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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/bme_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/phy_tree/fastme/bme.cpp Source File

61

-

A

[

g

->head->index][

f

->head->index]);

69

-

A

[

f

->head->index][

g

->head->index]);

75  int

up, down, left, right;

80

e->

distance

= 0.25*(

A

[up][left] +

A

[up][right] +

A

[left][down] +

A

[right][down]) - 0.5*(

A

[down][up] +

A

[left][right]);

115  if

(

T

->root == e->

tail

)

159  meNode

*root,

double

dcoeff,

int

direction)

193  meNode

*newNode,

double

dcoeff,

int

direction)

246  meEdge

*sib, *par, *left, *right;

277 double wf3

(

double

D_AB,

double

D_AC,

double

D_kB,

double

D_kC)

279  return

(D_AC + D_kB - D_AB - D_kC);

302

sprintf(nodeLabel,

"I%d"

,

T

->size+1);

303

sprintf(edgeLabel1,

"E%d"

,

T

->size);

304

sprintf(edgeLabel2,

"E%d"

,

T

->size+1);

309

newPendantEdge =

makeEdge

(edgeLabel1,newNode,v,0.0);

310

newInternalEdge =

makeEdge

(edgeLabel2,newNode,e->

head

,0.0);

324  T

->size =

T

->size + 2;

329

newNode->

leftEdge

= newInternalEdge;

334

newNode->

leftEdge

= newInternalEdge;

370

sprintf(e->

label

,

"E1"

);

384

e_min =

T

->root->leftEdge;

401

printf(

"Inserting %s between %s and %s on %s\n"

,v->

label

,e_min->

tail

->

label

,

413  if

(!(

leaf

(

g

->tail)))

429

e =

T

->root->leftEdge;

431  while

(

NULL

!=

f

) {

432  if

(

leaf

(

f

->head))

437

u =

f

->head->leftEdge->head;

438

v =

f

->head->rightEdge->head;

445  while

(

T

->root->leftEdge != e) {

447  while

(

T

->root->leftEdge !=

f

) {

452  if

(

leaf

(

f

->head))

458

u =

f

->head->leftEdge->head;

461

v =

f

->head->rightEdge->head;

478  while

(

T

->root->leftEdge != e)

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

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

meEdge * siblingEdge(meEdge *e)

void updateSubTree(double **A, meEdge *nearEdge, meNode *v, meNode *root, meNode *newNode, double dcoeff, int direction)

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

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

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

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

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

void updatePair(double **A, meEdge *nearEdge, meEdge *farEdge, meNode *v, meNode *root, double dcoeff, int direction)

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

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

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

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

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

double wf3(double D_AB, double D_AC, double D_kB, double D_kC)

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

void calcUpAverages(double **D, double **A, meEdge *e, meEdge *g)

meEdge * makeEdge(const char *label, meNode *tail, meNode *head, double weight)

meNode * makeNewNode(const char *label, int i)

#define NODE_LABEL_LENGTH

#define EDGE_LABEL_LENGTH

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

struct meEdge * rightEdge

struct meEdge * parentEdge

int g(Seg_Gsm *spe, Seq_Mtf *psm, Thd_Gsm *tdg)

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