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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cuDistmat_8cpp_source.html below:

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

130 for

(j=0; j<

; ++j) {

144 for

(j=0; j<

; ++j) {

210

cerr <<

"Error: "

<< dim <<

" is an invalidof matrix dimensionality.\n"

;

220

nexpect = dim*(dim-1)/2;

226 while

(col < row && is >>

value

) {

237 while

(

row

!= dim && is >>

value

) {

244 if

(

row

!= dim) is >> seqId;

248 if

(

count

!= nexpect) {

249

cerr <<

"Error: "

<< nexpect <<

" values expected; "

count

" found.\n"

;

265 int

prec = os.precision();

266 string

seqId, cdAcc, notFound =

"<not found>"

;

271

IOS_BASE::fmtflags initFlags = os.setf(IOS_BASE::scientific,

272

IOS_BASE::floatfield);

280

os.setf(IOS_BASE::left, IOS_BASE::adjustfield);

281

os << setw(12) << cdAcc <<

" "

;

285

os.setf(IOS_BASE::left, IOS_BASE::adjustfield);

286

os << setw(12) << seqId <<

" "

;

287

os.setf(initFlags, IOS_BASE::adjustfield);

288 for

(

int

col=0; col<

row

; ++col) {

289

os << setw(10) << (*(const_cast<DistanceMatrix*>(

this

)))[

row

][col] <<

" "

;

299

os.setf(IOS_BASE::left, IOS_BASE::adjustfield);

300

os << setw(12) << cdAcc <<

" "

;

304

os.setf(IOS_BASE::left, IOS_BASE::adjustfield);

305

os << setw(12) << seqId <<

" "

;

306

os.setf(initFlags, IOS_BASE::adjustfield);

307 for

(

int

col=0; col<nrows; ++col) {

308

os << setw(10) << (*(const_cast<DistanceMatrix*>(

this

)))[

row

][col] <<

" "

;

void GetExtremalEntries(double &max, double &min, bool ignoreDiagonal=false)

void ReSize(const int NumRows, const int NumCols)

bool Get_GI_or_PDB_String_FromAlignment(int row, std::string &result) const

const RowSource & GetRowSource(int row) const

string GetAccession(int &Version) const

void printMat(bool triangular=true)

static bool DistMethodUsesScoringMatrix(EDistMethod method)

ScoreMatrix * m_scoreMatrix

static bool RequireAlignedBlocks(EDistMethod method)

void SetNTermExt(int ext)

virtual ~DistanceMatrix()

static const int OUTPUT_PRECISION

static const bool USE_ALIGNED_DEFAULT

void ReplaceZeroWithTinyValue(const double tiny=TINY_DISTANCE)

EScoreMatrixType GetMatrixType()

bool ResetMatrixType(EScoreMatrixType newType)

void SetCTermExt(int ext)

AlignmentCollection * m_aligns

string GetDistMethodName()

static void writeMat(ofstream &ofs, const DistanceMatrix &dm, bool triangular)

std::vector< std::string > m_ConvertedSequences

static const int INITIAL_SCORE_BOUND

static const double HUGE_DISTANCE

static const int NO_EXTENSION

static void readMat(ifstream &ifs, DistanceMatrix &dm, bool triangular)

static const double TINY_DISTANCE

static bool ExtensionsAllowed(EDistMethod method)

void SetData(AlignmentCollection *aligns)

virtual void initialize()

EScoreMatrixType GetType() const

const string DISTANCE_METHOD_NAMES[]

#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.

const GenericPointer< typename T::ValueType > T2 value

#define row(bind, expected)

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