NCBI C++ ToolKit
Functions
gme.cpp File Reference
#include <ncbi_pch.hpp>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "graph.h"
#include "fastme.h"
+ Include dependency graph for gme.cpp:

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Functions

meEdge * siblingEdge (meEdge *e)
 
boolean leaf (meNode *v)
 
meEdge * depthFirstTraverse (meTree *T, meEdge *e)
 
meEdge * topFirstTraverse (meTree *T, meEdge *e)
 
void fillTableUp (meEdge *e, meEdge *f, double **A, double **D, meTree *T)
 
void updateSizes (meEdge *e, int direction)
 
void OLSext (meEdge *e, double **A)
 
double wf (double lambda, double D_LR, double D_LU, double D_LD, double D_RU, double D_RD, double D_DU)
 
void OLSint (meEdge *e, double **A)
 
void assignOLSWeights (meTree *T, double **A)
 
void makeOLSAveragesTable (meTree *T, double **D, double **A)
 
void GMEcalcDownAverage (meNode *v, meEdge *e, double **D, double **A)
 
void GMEcalcUpAverage (meNode *v, meEdge *e, double **D, double **A)
 
void GMEcalcNewvAverages (meTree *T, meNode *v, double **D, double **A)
 
double wf4 (double lambda, double lambda2, double D_AB, double D_AC, double D_BC, double D_Av, double D_Bv, double D_Cv)
 
void testEdge (meEdge *e, meNode *v, double **A)
 
void printDoubleTable (double **A, int d)
 
void GMEsplitEdge (meTree *T, meNode *v, meEdge *e, double **A)
 
meTree * GMEaddSpecies (meTree *T, meNode *v, double **D, double **A)
 
void updateSubTreeAverages (double **A, meEdge *e, meNode *v, int direction)
 
void GMEupdateAveragesMatrix (double **A, meEdge *e, meNode *v, meNode *newNode)
 
void assignBottomsize (meEdge *e)
 
void assignTopsize (meEdge *e, int numLeaves)
 
void assignAllSizeFields (meTree *T)
 

Function Documentation

◆ assignAllSizeFields()

void assignAllSizeFields ( meTree *  T)

Definition at line 676 of file gme.cpp.

References assignBottomsize(), assignTopsize(), and T.

Referenced by fastme_run().

◆ assignBottomsize()

void assignBottomsize ( meEdge *  e)

Definition at line 653 of file gme.cpp.

References meEdge::bottomsize, meEdge::head, leaf(), meNode::leftEdge, and meNode::rightEdge.

Referenced by assignAllSizeFields().

◆ assignOLSWeights()

void assignOLSWeights ( meTree *  T,
double **  A 
)

Definition at line 106 of file gme.cpp.

References depthFirstTraverse(), meEdge::head, leaf(), NULL, OLSext(), OLSint(), T, and meEdge::tail.

Referenced by fastme_run().

◆ assignTopsize()

void assignTopsize ( meEdge *  e,
int  numLeaves 
)

Definition at line 666 of file gme.cpp.

References meEdge::bottomsize, meEdge::head, meNode::leftEdge, NULL, meNode::rightEdge, and meEdge::topsize.

Referenced by assignAllSizeFields().

◆ depthFirstTraverse()

meEdge* depthFirstTraverse ( meTree *  T,
meEdge *  e 
)

Definition at line 65 of file traverse.cpp.

Referenced by assignOLSWeights(), GMEcalcNewvAverages(), and makeOLSAveragesTable().

◆ fillTableUp()

void fillTableUp ( meEdge *  e,
meEdge *  f,
double **  A,
double **  D,
meTree *  T 
)

Definition at line 56 of file NNI.cpp.

References meEdge::bottomsize, f(), g(), meEdge::head, meNode::index, meNode::index2, leaf(), meNode::leftEdge, meNode::rightEdge, siblingEdge(), and T.

Referenced by makeOLSAveragesTable().

◆ GMEaddSpecies()

meTree* GMEaddSpecies ( meTree *  T,
meNode *  v,
double **  D,
double **  A 
)

Definition at line 294 of file gme.cpp.

References meEdge::bottomsize, GMEcalcNewvAverages(), GMEsplitEdge(), meEdge::head, meNode::index, meNode::index2, meNode::label, meEdge::label, meNode::leftEdge, makeEdge(), newTree(), NULL, meNode::parentEdge, meTree::root, meTree::size, T, testEdge(), topFirstTraverse(), meEdge::topsize, and meEdge::totalweight.

Referenced by fastme_run().

◆ GMEcalcDownAverage()

void GMEcalcDownAverage ( meNode *  v,
meEdge *  e,
double **  D,
double **  A 
)

Definition at line 190 of file gme.cpp.

References meEdge::bottomsize, meEdge::head, meNode::index, meNode::index2, leaf(), meNode::leftEdge, and meNode::rightEdge.

Referenced by GMEcalcNewvAverages().

◆ GMEcalcNewvAverages()

void GMEcalcNewvAverages ( meTree *  T,
meNode *  v,
double **  D,
double **  A 
)

Definition at line 224 of file gme.cpp.

References depthFirstTraverse(), GMEcalcDownAverage(), GMEcalcUpAverage(), NULL, T, and topFirstTraverse().

Referenced by GMEaddSpecies().

◆ GMEcalcUpAverage()

void GMEcalcUpAverage ( meNode *  v,
meEdge *  e,
double **  D,
double **  A 
)

Definition at line 206 of file gme.cpp.

References meEdge::bottomsize, meEdge::head, meNode::index, meNode::index2, NULL, meNode::parentEdge, siblingEdge(), meEdge::tail, and meEdge::topsize.

Referenced by GMEcalcNewvAverages().

◆ GMEsplitEdge()

void GMEsplitEdge ( meTree *  T,
meNode *  v,
meEdge *  e,
double **  A 
)

Definition at line 446 of file gme.cpp.

References meEdge::bottomsize, DOWN, EDGE_LABEL_LENGTH, GMEupdateAveragesMatrix(), meEdge::head, meNode::label, meEdge::label, meNode::leftEdge, makeEdge(), makeNewNode(), NODE_LABEL_LENGTH, meNode::parentEdge, meNode::rightEdge, T, meEdge::tail, meEdge::topsize, UP, and updateSizes().

Referenced by GMEaddSpecies().

◆ GMEupdateAveragesMatrix()

void GMEupdateAveragesMatrix ( double **  A,
meEdge *  e,
meNode *  v,
meNode *  newNode 
)

Definition at line 368 of file gme.cpp.

References meEdge::bottomsize, meEdge::head, meNode::index, LEFT, meNode::leftEdge, NULL, meNode::parentEdge, RIGHT, meNode::rightEdge, siblingEdge(), SKEW, meEdge::tail, meEdge::topsize, UP, and updateSubTreeAverages().

Referenced by GMEsplitEdge().

◆ leaf()

boolean leaf ( meNode *  v)

Definition at line 44 of file graph.cpp.

Referenced by assignBottomsize(), assignOLSWeights(), GMEcalcDownAverage(), makeOLSAveragesTable(), and OLSext().

◆ makeOLSAveragesTable()

void makeOLSAveragesTable ( meTree *  T,
double **  D,
double **  A 
)

Definition at line 120 of file gme.cpp.

References meEdge::bottomsize, depthFirstTraverse(), f(), fillTableUp(), g(), meEdge::head, meNode::index, meNode::index2, leaf(), meNode::leftEdge, NULL, meNode::parentEdge, meNode::rightEdge, T, and meEdge::tail.

Referenced by buildAveragesTable(), fastme_run(), and NNIWithPartialMatrix().

◆ OLSext()

void OLSext ( meEdge *  e,
double **  A 
)

Definition at line 58 of file gme.cpp.

References meEdge::distance, f(), g(), meEdge::head, meNode::index, leaf(), meNode::leftEdge, meNode::rightEdge, siblingEdge(), and meEdge::tail.

Referenced by assignOLSWeights().

◆ OLSint()

void OLSint ( meEdge *  e,
double **  A 
)

Definition at line 87 of file gme.cpp.

References meEdge::bottomsize, meEdge::distance, meEdge::head, meNode::index, lambda(), meNode::leftEdge, meNode::parentEdge, meNode::rightEdge, siblingEdge(), meEdge::tail, meEdge::topsize, and wf().

Referenced by assignOLSWeights().

◆ printDoubleTable()

void printDoubleTable ( double **  A,
int  d 
)

Definition at line 281 of file gme.cpp.

References i.

◆ siblingEdge()

meEdge* siblingEdge ( meEdge *  e)

Definition at line 210 of file graph.cpp.

Referenced by GMEcalcUpAverage(), GMEupdateAveragesMatrix(), OLSext(), OLSint(), testEdge(), and updateSubTreeAverages().

◆ testEdge()

void testEdge ( meEdge *  e,
meNode *  v,
double **  A 
)

Definition at line 261 of file gme.cpp.

References meEdge::bottomsize, meEdge::head, meNode::index, lambda(), meNode::parentEdge, siblingEdge(), meEdge::tail, meEdge::topsize, meEdge::totalweight, and wf4().

Referenced by GMEaddSpecies().

◆ topFirstTraverse()

meEdge* topFirstTraverse ( meTree *  T,
meEdge *  e 
)

Definition at line 107 of file traverse.cpp.

Referenced by GMEaddSpecies(), and GMEcalcNewvAverages().

◆ 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().

◆ updateSubTreeAverages()

void updateSubTreeAverages ( double **  A,
meEdge *  e,
meNode *  v,
int  direction 
)

Definition at line 503 of file gme.cpp.

References meEdge::bottomsize, meEdge::head, meNode::index, LEFT, meNode::leftEdge, NULL, meNode::parentEdge, RIGHT, meNode::rightEdge, siblingEdge(), SKEW, meEdge::tail, meEdge::topsize, and UP.

Referenced by GMEupdateAveragesMatrix().

◆ wf()

double wf ( double  lambda,
double  D_LR,
double  D_LU,
double  D_LD,
double  D_RU,
double  D_RD,
double  D_DU 
)

Definition at line 78 of file gme.cpp.

References lambda(), and weight.

Referenced by CTextUtil::AddWordFrequencies(), CWindowManagerService::InitService(), and OLSint().

◆ wf4()

double wf4 ( double  lambda,
double  lambda2,
double  D_AB,
double  D_AC,
double  D_BC,
double  D_Av,
double  D_Bv,
double  D_Cv 
)

Definition at line 247 of file gme.cpp.

References lambda().

Referenced by testEdge().

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