NCBI C++ ToolKit
Macros | Enumerations | Functions
blast_program.h File Reference

Definitions for various programs supported by core BLAST. More...

#include <algo/blast/core/ncbi_std.h>
#include <algo/blast/core/blast_export.h>
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Macros

#define PROTEIN_QUERY_MASK   (0x1<<0)
 This bit is on if the query is protein. More...
 
#define PROTEIN_SUBJECT_MASK   (0x1<<1)
 This bit is on if the subject is protein. More...
 
#define NUCLEOTIDE_QUERY_MASK   (0x1<<2)
 This bit is on if the query is nucleotide. More...
 
#define NUCLEOTIDE_SUBJECT_MASK   (0x1<<3)
 This bit is on if the subject is nucleotide. More...
 
#define TRANSLATED_QUERY_MASK   (0x1<<4)
 This bit is on if the query is translated. More...
 
#define TRANSLATED_SUBJECT_MASK   (0x1<<5)
 This bit is on if the subject is translated. More...
 
#define PSSM_QUERY_MASK   (0x1<<6)
 This bit is on if the query is a PSSM (PSI-BLAST) More...
 
#define PSSM_SUBJECT_MASK   (0x1<<7)
 This bit is on if the subject is a PSSM (RPS-BLAST) More...
 
#define PATTERN_QUERY_MASK   (0x1<<8)
 This bit is on if the query includes a pattern (PHI-BLAST) More...
 
#define MAPPING_MASK   (0x1<<9)
 This bit is on for fast mapping of short reads. More...
 

Enumerations

enum  EBlastProgramType {
  eBlastTypeBlastp = ( (0x1<<0) | (0x1<<1) ) , eBlastTypeBlastn = ( (0x1<<2) | (0x1<<3) ) , eBlastTypeBlastx , eBlastTypeTblastn ,
  eBlastTypeTblastx , eBlastTypePsiBlast = ( (0x1<<6) | eBlastTypeBlastp) , eBlastTypePsiTblastn = ( (0x1<<6) | eBlastTypeTblastn) , eBlastTypeRpsBlast = ( (0x1<<7) | eBlastTypeBlastp) ,
  eBlastTypeRpsTblastn = ( (0x1<<7) | eBlastTypeBlastx) , eBlastTypePhiBlastp = ( (0x1<<8) | eBlastTypeBlastp) , eBlastTypePhiBlastn = ( (0x1<<8) | eBlastTypeBlastn) , eBlastTypeMapping = (eBlastTypeBlastn | (0x1<<9) ) ,
  eBlastTypeUndefined = 0x0
}
 Defines the engine's notion of the different applications of the BLAST algorithm. More...
 

Functions

Boolean Blast_QueryIsProtein (EBlastProgramType p)
 Returns true if the query is protein. More...
 
Boolean Blast_QueryIsNucleotide (EBlastProgramType p)
 Returns true if the query is nucleotide. More...
 
Boolean Blast_QueryIsPssm (EBlastProgramType p)
 Returns true if the query is PSSM. More...
 
Boolean Blast_SubjectIsProtein (EBlastProgramType p)
 Returns true if the subject is protein. More...
 
Boolean Blast_SubjectIsNucleotide (EBlastProgramType p)
 Returns true if the subject is nucleotide. More...
 
Boolean Blast_SubjectIsPssm (EBlastProgramType p)
 Returns true if the subject is PSSM. More...
 
Boolean Blast_QueryIsTranslated (EBlastProgramType p)
 Returns true if the query is translated. More...
 
Boolean Blast_SubjectIsTranslated (EBlastProgramType p)
 Returns true if the subject is translated. More...
 
Boolean Blast_ProgramIsPsiBlast (EBlastProgramType p)
 Returns true if program is PSI-BLAST (i.e. More...
 
Boolean Blast_ProgramIsPhiBlast (EBlastProgramType p)
 Returns true if program is PHI-BLAST (i.e. More...
 
Boolean Blast_ProgramIsRpsBlast (EBlastProgramType p)
 Returns true if program is RPS-BLAST (i.e. More...
 
Boolean Blast_ProgramIsMapping (EBlastProgramType p)
 
Boolean Blast_QueryIsPattern (EBlastProgramType p)
 
Boolean Blast_ProgramIsNucleotide (EBlastProgramType p)
 
Boolean Blast_ProgramIsValid (EBlastProgramType p)
 Returns true if program is not undefined. More...
 

Detailed Description

Definitions for various programs supported by core BLAST.

Definition in file blast_program.h.

Macro Definition Documentation

◆ MAPPING_MASK

#define MAPPING_MASK   (0x1<<9)

This bit is on for fast mapping of short reads.

Definition at line 66 of file blast_program.h.

◆ NUCLEOTIDE_QUERY_MASK

#define NUCLEOTIDE_QUERY_MASK   (0x1<<2)

This bit is on if the query is nucleotide.

Definition at line 52 of file blast_program.h.

◆ NUCLEOTIDE_SUBJECT_MASK

#define NUCLEOTIDE_SUBJECT_MASK   (0x1<<3)

This bit is on if the subject is nucleotide.

Definition at line 54 of file blast_program.h.

◆ PATTERN_QUERY_MASK

#define PATTERN_QUERY_MASK   (0x1<<8)

This bit is on if the query includes a pattern (PHI-BLAST)

Definition at line 64 of file blast_program.h.

◆ PROTEIN_QUERY_MASK

#define PROTEIN_QUERY_MASK   (0x1<<0)

This bit is on if the query is protein.

Definition at line 48 of file blast_program.h.

◆ PROTEIN_SUBJECT_MASK

#define PROTEIN_SUBJECT_MASK   (0x1<<1)

This bit is on if the subject is protein.

Definition at line 50 of file blast_program.h.

◆ PSSM_QUERY_MASK

#define PSSM_QUERY_MASK   (0x1<<6)

This bit is on if the query is a PSSM (PSI-BLAST)

Definition at line 60 of file blast_program.h.

◆ PSSM_SUBJECT_MASK

#define PSSM_SUBJECT_MASK   (0x1<<7)

This bit is on if the subject is a PSSM (RPS-BLAST)

Definition at line 62 of file blast_program.h.

◆ TRANSLATED_QUERY_MASK

#define TRANSLATED_QUERY_MASK   (0x1<<4)

This bit is on if the query is translated.

Definition at line 56 of file blast_program.h.

◆ TRANSLATED_SUBJECT_MASK

#define TRANSLATED_SUBJECT_MASK   (0x1<<5)

This bit is on if the subject is translated.

Definition at line 58 of file blast_program.h.

Enumeration Type Documentation

◆ EBlastProgramType

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

Enumerator
eBlastTypeBlastp 
eBlastTypeBlastn 
eBlastTypeBlastx 
eBlastTypeTblastn 
eBlastTypeTblastx 
eBlastTypePsiBlast 
eBlastTypePsiTblastn 
eBlastTypeRpsBlast 
eBlastTypeRpsTblastn 
eBlastTypePhiBlastp 
eBlastTypePhiBlastn 
eBlastTypeMapping 
eBlastTypeUndefined 

Definition at line 72 of file blast_program.h.

Function Documentation

◆ Blast_ProgramIsMapping()

Boolean Blast_ProgramIsMapping ( EBlastProgramType  p)

◆ Blast_ProgramIsNucleotide()

Boolean Blast_ProgramIsNucleotide ( EBlastProgramType  p)

◆ Blast_ProgramIsPhiBlast()

Boolean Blast_ProgramIsPhiBlast ( EBlastProgramType  p)

◆ Blast_ProgramIsPsiBlast()

Boolean Blast_ProgramIsPsiBlast ( EBlastProgramType  p)

Returns true if program is PSI-BLAST (i.e.

: involves a PSSM as query)

Parameters
pprogram type [in]

Definition at line 67 of file blast_program.c.

References PSSM_QUERY_MASK, and SAFE_CAST_INT_TO_BOOLEAN.

◆ Blast_ProgramIsRpsBlast()

Boolean Blast_ProgramIsRpsBlast ( EBlastProgramType  p)

◆ Blast_ProgramIsValid()

Boolean Blast_ProgramIsValid ( EBlastProgramType  p)

◆ Blast_QueryIsNucleotide()

Boolean Blast_QueryIsNucleotide ( EBlastProgramType  p)

◆ Blast_QueryIsPattern()

Boolean Blast_QueryIsPattern ( EBlastProgramType  p)

◆ Blast_QueryIsProtein()

Boolean Blast_QueryIsProtein ( EBlastProgramType  p)

◆ Blast_QueryIsPssm()

Boolean Blast_QueryIsPssm ( EBlastProgramType  p)

◆ Blast_QueryIsTranslated()

Boolean Blast_QueryIsTranslated ( EBlastProgramType  p)

◆ Blast_SubjectIsNucleotide()

Boolean Blast_SubjectIsNucleotide ( EBlastProgramType  p)

◆ Blast_SubjectIsProtein()

Boolean Blast_SubjectIsProtein ( EBlastProgramType  p)

◆ Blast_SubjectIsPssm()

Boolean Blast_SubjectIsPssm ( EBlastProgramType  p)

Returns true if the subject is PSSM.

Parameters
pprogram type [in]

Definition at line 56 of file blast_program.c.

References PSSM_SUBJECT_MASK, and SAFE_CAST_INT_TO_BOOLEAN.

Referenced by SplitQuery_GetChunkSize(), and SplitQuery_ShouldSplit().

◆ Blast_SubjectIsTranslated()

Boolean Blast_SubjectIsTranslated ( EBlastProgramType  p)
Modified on Mon Jul 22 05:01:53 2024 by modify_doxy.py rev. 669887