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NCBI C++ ToolKit: src/algo/phy_tree/dist_methods.cpp File Reference

USING_SCOPE (objects) void s_ThrowIfNotAllFinite (const CDistMethods::TMatrix &mat) boolean leaf (meNode *v) meTree * fastme_run (double **D_in, int numSpecies_in, char **labels, int btype_in, int wtype_in, int ntype_in) double ** initDoubleMatrix (int d) void freeMatrix (double **D, int size) void freeTree (meTree *T) static void s_AddFastMeSubtree (fastme::meNode *me_node, CDistMethods::TTree *node, const vector< string > &labels) static CDistMethods::TTree * s_ConvertFastMeTree (fastme::meTree *me_tree, const vector< string > &labels) static void s_AddNodeToBtc (CRef< CBioTreeContainer > btc, const TPhyTreeNode *ptn, int parent_uid, int &next_uid) Recursive function for adding TPhyTreeNodes to BioTreeContainer. More...
CRef< CBioTreeContainer > MakeBioTreeContainer (const TPhyTreeNode *tree) Conversion from TPhyTreeNode to CBioTreeContainer. More...
CRef< CBioTreeContainer > MakeDistanceSensitiveBioTreeContainer (const TPhyTreeNode *tree) Conversion from TPhyTreeNode to CBioTreeContainer, potentially without dist feature key. More...
◆ boolean ◆ fastme_run() meTree* fastme_run ( double ** D_in, int numSpecies_in, char ** labels, int btype_in, int wtype_in, int ntype_in )

Definition at line 240 of file fastme.cpp.

References A, assignAllSizeFields(), assignBMEWeights(), assignOLSWeights(), BAL, BMEaddSpecies(), bNNI(), D, exit(), EXIT_FAILURE, meSet::firstNode, freeMatrix(), freeSet(), GMEaddSpecies(), initDoubleMatrix(), loadMatrix(), makeBMEAveragesTable(), makeOLSAveragesTable(), malloc(), NNI(), NONE, NULL, OLS, meSet::secondNode, T, and USER.

Referenced by CDistMethods::FastMeTree().

◆ freeMatrix() void freeMatrix ( double ** D, int size ) ◆ freeTree() ◆ initDoubleMatrix() double** initDoubleMatrix ( int d ) ◆ leaf()

Definition at line 44 of file graph.cpp.

Referenced by CPriorityNode::Erase(), CPriorityTree::Erase(), SeqTree::getLeafById(), TaxTreeData::getParentAtRank(), CPriorityTree::Insert(), CPriority_I::InsertBefore(), mdb_cursor_count(), mdb_cursor_del(), mdb_cursor_first(), mdb_cursor_get(), mdb_cursor_last(), mdb_cursor_next(), mdb_cursor_prev(), mdb_cursor_put(), mdb_cursor_set(), mdb_env_cwalk(), mdb_node_read(), mdb_page_alloc(), mdb_page_search(), mdb_pages_xkeep(), DeBruijn::CDBGraphDigger::OneStepBranchExtend(), CDistMethods::RerootTree(), s_AddFastMeSubtree(), SeqTree::selectByRowID(), CPriorityNode::SetLeaf(), tdefl_calculate_minimum_redundancy(), CVariationUtilities::x_FixAlleles(), CSeq_loc_Mapper::x_InitializeSeqMapDown(), and CConcurrentMap< Key, Value, Comparator, Allocator, CntChildsInNode, MaxTreeHeight, DeletionDelay, DelStoreCapacity >::x_ScanForInsertSpace().

◆ MakeBioTreeContainer() ◆ MakeDistanceSensitiveBioTreeContainer() ◆ s_AddFastMeSubtree() ◆ s_AddNodeToBtc() ◆ s_ConvertFastMeTree() ◆ s_ThrowIfNotAllFinite() ◆ USING_SCOPE()

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