Public Member Functions | Public Attributes | List of all members
statistics::Gaps Class Reference

Class to handle gaps statistics. More...

#include <Gaps.h>

Public Member Functions

 Gaps (Alignment *pAlignment, Gaps *pGaps)
 
 Gaps (Alignment *parent)
 
 ~Gaps ()
 
bool applyWindow (int)
 
int * getGapsWindow ()
 
double calcCutPoint (float, float)
 
int calcCutPointMixSlope ()
 
int calcCutPoint2ndSlope ()
 
void printGapsColumns ()
 
void printGapsAcl ()
 
bool isDefinedWindow ()
 
void CalculateVectors ()
 

Public Attributes

Alignment * alig
 
int maxGaps = -1
 
int halfWindow = -1
 
int * gapsInColumn = nullptr
 
int * numColumnsWithGaps = nullptr
 
int * gapsWindow = nullptr
 
int * refCounter
 

Detailed Description

Class to handle gaps statistics.

Definition at line 42 of file Gaps.h.

Constructor & Destructor Documentation

◆ Gaps() [1/2]

statistics::Gaps::Gaps ( Alignment *  pAlignment,
Gaps *  pGaps 
)

Definition at line 58 of file Gaps.cpp.

References alig, gapsInColumn, gapsWindow, maxGaps, numColumnsWithGaps, and refCounter.

Referenced by statistics::Manager::Manager().

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◆ Gaps() [2/2]

statistics::Gaps::Gaps ( Alignment *  parent)
explicit

Definition at line 38 of file Gaps.cpp.

References alig, gapsInColumn, halfWindow, utils::initlVect(), maxGaps, numColumnsWithGaps, Alignment::originalNumberOfResidues, Alignment::originalNumberOfSequences, and refCounter.

Referenced by statistics::Manager::calculateGapStats().

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◆ ~Gaps()

statistics::Gaps::~Gaps ( )

Definition at line 79 of file Gaps.cpp.

References gapsInColumn, gapsWindow, numColumnsWithGaps, and refCounter.

Member Function Documentation

◆ applyWindow()

bool statistics::Gaps::applyWindow ( int  halfW)

Definition at line 93 of file Gaps.cpp.

References alig, debug, gapsInColumn, gapsWindow, GapWindowTooBig, halfWindow, utils::initlVect(), maxGaps, numColumnsWithGaps, Alignment::originalNumberOfResidues, Alignment::originalNumberOfSequences, reporting::reportManager::report(), and utils::roundInt().

Referenced by statistics::Manager::calculateGapStats(), and getGapsWindow().

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◆ calcCutPoint()

double statistics::Gaps::calcCutPoint ( float  minInputAlignment,
float  gapThreshold 
)

Definition at line 181 of file Gaps.cpp.

References alig, utils::max(), Alignment::numberOfSequences, numColumnsWithGaps, Alignment::originalNumberOfResidues, Alignment::originalNumberOfSequences, and utils::roundInt().

Referenced by Cleaner::clean(), and Cleaner::cleanGaps().

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◆ calcCutPoint2ndSlope()

int statistics::Gaps::calcCutPoint2ndSlope ( )

Definition at line 316 of file Gaps.cpp.

References alig, utils::initlVect(), maxGaps, Alignment::numberOfSequences, numColumnsWithGaps, and Alignment::originalNumberOfResidues.

Referenced by Cleaner::clean2ndSlope(), and Cleaner::cleanCombMethods().

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◆ calcCutPointMixSlope()

int statistics::Gaps::calcCutPointMixSlope ( )

Definition at line 226 of file Gaps.cpp.

References alig, utils::initlVect(), maxGaps, numColumnsWithGaps, Alignment::originalNumberOfResidues, and Alignment::originalNumberOfSequences.

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◆ CalculateVectors()

void statistics::Gaps::CalculateVectors ( )

Definition at line 593 of file Gaps.cpp.

References alig, gapsInColumn, maxGaps, numColumnsWithGaps, Alignment::originalNumberOfResidues, Alignment::originalNumberOfSequences, Alignment::saveSequences, and Alignment::sequences.

Referenced by statistics::Manager::calculateGapStats().

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◆ getGapsWindow()

int * statistics::Gaps::getGapsWindow ( )

Definition at line 163 of file Gaps.cpp.

References applyWindow(), gapsInColumn, gapsWindow, halfWindow, and isDefinedWindow().

Referenced by Alignment::alignmentSummaryHTML(), Alignment::alignmentSummarySVG(), statistics::Similarity::calculateVectors(), Cleaner::clean(), Cleaner::clean2ndSlope(), Cleaner::cleanCombMethods(), Cleaner::cleanGaps(), Cleaner::cleanNoAllGaps(), Cleaner::removeOnlyTerminal(), and Alignment::statSVG().

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◆ isDefinedWindow()

bool statistics::Gaps::isDefinedWindow ( )

Definition at line 155 of file Gaps.cpp.

References halfWindow.

Referenced by getGapsWindow().

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◆ printGapsAcl()

void statistics::Gaps::printGapsAcl ( )

Definition at line 464 of file Gaps.cpp.

References alig, Alignment::filename, maxGaps, numColumnsWithGaps, Alignment::originalNumberOfResidues, and Alignment::originalNumberOfSequences.

Referenced by statistics::Manager::printStatisticsGapsTotal().

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◆ printGapsColumns()

void statistics::Gaps::printGapsColumns ( )

Definition at line 387 of file Gaps.cpp.

References alig, utils::copyVect(), Alignment::filename, gapsInColumn, gapsWindow, halfWindow, Alignment::originalNumberOfResidues, and Alignment::originalNumberOfSequences.

Referenced by statistics::Manager::printStatisticsGapsColumns().

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Member Data Documentation

◆ alig

Alignment* statistics::Gaps::alig

Definition at line 47 of file Gaps.h.

Referenced by applyWindow(), calcCutPoint(), calcCutPoint2ndSlope(), calcCutPointMixSlope(), CalculateVectors(), Gaps(), printGapsAcl(), and printGapsColumns().

◆ gapsInColumn

int* statistics::Gaps::gapsInColumn = nullptr

Definition at line 52 of file Gaps.h.

Referenced by applyWindow(), CalculateVectors(), Gaps(), getGapsWindow(), printGapsColumns(), and ~Gaps().

◆ gapsWindow

int* statistics::Gaps::gapsWindow = nullptr

Definition at line 54 of file Gaps.h.

Referenced by applyWindow(), Gaps(), getGapsWindow(), printGapsColumns(), and ~Gaps().

◆ halfWindow

int statistics::Gaps::halfWindow = -1

Definition at line 50 of file Gaps.h.

Referenced by applyWindow(), Gaps(), getGapsWindow(), isDefinedWindow(), and printGapsColumns().

◆ maxGaps

int statistics::Gaps::maxGaps = -1

Definition at line 49 of file Gaps.h.

Referenced by applyWindow(), calcCutPoint2ndSlope(), calcCutPointMixSlope(), CalculateVectors(), Gaps(), and printGapsAcl().

◆ numColumnsWithGaps

int* statistics::Gaps::numColumnsWithGaps = nullptr

Definition at line 53 of file Gaps.h.

Referenced by applyWindow(), calcCutPoint(), calcCutPoint2ndSlope(), calcCutPointMixSlope(), CalculateVectors(), Gaps(), printGapsAcl(), and ~Gaps().

◆ refCounter

int* statistics::Gaps::refCounter

Definition at line 55 of file Gaps.h.

Referenced by Gaps(), and ~Gaps().

The documentation for this class was generated from the following files: