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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/newickstring_8cpp_source.html below:

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

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63  if

((

' '

== c) || (

'\t'

== c) || (

'\n'

== c))

89

strcpy(

label

,

"Default Label"

);

93  if

(

'('

== treeString[0])

104  if

(

'('

!= treeString[0])

106

fprintf(stderr,

"Error reading subtree.\n"

);

113  if

(

'('

== treeString[

i

])

122  while

((

'('

!= treeString[

i

]) && (

')'

!= treeString[

i

]))

124  if

(

'('

== treeString[

i

])

126  else if

(

')'

== treeString[

i

])

148  if

(

':'

== treeString[

i

])

150

sprintf(thisNode->

label

,

"I%d"

,(*uCount)++);

155  while

((

':'

!= treeString[

i

]) && (

','

!= treeString[

i

]))

159  for

(

i

= left;

i

< right;

i

++)

161

thisNode->

label

[j++] = treeString[

i

];

162

thisNode->

label

[j] =

'\0'

;

164  if

(

':'

== treeString[right])

173

((

','

!= treeString[

i

]) && (

')'

!= treeString[

i

]))

176  if

(

','

== treeString[right])

181  for

(

i

= left;

i

< right;

i

++)

182

stringWeight[j++] = treeString[

i

];

183

stringWeight[j] =

'\0'

;

184

thisWeight = atof(stringWeight);

185

thisEdge =

makeEdge

(

label

,centerNode,thisNode,thisWeight);

195

fprintf(stderr,

"Error: meNode %s has too many (>3) children.\n"

,centerNode->

label

);

223  if

(

NULL

== nextString)

226  while

(1 == fscanf(ifile,

"%c"

,&c))

237

nextString[

i

++] =

' '

;

240

nextString[

i

++] = c;

245  if

(

'('

!= nextString[0])

247

fprintf(stderr,

"Error reading input file - does not start with '('.\n"

);

251  for

(

i

= 0;

i

< inputLength;

i

++)

253  if

(

'('

== nextString[

i

])

255  else if

(

')'

== nextString[

i

])

259  else if

(0 == parCount)

262  if

(

';'

== nextString[

i

])

263

strcpy(rootLabel,

"URoot"

);

266  while

(

';'

!= nextString[

i

])

268

rootLabel[j++] = nextString[

i

-1];

269

rootLabel[j] =

'\0'

;

273  else if

(parCount < 0)

275

fprintf(stderr,

"Error reading meTree input file. Too many right parentheses.\n"

);

280

strcpy(centerNode->

label

,rootLabel);

281  T

->root = centerNode;

290

fprintf(stderr,

"Error with Newick Printing routine.\n"

);

295

fprintf(ofile,

"("

);

297

fprintf(ofile,

", "

);

299

fprintf(ofile,

")"

);

301

fprintf(ofile,

" "

);

302

fprintf(ofile,

"%s "

,e->

head

->

label

);

303

fprintf(ofile,

":%lf"

,e->

distance

);

309  int

slength, llength, rlength;

313  if

(!(

NULL

== left))

318

s[1 + llength] =

','

;

321

s[2 + rlength + llength]=

')'

;

322

slength = 3 + rlength + llength;

325  while

(

'\0'

!= s[slength])

335

e =

T

->root->leftEdge;

336

rootchild = e->

head

;

337

fprintf(ofile,

"(%s: %lf"

,

T

->root->label,e->

distance

);

341

fprintf(ofile,

","

);

347

fprintf(ofile,

","

);

350

fprintf(ofile,

")"

);

352

fprintf(ofile,

"%s"

,rootchild->

label

);

353

fprintf(ofile,

";\n"

);

359  int i

,slength, llength, rlength;

361

e =

T

->root->leftEdge;

364

+ 2*

T

->size +

T

->size + (

T

->size-1) + 1;

369

s = (

char

*)

malloc

(slength*

sizeof

(

char

));

374  if

(!(

NULL

== left))

378

s[1 + llength] =

','

;

381

s[2 + rlength + llength]=

','

;

382  i

= 3 + rlength + llength;

#define ReadOpenParenthesis

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

meNode * makeNode(const char *label, meEdge *parentEdge, int index)

#define NODE_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.

static const char label[]

void NewickPrintTree(meTree *T, FILE *ofile)

meTree * loadNewickTree(FILE *ifile, int numLeaves)

meNode * decodeNewickSubtree(char *treeString, meTree *T, int *uCount)

boolean whiteSpace(char c)

void NewickPrintSubtree(meTree *T, meEdge *e, FILE *ofile)

int NewickPrintSubtreeString(meTree *T, meEdge *e, char *s)

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

char * NewickPrintTreeString(meTree *T)

struct meEdge * rightEdge

struct meEdge * parentEdge

struct meEdge * middleEdge

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