ngs_server 0.1

data/ext/bamtools/src/third_party/jsoncpp/cmake_install.cmake

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+# Install script for directory: /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp
+
+# Set the install prefix
+IF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+  SET(CMAKE_INSTALL_PREFIX "/usr/local")
+ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
+
+# Set the install configuration name.
+IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+  IF(BUILD_TYPE)
+    STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
+           CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
+  ELSE(BUILD_TYPE)
+    SET(CMAKE_INSTALL_CONFIG_NAME "Release")
+  ENDIF(BUILD_TYPE)
+  MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
+ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+
+# Set the component getting installed.
+IF(NOT CMAKE_INSTALL_COMPONENT)
+  IF(COMPONENT)
+    MESSAGE(STATUS "Install component: \"${COMPONENT}\"")
+    SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
+  ELSE(COMPONENT)
+    SET(CMAKE_INSTALL_COMPONENT)
+  ENDIF(COMPONENT)
+ENDIF(NOT CMAKE_INSTALL_COMPONENT)
+

data/ext/bamtools/src/third_party/jsoncpp/json.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_JSON_H_INCLUDED
+# define JSON_JSON_H_INCLUDED
+
+//# include "autolink.h"
+# include "json_value.h"
+# include "json_reader.h"
+# include "json_writer.h"
+# include "json_features.h"
+
+#endif // JSON_JSON_H_INCLUDED

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

@@ -0,0 +1,130 @@
+// 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 JSONCPP_BATCHALLOCATOR_H_INCLUDED
+# define JSONCPP_BATCHALLOCATOR_H_INCLUDED
+
+# include <stdlib.h>
+# include <assert.h>
+
+# ifndef JSONCPP_DOC_EXCLUDE_IMPLEMENTATION
+
+namespace Json {
+
+/* Fast memory allocator.
+ *
+ * This memory allocator allocates memory for a batch of object (specified by
+ * the page size, the number of object in each page).
+ *
+ * It does not allow the destruction of a single object. All the allocated objects
+ * can be destroyed at once. The memory can be either released or reused for future
+ * allocation.
+ * 
+ * The in-place new operator must be used to construct the object using the pointer
+ * returned by allocate.
+ */
+template<typename AllocatedType
+        ,const unsigned int objectPerAllocation>
+class BatchAllocator
+{
+public:
+   typedef AllocatedType Type;
+
+   BatchAllocator( unsigned int objectsPerPage = 255 )
+      : freeHead_( 0 )
+      , objectsPerPage_( objectsPerPage )
+   {
+//      printf( "Size: %d => %s\n", sizeof(AllocatedType), typeid(AllocatedType).name() );
+      assert( sizeof(AllocatedType) * objectPerAllocation >= sizeof(AllocatedType *) ); // We must be able to store a slist in the object free space.
+      assert( objectsPerPage >= 16 );
+      batches_ = allocateBatch( 0 );   // allocated a dummy page
+      currentBatch_ = batches_;
+   }
+
+   ~BatchAllocator()
+   {
+      for ( BatchInfo *batch = batches_; batch;  )
+      {
+         BatchInfo *nextBatch = batch->next_;
+         free( batch );
+         batch = nextBatch;
+      }
+   }
+
+   /// allocate space for an array of objectPerAllocation object.
+   /// @warning it is the responsability of the caller to call objects constructors.
+   AllocatedType *allocate()
+   {
+      if ( freeHead_ ) // returns node from free list.
+      {
+         AllocatedType *object = freeHead_;
+         freeHead_ = *(AllocatedType **)object;
+         return object;
+      }
+      if ( currentBatch_->used_ == currentBatch_->end_ )
+      {
+         currentBatch_ = currentBatch_->next_;
+         while ( currentBatch_  &&  currentBatch_->used_ == currentBatch_->end_ )
+            currentBatch_ = currentBatch_->next_;
+
+         if ( !currentBatch_  ) // no free batch found, allocate a new one
+         { 
+            currentBatch_ = allocateBatch( objectsPerPage_ );
+            currentBatch_->next_ = batches_; // insert at the head of the list
+            batches_ = currentBatch_;
+         }
+      }
+      AllocatedType *allocated = currentBatch_->used_;
+      currentBatch_->used_ += objectPerAllocation;
+      return allocated;
+   }
+
+   /// Release the object.
+   /// @warning it is the responsability of the caller to actually destruct the object.
+   void release( AllocatedType *object )
+   {
+      assert( object != 0 );
+      *(AllocatedType **)object = freeHead_;
+      freeHead_ = object;
+   }
+
+private:
+   struct BatchInfo
+   {
+      BatchInfo *next_;
+      AllocatedType *used_;
+      AllocatedType *end_;
+      AllocatedType buffer_[objectPerAllocation];
+   };
+
+   // disabled copy constructor and assignement operator.
+   BatchAllocator( const BatchAllocator & );
+   void operator =( const BatchAllocator &);
+
+   static BatchInfo *allocateBatch( unsigned int objectsPerPage )
+   {
+      const unsigned int mallocSize = sizeof(BatchInfo) - sizeof(AllocatedType)* objectPerAllocation
+                                + sizeof(AllocatedType) * objectPerAllocation * objectsPerPage;
+      BatchInfo *batch = static_cast<BatchInfo*>( malloc( mallocSize ) );
+      batch->next_ = 0;
+      batch->used_ = batch->buffer_;
+      batch->end_ = batch->buffer_ + objectsPerPage;
+      return batch;
+   }
+
+   BatchInfo *batches_;
+   BatchInfo *currentBatch_;
+   /// Head of a single linked list within the allocated space of freeed object
+   AllocatedType *freeHead_;
+   unsigned int objectsPerPage_;
+};
+
+
+} // namespace Json
+
+# endif // ifndef JSONCPP_DOC_INCLUDE_IMPLEMENTATION
+
+#endif // JSONCPP_BATCHALLOCATOR_H_INCLUDED
+

data/ext/bamtools/src/third_party/jsoncpp/json_config.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_CONFIG_H_INCLUDED
+#define JSON_CONFIG_H_INCLUDED
+
+// Last Modified: Derek Barnett, 19 November 2010
+
+#include "shared/bamtools_global.h"
+#ifdef BAMTOOLS_JSONCPP_LIBRARY
+#  define JSON_API BAMTOOLS_LIBRARY_EXPORT
+#else
+#  define JSON_API BAMTOOLS_LIBRARY_IMPORT
+#endif
+
+#if defined(_MSC_VER)  &&  _MSC_VER <= 1200 // MSVC 6
+// Microsoft Visual Studio 6 only support conversion from __int64 to double
+// (no conversion from unsigned __int64).
+#  define JSON_USE_INT64_DOUBLE_CONVERSION 1
+#endif // if defined(_MSC_VER)  &&  _MSC_VER < 1200 // MSVC 6
+
+namespace Json {
+
+#if defined(JSON_NO_INT64)
+   typedef int Int;
+   typedef unsigned int UInt;
+#else // if defined(JSON_NO_INT64)
+   // For Microsoft Visual use specific types as long long is not supported
+#  if defined(_MSC_VER) // Microsoft Visual Studio
+     typedef __int64 Int;
+     typedef unsigned __int64 UInt;
+#  else // if defined(_MSC_VER) // Other platforms, use long long
+     typedef long long int Int;
+     typedef unsigned long long int UInt;
+#  endif // if defined(_MSC_VER)
+#endif // if defined(JSON_NO_INT64)
+
+} // end namespace Json
+
+#endif // JSON_CONFIG_H_INCLUDED

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

@@ -0,0 +1,47 @@
+// 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 CPPTL_JSON_FEATURES_H_INCLUDED
+# define CPPTL_JSON_FEATURES_H_INCLUDED
+
+# include "json_forwards.h"
+
+namespace Json {
+
+   /** \brief Configuration passed to reader and writer.
+    * This configuration object can be used to force the Reader or Writer
+    * to behave in a standard conforming way.
+    */
+   class JSON_API Features
+   {
+   public:
+      /** \brief A configuration that allows all features and assumes all strings are UTF-8.
+       * - C & C++ comments are allowed
+       * - Root object can be any JSON value
+       * - Assumes Value strings are encoded in UTF-8
+       */
+      static Features all();
+
+      /** \brief A configuration that is strictly compatible with the JSON specification.
+       * - Comments are forbidden.
+       * - Root object must be either an array or an object value.
+       * - Assumes Value strings are encoded in UTF-8
+       */
+      static Features strictMode();
+
+      /** \brief Initialize the configuration like JsonConfig::allFeatures;
+       */
+      Features();
+
+      /// \c true if comments are allowed. Default: \c true.
+      bool allowComments_;
+
+      /// \c true if root must be either an array or an object value. Default: \c false.
+      bool strictRoot_;
+   };
+
+} // namespace Json
+
+#endif // CPPTL_JSON_FEATURES_H_INCLUDED

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

@@ -0,0 +1,42 @@
+// 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_FORWARDS_H_INCLUDED
+# define JSON_FORWARDS_H_INCLUDED
+
+# include "json_config.h"
+
+namespace Json {
+
+   // writer.h
+   class FastWriter;
+   class StyledWriter;
+
+   // reader.h
+   class Reader;
+
+   // features.h
+   class Features;
+
+   // value.h
+   typedef unsigned int ArrayIndex;
+   class StaticString;
+   class Path;
+   class PathArgument;
+   class Value;
+   class ValueIteratorBase;
+   class ValueIterator;
+   class ValueConstIterator;
+#ifdef JSON_VALUE_USE_INTERNAL_MAP
+   class ValueMapAllocator;
+   class ValueInternalLink;
+   class ValueInternalArray;
+   class ValueInternalMap;
+#endif // #ifdef JSON_VALUE_USE_INTERNAL_MAP
+
+} // namespace Json
+
+
+#endif // JSON_FORWARDS_H_INCLUDED