Merge commit '0f66a4785cbefc6772ee790d55c16cc7239c1dba'

# Conflicts:
#	dependencies/libjson/ide/json.xcodeproj/project.pbxproj
#	src/core/probabilistic_model.cpp
#	src/models/hierarchical_hmm.cpp
#	src/models/hierarchical_hmm.h

CMakeLists.txt

@@ -1,8 +1,19 @@
-cmake_minimum_required (VERSION 2.6)
+cmake_minimum_required(VERSION 3.1.0 FATAL_ERROR)
 
 # Project declaration
 project(xmm)
 
+include(CheckCXXCompilerFlag)
+CHECK_CXX_COMPILER_FLAG("-std=c++11" COMPILER_SUPPORTS_CXX11)
+CHECK_CXX_COMPILER_FLAG("-std=c++0x" COMPILER_SUPPORTS_CXX0X)
+if(COMPILER_SUPPORTS_CXX11)
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+elseif(COMPILER_SUPPORTS_CXX0X)
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++0x")
+else()
+        message(STATUS "The compiler ${CMAKE_CXX_COMPILER} has no C++11 support. Please use a different C++ compiler.")
+endif()
+
 # The version number.
 set (xmm_VERSION_MAJOR 0)
 set (xmm_VERSION_MINOR 1)
@@ -15,16 +26,19 @@ if (NOT CMAKE_BUILD_TYPE)
     set(CMAKE_BUILD_TYPE "Release")
 endif()
 
-add_subdirectory(dependencies/libjson)
-
 # Include JSON
-include_directories(./dependencies/libjson/src)
-link_directories(${CMAKE_CURRENT_SOURCE_DIR}/dependencies/libjson/bin/${CMAKE_BUILD_TYPE})
+include_directories(./dependencies/jsoncpp/include)
+include_directories(./dependencies/jsoncpp/src)
 
 # Declare library
 include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src)
-include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/core)
-include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/models)
+include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/core/common)
+include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/core/distributions)
+include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/core/model)
+include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/core/trainingset)
+include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/models/gmm)
+include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/models/hmm)
+include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/models/kmeans)
 
 set(LIBRARY_OUTPUT_PATH ${CMAKE_CURRENT_SOURCE_DIR}/bin/${CMAKE_BUILD_TYPE})
 add_definitions(-DUSE_PTHREAD)
@@ -35,22 +49,21 @@ file(
     src/*
 )
 
-add_library(
-    xmm
-    STATIC
-    ${xmm_source_files}
+file(
+    GLOB_RECURSE
+    jsoncpp_source_files
+    dependencies/jsoncpp/src/*
 )
 
-# linking configuration
-target_link_libraries(
+add_library(
     xmm
-    json pthread
+    STATIC
+    ${xmm_source_files} ${jsoncpp_source_files}
 )
 
 # Declare Unit tests
 set(EXECUTABLE_OUTPUT_PATH bin/${CMAKE_BUILD_TYPE})
 include_directories(${CMAKE_CURRENT_SOURCE_DIR}/dependencies/catch)
-link_directories(${CMAKE_CURRENT_SOURCE_DIR}/dependencies/libjson/bin/${CMAKE_BUILD_TYPE} ${LIBRARY_OUTPUT_PATH})
 
 # message(${LINK_DIRECTORIES})
 
@@ -61,19 +74,19 @@ file(
 )
 
 add_executable(
-    test
+    tests
     EXCLUDE_FROM_ALL
     ${xmm_test_files}
 )
 
 # linking configuration
 target_link_libraries(
-    test
+    tests
     xmm
 )
 
-set_target_properties(test PROPERTIES OUTPUT_NAME xmm_testing)
-add_custom_command(TARGET test POST_BUILD COMMAND ${EXECUTABLE_OUTPUT_PATH}/xmm_testing)
+set_target_properties(tests PROPERTIES OUTPUT_NAME xmm_testing)
+add_custom_command(TARGET tests POST_BUILD COMMAND ${EXECUTABLE_OUTPUT_PATH}/xmm_testing)
 
 # add a target to generate API documentation with Doxygen
 find_package(Doxygen)
@@ -91,11 +104,6 @@ if(DOXYGEN_FOUND)
                       DEPENDS ${tracking_source_files}
                       WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc/
                       COMMENT "Generating API documentation with Doxygen" VERBATIM)
-    add_custom_target(docapi
-                      COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/doc/Doxyfile-API
-                      DEPENDS ${tracking_source_files}
-                      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc/
-                      COMMENT "Generating API documentation with Doxygen" VERBATIM)
 else(DOXYGEN_FOUND)
     message(STATUS "Doxygen not found, doc will not be included in the Makefile")
 endif(DOXYGEN_FOUND)

dependencies/jsoncpp/LICENSE

@@ -0,0 +1,55 @@
+The JsonCpp library's source code, including accompanying documentation, 
+tests and demonstration applications, are licensed under the following
+conditions...
+
+The author (Baptiste Lepilleur) explicitly disclaims copyright in all 
+jurisdictions which recognize such a disclaimer. In such jurisdictions, 
+this software is released into the Public Domain.
+
+In jurisdictions which do not recognize Public Domain property (e.g. Germany as of
+2010), this software is Copyright (c) 2007-2010 by Baptiste Lepilleur, and is
+released under the terms of the MIT License (see below).
+
+In jurisdictions which recognize Public Domain property, the user of this 
+software may choose to accept it either as 1) Public Domain, 2) under the 
+conditions of the MIT License (see below), or 3) under the terms of dual 
+Public Domain/MIT License conditions described here, as they choose.
+
+The MIT License is about as close to Public Domain as a license can get, and is
+described in clear, concise terms at:
+
+   http://en.wikipedia.org/wiki/MIT_License
+
+The full text of the MIT License follows:
+
+========================================================================
+Copyright (c) 2007-2010 Baptiste Lepilleur
+
+Permission is hereby granted, free of charge, to any person
+obtaining a copy of this software and associated documentation
+files (the "Software"), to deal in the Software without
+restriction, including without limitation the rights to use, copy,
+modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+========================================================================
+(END LICENSE TEXT)
+
+The MIT license is compatible with both the GPL and commercial
+software, affording one all of the rights of Public Domain with the
+minor nuisance of being required to keep the above copyright notice
+and license text in the source code. Note also that by accepting the
+Public Domain "license" you can re-license your copy using whatever
+license you like.

dependencies/jsoncpp/include/assertions.h

@@ -0,0 +1,54 @@
+// 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_ASSERTIONS_H_INCLUDED
+#define CPPTL_JSON_ASSERTIONS_H_INCLUDED
+
+#include <stdlib.h>
+#include <sstream>
+
+#if !defined(JSON_IS_AMALGAMATION)
+#include "config.h"
+#endif // if !defined(JSON_IS_AMALGAMATION)
+
+/** It should not be possible for a maliciously designed file to
+ *  cause an abort() or seg-fault, so these macros are used only
+ *  for pre-condition violations and internal logic errors.
+ */
+#if JSON_USE_EXCEPTION
+
+// @todo <= add detail about condition in exception
+# define JSON_ASSERT(condition)                                                \
+  {if (!(condition)) {Json::throwLogicError( "assert json failed" );}}
+
+# define JSON_FAIL_MESSAGE(message)                                            \
+  {                                                                            \
+    std::ostringstream oss; oss << message;                                    \
+    Json::throwLogicError(oss.str());                                          \
+    abort();                                                                   \
+  }
+
+#else // JSON_USE_EXCEPTION
+
+# define JSON_ASSERT(condition) assert(condition)
+
+// The call to assert() will show the failure message in debug builds. In
+// release builds we abort, for a core-dump or debugger.
+# define JSON_FAIL_MESSAGE(message)                                            \
+  {                                                                            \
+    std::ostringstream oss; oss << message;                                    \
+    assert(false && oss.str().c_str());                                        \
+    abort();                                                                   \
+  }
+
+
+#endif
+
+#define JSON_ASSERT_MESSAGE(condition, message)                                \
+  if (!(condition)) {                                                          \
+    JSON_FAIL_MESSAGE(message);                                                \
+  }
+
+#endif // CPPTL_JSON_ASSERTIONS_H_INCLUDED

dependencies/jsoncpp/include/autolink.h

@@ -0,0 +1,25 @@
+// 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_AUTOLINK_H_INCLUDED
+#define JSON_AUTOLINK_H_INCLUDED
+
+#include "config.h"
+
+#ifdef JSON_IN_CPPTL
+#include <cpptl/cpptl_autolink.h>
+#endif
+
+#if !defined(JSON_NO_AUTOLINK) && !defined(JSON_DLL_BUILD) &&                  \
+    !defined(JSON_IN_CPPTL)
+#define CPPTL_AUTOLINK_NAME "json"
+#undef CPPTL_AUTOLINK_DLL
+#ifdef JSON_DLL
+#define CPPTL_AUTOLINK_DLL
+#endif
+#include "autolink.h"
+#endif
+
+#endif // JSON_AUTOLINK_H_INCLUDED

dependencies/jsoncpp/include/config.h

@@ -0,0 +1,138 @@
+// 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
+
+/// If defined, indicates that json library is embedded in CppTL library.
+//# define JSON_IN_CPPTL 1
+
+/// If defined, indicates that json may leverage CppTL library
+//#  define JSON_USE_CPPTL 1
+/// If defined, indicates that cpptl vector based map should be used instead of
+/// std::map
+/// as Value container.
+//#  define JSON_USE_CPPTL_SMALLMAP 1
+
+// If non-zero, the library uses exceptions to report bad input instead of C
+// assertion macros. The default is to use exceptions.
+#ifndef JSON_USE_EXCEPTION
+#define JSON_USE_EXCEPTION 1
+#endif
+
+/// If defined, indicates that the source file is amalgated
+/// to prevent private header inclusion.
+/// Remarks: it is automatically defined in the generated amalgated header.
+// #define JSON_IS_AMALGAMATION
+
+#ifdef JSON_IN_CPPTL
+#include <cpptl/config.h>
+#ifndef JSON_USE_CPPTL
+#define JSON_USE_CPPTL 1
+#endif
+#endif
+
+#ifdef JSON_IN_CPPTL
+#define JSON_API CPPTL_API
+#elif defined(JSON_DLL_BUILD)
+#if defined(_MSC_VER)
+#define JSON_API __declspec(dllexport)
+#define JSONCPP_DISABLE_DLL_INTERFACE_WARNING
+#endif // if defined(_MSC_VER)
+#elif defined(JSON_DLL)
+#if defined(_MSC_VER)
+#define JSON_API __declspec(dllimport)
+#define JSONCPP_DISABLE_DLL_INTERFACE_WARNING
+#endif // if defined(_MSC_VER)
+#endif // ifdef JSON_IN_CPPTL
+#if !defined(JSON_API)
+#define JSON_API
+#endif
+
+// If JSON_NO_INT64 is defined, then Json only support C++ "int" type for
+// integer
+// Storages, and 64 bits integer support is disabled.
+// #define JSON_NO_INT64 1
+
+#if defined(_MSC_VER) // MSVC
+#  if _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
+    // Disable warning 4786 for VS6 caused by STL (identifier was truncated to '255'
+    // characters in the debug information)
+    // All projects I've ever seen with VS6 were using this globally (not bothering
+    // with pragma push/pop).
+#    pragma warning(disable : 4786)
+#  endif // MSVC 6
+
+#  if _MSC_VER >= 1500 // MSVC 2008
+    /// Indicates that the following function is deprecated.
+#    define JSONCPP_DEPRECATED(message) __declspec(deprecated(message))
+#  endif
+
+#endif // defined(_MSC_VER)
+
+
+#ifndef JSON_HAS_RVALUE_REFERENCES
+
+#if defined(_MSC_VER) && _MSC_VER >= 1600 // MSVC >= 2010
+#define JSON_HAS_RVALUE_REFERENCES 1
+#endif // MSVC >= 2010
+
+#ifdef __clang__
+#if __has_feature(cxx_rvalue_references)
+#define JSON_HAS_RVALUE_REFERENCES 1
+#endif  // has_feature
+
+#elif defined __GNUC__ // not clang (gcc comes later since clang emulates gcc)
+#if defined(__GXX_EXPERIMENTAL_CXX0X__) || (__cplusplus >= 201103L)
+#define JSON_HAS_RVALUE_REFERENCES 1
+#endif  // GXX_EXPERIMENTAL
+
+#endif // __clang__ || __GNUC__
+
+#endif // not defined JSON_HAS_RVALUE_REFERENCES
+
+#ifndef JSON_HAS_RVALUE_REFERENCES
+#define JSON_HAS_RVALUE_REFERENCES 0
+#endif
+
+#ifdef __clang__
+#elif defined __GNUC__ // not clang (gcc comes later since clang emulates gcc)
+#  if (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 5))
+#    define JSONCPP_DEPRECATED(message)  __attribute__ ((deprecated(message)))
+#  elif (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 1))
+#    define JSONCPP_DEPRECATED(message)  __attribute__((__deprecated__))
+#  endif  // GNUC version
+#endif // __clang__ || __GNUC__
+
+#if !defined(JSONCPP_DEPRECATED)
+#define JSONCPP_DEPRECATED(message)
+#endif // if !defined(JSONCPP_DEPRECATED)
+
+namespace Json {
+typedef int Int;
+typedef unsigned int UInt;
+#if defined(JSON_NO_INT64)
+typedef int LargestInt;
+typedef unsigned int LargestUInt;
+#undef JSON_HAS_INT64
+#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 Int64;
+typedef unsigned __int64 UInt64;
+#else                 // if defined(_MSC_VER) // Other platforms, use long long
+typedef long long int Int64;
+typedef unsigned long long int UInt64;
+#endif // if defined(_MSC_VER)
+typedef Int64 LargestInt;
+typedef UInt64 LargestUInt;
+#define JSON_HAS_INT64
+#endif // if defined(JSON_NO_INT64)
+} // end namespace Json
+
+#endif // JSON_CONFIG_H_INCLUDED