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NCBI C++ ToolKit: include/algo/blast/blastinput/blast_input_aux.hpp Source File

: m_FileName(

), m_Version(use_versions ? 1 : 0) {}

constexpr

kDfltMaxLength = 256;

fname.

().size() < m_MaxLength;

: m_MinValue(

), m_MaxValue(

), m_Inclusive(inclusive) {}

: m_MinValue(

), m_MaxValue(

), m_Inclusive(inclusive) {}

retval =

;

( !m_Inclusive ) {

retval = (

> m_MinValue &&

< m_MaxValue);

retval = (

>= m_MinValue &&

<= m_MaxValue);

( !m_Inclusive ) {

); \

virtual bool Verify(const string& value) const { \

DataType value2check = String2DataTypeFn(value); \

ITERATE(set<DataType>, itr, m_AllowedValues) { \

if (*itr == value2check) { \

virtual string GetUsage(void) const { \

CNcbiOstrstream os; \

os << "Permissible values: "; \

ITERATE(set<DataType>, itr, m_AllowedValues) { \

os << "'" << *itr << "' "; \

return CNcbiOstrstreamToString(os); \

use_default =

,

task =

,

mt_mode =

);

use_lcase_masking,

gaps_to_Ns =

);

void CheckForEmptySequences(const TSeqLocVector &sequences, string &warnings)

Inspect the sequences parameter for empty sequences.

TSeqRange ParseSequenceRangeOpenEnd(const string &range_str, const char *error_prefix=NULL)

Parse and extract a sequence range from argument provided to this function.

bool HasRawSequenceData(const objects::CBioseq &bioseq)

Returns true if the Bioseq passed as argument has the full, raw sequence data in its Seq-inst field.

TSeqRange ParseSequenceRange(const string &range_str, const char *error_prefix=NULL)

Parse and extract a sequence range from argument provided to this function.

string CalculateFormattingParams(TSeqPos max_target_seqs, TSeqPos *num_descriptions, TSeqPos *num_alignments, TSeqPos *num_overview=NULL)

Calculates the formatting parameters based on the maximum number of target sequences selected (a....

#define DEFINE_CARGALLOW_SET_CLASS(ClassName, DataType, String2DataTypeFn)

Macro to create a subclass of CArgAllow that allows the specification of sets of data.

int GetQueryBatchSize(EProgram program, bool is_ungapped=false, bool remote=false, bool use_default=true, string task="", bool mt_mode=false)

Retrieve the appropriate batch size for the specified task.

CRef< objects::CScope > ReadSequencesToBlast(CNcbiIstream &in, bool read_proteins, const TSeqRange &range, bool parse_deflines, bool use_lcase_masking, CRef< CBlastQueryVector > &sequences, bool gaps_to_Ns=false)

Read sequence input for BLAST.

EProgram

This enumeration is to evolve into a task/program specific list that specifies sets of default parame...

Class to constrain the length of the file name passed to a given CArgDescriptions key.

virtual bool Verify(const string &value) const

Overloaded method from CArgAllow.

virtual string GetUsage(void) const

Overloaded method from CArgAllow.

Uint4 m_MaxLength

Maximum string length value for this object.

CArgAllowMaximumFileNameLength(Uint4 max=kDfltMaxLength)

Class to constrain the values of an argument to those in between the values specified in the construc...

double m_MaxValue

Maximum value for this object.

CArgAllowValuesBetween(int min, int max, bool inclusive=false)

Constructor taking an integer.

bool m_Inclusive

Whether the values above should be included or not.

CArgAllowValuesBetween(double min, double max, bool inclusive=false)

Constructor taking a double.

double m_MinValue

Minimum value for this object.

virtual string GetUsage(void) const

Overloaded method from CArgAllow.

virtual bool Verify(const string &value) const

Overloaded method from CArgAllow.

Class to constrain the values of an argument to those greater than or equal to the value specified in...

virtual bool Verify(const string &value) const

Overloaded method from CArgAllow.

double m_MinValue

Minimum value for this object.

virtual string GetUsage(void) const

Overloaded method from CArgAllow.

CArgAllowValuesGreaterThanOrEqual(int min)

Constructor taking an integer.

CArgAllowValuesGreaterThanOrEqual(double min)

Constructor taking a double.

Class to constrain the values of an argument to those less than or equal to the value specified in th...

double m_MaxValue

Maximum value for this object.

CArgAllowValuesLessThanOrEqual(double max)

Constructor taking a double.

virtual string GetUsage(void) const

Overloaded method from CArgAllow.

CArgAllowValuesLessThanOrEqual(int max)

Constructor taking an integer.

virtual bool Verify(const string &value) const

Overloaded method from CArgAllow.

Auxiliary class to store the name of an output file, which is reset every time its GetStream method i...

CAutoOutputFileReset & operator=(const CAutoOutputFileReset &rhs)

Prohibit assignment operator.

CAutoOutputFileReset(const CAutoOutputFileReset &rhs)

Prohibit copy constructor.

unique_ptr< CNcbiOstream > m_FileStream

The output stream.

string m_FileName

The file's name.

int m_Version

File version if larger than zero.

CAutoOutputFileReset(const string &file_name, bool use_versions=false)

Constructor.

unsigned int TSeqPos

Type for sequence locations and lengths.

string GetName(void) const

Get the base entry name with extension (if any).

uint32_t Uint4

4-byte (32-bit) unsigned integer

#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::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static double StringToDouble(const CTempStringEx str, TStringToNumFlags flags=0)

Convert string to double.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

#define NCBI_BLASTINPUT_EXPORT

const GenericPointer< typename T::ValueType > T2 value

Defines command line argument related classes.

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

Definition of SSeqLoc structure.

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

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