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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cuCdFromFasta_8hpp_source.html below:

NCBI C++ ToolKit: include/algo/structure/cd_utils/cuCdFromFasta.hpp Source File

Go to the documentation of this file.

Go to the SVN repository for this file.

35 #ifndef CU_CDFROMFASTA_HPP 36 #define CU_CDFROMFASTA_HPP 60 string

s =

"Cd accession = "

+ cdAcc +

"\n"

;

61

s.append(

"Cd name = "

+ cdName +

"\n"

);

62

s.append(

"use local ids? "

+ ((useLocalIds) ?

string

(

"Yes\n"

) :

string

(

"No\n"

)));

63

s.append(

"use as is? "

+ ((useAsIs) ?

string

(

"Yes\n"

) :

string

(

"No\n"

)));

64

s.append(

"masterMethod = "

NStr::UIntToString

((

unsigned int

) masterMethod) +

"\n"

);

82 bool

ImportAlignmentData(

const string

& fastaFile,

bool

cleanUp =

false

);

85 bool

UpdateSourceId(

const string

& sourceId,

int version

= 0);

88 bool

WriteToFile(

const string

& outputFile)

const

;

90 bool WasInputError

()

const

{

return

m_fastaInputErrorMsg.length() > 0; }

101 string

GetDeflineReadFromFile(

unsigned int

index)

const

;

102 string

GetSequenceReadFromFile(

unsigned int

index)

const

;

108 string

GetColumnReadFromFile(

unsigned int column

)

const

;

123 void

ResetInitialMasterSequenceIndex();

148 void

InitializeParameters(

const

Fasta2CdParams* params =

NULL

);

Concrete implementations of the CFastaIOWrapper virtual class.

unsigned int m_initialMasterSequenceIndex

void SetParameters(const Fasta2CdParams &params)

CCdFromFasta(const CCdFromFasta &value)

bool WasInputError() const

unsigned int GetInitialMasterSequenceIndex() const

CBasicFastaWrapper * m_fastaIO

string m_fastaInputErrorMsg

CSeqAnnotFromFasta::MasteringMethod TMasterMethod

Fasta2CdParams m_parameters

string GetFastaInputErrorMsg() const

CCdFromFasta & operator=(const CCdFromFasta &value)

static const char * column

static const column_t columns[]

#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 UIntToString(unsigned int value, TNumToStringFlags flags=0, int base=10)

Convert UInt to string.

#define NCBI_CDUTILS_EXPORT

const string version

version string

const GenericPointer< typename T::ValueType > T2 value

TMasterMethod masterMethod

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