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NCBI C++ ToolKit: src/algo/cobalt/options.cpp Source File

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range1 = it->seq1_stop - it->seq1_start;

range2 = it->seq2_stop - it->seq2_start;

(range1 < 0 || range2 < 0) {

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((range1 == 1 && range2 != 1) || (range1 != 1 && range2 == 1)) {

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Multiple aligner exceptions.

Options and parameters for multiple alignement.

@ eFastME

Fast Minimum Evolution.

@ eClusters

Clustering dendrogram.

EInClustAlnMethod m_InClustAlnMethod

double m_MaxInClusterDist

vector< string > m_Messages

CMultiAlignerOptions(void)

Create options with default mode.

void SetDefaultCddPatterns(void)

Set default patterns for identification of conserved domains.

void x_InitParams(TMode mode)

Initiate parameter values based on the specified mode.

bool Validate(void)

Validate parameter values.

void SetUseQueryClusters(bool use)

Set use of query clustering option.

unsigned int m_KmerLength

vector< CPattern > m_Patterns

double m_LocalResFreqBoost

bool CanGetDomainHits(void) const

Are pre-computed domain hits set.

TKMethods::EDistMeasures m_ClustDistMeasure

@ fNoPatterns

Do not use conserved domain patterns.

@ fNoRealign

Do not realign with different tree root.

@ fNoQueryClusters

No query clustering.

@ fNoIterate

Do not use Iterative alignment.

@ fFastAlign

Do Fast and rough profile-profile alignment.

@ fNoRpsBlast

Do not use RPS Blast.

@ fNonStandard

Not used as input, indicates that.

vector< SConstraint > TConstraints

@ eMulti

Alignment guide tree for each cluster is attached to the main alignment guide tree.

TKMethods::ECompressedAlphabet m_KmerAlphabet

static const int kDefaultUserConstraintsScore

double m_DomainResFreqBoost

@ eFractionCommonKmersLocal

@ eFractionCommonKmersGlobal

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

#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.

Options for CMultiAligner.

#define COBALT_GAP_EXTNT

Gap extension score.

#define COBALT_KMER_LEN

K-mer length for sequence clustering.

#define COBALT_END_GAP_OPEN

End gap opening score.

#define COBALT_PSEUDO_COUNT

Pseudocount constant used in multiple alignment.

#define COBALT_CONSERVED_CUTOFF

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

#define COBALT_LOCAL_BOOST

Weight for sequence residues when creating MSA profules.

#define COBALT_BLAST_EVALUE

Blastp e-value cutoff for creating contraints.

#define COBALT_RPS_EVALUE

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

#define COBALT_GAP_OPEN

Gap opening score.

#define COBALT_DOMAIN_HITLIST_SIZE

Hitlist size for Rps-Blast searches.

#define COBALT_TREE_METHOD

Default method for computing progressive alignment tree.

#define COBALT_END_GAP_EXTNT

End gap extension score.

#define COBALT_DOMAIN_BOOST

Weight for domain residue frequecies when creating MSA profiles.

#define COBALT_KMER_ALPH

K-mer alphabet for sequence clustering.

#define COBALT_DEFAULT_MATRIX

Default substitution matrix used in multiple alignment.

#define COBALT_MAX_CLUSTER_DIAM

Maximum cluster diameter for pre-alignment sequence clustering.

Interface for default CDD patterns.

void AssignDefaultPatterns(vector< CMultiAlignerOptions::CPattern > &patterns)

Asignes default patterns to a given vector.

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