Merge branch 'eigenvalues'

This brings in the Eigen3 implementation of kernel/distance matrices

CMakeLists.txt

@@ -63,6 +63,10 @@ FIND_PACKAGE(ZLIB 1.2.3 REQUIRED)
 INCLUDE_DIRECTORIES(${ZLIB_INCLUDE_DIRS})
 SET(KMERCLUST_DEPENDS_LIBS ${KMERCLUST_DEPENDS_LIBS} ${ZLIB_LIBRARIES})
 
+FIND_PACKAGE(Eigen3 3.0.0 REQUIRED)
+INCLUDE_DIRECTORIES(${EIGEN3_INCLUDE_DIR})
+# Eigen is header only, no need for libs
+
 SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${ZLIB_C_FLAGS}")
 SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${ZLIB_C_FLAGS} -DSEQAN_HAS_ZLIB=1")
 

cmake/FindEigen3.cmake

@@ -0,0 +1,91 @@
+# - Try to find Eigen3 lib
+#
+# This module supports requiring a minimum version, e.g. you can do
+#   find_package(Eigen3 3.1.2)
+# to require version 3.1.2 or newer of Eigen3.
+#
+# Once done this will define
+#
+#  EIGEN3_FOUND - system has eigen lib with correct version
+#  EIGEN3_INCLUDE_DIR - the eigen include directory
+#  EIGEN3_VERSION - eigen version
+#
+# This module reads hints about search locations from 
+# the following enviroment variables:
+#
+# EIGEN3_ROOT
+# EIGEN3_ROOT_DIR
+
+# Copyright (c) 2006, 2007 Montel Laurent, <[email protected]>
+# Copyright (c) 2008, 2009 Gael Guennebaud, <[email protected]>
+# Copyright (c) 2009 Benoit Jacob <[email protected]>
+# Redistribution and use is allowed according to the terms of the 2-clause BSD license.
+
+if(NOT Eigen3_FIND_VERSION)
+  if(NOT Eigen3_FIND_VERSION_MAJOR)
+    set(Eigen3_FIND_VERSION_MAJOR 2)
+  endif(NOT Eigen3_FIND_VERSION_MAJOR)
+  if(NOT Eigen3_FIND_VERSION_MINOR)
+    set(Eigen3_FIND_VERSION_MINOR 91)
+  endif(NOT Eigen3_FIND_VERSION_MINOR)
+  if(NOT Eigen3_FIND_VERSION_PATCH)
+    set(Eigen3_FIND_VERSION_PATCH 0)
+  endif(NOT Eigen3_FIND_VERSION_PATCH)
+
+  set(Eigen3_FIND_VERSION "${Eigen3_FIND_VERSION_MAJOR}.${Eigen3_FIND_VERSION_MINOR}.${Eigen3_FIND_VERSION_PATCH}")
+endif(NOT Eigen3_FIND_VERSION)
+
+macro(_eigen3_check_version)
+  file(READ "${EIGEN3_INCLUDE_DIR}/Eigen/src/Core/util/Macros.h" _eigen3_version_header)
+
+  string(REGEX MATCH "define[ \t]+EIGEN_WORLD_VERSION[ \t]+([0-9]+)" _eigen3_world_version_match "${_eigen3_version_header}")
+  set(EIGEN3_WORLD_VERSION "${CMAKE_MATCH_1}")
+  string(REGEX MATCH "define[ \t]+EIGEN_MAJOR_VERSION[ \t]+([0-9]+)" _eigen3_major_version_match "${_eigen3_version_header}")
+  set(EIGEN3_MAJOR_VERSION "${CMAKE_MATCH_1}")
+  string(REGEX MATCH "define[ \t]+EIGEN_MINOR_VERSION[ \t]+([0-9]+)" _eigen3_minor_version_match "${_eigen3_version_header}")
+  set(EIGEN3_MINOR_VERSION "${CMAKE_MATCH_1}")
+
+  set(EIGEN3_VERSION ${EIGEN3_WORLD_VERSION}.${EIGEN3_MAJOR_VERSION}.${EIGEN3_MINOR_VERSION})
+  if(${EIGEN3_VERSION} VERSION_LESS ${Eigen3_FIND_VERSION})
+    set(EIGEN3_VERSION_OK FALSE)
+  else(${EIGEN3_VERSION} VERSION_LESS ${Eigen3_FIND_VERSION})
+    set(EIGEN3_VERSION_OK TRUE)
+  endif(${EIGEN3_VERSION} VERSION_LESS ${Eigen3_FIND_VERSION})
+
+  if(NOT EIGEN3_VERSION_OK)
+
+    message(STATUS "Eigen3 version ${EIGEN3_VERSION} found in ${EIGEN3_INCLUDE_DIR}, "
+                   "but at least version ${Eigen3_FIND_VERSION} is required")
+  endif(NOT EIGEN3_VERSION_OK)
+endmacro(_eigen3_check_version)
+
+if (EIGEN3_INCLUDE_DIR)
+
+  # in cache already
+  _eigen3_check_version()
+  set(EIGEN3_FOUND ${EIGEN3_VERSION_OK})
+
+else (EIGEN3_INCLUDE_DIR)
+
+  find_path(EIGEN3_INCLUDE_DIR NAMES signature_of_eigen3_matrix_library
+      HINTS
+      ENV EIGEN3_ROOT 
+      ENV EIGEN3_ROOT_DIR
+      PATHS
+      ${CMAKE_INSTALL_PREFIX}/include
+      ${KDE4_INCLUDE_DIR}
+      src/ext
+      PATH_SUFFIXES eigen3 eigen
+    )
+
+  if(EIGEN3_INCLUDE_DIR)
+    _eigen3_check_version()
+  endif(EIGEN3_INCLUDE_DIR)
+
+  include(FindPackageHandleStandardArgs)
+  find_package_handle_standard_args(Eigen3 DEFAULT_MSG EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK)
+
+  mark_as_advanced(EIGEN3_INCLUDE_DIR)
+
+endif(EIGEN3_INCLUDE_DIR)
+

src/ext/eigen3/COPYING.BSD

@@ -0,0 +1,26 @@
+/*
+ Copyright (c) 2011, Intel Corporation. All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without modification,
+ are permitted provided that the following conditions are met:
+
+ * Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+ * Neither the name of Intel Corporation nor the names of its contributors may
+   be used to endorse or promote products derived from this software without
+   specific prior written permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/