NCBI C++ ToolKit
Classes | Functions | Variables
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:

Go to the source code of this file.

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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 
)

◆ x_FillNewDistanceMatrix()

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

◆ 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

◆ 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

◆ 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

◆ x_SetScoreMatrix()

void x_SetScoreMatrix ( const char *  matrix_name,
CPSSMAligner aligner 
)

Variable Documentation

◆ kScaleFactor

const int kScaleFactor = 100
static

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 48 of file hyperclust.cpp.

Modified on Sat Mar 02 10:55:43 2024 by modify_doxy.py rev. 669887