--- /dev/null
+// ***************************************************************************
+// bamtools_options.h (c) 2010 Derek Barnett, Erik Garrison
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 1 June 2010
+// ---------------------------------------------------------------------------
+// Parses command line arguments and creates a help menu
+// ---------------------------------------------------------------------------
+// Modified from:
+// The Mosaik suite's command line parser class: COptions
+// (c) 2006 - 2009 Michael Str�mberg
+// Marth Lab, Department of Biology, Boston College
+// Dual licenced under the GNU General Public License 2.0+ license or as
+// a commercial license with the Marth Lab.
+//
+// * Modified to fit BamTools code-style, otherwise code is same. (DB)
+// ***************************************************************************
+
+#ifndef BAMTOOLS_OPTIONS_H
+#define BAMTOOLS_OPTIONS_H
+
+#include <map>
+#include <string>
+#include <vector>
+#include "bamtools_variant.h"
+
+#ifndef WIN32
+ #include <stdint.h>
+#endif
+
+namespace BamTools {
+
+#define ARGUMENT_LENGTH 35
+#define DESC_LENGTH_FIRST_ROW 50
+#define DESC_LENGTH 39
+#define MAX_LINE_LENGTH 78
+
+#ifdef WIN32
+ #define snprintf _snprintf
+ typedef __int64 int64_t;
+ typedef unsigned __int64 uint64_t;
+ #define strtoui64 _strtoui64
+#else
+ #define strtoui64 strtoull
+#endif
+
+struct Option {
+
+ // data members
+ std::string Argument;
+ std::string ValueDescription;
+ std::string Description;
+ bool StoreValue;
+ bool HasDefaultValue;
+ Variant DefaultValue;
+
+ // constructor
+ Option(void)
+ : StoreValue(true)
+ , HasDefaultValue(false)
+ { }
+};
+
+struct OptionValue {
+
+ // data members
+ bool* pFoundArgument;
+ void* pValue;
+ std::string ValueTypeDescription;
+ bool UseVector;
+ bool StoreValue;
+ bool IsRequired;
+ Variant VariantValue;
+
+ // constructor
+ OptionValue(void)
+ : pFoundArgument(NULL)
+ , pValue(NULL)
+ , UseVector(false)
+ , StoreValue(true)
+ , IsRequired(false)
+ { }
+};
+
+struct OptionGroup {
+ std::string Name;
+ std::vector<Option> Options;
+};
+
+class Options {
+
+ // add option/argument rules
+ public:
+ // adds a simple option to the parser
+ static void AddOption(const std::string& argument,
+ const std::string& optionDescription,
+ bool& foundArgument,
+ OptionGroup* group);
+
+ // adds a value option to the parser
+ template<typename T>
+ static void AddValueOption(const std::string& argument,
+ const std::string& valueDescription,
+ const std::string& optionDescription,
+ const std::string& valueTypeDescription,
+ bool& foundArgument,
+ T& val,
+ OptionGroup* group);
+
+ // adds a value option to the parser (with a default value)
+ template<typename T, typename D>
+ static void AddValueOption(const std::string& argument,
+ const std::string& valueDescription,
+ const std::string& optionDescription,
+ const std::string& valueTypeDescription,
+ bool& foundArgument,
+ T& val,
+ OptionGroup* group,
+ D& defaultValue);
+
+ // other API methods
+ public:
+ // creates an option group
+ static OptionGroup* CreateOptionGroup(const std::string& groupName);
+ // displays the help menu
+ static void DisplayHelp(void);
+ // parses the command line
+ static void Parse(int argc, char* argv[], int offset = 0);
+ // sets the program info
+ static void SetProgramInfo(const std::string& programName, const std::string& description, const std::string& arguments);
+ // returns string representation of stdin
+ static const std::string& StandardIn(void);
+ // returns string representation of stdout
+ static const std::string& StandardOut(void);
+
+ // static data members
+ private:
+ // the program name
+ static std::string m_programName;
+ // the main description
+ static std::string m_description;
+ // the example arguments
+ static std::string m_exampleArguments;
+ // stores the option groups
+ static std::vector<OptionGroup> m_optionGroups;
+ // stores the options in a map
+ static std::map<std::string, OptionValue> m_optionsMap;
+ // string representation of stdin
+ static std::string m_stdin;
+ // string representation of stdout
+ static std::string m_stdout;
+};
+
+// adds a value option to the parser
+template<typename T>
+void Options::AddValueOption(const std::string& argument,
+ const std::string& valueDescription,
+ const std::string& optionDescription,
+ const std::string& valueTypeDescription,
+ bool& foundArgument,
+ T& val,
+ OptionGroup* group)
+{
+ Option o;
+ o.Argument = argument;
+ o.ValueDescription = valueDescription;
+ o.Description = optionDescription;
+ group->Options.push_back(o);
+
+ OptionValue ov;
+ ov.pFoundArgument = &foundArgument;
+ ov.pValue = (void*)&val;
+ ov.VariantValue = val;
+ ov.IsRequired = (valueTypeDescription.empty() ? false : true);
+ ov.ValueTypeDescription = valueTypeDescription;
+ m_optionsMap[argument] = ov;
+}
+
+// adds a value option to the parser (with a default value)
+template<typename T, typename D>
+void Options::AddValueOption(const std::string& argument,
+ const std::string& valueDescription,
+ const std::string& optionDescription,
+ const std::string& valueTypeDescription,
+ bool& foundArgument,
+ T& val,
+ OptionGroup* group,
+ D& defaultValue)
+{
+ Option o;
+ o.Argument = argument;
+ o.ValueDescription = valueDescription;
+ o.Description = optionDescription;
+ o.DefaultValue = defaultValue;
+ o.HasDefaultValue = true;
+ group->Options.push_back(o);
+
+ OptionValue ov;
+ ov.pFoundArgument = &foundArgument;
+ ov.pValue = (void*)&val;
+ ov.VariantValue = val;
+ ov.IsRequired = (valueTypeDescription.empty() ? false : true);
+ ov.ValueTypeDescription = valueTypeDescription;
+ m_optionsMap[argument] = ov;
+}
+
+} // namespace BamTools
+
+#endif // BAMTOOLS_OPTIONS_H
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projects / bamtools.git / blobdiff