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
◆ TSeqAlignVector
| typedef vector< CRef<objects::CSeq_align_set> > TSeqAlignVector |
Vector of Seq-align-sets.
Definition at line 274 of file blast_types.hpp.
Enumeration Type Documentation
◆ EProgram
| 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.
◆ EResultType
| enum EResultType |
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 267 of file blast_types.hpp.
