_LEAF_EDGES, sonNode(), STRUCTURE, and undefine_branchlengths().
Referenced by calc_branchlengths(), and insert_species_into_tree().
does K.L. recursion
KL  parameters defining how recursion is done 
rec_depth  current recursion depth (starts with 0) 
pars_best  current parsimony value of topology 
Definition at line 1096 of file AP_tree_nlen.cxx.
References AP_main::accept_if(), ap_assert, AP_DYNAMIK, ap_main, AP_STATIC, QuadraticThreshold::calculate(), CUSTOM_DEPTHS, idx2side(), implicated, KL_params::inc_rec_depth, is_leaf_edge(), kl_rec(), KL_params::max_rec_depth, min, next_to_folded_group(), NULp, KL_params::rec_type, KL_params::rec_width, AP_main::remember(), AP_main::revert(), rootNode(), sonNode(), KL_params::stopAtFoldedGroups, swap(), and KL_params::thresFunctor.
Referenced by ArbParsimony::kernighan_optimize_tree(), and kl_rec().

inline 
Definition at line 340 of file ap_tree_nlen.hxx.
References ANY_EDGE, AP_BL_BL_ONLY, nni_rec(), and NULp.
Mutations AP_tree_edge::nni_mutPerSite  (  Mutations  pars_one, 
AP_BL_MODE  mode,  
MutationsPerSite *  mps  
) 
Definition at line 502 of file AP_tree_edge.cxx.
References AP_main::accept_if(), ap_assert, AP_BL_BL_ONLY, AP_BL_BOOTSTRAP_LIMIT, AP_BL_NNI_ONLY, AP_LEFT, ap_main, AP_RIGHT, AP_tree_nlen, MutationsPerSite::data(), is_leaf_edge(), NULp, AP_main::remember(), AP_main::revert(), rootNode(), and sonNode().
Referenced by nni_rec().
Definition at line 592 of file AP_tree_edge.cxx.
References arb_progress::aborted(), ap_assert, AP_LEFT, AP_RIGHT, AP_tree_nlen, GB_random(), EdgeChain::restart(), EdgeChain::size(), and SKIP_LEAF_EDGES.

inline 
Definition at line 346 of file ap_tree_nlen.hxx.
Referenced by ArbParsimony::kernighan_optimize_tree().

friend 
Definition at line 283 of file ap_tree_nlen.hxx.
Referenced by mixTree(), nni_mutPerSite(), and nni_rec().

friend 
Definition at line 284 of file ap_tree_nlen.hxx.

friend 
Definition at line 572 of file AP_tree_edge.cxx.

friend 

friend 

friend 