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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/fastme_8cpp_source.html below:

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

67 double

loadMatrix

(

double

**table_in,

char

**labels,

int

*size_in,

meSet

);

88 while

(counter < argc)

90 switch

(argv[counter][1])

94 if

(

NULL

!= argv[counter])

98

fprintf(stderr,

"Error: -d flag requires argument.\n"

);

105 if

(

NULL

!= argv[counter])

109

fprintf(stderr,

"Error: -o flag requires argument.\n"

);

116 if

(

NULL

!= argv[counter])

120

fprintf(stderr,

"Error: -i flag requires argument.\n"

);

128 switch

(argv[counter][0])

141

fprintf(stderr,

"Unknown argument to -w option: please"

);

142

fprintf(stderr,

" use (b)alanced or (O)LS\n"

);

149 switch

(argv[counter][0])

162

fprintf(stderr,

"Unknown argument to -b option: please"

);

163

fprintf(stderr,

" use BME or GME\n"

);

170

*numDataSets =

= 0;

171 while

(argv[counter][

])

172

*numDataSets = 10* (*numDataSets) + (argv[counter][

++] -

'0'

);

177 switch

(argv[counter][0])

194

fprintf(stderr,

"Unknown argument to -s option: please"

);

195

fprintf(stderr,

" use BME, GME, or none\n"

);

206

fprintf(stderr,

"Usage: fastme -binostv\n"

);

207

fprintf(stderr,

"-b specify method for building initial tree: "

);

208

fprintf(stderr,

"BME or GME(default).\n"

);

209

fprintf(stderr,

"-i filename of distance matrix\n"

);

210

fprintf(stderr,

"-n number of trees/matrices input (default = 1)\n"

);

211

fprintf(stderr,

"-o filename for meTree output\n"

);

212

fprintf(stderr,

"-s specify type of meTree swapping (NNIs): "

);

213

fprintf(stderr,

"(b)alanced, (O)LS, or (n)one. (Default is balanced.)\n"

);

214

fprintf(stderr,

"-t (optional) filename of starting meTree topology\n"

);

216

fprintf(stderr,

"-v for verbose output\n"

);

217

fprintf(stderr,

"-w (b)alanced or (O)LS weights (if not doing NNIs on input topology) \n"

);

218

fprintf(stderr,

"-help to get this message\n"

);

228 A

= (

double

**)

malloc

(d*

sizeof

(

double

*));

229 for

(

=0;

<d;

++)

231 A

[

] = (

double

malloc

(d*

sizeof

(

double

));

240 meTree

fastme_run

(

double

** D_in,

int

numSpecies_in,

char

**labels,

int

btype_in,

int

wtype_in,

int

ntype_in)

248 meSet

*species, *slooper;

259 int

ntype = ntype_in, btype = btype_in, wtype = wtype_in;

261

numSpecies = numSpecies_in;

291 while

( setCounter < numSets ) {

314 for

(slooper = species;

NULL

!= slooper; slooper = slooper->

secondNode

)

318 for

(slooper = species;

NULL

!= slooper; slooper = slooper->

secondNode

)

337 NNI

(

,&nniCount);

361

fprintf(stderr,

"Error in program: variable 'btype' has illegal "

);

362

fprintf(stderr,

"value %d.\n"

,btype);

367

fprintf(stderr,

"Error in program: variable 'ntype' has illegal "

);

368

fprintf(stderr,

"value %d.\n"

,ntype);

383

printf(

"Performed %d NNIs on data meSet %d\n"

,nniCount,setCounter);

void freeMatrix(double **D, int size)

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

void assignAllSizeFields(meTree *T)

void partitionSizes(meTree *T)

void compareSets(meTree *T, meSet *S, FILE *ofile)

void chooseSettings(int argc, char **argv, int *btype, int *ntype, int *wtype, int *numDataSets, char **filenames)

double ** initDoubleMatrix(int d)

void NewickPrintTree(meTree *T, FILE *ofile)

double ** loadMatrix(double **table_in, char **labels, int *size_in, meSet *S)

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

meTree * loadNewickTree(FILE *ifile, int numLeaves)

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

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

double ** loadMatrixOLD(FILE *ifile, int *size, meSet *S)

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

meTree * detrifurcate(meTree *T)

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

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

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

char * NewickPrintTreeString(meTree *T)

meTree * fastme_run(double **D_in, int numSpecies_in, char **labels, int btype_in, int wtype_in, int ntype_in)

#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.

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

struct meSet * secondNode

struct meNode * firstNode

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