readAlMain.cpp File Reference

#include "FormatHandling/FormatManager.h"
#include "Alignment/Alignment.h"
#include "defines.h"
#include "values.h"
#include <iostream>
#include <cstring>
#include <iomanip>

Go to the source code of this file.

Functions
int	parseArguments (int argc, char *argv[], FormatHandling::FormatManager *machine, std::vector< std::string > *inFiles, std::vector< std::string > *outFormats, std::string *outPattern)
int	checkArguments (FormatHandling::FormatManager *machine, std::vector< std::string > *inFiles, std::vector< std::string > *outFormats, std::string *outPattern)
void	menu ()
int	main (int argc, char *argv[])

Function Documentation

checkArguments()

int checkArguments	(	FormatHandling::FormatManager *	machine,
		std::vector< std::string > *	inFiles,
		std::vector< std::string > *	outFormats,
		std::string *	outPattern
	)

Definition at line 222 of file readAlMain.cpp.

References FormatHandling::FormatManager::format, FormatHandling::FormatManager::hasOutputFile, FormatHandling::FormatManager::info, and FormatHandling::FormatManager::type.

Referenced by main().

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main()

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

Definition at line 359 of file readAlMain.cpp.

References AA, checkArguments(), DEG, DNA, FormatHandling::FormatManager::format, FormatHandling::FormatManager::FormatManager(), Alignment::getAlignmentType(), FormatHandling::FormatManager::getFileFormatName(), FormatHandling::FormatManager::info, Alignment::isAligned, FormatHandling::FormatManager::loadAlignment(), FormatHandling::FormatManager::loadAndSaveMultipleAlignments(), menu(), parseArguments(), Alignment::printAlignmentInfo(), FormatHandling::FormatManager::reverse, RNA, FormatHandling::FormatManager::saveAlignment(), and FormatHandling::FormatManager::type.

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menu()

void menu

(

void

)

Definition at line 249 of file readAlMain.cpp.

References FormatHandling::FormatManager::FormatManager(), FormatHandling::FormatManager::getInputFormatsAvailable(), and FormatHandling::FormatManager::getOutputFormatsAvailable().

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parseArguments()

int parseArguments	(	int	argc,
		char *	argv[],
		FormatHandling::FormatManager *	machine,
		std::vector< std::string > *	inFiles,
		std::vector< std::string > *	outFormats,
		std::string *	outPattern
	)

Definition at line 39 of file readAlMain.cpp.

References FormatHandling::FormatManager::format, FormatHandling::FormatManager::info, FormatHandling::FormatManager::keepHeader, FormatHandling::FormatManager::reverse, and FormatHandling::FormatManager::type.

Referenced by main().

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