/usr/include/mash/Command.h is in libmash-dev 2.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
// Sergey Koren, and Adam Phillippy
//
// See the LICENSE.txt file included with this software for license information.
#ifndef INCLUDED_Command
#define INCLUDED_Command
#include <map>
#include <string>
#include <vector>
#include <set>
namespace mash {
class Command
{
// A base class for handling command line parsing and usage messages. Specific
// commands can be implemented by subclassing and overriding the run() method.
// The run() method will be called by this base class from run(argc, argv) once
// it has parsed options, which can be accessed from the 'options' map using the
// name strings given when adding them (not 'identifier', which is its parsing
// name to appear after the '-'). Arguments (i.e. operands given after the
// options on the command line) will be available in the 'arguments' vector.
public:
class Option
{
public:
enum Type
{
Boolean,
Number,
Integer,
Size,
File,
String
}
type;
std::string category;
std::string identifier;
std::string description;
std::string argument;
std::string argumentDefault;
float argumentAsNumber;
float argumentMin;
float argumentMax;
bool active;
bool changed;
Option() {}
Option(Type typeNew, std::string identifierNew, std::string categoryNew, std::string descriptionNew, std::string argumentDefaultNew = "", float argumentMinNew = 0, float argumentMaxNew = 0);
float getArgumentAsNumber() const {return argumentAsNumber;}
void setArgument(std::string argumentNew);
};
Command();
virtual ~Command() {};
void addOption(std::string name, Option option);
const Option & getOption(std::string name) const;
inline bool hasOption(std::string name) const {return options.count(name);}
void print() const;
virtual int run() const = 0;
int run(int argc, const char ** argv);
std::string name;
std::string summary;
std::string description;
std::string argumentString;
protected:
void useOption(std::string name);
void useSketchOptions();
std::map<std::string, Option> options;
std::map<std::string, Option> optionsAvailable;
std::vector<std::string> arguments;
private:
void addAvailableOption(std::string name, Option option);
void addCategory(std::string name, std::string displayName);
std::map<std::string, std::string> optionNamesByIdentifier;
std::map<std::string, std::vector<std::string> > optionNamesByCategory;
std::vector<std::string> categories;
std::map<std::string, std::string> categoryDisplayNames;
};
inline const Command::Option & Command::getOption(std::string name) const {return options.at(name);}
void splitFile(const std::string & file, std::vector<std::string> & lines);
void printColumns(const std::vector<std::vector<std::string>> & columns, int indent = 2, int spacing = 2, const char * missing = "-", int max = 80);
void printColumns(const std::vector<std::vector<std::string>> & columns, const std::vector<std::pair<int, std::string>> & dividers, int indent = 2, int spacing = 2, const char * missing = "-", int max = 80);
} // namespace mash
#endif
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