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NCBI C++ ToolKit: include/algo/blast/api/blast_types.hpp Source File

& message)

SetQueryId(

&

);

GetQueryId()

;

& message);

HasMessages()

;

RemoveDuplicates();

!(*

== rhs);

Definitions used throughout BLAST.

Defines to provide correct exporting from BLAST DLL in Windows.

#define NCBI_XBLAST_EXPORT

NULL operations for other cases.

BLAST filtering functions.

BlastSeqLoc * BlastSeqLocFree(BlastSeqLoc *loc)

Deallocate all BlastSeqLoc objects in a chain.

Structures for BLAST messages.

EBlastSeverity

Blast error message severities .

EBlastProgramType

Defines the engine's notion of the different applications of the BLAST algorithm.

vector< CRef< objects::CSeq_align_set > > TSeqAlignVector

Vector of Seq-align-sets.

EResultType

Specifies the style of Seq-aligns that should be built from the internal BLAST data structures.

@ eDatabaseSearch

Seq-aligns in the style of a database search.

@ eSequenceComparison

Seq-aligns in the BLAST 2 Sequence style (one alignment per query-subject pair)

EProgram

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

@ eBlastNotSet

Not yet set.

@ eBlastProgramMax

Undefined program.

@ eVecScreen

Vector screening.

@ eTblastx

Translated nucl-Translated nucl.

@ eBlastn

Nucl-Nucl (traditional blastn)

@ eRPSBlast

protein-pssm (reverse-position-specific BLAST)

@ ePHIBlastn

Nucleotide PHI BLAST.

@ eBlastp

Protein-Protein.

@ ePHIBlastp

Protein PHI BLAST.

@ eMapper

Jumper alignment for mapping.

@ eTblastn

Protein-Translated nucl.

@ eMegablast

Nucl-Nucl (traditional megablast)

@ eDeltaBlast

Delta Blast.

@ ePSITblastn

PSI Tblastn.

@ eKBlastp

KMER screening and BLASTP.

@ eDiscMegablast

Nucl-Nucl using discontiguous megablast.

@ eRPSTblastn

nucleotide-pssm (RPS blast with translated query)

@ eBlastx

Translated nucl-Protein.

Wrapper for BlastSeqLoc structure.

CBlastSeqLocWrap(BlastSeqLoc *locs)

Instance constructor.

virtual ~CBlastSeqLocWrap()

Instance destructor.

BlastSeqLoc * locs_

Wrapped pointer.

BlastSeqLoc * getLocs() const

Get access to the held object.

Error or Warning Message from search.

string m_Message

A message describing the error to the application user.

bool operator<(const CSearchMessage &rhs) const

Compare two error messages for order.

EBlastSeverity m_Severity

The severity of this error or warning message.

string & SetMessage(void)

Set the error message.

void SetSeverity(EBlastSeverity sev)

Adjust the severity of this message.

CSearchMessage()

Construct an empty search message object.

int m_ErrorId

A unique identifier specifying what kind of error this is.

string GetSeverityString() const

Get the severity of this message as a string.

bool operator!=(const CSearchMessage &rhs) const

Compare two error messages for inequality.

CSearchMessage(EBlastSeverity severity, int error_id, const string &message)

Construct a search message object.

bool operator==(const CSearchMessage &rhs) const

Compare two error messages for equality.

int GetErrorId() const

Get the error identifier.

string GetMessage(bool withSeverity=true) const

Get the error message.

EBlastSeverity GetSeverity() const

Get the severity of this message.

static string GetSeverityString(EBlastSeverity severity)

Get the symbolic name for a level of severity as a string.

Class for the messages for an individual query sequence.

string m_IdString

The query identifier.

typedef for the messages for an entire BLAST search, which could be comprised of multiple query seque...

Include a standard set of the NCBI C++ Toolkit most basic headers.

EBlastProgramType EProgramToEBlastProgramType(EProgram p)

Convert EProgram to EBlastProgramType.

string EProgramToTaskName(EProgram p)

Convert a EProgram enumeration value to a task name (as those used in the BLAST command line binaries...

EProgram ProgramNameToEnum(const std::string &program_name)

Map a string into an element of the ncbi::blast::EProgram enumeration (except eBlastProgramMax).

void ThrowIfInvalidTask(const string &task)

Validates that the task provided is indeed a valid task, otherwise throws a CBlastException.

#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.

Used to hold a set of positions, mostly used for filtering.

string ToString(const wxRect &rc)

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