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Changeset 2881

Timestamp:

Nov 18, 2012, 2:28:05 AM (9 years ago)

Author:

Peter

Message:

Define PP variables in config.h rather than in CPPFLAGS. Include
config.h into all source files. Only ammend CXXFLAGS with '-Wall
-pedantic' when --enable-debug. In default mode we respect CXXFLAGS
value set by user, or set to default value '-O3'.

Location:

trunk

Files:

: 190 edited

configure.ac (modified) (4 diffs)
test/alignment.cc (modified) (1 diff)
test/alignment2.cc (modified) (1 diff)
test/averager.cc (modified) (1 diff)
test/averager1.cc (modified) (1 diff)
test/averager3.cc (modified) (1 diff)
test/averager4.cc (modified) (1 diff)
test/codon.cc (modified) (1 diff)
test/commandline.cc (modified) (1 diff)
test/concept.cc (modified) (1 diff)
test/consensus_inputranker.cc (modified) (1 diff)
test/crossvalidation.cc (modified) (1 diff)
test/data_lookup_1d.cc (modified) (1 diff)
test/data_weight.cc (modified) (1 diff)
test/data_weight_proxy.cc (modified) (1 diff)
test/deleter.cc (modified) (1 diff)
test/distance.cc (modified) (1 diff)
test/dna.cc (modified) (1 diff)
test/ensemble.cc (modified) (1 diff)
test/feature_selection.cc (modified) (1 diff)
test/fileutil.cc (modified) (1 diff)
test/fisher.cc (modified) (1 diff)
test/genomic_position.cc (modified) (1 diff)
test/getline_iterator.cc (modified) (1 diff)
test/gff.cc (modified) (1 diff)
test/help.cc (modified) (1 diff)
test/histogram.cc (modified) (1 diff)
test/igp.cc (modified) (1 diff)
test/index.cc (modified) (1 diff)
test/inputranker.cc (modified) (1 diff)
test/interpolation.cc (modified) (1 diff)
test/iterator.cc (modified) (1 diff)
test/kendall.cc (modified) (1 diff)
test/kernel.cc (modified) (1 diff)
test/kernel_lookup.cc (modified) (1 diff)
test/kernel_pca.cc (modified) (1 diff)
test/knn.cc (modified) (1 diff)
test/kolmogorov_smirnov.cc (modified) (1 diff)
test/matrix.cc (modified) (1 diff)
test/matrix_lookup.cc (modified) (1 diff)
test/matrix_lookup_weighted.cc (modified) (1 diff)
test/matrix_weighted.cc (modified) (1 diff)
test/merge.cc (modified) (1 diff)
test/nbc.cc (modified) (1 diff)
test/ncc.cc (modified) (1 diff)
test/nni.cc (modified) (1 diff)
test/normalization.cc (modified) (1 diff)
test/pca.cc (modified) (1 diff)
test/range.cc (modified) (1 diff)
test/regression.cc (modified) (1 diff)
test/rnd.cc (modified) (1 diff)
test/rng-mt.cc (modified) (1 diff)
test/roc.cc (modified) (1 diff)
test/score.cc (modified) (1 diff)
test/segment.cc (modified) (1 diff)
test/smart_ptr.cc (modified) (1 diff)
test/smoother.cc (modified) (1 diff)
test/spearman.cc (modified) (1 diff)
test/split.cc (modified) (1 diff)
test/statistics.cc (modified) (1 diff)
test/stream_redirect.cc (modified) (1 diff)
test/subset_generator.cc (modified) (1 diff)
test/svd.cc (modified) (1 diff)
test/svm.cc (modified) (1 diff)
test/svm_multi_class.cc (modified) (1 diff)
test/target.cc (modified) (1 diff)
test/ttest.cc (modified) (1 diff)
test/tukey.cc (modified) (1 diff)
test/utility.cc (modified) (1 diff)
test/vector.cc (modified) (1 diff)
test/version.cc (modified) (1 diff)
test/view.cc (modified) (1 diff)
yat/classifier/BootstrapSampler.cc (modified) (1 diff)
yat/classifier/ConsensusInputRanker.cc (modified) (1 diff)
yat/classifier/CrossValidationSampler.cc (modified) (1 diff)
yat/classifier/DataLookup1D.cc (modified) (1 diff)
yat/classifier/DataLookupWeighted1D.cc (modified) (1 diff)
yat/classifier/FeatureSelector.cc (modified) (1 diff)
yat/classifier/FeatureSelectorIR.cc (modified) (1 diff)
yat/classifier/FeatureSelectorRandom.cc (modified) (1 diff)
yat/classifier/GaussianKernelFunction.cc (modified) (1 diff)
yat/classifier/InputRanker.cc (modified) (1 diff)
yat/classifier/KNN_ReciprocalDistance.cc (modified) (1 diff)
yat/classifier/KNN_ReciprocalRank.cc (modified) (1 diff)
yat/classifier/KNN_Uniform.cc (modified) (1 diff)
yat/classifier/Kernel.cc (modified) (1 diff)
yat/classifier/KernelLookup.cc (modified) (1 diff)
yat/classifier/Kernel_MEV.cc (modified) (1 diff)
yat/classifier/Kernel_SEV.cc (modified) (1 diff)
yat/classifier/MatrixLookup.cc (modified) (1 diff)
yat/classifier/MatrixLookupWeighted.cc (modified) (1 diff)
yat/classifier/NBC.cc (modified) (1 diff)
yat/classifier/PolynomialKernelFunction.cc (modified) (1 diff)
yat/classifier/SVM.cc (modified) (1 diff)
yat/classifier/SVindex.cc (modified) (1 diff)
yat/classifier/Sampler.cc (modified) (1 diff)
yat/classifier/SupervisedClassifier.cc (modified) (1 diff)
yat/classifier/SvmMultiClass.cc (modified) (1 diff)
yat/classifier/Target.cc (modified) (1 diff)
yat/classifier/utility.cc (modified) (1 diff)
yat/normalizer/QuantileNormalizer.cc (modified) (1 diff)
yat/normalizer/qQuantileNormalizer.cc (modified) (1 diff)
yat/omic/Codon.cc (modified) (1 diff)
yat/omic/DNA.cc (modified) (1 diff)
yat/omic/GFF.cc (modified) (1 diff)
yat/omic/GFF2.cc (modified) (1 diff)
yat/omic/GFF3.cc (modified) (1 diff)
yat/omic/GenomicPosition.cc (modified) (1 diff)
yat/random/random.cc (modified) (1 diff)
yat/regression/AkimaInterpolation.cc (modified) (1 diff)
yat/regression/AkimaPeriodicInterpolation.cc (modified) (1 diff)
yat/regression/CSplineInterpolation.cc (modified) (1 diff)
yat/regression/CSplinePeriodicInterpolation.cc (modified) (1 diff)
yat/regression/GSLInterpolation.cc (modified) (1 diff)
yat/regression/KernelBox.cc (modified) (1 diff)
yat/regression/KernelTriCube.cc (modified) (1 diff)
yat/regression/Linear.cc (modified) (1 diff)
yat/regression/LinearInterpolation.cc (modified) (1 diff)
yat/regression/LinearWeighted.cc (modified) (1 diff)
yat/regression/Local.cc (modified) (1 diff)
yat/regression/MultiDimensional.cc (modified) (1 diff)
yat/regression/MultiDimensionalWeighted.cc (modified) (1 diff)
yat/regression/Naive.cc (modified) (1 diff)
yat/regression/NaiveWeighted.cc (modified) (1 diff)
yat/regression/OneDimensional.cc (modified) (1 diff)
yat/regression/OneDimensionalWeighted.cc (modified) (1 diff)
yat/regression/Polynomial.cc (modified) (1 diff)
yat/regression/PolynomialInterpolation.cc (modified) (1 diff)
yat/regression/PolynomialWeighted.cc (modified) (1 diff)
yat/regression/TukeyBiweight.cc (modified) (1 diff)
yat/statistics/AUC.cc (modified) (1 diff)
yat/statistics/Averager.cc (modified) (1 diff)
yat/statistics/Averager1.cc (modified) (1 diff)
yat/statistics/Averager3.cc (modified) (1 diff)
yat/statistics/Averager4.cc (modified) (1 diff)
yat/statistics/AveragerPair.cc (modified) (1 diff)
yat/statistics/AveragerPairWeighted.cc (modified) (1 diff)
yat/statistics/AveragerWeighted.cc (modified) (1 diff)
yat/statistics/Fisher.cc (modified) (1 diff)
yat/statistics/FoldChange.cc (modified) (1 diff)
yat/statistics/Histogram.cc (modified) (1 diff)
yat/statistics/Kendall.cc (modified) (1 diff)
yat/statistics/Pearson.cc (modified) (1 diff)
yat/statistics/PearsonCorrelation.cc (modified) (1 diff)
yat/statistics/Percentiler.cc (modified) (1 diff)
yat/statistics/ROC.cc (modified) (1 diff)
yat/statistics/SAMScore.cc (modified) (1 diff)
yat/statistics/SNRScore.cc (modified) (1 diff)
yat/statistics/Score.cc (modified) (1 diff)
yat/statistics/Smoother.cc (modified) (1 diff)
yat/statistics/Spearman.cc (modified) (1 diff)
yat/statistics/VectorFunction.cc (modified) (1 diff)
yat/statistics/WilcoxonFoldChange.cc (modified) (1 diff)
yat/statistics/tScore.cc (modified) (1 diff)
yat/statistics/tTest.cc (modified) (1 diff)
yat/statistics/utility.cc (modified) (1 diff)
yat/utility/Aligner.cc (modified) (1 diff)
yat/utility/Alignment.cc (modified) (1 diff)
yat/utility/ColumnStream.cc (modified) (1 diff)
yat/utility/CommandLine.cc (modified) (1 diff)
yat/utility/DataWeight.cc (modified) (1 diff)
yat/utility/Deleter.cc (modified) (1 diff)
yat/utility/Exception.cc (modified) (1 diff)
yat/utility/GetlineIterator.cc (modified) (1 diff)
yat/utility/Index.cc (modified) (1 diff)
yat/utility/KernelPCA.cc (modified) (1 diff)
yat/utility/Matrix.cc (modified) (1 diff)
yat/utility/MatrixWeighted.cc (modified) (1 diff)
yat/utility/NNI.cc (modified) (1 diff)
yat/utility/Option.cc (modified) (1 diff)
yat/utility/OptionFile.cc (modified) (1 diff)
yat/utility/OptionHelp.cc (modified) (1 diff)
yat/utility/OptionInFile.cc (modified) (1 diff)
yat/utility/OptionOutFile.cc (modified) (1 diff)
yat/utility/OptionSwitch.cc (modified) (1 diff)
yat/utility/PCA.cc (modified) (1 diff)
yat/utility/SVD.cc (modified) (1 diff)
yat/utility/TypeInfo.cc (modified) (1 diff)
yat/utility/Vector.cc (modified) (1 diff)
yat/utility/VectorBase.cc (modified) (1 diff)
yat/utility/VectorConstView.cc (modified) (1 diff)
yat/utility/VectorMutable.cc (modified) (1 diff)
yat/utility/VectorView.cc (modified) (1 diff)
yat/utility/WeNNI.cc (modified) (1 diff)
yat/utility/kNNI.cc (modified) (1 diff)
yat/utility/sort_index.cc (modified) (1 diff)
yat/utility/split.cc (modified) (1 diff)
yat/utility/stl_utility.cc (modified) (1 diff)
yat/utility/utility.cc (modified) (1 diff)
yat/utility/version.cc (modified) (1 diff)

Legend:

: Unmodified
: Added
: Removed

trunk/configure.ac

-                      r2878
+                      r2881
 AC_SUBST(DISTCHECK_CONFIGURE_FLAGS)
+# Let user overide default CXXFLAGS
+if test "${CXXFLAGS+set}" != set; then
+  CXXFLAGS=""  # Setting CXXFLAGS here to prevent expansion in AC_PROG_CXX
+fi
+# record if CXXFLAGS was set by user for further use below
+AS_IF([test "${CXXFLAGS+set}" = set], [
+  CXXFLAGS_set_by_user=yes
+],[
+  CXXFLAGS_set_by_user=no
+  # set CXXFLAGS to avoid expansion in AC_PROG_CXX
+  CXXFLAGS=
+])
 # Checks for programs.
 AC_PROG_CXX
 …
 fi
+AC_DEFINE([HAVE_INLINE], [1], [Define if inline is available on system])
+AC_ARG_ENABLE([debug],
+  [AS_HELP_STRING([--enable-debug],[turn on debug options and code])])
 # we use prefix INTERNAL_ for variables that are solely needed for
 # building yat, i.e., they are not needed for a user of yat and are
 # not propagated to yat-config or yat.m4.
+AS_IF([test x"$ax_cv_cxx_compiler_vendor" = x"gnu"], [
+  YAT_CXX_ADD_FLAG([INTERNAL_CXXFLAGS], [-Wall -pedantic])
+])
+YAT_CPP_ADD_FLAG([INTERNAL_CPPFLAGS], [-DHAVE_INLINE=1])
+AC_ARG_ENABLE([debug],
+  [AS_HELP_STRING([--enable-debug],[turn on debug options and code])])
+if test "${enable_debug}" = "yes" ; then
+  YAT_CPP_ADD_FLAG([INTERNAL_CPPFLAGS], [-DYAT_DEBUG=1])
+  YAT_CXX_ADD_FLAG([INTERNAL_CXXFLAGS], [-g -O])
+else
+AS_IF([test "${enable_debug}" = "yes"], [
+  AC_DEFINE([YAT_DEBUG], [1], [Define to activate yat assertioons])
+  YAT_CXX_ADD_FLAG([INTERNAL_CXXFLAGS], [-Wall -pedantic -g -O])
+], [
   # avoid defining GSL_RANGE_CHECK_OFF if GSL_RANGE_CHECK is already defined
   AC_CHECK_DECL([GSL_RANGE_CHECK],[],
+                [YAT_CPP_ADD_FLAG([INTERNAL_CPPFLAGS],[-DGSL_RANGE_CHECK_OFF])])
+  YAT_CPP_ADD_FLAG([INTERNAL_CPPFLAGS], [-DNDEBUG])
+  YAT_CXX_ADD_FLAG([INTERNAL_CXXFLAGS], [-O3])
+fi
+                [AC_DEFINE([GSL_RANGE_CHECK_OFF], [1],
+                           [Define to turn off GSL range checks])])
+  AC_DEFINE([NDEBUG], [1], [Define to turn off assertions])
+  # If CXXFLAGS not set by user, set it to default value
+  AS_IF([test x$CXXFLAGS_set_by_user != xyes], [
+    YAT_CXX_ADD_FLAG([INTERNAL_CXXFLAGS],[-O3])
+  ])
+])
 # turn off compiler warning #654 from intel compiler
 …
 ])
+# some versions of boost uses long long - turn off compiler warnings
+# with -Wno-long-long
+yat_save_CXXFLAGS=$CXXFLAGS
+AC_MSG_CHECKING([whether boost uses long long])
+CXXFLAGS="$INTERNAL_CXXFLAGS $CXXFLAGS"
+AC_COMPILE_IFELSE([AC_LANG_PROGRAM(
+  [
+    @%:@include <boost/iterator/transform_iterator.hpp>
+    @%:@include <boost/thread.hpp>
+    @%:@include <cmath>
+    @%:@include <functional>
+    @%:@include <vector>
+  ],[
+AS_IF([test x$enable_debug = xyes], [
+  # some versions of boost uses long long - turn off compiler warnings
+  # with -Wno-long-long
+  yat_save_CXXFLAGS=$CXXFLAGS
+  AC_MSG_CHECKING([whether boost uses long long])
+  CXXFLAGS="$INTERNAL_CXXFLAGS $CXXFLAGS"
+  AC_COMPILE_IFELSE([AC_LANG_PROGRAM(
+    [
+      @%:@include <boost/iterator/transform_iterator.hpp>
+      @%:@include <boost/thread.hpp>
+      @%:@include <cmath>
+      @%:@include <functional>
+      @%:@include <vector>
+    ],[
       using namespace boost;
       typedef std::pointer_to_unary_function<double, double> F;
 …
       int x = boost::thread::hardware_concurrency();
       ++x;
+  ])],
+[AC_MSG_RESULT([no])],
+[AC_MSG_RESULT([yes])
+ YAT_CXX_ADD_FLAG([INTERNAL_CXXFLAGS], [-Wno-long-long])
+])
+# restore CXXFLAGS
+CXXFLAGS=$yat_save_CXXFLAGS
+    ])],
+  [AC_MSG_RESULT([no])],
+  [AC_MSG_RESULT([yes])
+   YAT_CXX_ADD_FLAG([INTERNAL_CXXFLAGS], [-Wno-long-long])
+  ])
+  # restore CXXFLAGS
+  CXXFLAGS=$yat_save_CXXFLAGS
+])
 #doxygen stuff

trunk/test/alignment.cc

r2853	r2881
22	22	along with yat. If not, see <http://www.gnu.org/licenses/>.
23	23	*/
	24
	25	#include <config.h>
24	26
25	27	#include "Suite.h"

trunk/test/alignment2.cc

r2853	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/averager.cc

r2809	r2881
22	22	along with yat. If not, see <http://www.gnu.org/licenses/>.
23	23	*/
	24
	25	#include <config.h>
24	26
25	27	#include "Suite.h"

trunk/test/averager1.cc

r2809	r2881
17	17	along with yat. If not, see <http://www.gnu.org/licenses/>.
18	18	*/
	19
	20	#include <config.h>
19	21
20	22	#include "Suite.h"

trunk/test/averager3.cc

r2809	r2881
17	17	along with yat. If not, see <http://www.gnu.org/licenses/>.
18	18	*/
	19
	20	#include <config.h>
19	21
20	22	#include "Suite.h"

trunk/test/averager4.cc

r2809	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/codon.cc

r2470	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/commandline.cc

r2739	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "Suite.h"

trunk/test/concept.cc

r2370	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/consensus_inputranker.cc

r2370	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "Suite.h"

trunk/test/crossvalidation.cc

r2370	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "yat/classifier/CrossValidationSampler.h"

trunk/test/data_lookup_1d.cc

r2608	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "Suite.h"

trunk/test/data_weight.cc

r2370	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/data_weight_proxy.cc

r2370	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/deleter.cc

r2858	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/distance.cc

r2608	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "Suite.h"

trunk/test/dna.cc

r2787	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/ensemble.cc

r2370	r2881
22	22	along with yat. If not, see <http://www.gnu.org/licenses/>.
23	23	*/
	24
	25	#include <config.h>
24	26
25	27	#include "Suite.h"

trunk/test/feature_selection.cc

r2370	r2881
22	22	along with yat. If not, see <http://www.gnu.org/licenses/>.
23	23	*/
	24
	25	#include <config.h>
24	26
25	27	#include "Suite.h"

trunk/test/fileutil.cc

r2608	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "Suite.h"

trunk/test/fisher.cc

r2787	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/genomic_position.cc

r2370	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/getline_iterator.cc

r2370	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/gff.cc

r2703	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/help.cc

r2458	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "yat/utility/CommandLine.h"

trunk/test/histogram.cc

r2370	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/igp.cc

r2370	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/index.cc

r2370	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/inputranker.cc

r2370	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "Suite.h"

trunk/test/interpolation.cc

r2608	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "Suite.h"

trunk/test/iterator.cc

r2370	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "Suite.h"

trunk/test/kendall.cc

r2787	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/kernel.cc

r2608	r2881
22	22	along with yat. If not, see <http://www.gnu.org/licenses/>.
23	23	*/
	24
	25	#include <config.h>
24	26
25	27	#include "Suite.h"

trunk/test/kernel_lookup.cc

r2608	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "Suite.h"

trunk/test/kernel_pca.cc

r2608	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/knn.cc

r2608	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "Suite.h"

trunk/test/kolmogorov_smirnov.cc

r2721	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/matrix.cc

r2735	r2881
22	22	along with yat. If not, see <http://www.gnu.org/licenses/>.
23	23	*/
	24
	25	#include <config.h>
24	26
25	27	#include "Suite.h"

trunk/test/matrix_lookup.cc

r2608	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "Suite.h"

trunk/test/matrix_lookup_weighted.cc

r2608	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/matrix_weighted.cc

r2608	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "Suite.h"

trunk/test/merge.cc

r2384	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/nbc.cc

r2370	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "Suite.h"

trunk/test/ncc.cc

r2384	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "Suite.h"

trunk/test/nni.cc

r2370	r2881
23	23	along with yat. If not, see <http://www.gnu.org/licenses/>.
24	24	*/
	25
	26	#include <config.h>
25	27
26	28	#include "Suite.h"

trunk/test/normalization.cc

r2608	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "Suite.h"

trunk/test/pca.cc

r2608	r2881
23	23	along with yat. If not, see <http://www.gnu.org/licenses/>.
24	24	*/
	25
	26	#include <config.h>
25	27
26	28	#include "Suite.h"

trunk/test/range.cc

r2608	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/regression.cc

r2787	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "Suite.h"

trunk/test/rnd.cc

r2370	r2881
23	23	along with yat. If not, see <http://www.gnu.org/licenses/>.
24	24	*/
	25
	26	#include <config.h>
25	27
26	28	#include "Suite.h"

trunk/test/rng-mt.cc

r2802	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/roc.cc

r2736	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "Suite.h"

trunk/test/score.cc

r2370	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "Suite.h"

trunk/test/segment.cc

r2613	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/smart_ptr.cc

r2370	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/smoother.cc

r2370	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/spearman.cc

r2649	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/split.cc

r2879	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/statistics.cc

r2476	r2881
23	23	along with yat. If not, see <http://www.gnu.org/licenses/>.
24	24	*/
	25
	26	#include <config.h>
25	27
26	28	#include "Suite.h"

trunk/test/stream_redirect.cc

r2370	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/subset_generator.cc

r2370	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "Suite.h"

trunk/test/svd.cc

r2370	r2881
23	23	along with yat. If not, see <http://www.gnu.org/licenses/>.
24	24	*/
	25
	26	#include <config.h>
25	27
26	28	#include "Suite.h"

trunk/test/svm.cc

r2370	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "Suite.h"

trunk/test/svm_multi_class.cc

r2608	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/target.cc

r2370	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/ttest.cc

r2370	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/tukey.cc

r2558	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Suite.h"

trunk/test/utility.cc

r2867	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "Suite.h"

trunk/test/vector.cc

r2370	r2881
23	23	along with yat. If not, see <http://www.gnu.org/licenses/>.
24	24	*/
	25
	26	#include <config.h>
25	27
26	28	#include "Suite.h"

trunk/test/version.cc

r2608	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "Suite.h"

trunk/test/view.cc

r2370	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "Suite.h"

trunk/yat/classifier/BootstrapSampler.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "BootstrapSampler.h"

trunk/yat/classifier/ConsensusInputRanker.cc

r2384	r2881
23	23	along with yat. If not, see <http://www.gnu.org/licenses/>.
24	24	*/
	25
	26	#include <config.h>
25	27
26	28	#include "ConsensusInputRanker.h"

trunk/yat/classifier/CrossValidationSampler.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "CrossValidationSampler.h"

trunk/yat/classifier/DataLookup1D.cc

r2121	r2881
22	22	along with yat. If not, see <http://www.gnu.org/licenses/>.
23	23	*/
	24
	25	#include <config.h>
24	26
25	27	#include "DataLookup1D.h"

trunk/yat/classifier/DataLookupWeighted1D.cc

r2119	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "DataLookupWeighted1D.h"

trunk/yat/classifier/FeatureSelector.cc

r2384	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "FeatureSelector.h"

trunk/yat/classifier/FeatureSelectorIR.cc

r2119	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "FeatureSelectorIR.h"

trunk/yat/classifier/FeatureSelectorRandom.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "FeatureSelectorRandom.h"

trunk/yat/classifier/GaussianKernelFunction.cc

r2119	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "GaussianKernelFunction.h"

trunk/yat/classifier/InputRanker.cc

r2119	r2881
22	22	along with yat. If not, see <http://www.gnu.org/licenses/>.
23	23	*/
	24
	25	#include <config.h>
24	26
25	27	#include "InputRanker.h"

trunk/yat/classifier/KNN_ReciprocalDistance.cc

r2119	r2881
22	22	*/
23	23
	24	#include <config.h>
	25
24	26	#include "KNN_ReciprocalDistance.h"
25	27	#include "Target.h"

trunk/yat/classifier/KNN_ReciprocalRank.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "KNN_ReciprocalRank.h"

trunk/yat/classifier/KNN_Uniform.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "KNN_Uniform.h"

trunk/yat/classifier/Kernel.cc

r2384	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "Kernel.h"

trunk/yat/classifier/KernelLookup.cc

r2861	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "KernelLookup.h"

trunk/yat/classifier/Kernel_MEV.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Kernel_MEV.h"

trunk/yat/classifier/Kernel_SEV.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Kernel_SEV.h"

trunk/yat/classifier/MatrixLookup.cc

r2863	r2881
22	22	along with yat. If not, see <http://www.gnu.org/licenses/>.
23	23	*/
	24
	25	#include <config.h>
24	26
25	27	#include "MatrixLookup.h"

trunk/yat/classifier/MatrixLookupWeighted.cc

r2862	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "MatrixLookupWeighted.h"

trunk/yat/classifier/NBC.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "NBC.h"

trunk/yat/classifier/PolynomialKernelFunction.cc

r2119	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "PolynomialKernelFunction.h"

trunk/yat/classifier/SVM.cc

r2384	r2881
23	23	along with yat. If not, see <http://www.gnu.org/licenses/>.
24	24	*/
	25
	26	#include <config.h>
25	27
26	28	#include "SVM.h"

trunk/yat/classifier/SVindex.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "SVindex.h"

trunk/yat/classifier/Sampler.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Sampler.h"

trunk/yat/classifier/SupervisedClassifier.cc

r2119	r2881
23	23	*/
24	24
	25	#include <config.h>
	26
25	27	#include "SupervisedClassifier.h"
26	28	#include "InputRanker.h"

trunk/yat/classifier/SvmMultiClass.cc

r2055	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "SvmMultiClass.h"

trunk/yat/classifier/Target.cc

r2119	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "Target.h"

trunk/yat/classifier/utility.cc

r2119	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "utility.h"

trunk/yat/normalizer/QuantileNormalizer.cc

r2119	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "QuantileNormalizer.h"

trunk/yat/normalizer/qQuantileNormalizer.cc

r2384	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "qQuantileNormalizer.h"

trunk/yat/omic/Codon.cc

r2608	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Codon.h"

trunk/yat/omic/DNA.cc

r2763	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "DNA.h"

trunk/yat/omic/GFF.cc

r2723	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "GFF.h"

trunk/yat/omic/GFF2.cc

r2482	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "GFF2.h"

trunk/yat/omic/GFF3.cc

r2608	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "GFF3.h"

trunk/yat/omic/GenomicPosition.cc

r2591	r2881
17	17	along with this program. If not, see <http://www.gnu.org/licenses/>.
18	18	*/
	19
	20	#include <config.h>
19	21
20	22	#include "GenomicPosition.h"

trunk/yat/random/random.cc

r2838	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "random.h"

trunk/yat/regression/AkimaInterpolation.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "AkimaInterpolation.h"

trunk/yat/regression/AkimaPeriodicInterpolation.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "AkimaPeriodicInterpolation.h"

trunk/yat/regression/CSplineInterpolation.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "CSplineInterpolation.h"

trunk/yat/regression/CSplinePeriodicInterpolation.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "CSplinePeriodicInterpolation.h"

trunk/yat/regression/GSLInterpolation.cc

r2119	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "GSLInterpolation.h"

trunk/yat/regression/KernelBox.cc

r2119	r2881
22	22	*/
23	23
	24	#include <config.h>
	25
24	26	#include "KernelBox.h"
25	27

trunk/yat/regression/KernelTriCube.cc

r2119	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "KernelTriCube.h"

trunk/yat/regression/Linear.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Linear.h"

trunk/yat/regression/LinearInterpolation.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "LinearInterpolation.h"

trunk/yat/regression/LinearWeighted.cc

r2119	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "LinearWeighted.h"

trunk/yat/regression/Local.cc

r2564	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "Local.h"

trunk/yat/regression/MultiDimensional.cc

r2564	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "MultiDimensional.h"

trunk/yat/regression/MultiDimensionalWeighted.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "MultiDimensionalWeighted.h"

trunk/yat/regression/Naive.cc

r2532	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "Naive.h"

trunk/yat/regression/NaiveWeighted.cc

r2119	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "NaiveWeighted.h"

trunk/yat/regression/OneDimensional.cc

r2564	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "OneDimensional.h"

trunk/yat/regression/OneDimensionalWeighted.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "OneDimensionalWeighted.h"

trunk/yat/regression/Polynomial.cc

r2564	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "Polynomial.h"

trunk/yat/regression/PolynomialInterpolation.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "PolynomialInterpolation.h"

trunk/yat/regression/PolynomialWeighted.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "PolynomialWeighted.h"

trunk/yat/regression/TukeyBiweight.cc

r2508	r2881
20	20	*/
21	21
	22	#include <config.h>
	23
22	24	#include "TukeyBiweight.h"
23	25

trunk/yat/statistics/AUC.cc

r2564	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include <iostream>

trunk/yat/statistics/Averager.cc

r2809	r2881
23	23	along with yat. If not, see <http://www.gnu.org/licenses/>.
24	24	*/
	25
	26	#include <config.h>
25	27
26	28	#include "Averager.h"

trunk/yat/statistics/Averager1.cc

r2810	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Averager1.h"

trunk/yat/statistics/Averager3.cc

r2809	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Averager3.h"

trunk/yat/statistics/Averager4.cc

r2809	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Averager4.h"

trunk/yat/statistics/AveragerPair.cc

r2644	r2881
22	22	along with yat. If not, see <http://www.gnu.org/licenses/>.
23	23	*/
	24
	25	#include <config.h>
24	26
25	27	#include "AveragerPair.h"

trunk/yat/statistics/AveragerPairWeighted.cc

r2571	r2881
23	23	along with yat. If not, see <http://www.gnu.org/licenses/>.
24	24	*/
	25
	26	#include <config.h>
25	27
26	28	#include "AveragerPairWeighted.h"

trunk/yat/statistics/AveragerWeighted.cc

r2798	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "AveragerWeighted.h"

trunk/yat/statistics/Fisher.cc

r2523	r2881
22	22	along with yat. If not, see <http://www.gnu.org/licenses/>.
23	23	*/
	24
	25	#include <config.h>
24	26
25	27	#include "Fisher.h"

trunk/yat/statistics/FoldChange.cc

r2119	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "FoldChange.h"

trunk/yat/statistics/Histogram.cc

r2411	r2881
23	23	along with yat. If not, see <http://www.gnu.org/licenses/>.
24	24	*/
	25
	26	#include <config.h>
25	27
26	28	#include "Histogram.h"

trunk/yat/statistics/Kendall.cc

r2766	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Kendall.h"

trunk/yat/statistics/Pearson.cc

r2119	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "Pearson.h"

trunk/yat/statistics/PearsonCorrelation.cc

r2119	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "PearsonCorrelation.h"

trunk/yat/statistics/Percentiler.cc

r2608	r2881
20	20	*/
21	21
	22	#include <config.h>
	23
22	24	#include "Percentiler.h"
23	25

trunk/yat/statistics/ROC.cc

r2838	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "ROC.h"

trunk/yat/statistics/SAMScore.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "SAMScore.h"

trunk/yat/statistics/SNRScore.cc

r2119	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "SNRScore.h"

trunk/yat/statistics/Score.cc

r2119	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "Score.h"

trunk/yat/statistics/Smoother.cc

r2202	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "Smoother.h"

trunk/yat/statistics/Spearman.cc

r2648	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Spearman.h"

trunk/yat/statistics/VectorFunction.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "VectorFunction.h"

trunk/yat/statistics/WilcoxonFoldChange.cc

r2119	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "WilcoxonFoldChange.h"

trunk/yat/statistics/tScore.cc

r2119	r2881
22	22	along with yat. If not, see <http://www.gnu.org/licenses/>.
23	23	*/
	24
	25	#include <config.h>
24	26
25	27	#include "tScore.h"

trunk/yat/statistics/tTest.cc

r2119	r2881
22	22	along with yat. If not, see <http://www.gnu.org/licenses/>.
23	23	*/
	24
	25	#include <config.h>
24	26
25	27	#include "tTest.h"

trunk/yat/statistics/utility.cc

r2787	r2881
22	22	along with yat. If not, see <http://www.gnu.org/licenses/>.
23	23	*/
	24
	25	#include <config.h>
24	26
25	27	#include "utility.h"

trunk/yat/utility/Aligner.cc

r2853	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Aligner.h"

trunk/yat/utility/Alignment.cc

r2816	r2881
23	23	along with yat. If not, see <http://www.gnu.org/licenses/>.
24	24	*/
	25
	26	#include <config.h>
25	27
26	28	#include "Alignment.h"

trunk/yat/utility/ColumnStream.cc

r2526	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "ColumnStream.h"

trunk/yat/utility/CommandLine.cc

r2853	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "CommandLine.h"

trunk/yat/utility/DataWeight.cc

r2119	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "DataWeight.h"

trunk/yat/utility/Deleter.cc

r2858	r2881
20	20	*/
21	21
	22	#include <config.h>
	23
22	24	#include "Deleter.h"
23	25

trunk/yat/utility/Exception.cc

r2526	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Exception.h"

trunk/yat/utility/GetlineIterator.cc

r1878	r2881
20	20	*/
21	21
	22
	23	#include <config.h>
22	24
23	25	#include "GetlineIterator.h"

trunk/yat/utility/Index.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "Index.h"

trunk/yat/utility/KernelPCA.cc

r2324	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include <iostream>

trunk/yat/utility/Matrix.cc

r2787	r2881
23	23	along with yat. If not, see <http://www.gnu.org/licenses/>.
24	24	*/
	25
	26	#include <config.h>
25	27
26	28	#include "Matrix.h"

trunk/yat/utility/MatrixWeighted.cc

r2384	r2881
24	24	*/
25	25
	26	#include <config.h>
	27
26	28	#include "MatrixWeighted.h"
27	29

trunk/yat/utility/NNI.cc

r2119	r2881
22	22	along with yat. If not, see <http://www.gnu.org/licenses/>.
23	23	*/
	24
	25	#include <config.h>
24	26
25	27	#include "NNI.h"

trunk/yat/utility/Option.cc

r2384	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "Option.h"

trunk/yat/utility/OptionFile.cc

r2384	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "OptionFile.h"

trunk/yat/utility/OptionHelp.cc

r2384	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "OptionHelp.h"

trunk/yat/utility/OptionInFile.cc

r2121	r2881
20	20	along with yat. If not, see <http://www.gnu.org/licenses/>.
21	21	*/
	22
	23	#include <config.h>
22	24
23	25	#include "OptionInFile.h"

trunk/yat/utility/OptionOutFile.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "OptionOutFile.h"

trunk/yat/utility/OptionSwitch.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "OptionSwitch.h"

trunk/yat/utility/PCA.cc

r2384	r2881
24	24	along with yat. If not, see <http://www.gnu.org/licenses/>.
25	25	*/
	26
	27	#include <config.h>
26	28
27	29	#include "PCA.h"

trunk/yat/utility/SVD.cc

r2451	r2881
25	25	along with yat. If not, see <http://www.gnu.org/licenses/>.
26	26	*/
	27
	28	#include <config.h>
27	29
28	30	#include "SVD.h"

trunk/yat/utility/TypeInfo.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "TypeInfo.h"

trunk/yat/utility/Vector.cc

r2787	r2881
23	23	along with yat. If not, see <http://www.gnu.org/licenses/>.
24	24	*/
	25
	26	#include <config.h>
25	27
26	28	#include "Vector.h"

trunk/yat/utility/VectorBase.cc

r2787	r2881
23	23	along with yat. If not, see <http://www.gnu.org/licenses/>.
24	24	*/
	25
	26	#include <config.h>
25	27
26	28	#include "VectorBase.h"

trunk/yat/utility/VectorConstView.cc

r2787	r2881
23	23	along with yat. If not, see <http://www.gnu.org/licenses/>.
24	24	*/
	25
	26	#include <config.h>
25	27
26	28	#include "VectorConstView.h"

trunk/yat/utility/VectorMutable.cc

r2787	r2881
23	23	along with yat. If not, see <http://www.gnu.org/licenses/>.
24	24	*/
	25
	26	#include <config.h>
25	27
26	28	#include "VectorMutable.h"

trunk/yat/utility/VectorView.cc

r2787	r2881
23	23	along with yat. If not, see <http://www.gnu.org/licenses/>.
24	24	*/
	25
	26	#include <config.h>
25	27
26	28	#include "VectorView.h"

trunk/yat/utility/WeNNI.cc

r2526	r2881
24	24	along with yat. If not, see <http://www.gnu.org/licenses/>.
25	25	*/
	26
	27	#include <config.h>
26	28
27	29	#include "WeNNI.h"

trunk/yat/utility/kNNI.cc

r2119	r2881
22	22	along with yat. If not, see <http://www.gnu.org/licenses/>.
23	23	*/
	24
	25	#include <config.h>
24	26
25	27	#include "kNNI.h"

trunk/yat/utility/sort_index.cc

r2608	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "sort_index.h"

trunk/yat/utility/split.cc

r2879	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "split.h"

trunk/yat/utility/stl_utility.cc

r2302	r2881
22	22	along with yat. If not, see <http://www.gnu.org/licenses/>.
23	23	*/
	24
	25	#include <config.h>
24	26
25	27	#include "stl_utility.h"

trunk/yat/utility/utility.cc

r2384	r2881
21	21	along with yat. If not, see <http://www.gnu.org/licenses/>.
22	22	*/
	23
	24	#include <config.h>
23	25
24	26	#include "utility.h"

trunk/yat/utility/version.cc

r2119	r2881
19	19	along with yat. If not, see <http://www.gnu.org/licenses/>.
20	20	*/
	21
	22	#include <config.h>
21	23
22	24	#include "version.h"

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