ngs_server 0.1

data/ext/bamtools/src/third_party/jsoncpp/json_writer.h

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+// Copyright 2007-2010 Baptiste Lepilleur
+// Distributed under MIT license, or public domain if desired and
+// recognized in your jurisdiction.
+// See file LICENSE for detail or copy at http://jsoncpp.sourceforge.net/LICENSE
+
+#ifndef JSON_WRITER_H_INCLUDED
+# define JSON_WRITER_H_INCLUDED
+
+# include "json_value.h"
+# include <vector>
+# include <string>
+# include <iostream>
+
+namespace Json {
+
+   class Value;
+
+   /** \brief Abstract class for writers.
+    */
+   class JSON_API Writer
+   {
+   public:
+      virtual ~Writer();
+
+      virtual std::string write( const Value &root ) = 0;
+   };
+
+   /** \brief Outputs a Value in <a HREF="http://www.json.org">JSON</a> format without formatting (not human friendly).
+    *
+    * The JSON document is written in a single line. It is not intended for 'human' consumption,
+    * but may be usefull to support feature such as RPC where bandwith is limited.
+    * \sa Reader, Value
+    */
+   class JSON_API FastWriter : public Writer
+   {
+   public:
+      FastWriter();
+      virtual ~FastWriter(){}
+
+      void enableYAMLCompatibility();
+
+   public: // overridden from Writer
+      virtual std::string write( const Value &root );
+
+   private:
+      void writeValue( const Value &value );
+
+      std::string document_;
+      bool yamlCompatiblityEnabled_;
+   };
+
+   /** \brief Writes a Value in <a HREF="http://www.json.org">JSON</a> format in a human friendly way.
+    *
+    * The rules for line break and indent are as follow:
+    * - Object value:
+    *     - if empty then print {} without indent and line break
+    *     - if not empty the print '{', line break & indent, print one value per line
+    *       and then unindent and line break and print '}'.
+    * - Array value:
+    *     - if empty then print [] without indent and line break
+    *     - if the array contains no object value, empty array or some other value types,
+    *       and all the values fit on one lines, then print the array on a single line.
+    *     - otherwise, it the values do not fit on one line, or the array contains
+    *       object or non empty array, then print one value per line.
+    *
+    * If the Value have comments then they are outputed according to their #CommentPlacement.
+    *
+    * \sa Reader, Value, Value::setComment()
+    */
+   class JSON_API StyledWriter: public Writer
+   {
+   public:
+      StyledWriter();
+      virtual ~StyledWriter(){}
+
+   public: // overridden from Writer
+      /** \brief Serialize a Value in <a HREF="http://www.json.org">JSON</a> format.
+       * \param root Value to serialize.
+       * \return String containing the JSON document that represents the root value.
+       */
+      virtual std::string write( const Value &root );
+
+   private:
+      void writeValue( const Value &value );
+      void writeArrayValue( const Value &value );
+      bool isMultineArray( const Value &value );
+      void pushValue( const std::string &value );
+      void writeIndent();
+      void writeWithIndent( const std::string &value );
+      void indent();
+      void unindent();
+      void writeCommentBeforeValue( const Value &root );
+      void writeCommentAfterValueOnSameLine( const Value &root );
+      bool hasCommentForValue( const Value &value );
+      static std::string normalizeEOL( const std::string &text );
+
+      typedef std::vector<std::string> ChildValues;
+
+      ChildValues childValues_;
+      std::string document_;
+      std::string indentString_;
+      int rightMargin_;
+      int indentSize_;
+      bool addChildValues_;
+   };
+
+   /** \brief Writes a Value in <a HREF="http://www.json.org">JSON</a> format in a human friendly way,
+        to a stream rather than to a string.
+    *
+    * The rules for line break and indent are as follow:
+    * - Object value:
+    *     - if empty then print {} without indent and line break
+    *     - if not empty the print '{', line break & indent, print one value per line
+    *       and then unindent and line break and print '}'.
+    * - Array value:
+    *     - if empty then print [] without indent and line break
+    *     - if the array contains no object value, empty array or some other value types,
+    *       and all the values fit on one lines, then print the array on a single line.
+    *     - otherwise, it the values do not fit on one line, or the array contains
+    *       object or non empty array, then print one value per line.
+    *
+    * If the Value have comments then they are outputed according to their #CommentPlacement.
+    *
+    * \param indentation Each level will be indented by this amount extra.
+    * \sa Reader, Value, Value::setComment()
+    */
+   class JSON_API StyledStreamWriter
+   {
+   public:
+      StyledStreamWriter( std::string indentation="\t" );
+      ~StyledStreamWriter(){}
+
+   public:
+      /** \brief Serialize a Value in <a HREF="http://www.json.org">JSON</a> format.
+       * \param out Stream to write to. (Can be ostringstream, e.g.)
+       * \param root Value to serialize.
+       * \note There is no point in deriving from Writer, since write() should not return a value.
+       */
+      void write( std::ostream &out, const Value &root );
+
+   private:
+      void writeValue( const Value &value );
+      void writeArrayValue( const Value &value );
+      bool isMultineArray( const Value &value );
+      void pushValue( const std::string &value );
+      void writeIndent();
+      void writeWithIndent( const std::string &value );
+      void indent();
+      void unindent();
+      void writeCommentBeforeValue( const Value &root );
+      void writeCommentAfterValueOnSameLine( const Value &root );
+      bool hasCommentForValue( const Value &value );
+      static std::string normalizeEOL( const std::string &text );
+
+      typedef std::vector<std::string> ChildValues;
+
+      ChildValues childValues_;
+      std::ostream* document_;
+      std::string indentString_;
+      int rightMargin_;
+      std::string indentation_;
+      bool addChildValues_;
+   };
+
+   std::string JSON_API valueToString( Int value );
+   std::string JSON_API valueToString( UInt value );
+   std::string JSON_API valueToString( double value );
+   std::string JSON_API valueToString( bool value );
+   std::string JSON_API valueToQuotedString( const char *value );
+
+   /// \brief Output using the StyledStreamWriter.
+   /// \see Json::operator>>()
+   std::ostream& operator<<( std::ostream&, const Value &root );
+
+} // namespace Json
+
+
+
+#endif // JSON_WRITER_H_INCLUDED

data/ext/bamtools/src/toolkit/CMakeFiles/CMakeDirectoryInformation.cmake

@@ -0,0 +1,25 @@
+# CMAKE generated file: DO NOT EDIT!
+# Generated by "Unix Makefiles" Generator, CMake Version 2.8
+
+# Relative path conversion top directories.
+SET(CMAKE_RELATIVE_PATH_TOP_SOURCE "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools")
+SET(CMAKE_RELATIVE_PATH_TOP_BINARY "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools")
+
+# Force unix paths in dependencies.
+SET(CMAKE_FORCE_UNIX_PATHS 1)
+
+# The C and CXX include file search paths:
+SET(CMAKE_C_INCLUDE_PATH
+  "src"
+  "src/api"
+  "src/utils"
+  "src/third_party"
+  )
+SET(CMAKE_CXX_INCLUDE_PATH ${CMAKE_C_INCLUDE_PATH})
+SET(CMAKE_Fortran_INCLUDE_PATH ${CMAKE_C_INCLUDE_PATH})
+
+# The C and CXX include file regular expressions for this directory.
+SET(CMAKE_C_INCLUDE_REGEX_SCAN "^.*$")
+SET(CMAKE_C_INCLUDE_REGEX_COMPLAIN "^$")
+SET(CMAKE_CXX_INCLUDE_REGEX_SCAN ${CMAKE_C_INCLUDE_REGEX_SCAN})
+SET(CMAKE_CXX_INCLUDE_REGEX_COMPLAIN ${CMAKE_C_INCLUDE_REGEX_COMPLAIN})