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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/NNI_8cpp_source.html below:

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

50 double wf

(

double lambda

,

double

D_LR,

double

D_LU,

double

D_LD,

51  double

D_RU,

double

D_RD,

double

D_DU);

59  if

(

T

->root ==

f

->tail)

71

(

g

->bottomsize*

A

[

f

->head->index][

g

->head->index]

78  g

=

f

->tail->parentEdge;

95  A

= (

double

**)

malloc

(

T

->size*

sizeof

(

double

*));

96  for

(

i

= 0;

i

<

T

->size;

i

++)

98  A

[

i

] = (

double

*)

malloc

(

T

->size*

sizeof

(

double

));

99  for

(j=0;j<

T

->size;j++)

106 double wf2

(

double lambda

,

double

D_AD,

double

D_BC,

double

D_AC,

double

D_BD,

107  double

D_AB,

double

D_CD)

120  double

D_LR, D_LU, D_LD, D_RD, D_RU, D_DU;

132  lambda

[0] = ((double)

b

*c +

a

*d)/((

a

+

b

)*(c+d));

133  lambda

[1] = ((double)

b

*c +

a

*d)/((

a

+ c)*(

b

+d));

134  lambda

[2] = ((double) c*d +

a

*

b

)/((

a

+ d)*(

b

+c));

143

w0 =

wf2

(

lambda

[0],D_RU,D_LD,D_LU,D_RD,D_DU,D_LR);

144

w1 =

wf2

(

lambda

[1],D_RU,D_LD,D_DU,D_LR,D_LU,D_RD);

145

w2 =

wf2

(

lambda

[2],D_DU,D_LR,D_LU,D_RD,D_RU,D_LD);

159

printf(

"Swap across %s. "

,e->

label

);

160

printf(

"Weight dropping by %lf.\n"

,w0 - w2);

161

printf(

"New weight should be %lf.\n"

,

T

->weight + w2 - w0);

171

printf(

"Swap across %s. "

,e->

label

);

172

printf(

"Weight dropping by %lf.\n"

,w0 - w2);

173

printf(

"New weight should be %lf.\n"

,

T

->weight + w2 - w0);

182

printf(

"Swap across %s. "

,e->

label

);

183

printf(

"Weight dropping by %lf.\n"

,w0 - w1);

184

printf(

"New weight should be %lf.\n"

,

T

->weight + w1 - w0);

224  while

(

swap

!= elooper)

242

elooper =

T

->root->leftEdge;

243  while

((elooper !=

swap

) && (elooper != e))

256  while

(

NULL

!= elooper)

275

printf(

"Branch swap across meEdge %s.\n"

,e->

label

);

277  if

(

LEFT

== direction)

287

printf(

"Branch swap: switching edges %s and %s.\n"

,skew->

label

,

swap

->label);

295  if

(

LEFT

== direction)

312 void reHeapElement

(

int

*p,

int

*q,

double

*v,

int

length,

int i

);

313 void pushHeap

(

int

*p,

int

*q,

double

*v,

int

length,

int i

);

314 void popHeap

(

int

*p,

int

*q,

double

*v,

int

length,

int i

);

318  double

*weights,

int

*

location

,

int

*possibleSwaps)

340 int makeThreshHeap

(

int

*p,

int

*q,

double

*v,

int

arraySize,

double

thresh);

355

weights = (

double

*)

malloc

((

T

->size+1)*

sizeof

(double));

357  for

(

i

=0;

i

<

T

->size+1;

i

++)

383  while

(weights[p[1]] < -1e-8)

385

centerEdge = edgeArray[p[1]];

387  T

->weight =

T

->weight + weights[p[1]];

392  popHeap

(p,q,weights,possibleSwaps--,1);

411  double

**avgDistArray;

meEdge * findBottomLeft(meEdge *e)

meEdge * siblingEdge(meEdge *e)

void NNItopSwitch(meTree *T, meEdge *e, int direction, double **A)

double ** buildAveragesTable(meTree *T, double **D)

void NNI(meTree *T, double **avgDistArray, int *count)

void pushHeap(int *p, int *q, double *v, int length, int i)

void NNIwithoutMatrix(meTree *T, double **D, int *count)

void reHeapElement(int *p, int *q, double *v, int length, int i)

int NNIEdgeTest(meEdge *e, meTree *T, double **A, double *weight)

int makeThreshHeap(int *p, int *q, double *v, int arraySize, double thresh)

meEdge * moveUpRight(meEdge *e)

double wf2(double lambda, double D_AD, double D_BC, double D_AC, double D_BD, double D_AB, double D_CD)

void NNIRetestEdge(int *p, int *q, meEdge *e, meTree *T, double **avgDistArray, double *weights, int *location, int *possibleSwaps)

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

void popHeap(int *p, int *q, double *v, int length, int i)

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

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

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

void permInverse(int *p, int *q, int length)

void NNIWithPartialMatrix(meTree *T, double **D, double **A, int *count)

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

void NNIupdateAverages(double **A, meEdge *e, meEdge *par, meEdge *skew, meEdge *swap, meEdge *fixed, meTree *T)

static const char location[]

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#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.

unsigned int

A callback function used to compare two keys in a database.

while(yy_chk[yy_base[yy_current_state]+yy_c] !=yy_current_state)

const struct ncbi::grid::netcache::search::fields::SIZE size

double lambda(size_t dimMatrix_, const Int4 *const *scoreMatrix_, const double *q_)

struct meEdge * rightEdge

struct meEdge * parentEdge

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

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