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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cuSeqTreeSlc_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/structure/cd_utils/cuSeqTreeSlc.cpp Source File

50 return a

;

129 for

(

int i

=0;

<nnodes; ++

) {

156 if

(idmin == jdmin) {

157

cerr <<

"Error: You cannot join node "

<< idmin <<

" to itself.\n"

;

161 if

(idmin < 0 || idmin > maxIndex || jdmin < 0 || jdmin > maxIndex || m_nextNode < 0 || m_nextNode > maxIndex+1) {

165

cerr <<

"Warning: Out of range index in Join: "

<< idmin <<

" " 166

<< jdmin <<

" "

m_nextNode

" Max allowed index: "

<< maxIndex << endl;

180 while

(tmpi == idmin || tmpi == jdmin) {

185

cit->distance = tmpd;

189

tmpi = -(idmin+jdmin);

190

cerr <<

"Error: iterator found (id= "

<< cit->rowID <<

") not attached to hub.\n"

;

193 m_items

[tmpi]->distance = tmpd;

199

cit->distance = tmpd;

201

tmpi = -(idmin+jdmin);

202

cerr <<

"Error: iterator found (id= "

<< cit->rowID <<

") not attached to hub for last nodes.\n"

;

205 m_items

[tmpi]->distance = tmpd;

210

tmpi = (tmpi==idmin) ? jdmin : -(idmin+jdmin);

219 int

* indexMap =

new int

[

m_nseqs

];

221

indexMap[

] =

+1;

223 for

(it=1; it<=

m_nseqs

-1; ++it) {

247 int

imin = 0, jmin = 0;

252 string

newickStr =

""

;

262

}

else if

m_dm

) {

274 double

* internalDistCorrection =

new double

[

m_nseqs

];

279 int

* indexMap =

new int

[

m_nseqs

]{ 0 };

283 if

(indexMap == 0 || internalDistCorrection == 0) {

289

indexMap[

] =

+1;

290

internalDistCorrection[

] = 0.0;

299

ppDists =

new double

m_nseqs

];

301

ppDists[

] =

new double

[

m_nseqs

];

312 for

(

int

it=1; it<=

m_nseqs

-1; ++it) {

319 for

(

=0;

<j; ++

) {

321 if

(ppDists[j][

] < minval) {

322

minval = ppDists[j][

];

332

pFunc(

count

, total);

334

idmin = indexMap[imin];

335

jdmin = indexMap[jmin];

345

ilen = 0.5*ppDists[imin][jmin] - internalDistCorrection[imin];

346

jlen = 0.5*ppDists[imin][jmin] - internalDistCorrection[jmin];

363 Join

(idmin, jdmin, ilen, jlen);

365

internalDistCorrection[imin] = 0.5*ppDists[imin][jmin];

372

ppDists[k][imin] =

myMin

(ppDists[k][imin], ppDists[k][jmin]);

373

ppDists[k][jmin] = 0.0;

374

ppDists[jmin][k] = 0.0;

375

ppDists[imin][k] = ppDists[k][imin];

378

ppDists[imin][imin] = 0.0;

392 delete

[] ppDists[

];

397 delete

[] internalDistCorrection;

double FastGet(const int RowIndex, const int ColIndex) const

static std::string toNestedString(const SeqTree &seqTree)

virtual void ComputeTree(SeqTree *tree, pProgressFunction pFunc)

virtual long GetNumLoopsForTreeCalc()

int numChildren(const TSeqIt &sit)

static const DistanceMatrix::TMatType INIT_MINIMA

static const ETreeMethod MY_TREE_METHOD

vector< SeqItem * > m_items

static const double REPLACE_NEG_DIST

virtual ~SLC_TreeAlgorithm()

static const int BAD_INDEX

virtual void SetDistMat(DistanceMatrix *dm)

static const Rootedness MY_ROOTEDNESS

static const int USED_ROW

virtual string toString()

void Join(int inode1, int inode2, double len1, double len2)

void midpointRootIfNeeded()

iter append_child(iter position)

pre_order_iterator begin() const

iter insert(iter position, const T &x)

unsigned int number_of_children(const iterator_base &) const

iter reparent(iter position, sibling_iterator begin, sibling_iterator end)

void(* pProgressFunction)(int Num, int Total)

double myMin(double a, double b)

#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.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

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