hyperclust.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbifile.hpp>
#include <objmgr/object_manager.hpp>
#include <objtools/data_loaders/blastdb/bdbloader.hpp>
#include <serial/iterator.hpp>
#include <objtools/readers/fasta.hpp>
#include <objtools/readers/reader_exception.hpp>
#include <algo/align/nw/nw_pssm_aligner.hpp>
#include <algo/cobalt/cobalt.hpp>
#include "cobalt_app_util.hpp"

Include dependency graph for hyperclust.cpp:

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Classes
class	CMultiApplication
struct	SAlignEntry

Functions
	USING_SCOPE (objects)
	USING_SCOPE (cobalt)
static blast::TSeqLocVector	x_GetSeqLocFromStream (CNcbiIstream &instream, CObjectManager &objmgr)
void	x_SetScoreMatrix (const char *matrix_name, CPSSMAligner &aligner)
static void	x_FillResidueFrequencies (double **freq_data, vector< CSequence > &query_data)
static void	x_NormalizeResidueFrequencies (double **freq_data, int freq_size)
static int	x_ScoreFromTranscriptCore (CPSSMAligner &aligner, double **freq1, int len1, double **freq2, int len2, int end_gap_open, int end_gap_extend)
static double **	x_GetProfile (vector< CSequence > &alignment)
int	x_AlignProfileProfile (double **freq1_data, int freq1_size, double **freq2_data, int freq2_size, CPSSMAligner &aligner, bool local_alignment)
static double	x_GetSelfScore (double **freq_data, int freq_size, SNCBIFullScoreMatrix &matrix)
static void	x_PrintTree (const TPhyTreeNode *tree, int level, vector< SAlignEntry > &aligns)
static void	x_FillNewDistanceMatrix (const TPhyTreeNode *node, CDistMethods::TMatrix &matrix)
int	main (int argc, const char *argv[])

Variables
	USING_NCBI_SCOPE
static const int	kScaleFactor = 100

Function Documentation

main()

int main	(	int	argc,
		const char *	argv[]
	)

Definition at line 704 of file hyperclust.cpp.

References CNcbiApplicationAPI::AppMain(), and eDS_Default.

USING_SCOPE() [1/2]

USING_SCOPE

(

cobalt

)

USING_SCOPE() [2/2]

USING_SCOPE

(

objects

)

x_AlignProfileProfile()

int x_AlignProfileProfile	(	double **	freq1_data,
		int	freq1_size,
		double **	freq2_data,
		int	freq2_size,
		CPSSMAligner &	aligner,
		bool	local_alignment
	)

Definition at line 355 of file hyperclust.cpp.

References CPSSMAligner::GetStartWg(), CPSSMAligner::GetStartWs(), kScaleFactor, CPSSMAligner::Run(), CPSSMAligner::SetSequences(), and x_ScoreFromTranscriptCore().

x_FillNewDistanceMatrix()

static void x_FillNewDistanceMatrix ( const TPhyTreeNode *  node, CDistMethods::TMatrix &  matrix  )

static

Definition at line 432 of file hyperclust.cpp.

References i, CTreeNode< TValue, TKeyGetterP >::IsLeaf(), CTree::ListTreeLeaves(), CTreeNode< TValue, TKeyGetterP >::SubNodeBegin(), and CTreeNode< TValue, TKeyGetterP >::SubNodeEnd().

x_FillResidueFrequencies()

static void x_FillResidueFrequencies ( double **  freq_data, vector< CSequence > &  query_data  )

static

Definition at line 179 of file hyperclust.cpp.

References i, and int.

Referenced by x_GetProfile().

x_GetProfile()

static double** x_GetProfile ( vector< CSequence > &  alignment )

static

Definition at line 325 of file hyperclust.cpp.

References i, kAlphabetSize, x_FillResidueFrequencies(), and x_NormalizeResidueFrequencies().

x_GetSelfScore()

static double x_GetSelfScore ( double **  freq_data, int  freq_size, SNCBIFullScoreMatrix &  matrix  )

static

Definition at line 377 of file hyperclust.cpp.

References i, kAlphabetSize, kScaleFactor, and SNCBIFullScoreMatrix::s.

x_GetSeqLocFromStream()

static blast::TSeqLocVector x_GetSeqLocFromStream ( CNcbiIstream &  instream, CObjectManager &  objmgr  )

static

Definition at line 120 of file hyperclust.cpp.

References CScope::AddDefaults(), CScope::AddTopLevelSeqEntry(), CStreamLineReader::AtEOF(), ConstBegin(), CFastaReader::fAssumeProt, CFastaReader::fForceType, CFastaReader::fNoParseID, CFastaReader::fParseRawID, NCBI_THROW, CFastaReader::ReadOneSeq(), and CSeq_loc::SetWhole().

x_NormalizeResidueFrequencies()

static void x_NormalizeResidueFrequencies ( double **  freq_data, int  freq_size  )

static

Definition at line 191 of file hyperclust.cpp.

References i, and kAlphabetSize.

Referenced by x_GetProfile().

x_PrintTree()

static void x_PrintTree ( const TPhyTreeNode *  tree, int  level, vector< SAlignEntry > &  aligns  )

static

Definition at line 397 of file hyperclust.cpp.

References i.

x_ScoreFromTranscriptCore()

static int x_ScoreFromTranscriptCore ( CPSSMAligner &  aligner, double **  freq1, int  len1, double **  freq2, int  len2, int  end_gap_open, int  end_gap_extend  )

static

Definition at line 211 of file hyperclust.cpp.

References CNWAligner::eTS_Delete, CNWAligner::eTS_Insert, CNWAligner::eTS_Match, CNWAligner::eTS_Replace, CPSSMAligner::GetMatrix(), CNWAligner::GetTranscript(), CNWAligner::GetWg(), CNWAligner::GetWs(), i, kAlphabetSize, kScaleFactor, n, NCBI_FSM_DIM, and SNCBIFullScoreMatrix::s.

Referenced by x_AlignProfileProfile().

x_SetScoreMatrix()

void x_SetScoreMatrix	(	const char *	matrix_name,
		CPSSMAligner &	aligner
	)

Definition at line 159 of file hyperclust.cpp.

References NCBISM_Blosum45, NCBISM_Blosum62, NCBISM_Blosum80, NCBISM_Pam250, NCBISM_Pam30, NCBISM_Pam70, CPSSMAligner::SetScoreMatrix(), and util::strcmp().

Variable Documentation

kScaleFactor

const int kScaleFactor = 100

static

Definition at line 176 of file hyperclust.cpp.

Referenced by InitializeBlastScoreBlk(), x_AlignProfileProfile(), x_GetSelfScore(), CPssmEngine::x_InitializeScoreBlock(), and x_ScoreFromTranscriptCore().

USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 48 of file hyperclust.cpp.