NCBI C++ ToolKit
Classes | Typedefs | Enumerations | Functions
blast_types.hpp File Reference

Definitions of special type used in BLAST. More...

#include <corelib/ncbistd.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <algo/blast/core/blast_export.h>
#include <algo/blast/core/blast_message.h>
#include <algo/blast/core/blast_def.h>
#include <algo/blast/core/blast_filter.h>
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Classes

class  CSearchMessage
 Error or Warning Message from search. More...
 
class  TQueryMessages
 Class for the messages for an individual query sequence. More...
 
class  TSearchMessages
 typedef for the messages for an entire BLAST search, which could be comprised of multiple query sequences More...
 
class  CBlastSeqLocWrap
 Wrapper for BlastSeqLoc structure. More...
 

Typedefs

typedef vector< CRef< objects::CSeq_align_set > > TSeqAlignVector
 Vector of Seq-align-sets. More...
 

Enumerations

enum  EProgram {
  eBlastNotSet = 0, eBlastn, eBlastp, eBlastx,
  eTblastn, eTblastx, eRPSBlast, eRPSTblastn,
  eMegablast, eDiscMegablast, ePSIBlast, ePSITblastn,
  ePHIBlastp, ePHIBlastn, eDeltaBlast, eVecScreen,
  eMapper, eKBlastp, eBlastProgramMax
}
 This enumeration is to evolve into a task/program specific list that specifies sets of default parameters to easily conduct searches using BLAST. More...
 
enum  EResultType { eDatabaseSearch, eSequenceComparison }
 Specifies the style of Seq-aligns that should be built from the internal BLAST data structures. More...
 

Functions

string EProgramToTaskName (EProgram p)
 Convert a EProgram enumeration value to a task name (as those used in the BLAST command line binaries) More...
 
EProgram ProgramNameToEnum (const std::string &program_name)
 Map a string into an element of the ncbi::blast::EProgram enumeration (except eBlastProgramMax). More...
 
void ThrowIfInvalidTask (const string &task)
 Validates that the task provided is indeed a valid task, otherwise throws a CBlastException. More...
 
EBlastProgramType EProgramToEBlastProgramType (EProgram p)
 Convert EProgram to EBlastProgramType. More...
 

Detailed Description

Definitions of special type used in BLAST.

Definition in file blast_types.hpp.

Typedef Documentation

typedef vector< CRef<objects::CSeq_align_set> > TSeqAlignVector

Vector of Seq-align-sets.

Definition at line 271 of file blast_types.hpp.

Enumeration Type Documentation

enum EProgram

This enumeration is to evolve into a task/program specific list that specifies sets of default parameters to easily conduct searches using BLAST.

Enumerator
eBlastNotSet 

Not yet set.

eBlastn 

Nucl-Nucl (traditional blastn)

eBlastp 

Protein-Protein.

eBlastx 

Translated nucl-Protein.

eTblastn 

Protein-Translated nucl.

eTblastx 

Translated nucl-Translated nucl.

eRPSBlast 

protein-pssm (reverse-position-specific BLAST)

eRPSTblastn 

nucleotide-pssm (RPS blast with translated query)

eMegablast 

Nucl-Nucl (traditional megablast)

eDiscMegablast 

Nucl-Nucl using discontiguous megablast.

ePSIBlast 

PSI Blast.

ePSITblastn 

PSI Tblastn.

ePHIBlastp 

Protein PHI BLAST.

ePHIBlastn 

Nucleotide PHI BLAST.

eDeltaBlast 

Delta Blast.

eVecScreen 

Vector screening.

eMapper 

Jumper alignment for mapping.

eKBlastp 

KMER screening and BLASTP.

eBlastProgramMax 

Undefined program.

Definition at line 56 of file blast_types.hpp.

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

Enumerator
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)

Definition at line 264 of file blast_types.hpp.

Modified on Sat Sep 23 14:28:27 2017 by modify_doxy.py rev. 546573