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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cuCdFromFasta_8cpp_source.html below:

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

isNull = (!params);

, nSeq = 1;

(fastaFile.size() == 0) {

(bs.

().Set().size() == 0) {

cerr <<

<< nSeq <<

<< endl;

(!bs.

().Set().front()->IsTitle())

;

(

<< nSeq <<

<<

<<

);

(

);

bs.

().Set().front()->SetTitle().resize(

-1);

gap =

;

= 0, nNoSuchColumn = 0;

(;

< nRead; ++

) {

(

< rowSequence.length()) {

(nNoSuchColumn == nRead) {

gap =

;

* letters(

);

rowSequence, columnString;

nColumns, col;

= 0, nNoSuchColumn = 0;

(;

< nRead; ++

) {

nColumns = activeSequences[0].length();

(col = 0; col < nColumns; ++col) {

columnString.

();

(col < activeSequences[

].length()) {

columnString += activeSequences[

][col];

(nNoSuchColumn == nRead) {

columnString.

();

(skipGappedColumns) {

nonLetterPosition = columnString.find_first_not_of(letters);

(nonLetterPosition !=

) {

columnString.erase();

(columnString.length() > 0) {

foundExisting =

;

= (sourceId.length() > 0);

CCdd_descr_set::Tdata::iterator

;

GID->SetAccession(sourceId);

((*i)->IsSource_id()) {

(*i)->SetSource_id().

();

(*i)->SetSource_id().Set().push_back(ID);

foundExisting =

;

(

&& !foundExisting) {

setOfIds->

().push_back(ID);

descr->SetSource_id(*setOfIds);

* cdExt =

;

cdOutFile, cdOutExt, err;

cdOutFile = (outputFile.size() > 0) ? outputFile :

;

(cdOutFile.length() > 0 && cdOutExt != cdExt) {

(!

(cdOutFile.c_str(), *

,

, &err)) {

cerr <<

<< cdOutFile << endl << err << endl;

Concrete implementations of the CFastaIOWrapper virtual class.

void SetFastaFlags(TReadFastaFlags flagsToSet)

bool AddCddDescr(CRef< CCdd_descr > &descr)

void SetAccession(string Accession, int Version)

string GetColumnReadFromFile(unsigned int column) const

void InitializeParameters(const Fasta2CdParams *params=NULL)

string GetDeflineReadFromFile(unsigned int index) const

unsigned int m_initialMasterSequenceIndex

void ResetInitialMasterSequenceIndex()

bool UpdateSourceId(const string &sourceId, int version=0)

bool WriteToFile(const string &outputFile) const

unsigned int GetColumnsReadFromFile(map< unsigned int, string > &columns, bool skipGappedColumns) const

string GetSequenceReadFromFile(unsigned int index) const

bool ImportAlignmentData(const string &fastaFile, bool cleanUp=false)

unsigned int GetAllColumnsReadFromFile(map< unsigned int, string > &columns) const

unsigned int GetGaplessColumnsReadFromFile(map< unsigned int, string > &gaplessColumns) const

CBasicFastaWrapper * m_fastaIO

string m_fastaInputErrorMsg

Fasta2CdParams m_parameters

const CRef< CSeq_entry > & GetSeqEntry() const

virtual unsigned int GetNumRead() const

virtual string GetActiveSequence(unsigned int index, bool removeWhitespace=true) const

virtual string GetActiveDefline(unsigned int index) const

static bool PurgeNonAlphaFromSequence(CBioseq &bioseq)

@ eMostAlignedAndFewestGaps

const CRef< CSeq_annot > & GetSeqAnnot() const

unsigned int GetMasterIndex() const

virtual bool MakeSeqAnnotFromFasta(CNcbiIstream &is, CFastaIOWrapper &fastaIO, MasteringMethod masterMethod, unsigned int masterIndex=(unsigned int) eUnassignedMaster)

static bool WriteASNToFile(const char *filename, const ASNClass &ASNobject, bool isBinary, std::string *err, ncbi::EFixNonPrint fixNonPrint=ncbi::eFNP_Default)

#define test(a, b, c, d, e)

static const char * column

static const column_t columns[]

static void SplitPath(const string &path, string *dir=0, string *base=0, string *ext=0)

Split a path string into its basic components.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

CFastaReader::TFlags TReadFastaFlags

@ fNoParseID

Generate an ID (whole defline -> title)

@ fForceType

Force specified type regardless of accession.

@ fAssumeProt

Assume prots unless accns indicate otherwise.

bool GoodVisibleChar(char c)

#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.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

NCBI_NS_STD::string::size_type SIZE_TYPE

bool IsSetDescription(void) const

status, references, etc.

TGid & SetGid(void)

Select the variant.

TSequences & SetSequences(void)

Assign a value to Sequences data member.

Tdata & Set(void)

Assign a value to data member.

TSeqannot & SetSeqannot(void)

Assign a value to Seqannot data member.

Tdata & Set(void)

Assign a value to data member.

TDescription & SetDescription(void)

Assign a value to Description data member.

TName & SetName(void)

Assign a value to Name data member.

virtual void Reset(void)

Reset the whole object.

TSet & SetSet(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

void ResetDescr(void)

Reset Descr data member.

bool IsSetDescr(void) const

descriptors Check if a value has been assigned to Descr data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

unsigned int

A callback function used to compare two keys in a database.

const string version

version string

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

std::istream & in(std::istream &in_, double &x_)

#define row(bind, expected)

TMasterMethod masterMethod

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