--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/include/mash/Command.h	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,107 @@
+// Copyright © 2015, Battelle National Biodefense Institute (BNBI);
+// 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