#include <ncbi_pch.hpp>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "graph.h"
#include "fastme.h"
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◆ addToSet() ◆ copyEdge() ◆ copyNode() ◆ detrifurcate()Definition at line 183 of file graph.cpp.
References exit(), EXIT_FAILURE, f, meEdge::head, meNode::label, leaf(), meNode::leftEdge, meNode::middleEdge, NULL, meNode::parentEdge, T, and meEdge::tail.
◆ freeSet() void freeSet ( meSet * S ) ◆ freeSubTree() void freeSubTree ( meEdge * e ) ◆ freeTree() ◆ leaf()Definition at line 44 of file graph.cpp.
References count, FALSE_FASTME, NULL, and TRUE_FASTME.
Referenced by assignBalWeights(), assignBMEWeights(), assignBottomsize(), assignOLSWeights(), BalWFext(), BMEcalcDownAverage(), bNNIEdgeTest(), calcUpAverages(), compareSets(), detrifurcate(), CPriorityNode::Erase(), CPriorityTree::Erase(), fillTableUp(), SeqTree::getLeafById(), TaxTreeData::getParentAtRank(), GMEcalcDownAverage(), CPriorityTree::Insert(), CPriority_I::InsertBefore(), makeBMEAveragesTable(), makeOLSAveragesTable(), 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(), NewickPrintSubtree(), NNIEdgeTest(), OLSext(), DeBruijn::CDBGraphDigger::OneStepBranchExtend(), partitionSizes(), CDistMethods::RerootTree(), s_AddFastMeSubtree(), SeqTree::selectByRowID(), CPriorityNode::SetLeaf(), tdefl_calculate_minimum_redundancy(), topFirstTraverse(), WFext(), CVariationUtilities::x_FixAlleles(), CSeq_loc_Mapper::x_InitializeSeqMapDown(), and CConcurrentMap< Key, Value, Comparator, Allocator, CntChildsInNode, MaxTreeHeight, DeletionDelay, DelStoreCapacity >::x_ScanForInsertSpace().
◆ makeEdge()Definition at line 90 of file graph.cpp.
References meEdge::distance, meEdge::head, head, meEdge::label, label, malloc(), meEdge::tail, meEdge::totalweight, and weight.
Referenced by BMEaddSpecies(), BMEsplitEdge(), copyEdge(), decodeNewickSubtree(), GMEaddSpecies(), and GMEsplitEdge().
◆ makeNewNode() ◆ makeNode()Definition at line 75 of file graph.cpp.
References meNode::index, meNode::index2, meNode::label, label, meNode::leftEdge, malloc(), meNode::middleEdge, NULL, meNode::parentEdge, and meNode::rightEdge.
Referenced by copyNode(), decodeNewickSubtree(), and makeNewNode().
◆ newTree() ◆ siblingEdge()Definition at line 210 of file graph.cpp.
References meNode::leftEdge, meNode::rightEdge, and meEdge::tail.
Referenced by BalWFext(), BalWFint(), BMEcalcUpAverage(), BMEtestEdge(), BMEupdateAveragesMatrix(), bNNIEdgeTest(), bNNItopSwitch(), calcUpAverages(), fillTableUp(), GMEcalcUpAverage(), GMEupdateAveragesMatrix(), limitedFillTableUp(), NNI(), NNIEdgeTest(), NNItopSwitch(), OLSext(), OLSint(), testEdge(), updatePair(), updateSizes(), updateSubTree(), updateSubTreeAfterNNI(), updateSubTreeAverages(), WFext(), and WFint().
◆ updateSizes() void updateSizes ( meEdge * e, int direction )Definition at line 218 of file graph.cpp.
References meEdge::bottomsize, DOWN, f, meEdge::head, meNode::leftEdge, NULL, meNode::parentEdge, meNode::rightEdge, siblingEdge(), meEdge::tail, meEdge::topsize, and UP.
Referenced by GMEsplitEdge().
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