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jpayne@69
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1 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
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2 // all rights reserved. Authored by: Brian Ondov, Todd Treangen,
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3 // Sergey Koren, and Adam Phillippy
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4 //
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5 // See the LICENSE.txt file included with this software for license information.
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6
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7 #ifndef INCLUDED_Command
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8 #define INCLUDED_Command
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9
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10 #include <map>
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11 #include <string>
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12 #include <vector>
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13 #include <set>
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14
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15 namespace mash {
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16
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17 class Command
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18 {
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19
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20 // A base class for handling command line parsing and usage messages. Specific
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21 // commands can be implemented by subclassing and overriding the run() method.
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22 // The run() method will be called by this base class from run(argc, argv) once
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23 // it has parsed options, which can be accessed from the 'options' map using the
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24 // name strings given when adding them (not 'identifier', which is its parsing
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25 // name to appear after the '-'). Arguments (i.e. operands given after the
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26 // options on the command line) will be available in the 'arguments' vector.
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27
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28 public:
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29
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30 class Option
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31 {
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32 public:
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33
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34 enum Type
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35 {
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36 Boolean,
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37 Number,
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38 Integer,
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39 Size,
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40 File,
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41 String
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42 }
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43 type;
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44
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45 std::string category;
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46 std::string identifier;
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47 std::string description;
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48 std::string argument;
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49 std::string argumentDefault;
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50
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51 float argumentAsNumber;
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52 float argumentMin;
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53 float argumentMax;
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54
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55 bool active;
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56 bool changed;
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57
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58 Option() {}
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59 Option(Type typeNew, std::string identifierNew, std::string categoryNew, std::string descriptionNew, std::string argumentDefaultNew = "", float argumentMinNew = 0, float argumentMaxNew = 0);
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60
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61 float getArgumentAsNumber() const {return argumentAsNumber;}
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62 void setArgument(std::string argumentNew);
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63 };
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64
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65 Command();
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66 virtual ~Command() {};
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67
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68 void addOption(std::string name, Option option);
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69 const Option & getOption(std::string name) const;
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70 inline bool hasOption(std::string name) const {return options.count(name);}
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71 void print() const;
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72 virtual int run() const = 0;
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73 int run(int argc, const char ** argv);
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74
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75 std::string name;
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76 std::string summary;
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77 std::string description;
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78 std::string argumentString;
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79
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80 protected:
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81
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82 void useOption(std::string name);
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83 void useSketchOptions();
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84
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85 std::map<std::string, Option> options;
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86 std::map<std::string, Option> optionsAvailable;
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87 std::vector<std::string> arguments;
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88
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89 private:
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90
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91 void addAvailableOption(std::string name, Option option);
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92 void addCategory(std::string name, std::string displayName);
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93
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94 std::map<std::string, std::string> optionNamesByIdentifier;
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95 std::map<std::string, std::vector<std::string> > optionNamesByCategory;
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96 std::vector<std::string> categories;
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97 std::map<std::string, std::string> categoryDisplayNames;
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98 };
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99
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100 inline const Command::Option & Command::getOption(std::string name) const {return options.at(name);}
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101 void splitFile(const std::string & file, std::vector<std::string> & lines);
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102 void printColumns(const std::vector<std::vector<std::string>> & columns, int indent = 2, int spacing = 2, const char * missing = "-", int max = 80);
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103 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);
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104
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105 } // namespace mash
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106
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107 #endif
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