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// ==========================================================================
// %(TITLE)s
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of Knut Reinert or the FU Berlin nor the names of
// its contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: %(AUTHOR)s
// ==========================================================================
#include <seqan/basic.h>
#include <seqan/sequence.h>
#include <seqan/arg_parse.h>
// ==========================================================================
// Classes
// ==========================================================================
// --------------------------------------------------------------------------
// Class AppOptions
// --------------------------------------------------------------------------
// This struct stores the options from the command line.
//
// You might want to rename this to reflect the name of your app.
struct AppOptions
{
// Verbosity level. 0 -- quiet, 1 -- normal, 2 -- verbose, 3 -- very verbose.
int verbosity;
// The first (and only) argument of the program is stored here.
seqan2::CharString text;
AppOptions() :
verbosity(1)
{}
};
// ==========================================================================
// Functions
// ==========================================================================
// --------------------------------------------------------------------------
// Function parseCommandLine()
// --------------------------------------------------------------------------
seqan2::ArgumentParser::ParseResult
parseCommandLine(AppOptions & options, int argc, char const ** argv)
{
// Setup ArgumentParser.
seqan2::ArgumentParser parser("%(NAME)s");
// Set short description, version, and date.
setShortDescription(parser, "Put a Short Description Here");
setVersion(parser, "0.1");
setDate(parser, "July 2012");
// Define usage line and long description.
addUsageLine(parser, "[\\fIOPTIONS\\fP] \"\\fITEXT\\fP\"");
addDescription(parser, "This is the application skelleton and you should modify this string.");
// We require one argument.
addArgument(parser, seqan2::ArgParseArgument(seqan2::ArgParseArgument::STRING, "TEXT"));
addOption(parser, seqan2::ArgParseOption("q", "quiet", "Set verbosity to a minimum."));
addOption(parser, seqan2::ArgParseOption("v", "verbose", "Enable verbose output."));
addOption(parser, seqan2::ArgParseOption("vv", "very-verbose", "Enable very verbose output."));
// Add Examples Section.
addTextSection(parser, "Examples");
addListItem(parser, "\\fB%(NAME)s\\fP \\fB-v\\fP \\fItext\\fP",
"Call with \\fITEXT\\fP set to \"text\" with verbose output.");
// Parse command line.
seqan2::ArgumentParser::ParseResult res = seqan2::parse(parser, argc, argv);
// Only extract options if the program will continue after parseCommandLine()
if (res != seqan2::ArgumentParser::PARSE_OK)
return res;
// Extract option values.
if (isSet(parser, "quiet"))
options.verbosity = 0;
if (isSet(parser, "verbose"))
options.verbosity = 2;
if (isSet(parser, "very-verbose"))
options.verbosity = 3;
seqan2::getArgumentValue(options.text, parser, 0);
return seqan2::ArgumentParser::PARSE_OK;
}
// --------------------------------------------------------------------------
// Function main()
// --------------------------------------------------------------------------
// Program entry point.
int main(int argc, char const ** argv)
{
// Parse the command line.
seqan2::ArgumentParser parser;
AppOptions options;
seqan2::ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
// If there was an error parsing or built-in argument parser functionality
// was triggered then we exit the program. The return code is 1 if there
// were errors and 0 if there were none.
if (res != seqan2::ArgumentParser::PARSE_OK)
return res == seqan2::ArgumentParser::PARSE_ERROR;
std::cout << "EXAMPLE PROGRAM\n"
<< "===============\n\n";
// Print the command line arguments back to the user.
if (options.verbosity > 0)
{
std::cout << "__OPTIONS____________________________________________________________________\n"
<< '\n'
<< "VERBOSITY\t" << options.verbosity << '\n'
<< "TEXT \t" << options.text << "\n\n";
}
return 0;
}
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