NCBI C++ ToolKit
Classes | Macros
options.hpp File Reference

Options for CMultiAligner. More...

#include <corelib/ncbiobj.hpp>
#include <algo/cobalt/kmercounts.hpp>
#include <algo/align/nw/nw_pssm_aligner.hpp>
#include <objects/blast/Blast4_archive.hpp>
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Classes

class  CMultiAlignerOptions
 Options and parameters for multiple alignement. More...
 
class  CMultiAlignerOptions::CPattern
 Representation of CDD pattern. More...
 
struct  CMultiAlignerOptions::CPattern::SPattern
 
struct  CMultiAlignerOptions::SConstraint
 Structure for representing single user constraint for pair-wise alignment. More...
 

Macros

#define COBALT_RPS_EVALUE   0.01
 Default values for cobalt parameters Rps-Blast e-value cutoff for creating contraints. More...
 
#define COBALT_DOMAIN_BOOST   0.5
 Weight for domain residue frequecies when creating MSA profiles. More...
 
#define COBALT_DOMAIN_HITLIST_SIZE   500
 Hitlist size for Rps-Blast searches. More...
 
#define COBALT_BLAST_EVALUE   0.005
 Blastp e-value cutoff for creating contraints. More...
 
#define COBALT_LOCAL_BOOST   1.0
 Weight for sequence residues when creating MSA profules. More...
 
#define COBALT_PSEUDO_COUNT   2.0
 Pseudocount constant used in multiple alignment. More...
 
#define COBALT_CONSERVED_CUTOFF   0.67
 Conservation score cutoff used for selecting conserved columns in initial MSA. More...
 
#define COBALT_TREE_METHOD   CMultiAlignerOptions::eClusters
 Default method for computing progressive alignment tree. More...
 
#define COBALT_DEFAULT_MATRIX   "BLOSUM62"
 Default substitution matrix used in multiple alignment. More...
 
#define COBALT_END_GAP_OPEN   -5
 End gap opening score. More...
 
#define COBALT_END_GAP_EXTNT   -1
 End gap extension score. More...
 
#define COBALT_GAP_OPEN   -11
 Gap opening score. More...
 
#define COBALT_GAP_EXTNT   -1
 Gap extension score. More...
 
#define COBALT_MAX_CLUSTER_DIAM   0.8
 Maximum cluster diameter for pre-alignment sequence clustering. More...
 
#define COBALT_KMER_LEN   4
 K-mer length for sequence clustering. More...
 
#define COBALT_KMER_ALPH   CMultiAlignerOptions::TKMethods::eSE_B15
 K-mer alphabet for sequence clustering. More...
 

Detailed Description

Options for CMultiAligner.

Definition in file options.hpp.

Macro Definition Documentation

◆ COBALT_BLAST_EVALUE

#define COBALT_BLAST_EVALUE   0.005

Blastp e-value cutoff for creating contraints.

Definition at line 57 of file options.hpp.

◆ COBALT_CONSERVED_CUTOFF

#define COBALT_CONSERVED_CUTOFF   0.67

Conservation score cutoff used for selecting conserved columns in initial MSA.

Definition at line 65 of file options.hpp.

◆ COBALT_DEFAULT_MATRIX

#define COBALT_DEFAULT_MATRIX   "BLOSUM62"

Default substitution matrix used in multiple alignment.

Definition at line 71 of file options.hpp.

◆ COBALT_DOMAIN_BOOST

#define COBALT_DOMAIN_BOOST   0.5

Weight for domain residue frequecies when creating MSA profiles.

Definition at line 52 of file options.hpp.

◆ COBALT_DOMAIN_HITLIST_SIZE

#define COBALT_DOMAIN_HITLIST_SIZE   500

Hitlist size for Rps-Blast searches.

Definition at line 54 of file options.hpp.

◆ COBALT_END_GAP_EXTNT

#define COBALT_END_GAP_EXTNT   -1

End gap extension score.

Definition at line 75 of file options.hpp.

◆ COBALT_END_GAP_OPEN

#define COBALT_END_GAP_OPEN   -5

End gap opening score.

Definition at line 73 of file options.hpp.

◆ COBALT_GAP_EXTNT

#define COBALT_GAP_EXTNT   -1

Gap extension score.

Definition at line 79 of file options.hpp.

◆ COBALT_GAP_OPEN

#define COBALT_GAP_OPEN   -11

Gap opening score.

Definition at line 77 of file options.hpp.

◆ COBALT_KMER_ALPH

#define COBALT_KMER_ALPH   CMultiAlignerOptions::TKMethods::eSE_B15

K-mer alphabet for sequence clustering.

Definition at line 86 of file options.hpp.

◆ COBALT_KMER_LEN

#define COBALT_KMER_LEN   4

K-mer length for sequence clustering.

Definition at line 84 of file options.hpp.

◆ COBALT_LOCAL_BOOST

#define COBALT_LOCAL_BOOST   1.0

Weight for sequence residues when creating MSA profules.

Definition at line 59 of file options.hpp.

◆ COBALT_MAX_CLUSTER_DIAM

#define COBALT_MAX_CLUSTER_DIAM   0.8

Maximum cluster diameter for pre-alignment sequence clustering.

Definition at line 82 of file options.hpp.

◆ COBALT_PSEUDO_COUNT

#define COBALT_PSEUDO_COUNT   2.0

Pseudocount constant used in multiple alignment.

Definition at line 62 of file options.hpp.

◆ COBALT_RPS_EVALUE

#define COBALT_RPS_EVALUE   0.01

Default values for cobalt parameters Rps-Blast e-value cutoff for creating contraints.

Definition at line 50 of file options.hpp.

◆ COBALT_TREE_METHOD

#define COBALT_TREE_METHOD   CMultiAlignerOptions::eClusters

Default method for computing progressive alignment tree.

Definition at line 68 of file options.hpp.

Modified on Sat Jul 13 13:34:41 2024 by modify_doxy.py rev. 669887