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

-

[

->head->index][

->head->index]);

(

,

D_LR,

D_LU,

D_LD,

D_RU,

D_RD,

D_DU)

*left, *right, *sib;

(

(

->head))

=

->head->leftEdge;

h =

->head->rightEdge;

(

,

lambda2,

D_AB,

D_AC,

D_BC,

D_Av,

D_Bv,

D_Cv)

(((1 -

) * (D_AC + D_Bv) + (lambda2 - 1)*(D_AB + D_Cv)

+ (

- lambda2)*(D_BC + D_Av)));

(

=0;

<d;

++)

printf(

,

[

][j]);

printf(

,v->

);

sprintf(e->

,

);

e_min =

->root->leftEdge;

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

sprintf(nodelabel,

,

->size+1);

sprintf(edgelabel,

,

->size);

newPendantEdge =

(edgelabel,newNode,v,0.0);

sprintf(edgelabel,

,

->size+1);

newInternalEdge =

(edgelabel,newNode,e->

,0.0);

printf(

,

->size =

->size + 2;

newNode->

= newInternalEdge;

newNode->

= newInternalEdge;

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

void printDoubleTable(double **A, int d)

void assignAllSizeFields(meTree *T)

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

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

void assignTopsize(meEdge *e, int numLeaves)

meEdge * siblingEdge(meEdge *e)

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

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

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

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

void assignBottomsize(meEdge *e)

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

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

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

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

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

void updateSizes(meEdge *e, int direction)

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

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

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

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.

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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