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Changeset 1437 for trunk/yat

Timestamp:

Aug 25, 2008, 7:55:00 PM (15 years ago)

Author:

Peter

Message:

merge patch release 0.4.2 to trunk. Delta 0.4.2-0.4.1

Location:

trunk/yat

Files:

: 197 edited

Makefile.am (modified) (1 diff)
classifier/BootstrapSampler.cc (modified) (1 diff)
classifier/BootstrapSampler.h (modified) (1 diff)
classifier/ConsensusInputRanker.cc (modified) (1 diff)
classifier/ConsensusInputRanker.h (modified) (1 diff)
classifier/CrossValidationSampler.cc (modified) (1 diff)
classifier/CrossValidationSampler.h (modified) (1 diff)
classifier/DataLookup1D.cc (modified) (1 diff)
classifier/DataLookup1D.h (modified) (1 diff)
classifier/DataLookupWeighted1D.cc (modified) (1 diff)
classifier/DataLookupWeighted1D.h (modified) (1 diff)
classifier/EnsembleBuilder.h (modified) (1 diff)
classifier/FeatureSelector.cc (modified) (1 diff)
classifier/FeatureSelector.h (modified) (1 diff)
classifier/FeatureSelectorIR.cc (modified) (1 diff)
classifier/FeatureSelectorIR.h (modified) (1 diff)
classifier/FeatureSelectorRandom.cc (modified) (1 diff)
classifier/FeatureSelectorRandom.h (modified) (1 diff)
classifier/GaussianKernelFunction.cc (modified) (1 diff)
classifier/GaussianKernelFunction.h (modified) (1 diff)
classifier/IGP.h (modified) (1 diff)
classifier/IRRank.h (modified) (1 diff)
classifier/IRRetrieve.h (modified) (1 diff)
classifier/InputRanker.cc (modified) (1 diff)
classifier/InputRanker.h (modified) (1 diff)
classifier/KNN.h (modified) (1 diff)
classifier/KNN_ReciprocalDistance.cc (modified) (2 diffs)
classifier/KNN_ReciprocalDistance.h (modified) (1 diff)
classifier/KNN_ReciprocalRank.cc (modified) (1 diff)
classifier/KNN_ReciprocalRank.h (modified) (1 diff)
classifier/KNN_Uniform.cc (modified) (1 diff)
classifier/KNN_Uniform.h (modified) (1 diff)
classifier/Kernel.cc (modified) (1 diff)
classifier/Kernel.h (modified) (1 diff)
classifier/KernelFunction.h (modified) (1 diff)
classifier/KernelLookup.cc (modified) (1 diff)
classifier/KernelLookup.h (modified) (1 diff)
classifier/Kernel_MEV.cc (modified) (1 diff)
classifier/Kernel_MEV.h (modified) (1 diff)
classifier/Kernel_SEV.cc (modified) (1 diff)
classifier/Kernel_SEV.h (modified) (1 diff)
classifier/Makefile.am (modified) (1 diff)
classifier/MatrixLookup.cc (modified) (1 diff)
classifier/MatrixLookup.h (modified) (1 diff)
classifier/MatrixLookupWeighted.cc (modified) (1 diff)
classifier/MatrixLookupWeighted.h (modified) (1 diff)
classifier/NBC.cc (modified) (2 diffs)
classifier/NBC.h (modified) (1 diff)
classifier/NCC.h (modified) (1 diff)
classifier/PolynomialKernelFunction.cc (modified) (1 diff)
classifier/PolynomialKernelFunction.h (modified) (1 diff)
classifier/SVM.cc (modified) (1 diff)
classifier/SVM.h (modified) (1 diff)
classifier/SVindex.cc (modified) (1 diff)
classifier/SVindex.h (modified) (1 diff)
classifier/Sampler.cc (modified) (1 diff)
classifier/Sampler.h (modified) (1 diff)
classifier/SubsetGenerator.h (modified) (1 diff)
classifier/SupervisedClassifier.cc (modified) (1 diff)
classifier/SupervisedClassifier.h (modified) (1 diff)
classifier/Target.cc (modified) (1 diff)
classifier/Target.h (modified) (1 diff)
classifier/utility.cc (modified) (1 diff)
classifier/utility.h (modified) (1 diff)
random/Makefile.am (modified) (1 diff)
random/random.cc (modified) (1 diff)
random/random.h (modified) (1 diff)
regression/Kernel.h (modified) (1 diff)
regression/KernelBox.cc (modified) (1 diff)
regression/KernelBox.h (modified) (1 diff)
regression/KernelTriCube.cc (modified) (1 diff)
regression/KernelTriCube.h (modified) (1 diff)
regression/Linear.cc (modified) (1 diff)
regression/Linear.h (modified) (1 diff)
regression/LinearWeighted.cc (modified) (1 diff)
regression/LinearWeighted.h (modified) (1 diff)
regression/Local.cc (modified) (3 diffs)
regression/Local.h (modified) (2 diffs)
regression/Makefile.am (modified) (1 diff)
regression/MultiDimensional.cc (modified) (1 diff)
regression/MultiDimensional.h (modified) (1 diff)
regression/MultiDimensionalWeighted.cc (modified) (1 diff)
regression/MultiDimensionalWeighted.h (modified) (1 diff)
regression/Naive.cc (modified) (1 diff)
regression/Naive.h (modified) (1 diff)
regression/NaiveWeighted.cc (modified) (1 diff)
regression/NaiveWeighted.h (modified) (1 diff)
regression/OneDimensional.cc (modified) (1 diff)
regression/OneDimensional.h (modified) (1 diff)
regression/OneDimensionalWeighted.cc (modified) (1 diff)
regression/OneDimensionalWeighted.h (modified) (1 diff)
regression/Polynomial.cc (modified) (1 diff)
regression/Polynomial.h (modified) (1 diff)
regression/PolynomialWeighted.cc (modified) (1 diff)
regression/PolynomialWeighted.h (modified) (1 diff)
statistics/AUC.cc (modified) (1 diff)
statistics/AUC.h (modified) (1 diff)
statistics/Averager.cc (modified) (1 diff)
statistics/Averager.h (modified) (1 diff)
statistics/AveragerPair.cc (modified) (1 diff)
statistics/AveragerPair.h (modified) (1 diff)
statistics/AveragerPairWeighted.cc (modified) (1 diff)
statistics/AveragerPairWeighted.h (modified) (1 diff)
statistics/AveragerWeighted.cc (modified) (1 diff)
statistics/AveragerWeighted.h (modified) (1 diff)
statistics/EuclideanDistance.h (modified) (1 diff)
statistics/Fisher.cc (modified) (1 diff)
statistics/Fisher.h (modified) (1 diff)
statistics/FoldChange.cc (modified) (1 diff)
statistics/FoldChange.h (modified) (1 diff)
statistics/Histogram.cc (modified) (1 diff)
statistics/Histogram.h (modified) (1 diff)
statistics/KolmogorovSmirnov.cc (modified) (1 diff)
statistics/KolmogorovSmirnov.h (modified) (1 diff)
statistics/Makefile.am (modified) (1 diff)
statistics/Pearson.cc (modified) (1 diff)
statistics/Pearson.h (modified) (1 diff)
statistics/PearsonCorrelation.cc (modified) (1 diff)
statistics/PearsonCorrelation.h (modified) (1 diff)
statistics/PearsonDistance.h (modified) (1 diff)
statistics/ROC.cc (modified) (1 diff)
statistics/ROC.h (modified) (2 diffs)
statistics/SAMScore.cc (modified) (1 diff)
statistics/SAMScore.h (modified) (1 diff)
statistics/SNRScore.cc (modified) (1 diff)
statistics/SNRScore.h (modified) (1 diff)
statistics/Score.cc (modified) (1 diff)
statistics/Score.h (modified) (1 diff)
statistics/VectorFunction.cc (modified) (1 diff)
statistics/VectorFunction.h (modified) (1 diff)
statistics/WilcoxonFoldChange.cc (modified) (1 diff)
statistics/WilcoxonFoldChange.h (modified) (1 diff)
statistics/tScore.cc (modified) (1 diff)
statistics/tScore.h (modified) (1 diff)
statistics/tTest.cc (modified) (1 diff)
statistics/tTest.h (modified) (1 diff)
statistics/utility.cc (modified) (1 diff)
statistics/utility.h (modified) (1 diff)
utility/Alignment.cc (modified) (1 diff)
utility/Alignment.h (modified) (1 diff)
utility/ColumnStream.cc (modified) (1 diff)
utility/ColumnStream.h (modified) (1 diff)
utility/CommandLine.cc (modified) (1 diff)
utility/CommandLine.h (modified) (3 diffs)
utility/Container2DIterator.h (modified) (1 diff)
utility/Exception.h (modified) (1 diff)
utility/FileUtil.cc (modified) (4 diffs)
utility/FileUtil.h (modified) (1 diff)
utility/Index.cc (modified) (1 diff)
utility/Index.h (modified) (1 diff)
utility/IteratorPolicy.h (modified) (1 diff)
utility/Makefile.am (modified) (1 diff)
utility/Matrix.cc (modified) (1 diff)
utility/Matrix.h (modified) (2 diffs)
utility/NNI.cc (modified) (1 diff)
utility/NNI.h (modified) (1 diff)
utility/Option.cc (modified) (1 diff)
utility/Option.h (modified) (2 diffs)
utility/OptionArg.h (modified) (1 diff)
utility/OptionFile.cc (modified) (1 diff)
utility/OptionFile.h (modified) (1 diff)
utility/OptionHelp.cc (modified) (1 diff)
utility/OptionHelp.h (modified) (2 diffs)
utility/OptionInFile.cc (modified) (1 diff)
utility/OptionInFile.h (modified) (1 diff)
utility/OptionOutFile.cc (modified) (1 diff)
utility/OptionOutFile.h (modified) (1 diff)
utility/OptionSwitch.cc (modified) (1 diff)
utility/OptionSwitch.h (modified) (1 diff)
utility/PCA.cc (modified) (1 diff)
utility/PCA.h (modified) (1 diff)
utility/SVD.cc (modified) (1 diff)
utility/SVD.h (modified) (1 diff)
utility/SmartPtr.h (modified) (1 diff)
utility/StrideIterator.h (modified) (1 diff)
utility/TypeInfo.cc (modified) (1 diff)
utility/TypeInfo.h (modified) (2 diffs)
utility/Vector.cc (modified) (1 diff)
utility/Vector.h (modified) (1 diff)
utility/VectorBase.cc (modified) (1 diff)
utility/VectorBase.h (modified) (2 diffs)
utility/VectorConstView.cc (modified) (1 diff)
utility/VectorConstView.h (modified) (1 diff)
utility/VectorMutable.cc (modified) (1 diff)
utility/VectorMutable.h (modified) (1 diff)
utility/VectorView.cc (modified) (1 diff)
utility/VectorView.h (modified) (1 diff)
utility/WeNNI.cc (modified) (1 diff)
utility/WeNNI.h (modified) (1 diff)
utility/iterator_traits.h (modified) (1 diff)
utility/kNNI.cc (modified) (1 diff)
utility/kNNI.h (modified) (1 diff)
utility/stl_utility.cc (modified) (1 diff)
utility/stl_utility.h (modified) (1 diff)
utility/utility.cc (modified) (1 diff)
utility/utility.h (modified) (2 diffs)
utility/yat_assert.h (modified) (1 diff)

Legend:

: Unmodified
: Added
: Removed

trunk/yat/Makefile.am

r1429	r1437
7	7	# Copyright (C) 2005, 2006, 2007, 2008 Jari Häkkinen, Peter Johansson
8	8	#
9		# This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	# This file is part of the yat library, http://dev.thep.lu.se/yat
10	10	#
11	11	# The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/BootstrapSampler.cc

r1275	r1437
5	5	Copyright (C) 2008 Peter Johansson
6	6
7		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	7	This file is part of the yat library, http://dev.thep.lu.se/yat
8	8
9	9	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/BootstrapSampler.h

r1275	r1437
7	7	Copyright (C) 2007 Jari Häkkinen, Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/ConsensusInputRanker.cc

r1275	r1437
7	7	Copyright (C) 2007 Jari Häkkinen, Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/ConsensusInputRanker.h

r1275	r1437
9	9	Copyright (C) 2007 Jari Häkkinen, Peter Johansson
10	10
11		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	11	This file is part of the yat library, http://dev.thep.lu.se/yat
12	12
13	13	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/CrossValidationSampler.cc

r1275	r1437
5	5	Copyright (C) 2008 Peter Johansson
6	6
7		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	7	This file is part of the yat library, http://dev.thep.lu.se/yat
8	8
9	9	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/CrossValidationSampler.h

r1275	r1437
8	8	Copyright (C) 2007 Jari Häkkinen, Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/DataLookup1D.cc

r1275	r1437
7	7	Copyright (C) 2008 Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/DataLookup1D.h

r1275	r1437
10	10	Copyright (C) 2008 Peter Johansson
11	11
12		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	12	This file is part of the yat library, http://dev.thep.lu.se/yat
13	13
14	14	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/DataLookupWeighted1D.cc

r1275	r1437
6	6	Copyright (C) 2008 Peter Johansson
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/DataLookupWeighted1D.h

r1275	r1437
9	9	Copyright (C) 2008 Peter Johansson, Markus Ringnér
10	10
11		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	11	This file is part of the yat library, http://dev.thep.lu.se/yat
12	12
13	13	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/EnsembleBuilder.h

r1275	r1437
10	10	Copyright (C) 2008 Jari Häkkinen, Peter Johansson, Markus Ringnér
11	11
12		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	12	This file is part of the yat library, http://dev.thep.lu.se/yat
13	13
14	14	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/FeatureSelector.cc

r1275	r1437
5	5	Copyright (C) 2008 Peter Johansson
6	6
7		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	7	This file is part of the yat library, http://dev.thep.lu.se/yat
8	8
9	9	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/FeatureSelector.h

r1275	r1437
8	8	Copyright (C) 2008 Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/FeatureSelectorIR.cc

r1275	r1437
6	6	Copyright (C) 2008 Peter Johansson
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/FeatureSelectorIR.h

r1275	r1437
7	7	Copyright (C) 2006, 2007 Jari Häkkinen, Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/FeatureSelectorRandom.cc

r1275	r1437
5	5	Copyright (C) 2008 Peter Johansson
6	6
7		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	7	This file is part of the yat library, http://dev.thep.lu.se/yat
8	8
9	9	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/FeatureSelectorRandom.h

r1275	r1437
7	7	Copyright (C) 2006, 2007 Jari Häkkinen, Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/GaussianKernelFunction.cc

r1275	r1437
6	6	Copyright (C) 2006, 2007 Jari Häkkinen, Peter Johansson
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/GaussianKernelFunction.h

r1275	r1437
7	7	Copyright (C) 2004, 2005, 2006, 2007 Jari Häkkinen, Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/IGP.h

r1275	r1437
8	8	Copyright (C) 2008 Peter Johansson, Markus Ringnér
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/IRRank.h

r1275	r1437
7	7	Copyright (C) 2006, 2007 Jari Häkkinen, Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/IRRetrieve.h

r1275	r1437
7	7	Copyright (C) 2006, 2007 Jari Häkkinen, Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/InputRanker.cc

r1275	r1437
6	6	Copyright (C) 2006, 2007 Jari Häkkinen, Peter Johansson, Markus Ringnér
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/InputRanker.h

r1275	r1437
9	9	Copyright (C) 2008 Peter Johansson
10	10
11		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	11	This file is part of the yat library, http://dev.thep.lu.se/yat
12	12
13	13	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/KNN.h

r1275	r1437
7	7	Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson, Markus Ringnér
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/KNN_ReciprocalDistance.cc

-                      r1251
+                      r1437
 // $Id$
+// $Id$
+/*
+  Copyright (C) 2008 Markus Ringnér
+  This file is part of the yat library, http://dev.thep.lu.se/yat
+  The yat library is free software; you can redistribute it and/or
+  modify it under the terms of the GNU General Public License as
+  published by the Free Software Foundation; either version 2 of the
+  License, or (at your option) any later version.
+  The yat library is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+  General Public License for more details.
+  You should have received a copy of the GNU General Public License
+  along with this program; if not, write to the Free Software
+  Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
+-1307, USA.
+*/
 #include "KNN_ReciprocalDistance.h"
 …
 #include <vector>
-#include <iostream>
 namespace theplu {

trunk/yat/classifier/KNN_ReciprocalDistance.h

r1142	r1437
7	7	Copyright (C) 2008 Markus Ringnér
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/KNN_ReciprocalRank.cc

-                      r1156
+                      r1437
 // $Id$
+/*
+  Copyright (C) 2008 Markus Ringnér
+  This file is part of the yat library, http://dev.thep.lu.se/yat
+  The yat library is free software; you can redistribute it and/or
+  modify it under the terms of the GNU General Public License as
+  published by the Free Software Foundation; either version 2 of the
+  License, or (at your option) any later version.
+  The yat library is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+  General Public License for more details.
+  You should have received a copy of the GNU General Public License
+  along with this program; if not, write to the Free Software
+  Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
+-1307, USA.
+*/
 #include "KNN_ReciprocalRank.h"

trunk/yat/classifier/KNN_ReciprocalRank.h

r1142	r1437
7	7	Copyright (C) 2008 Markus Ringnér
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/KNN_Uniform.cc

-                      r1156
+                      r1437
 // $Id$
+/*
+  Copyright (C) 2008 Markus Ringnér
+  This file is part of the yat library, http://dev.thep.lu.se/yat
+  The yat library is free software; you can redistribute it and/or
+  modify it under the terms of the GNU General Public License as
+  published by the Free Software Foundation; either version 2 of the
+  License, or (at your option) any later version.
+  The yat library is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+  General Public License for more details.
+  You should have received a copy of the GNU General Public License
+  along with this program; if not, write to the Free Software
+  Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
+-1307, USA.
+*/
 #include "KNN_Uniform.h"

trunk/yat/classifier/KNN_Uniform.h

r1142	r1437
7	7	Copyright (C) 2008 Markus Ringnér
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/Kernel.cc

r1275	r1437
5	5	Copyright (C) 2008 Peter Johansson, Markus Ringnér
6	6
7		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	7	This file is part of the yat library, http://dev.thep.lu.se/yat
8	8
9	9	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/Kernel.h

r1275	r1437
10	10	Copyright (C) 2008 Jari Häkkinen, Peter Johansson, Markus Ringnér
11	11
12		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	12	This file is part of the yat library, http://dev.thep.lu.se/yat
13	13
14	14	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/KernelFunction.h

r1275	r1437
10	10	Copyright (C) 2006, 2007 Jari Häkkinen, Peter Johansson
11	11
12		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	12	This file is part of the yat library, http://dev.thep.lu.se/yat
13	13
14	14	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/KernelLookup.cc

r1275	r1437
5	5	Copyright (C) 2008 Peter Johansson
6	6
7		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	7	This file is part of the yat library, http://dev.thep.lu.se/yat
8	8
9	9	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/KernelLookup.h

r1275	r1437
10	10	Copyright (C) 2008 Peter Johansson
11	11
12		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	12	This file is part of the yat library, http://dev.thep.lu.se/yat
13	13
14	14	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/Kernel_MEV.cc

r1275	r1437
5	5	Copyright (C) 2008 Peter Johansson
6	6
7		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	7	This file is part of the yat library, http://dev.thep.lu.se/yat
8	8
9	9	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/Kernel_MEV.h

r1275	r1437
11	11	Copyright (C) 2008 Peter Johansson
12	12
13		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	13	This file is part of the yat library, http://dev.thep.lu.se/yat
14	14
15	15	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/Kernel_SEV.cc

r1275	r1437
4	4	Copyright (C) 2005, 2006, 2007, 2008 Jari Häkkinen, Peter Johansson
5	5
6		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	6	This file is part of the yat library, http://dev.thep.lu.se/yat
7	7
8	8	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/Kernel_SEV.h

r1275	r1437
10	10	Copyright (C) 2008 Peter Johansson
11	11
12		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	12	This file is part of the yat library, http://dev.thep.lu.se/yat
13	13
14	14	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/Makefile.am

r1324	r1437
5	5	# Copyright (C) 2005, 2006, 2007, 2008 Jari Häkkinen, Peter Johansson, Markus Ringnér
6	6	#
7		# This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	7	# This file is part of the yat library, http://dev.thep.lu.se/yat
8	8	#
9	9	# The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/MatrixLookup.cc

r1361	r1437
7	7	Copyright (C) 2008 Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/MatrixLookup.h

r1275	r1437
10	10	Copyright (C) 2008 Peter Johansson
11	11
12		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	12	This file is part of the yat library, http://dev.thep.lu.se/yat
13	13
14	14	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/MatrixLookupWeighted.cc

r1275	r1437
6	6	Copyright (C) 2008 Peter Johansson
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/MatrixLookupWeighted.h

r1275	r1437
9	9	Copyright (C) 2008 Peter Johansson
10	10
11		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	11	This file is part of the yat library, http://dev.thep.lu.se/yat
12	12
13	13	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/NBC.cc

-                      r1275
+                      r1437
   Copyright (C) 2008 Peter Johansson, Markus Ringnér
   This file is part of the yat library, http://trac.thep.lu.se/yat
+  This file is part of the yat library, http://dev.thep.lu.se/yat
   The yat library is free software; you can redistribute it and/or
 …
 #include <cassert>
 #include <cmath>
+#include <limits>
 #include <stdexcept>
 #include <vector>

trunk/yat/classifier/NBC.h

r1275	r1437
9	9	Copyright (C) 2008 Peter Johansson, Markus Ringnér
10	10
11		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	11	This file is part of the yat library, http://dev.thep.lu.se/yat
12	12
13	13	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/NCC.h

r1275	r1437
8	8	Copyright (C) 2006, 2007, 2008 Jari Häkkinen, Peter Johansson, Markus Ringnér
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/PolynomialKernelFunction.cc

r1275	r1437
6	6	Copyright (C) 2008 Peter Johansson
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/PolynomialKernelFunction.h

r1275	r1437
8	8	Copyright (C) 2004, 2005, 2006, 2007 Jari Häkkinen, Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/SVM.cc

r1275	r1437
7	7	Copyright (C) 2008 Jari Häkkinen, Peter Johansson, Markus Ringnér
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/SVM.h

r1275	r1437
10	10	Copyright (C) 2008 Peter Johansson
11	11
12		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	12	This file is part of the yat library, http://dev.thep.lu.se/yat
13	13
14	14	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/SVindex.cc

r1275	r1437
5	5	Copyright (C) 2008 Peter Johansson
6	6
7		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	7	This file is part of the yat library, http://dev.thep.lu.se/yat
8	8
9	9	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/SVindex.h

r1275	r1437
8	8	Copyright (C) 2008 Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/Sampler.cc

r1275	r1437
5	5	Copyright (C) 2008 Peter Johansson
6	6
7		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	7	This file is part of the yat library, http://dev.thep.lu.se/yat
8	8
9	9	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/Sampler.h

r1275	r1437
9	9	Copyright (C) 2008 Peter Johansson
10	10
11		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	11	This file is part of the yat library, http://dev.thep.lu.se/yat
12	12
13	13	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/SubsetGenerator.h

r1275	r1437
8	8	Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/SupervisedClassifier.cc

r1275	r1437
7	7	Copyright (C) 2008 Peter Johansson, Markus Ringnér
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/SupervisedClassifier.h

r1275	r1437
10	10	Copyright (C) 2008 Peter Johansson, Markus Ringnér
11	11
12		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	12	This file is part of the yat library, http://dev.thep.lu.se/yat
13	13
14	14	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/Target.cc

r1275	r1437
7	7	Copyright (C) 2008 Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/Target.h

r1343	r1437
10	10	Copyright (C) 2008 Peter Johansson
11	11
12		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	12	This file is part of the yat library, http://dev.thep.lu.se/yat
13	13
14	14	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/utility.cc

r1275	r1437
6	6	Copyright (C) 2008 Peter Johansson
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/classifier/utility.h

r1275	r1437
9	9	Copyright (C) 2008 Peter Johansson
10	10
11		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	11	This file is part of the yat library, http://dev.thep.lu.se/yat
12	12
13	13	The yat library is free software; you can redistribute it and/or

trunk/yat/random/Makefile.am

r1324	r1437
6	6	# Copyright (C) 2007 Jari Häkkinen, Peter Johansson
7	7	#
8		# This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	# This file is part of the yat library, http://dev.thep.lu.se/yat
9	9	#
10	10	# The yat library is free software; you can redistribute it

trunk/yat/random/random.cc

r1275	r1437
5	5	Copyright (C) 2008 Peter Johansson
6	6
7		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	7	This file is part of the yat library, http://dev.thep.lu.se/yat
8	8
9	9	The yat library is free software; you can redistribute it and/or

trunk/yat/random/random.h

r1342	r1437
8	8	Copyright (C) 2008 Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/Kernel.h

r1310	r1437
10	10	Copyright (C) 2007 Jari Häkkinen, Peter Johansson
11	11
12		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	12	This file is part of the yat library, http://dev.thep.lu.se/yat
13	13
14	14	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/KernelBox.cc

r1275	r1437
6	6	Copyright (C) 2007 Jari Häkkinen, Peter Johansson
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/KernelBox.h

r1275	r1437
10	10	Copyright (C) 2007 Jari Häkkinen, Peter Johansson
11	11
12		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	12	This file is part of the yat library, http://dev.thep.lu.se/yat
13	13
14	14	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/KernelTriCube.cc

r1275	r1437
6	6	Copyright (C) 2007 Jari Häkkinen, Peter Johansson
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/KernelTriCube.h

r1275	r1437
9	9	Copyright (C) 2007 Jari Häkkinen, Peter Johansson
10	10
11		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	11	This file is part of the yat library, http://dev.thep.lu.se/yat
12	12
13	13	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/Linear.cc

r1275	r1437
5	5	Copyright (C) 2008 Peter Johansson
6	6
7		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	7	This file is part of the yat library, http://dev.thep.lu.se/yat
8	8
9	9	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/Linear.h

r1275	r1437
8	8	Copyright (C) 2008 Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/LinearWeighted.cc

r1275	r1437
7	7	Copyright (C) 2008 Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/LinearWeighted.h

r1275	r1437
10	10	Copyright (C) 2008 Peter Johansson
11	11
12		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	12	This file is part of the yat library, http://dev.thep.lu.se/yat
13	13
14	14	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/Local.cc

-                      r1275
+                      r1437
   Copyright (C) 2008 Peter Johansson
   This file is part of the yat library, http://trac.thep.lu.se/yat
+  This file is part of the yat library, http://dev.thep.lu.se/yat
   The yat library is free software; you can redistribute it and/or
 …
     size_t nof_fits=data_.size()/step_size;
     x_ = utility::Vector(nof_fits);
     y_predicted_ = utility::Vector(x_.size());
     y_err_ = utility::Vector(x_.size());
+    x_.resize(nof_fits);
+    y_predicted_.resize(x_.size());
+    y_err_.resize(x_.size());
     sort(data_.begin(), data_.end());
     // coying data to 2 utility vectors ONCE to use views from
+    // copying data to 2 utility vectors ONCE to use views from
     utility::Vector x(data_.size());
     utility::Vector y(data_.size());
 …
       assert(i<y_predicted_.size());
       assert(i<y_err_.size());
+      x_(i) = x(i*step_size);
       y_predicted_(i) = regressor_->predict(x(i*step_size));
       y_err_(i) = sqrt(regressor_->standard_error2(x(i*step_size)));

trunk/yat/regression/Local.h

-                      r1275
+                      r1437
   Copyright (C) 2008 Peter Johansson
   This file is part of the yat library, http://trac.thep.lu.se/yat
+  This file is part of the yat library, http://dev.thep.lu.se/yat
   The yat library is free software; you can redistribute it and/or
 …
     ///
+    /// @param step_size Size of step between each fit
     /// @param nof_points Number of points used in each fit
-    /// @param step_size Size of step between each fit
     ///
     void fit(const size_t step_size, const size_t nof_points);

trunk/yat/regression/Makefile.am

r1324	r1437
6	6	# Copyright (C) 2007 Jari Häkkinen, Peter Johansson
7	7	#
8		# This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	# This file is part of the yat library, http://dev.thep.lu.se/yat
9	9	#
10	10	# The yat library is free software; you can redistribute it and/or

trunk/yat/regression/MultiDimensional.cc

r1275	r1437
5	5	Copyright (C) 2006, 2007, 2008 Jari Häkkinen, Peter Johansson
6	6
7		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	7	This file is part of the yat library, http://dev.thep.lu.se/yat
8	8
9	9	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/MultiDimensional.h

r1275	r1437
8	8	Copyright (C) 2008 Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/MultiDimensionalWeighted.cc

r1275	r1437
4	4	Copyright (C) 2006, 2007, 2008 Jari Häkkinen, Peter Johansson
5	5
6		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	6	This file is part of the yat library, http://dev.thep.lu.se/yat
7	7
8	8	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/MultiDimensionalWeighted.h

r1275	r1437
8	8	Copyright (C) 2008 Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/Naive.cc

r1275	r1437
6	6	Copyright (C) 2008 Peter Johansson
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/Naive.h

r1275	r1437
9	9	Copyright (C) 2008 Peter Johansson
10	10
11		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	11	This file is part of the yat library, http://dev.thep.lu.se/yat
12	12
13	13	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/NaiveWeighted.cc

r1275	r1437
6	6	Copyright (C) 2008 Peter Johansson
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/NaiveWeighted.h

r1275	r1437
9	9	Copyright (C) 2008 Peter Johansson
10	10
11		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	11	This file is part of the yat library, http://dev.thep.lu.se/yat
12	12
13	13	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/OneDimensional.cc

r1275	r1437
6	6	Copyright (C) 2008 Peter Johansson
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/OneDimensional.h

r1275	r1437
9	9	Copyright (C) 2008 Peter Johansson
10	10
11		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	11	This file is part of the yat library, http://dev.thep.lu.se/yat
12	12
13	13	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/OneDimensionalWeighted.cc

r1275	r1437
4	4	Copyright (C) 2007 Jari Häkkinen, Peter Johansson
5	5
6		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	6	This file is part of the yat library, http://dev.thep.lu.se/yat
7	7
8	8	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/OneDimensionalWeighted.h

r1275	r1437
9	9	Copyright (C) 2008 Peter Johansson
10	10
11		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	11	This file is part of the yat library, http://dev.thep.lu.se/yat
12	12
13	13	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/Polynomial.cc

r1275	r1437
6	6	Copyright (C) 2008 Peter Johansson
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/Polynomial.h

r1275	r1437
8	8	Copyright (C) 2008 Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/PolynomialWeighted.cc

r1275	r1437
5	5	Copyright (C) 2008 Peter Johansson
6	6
7		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	7	This file is part of the yat library, http://dev.thep.lu.se/yat
8	8
9	9	The yat library is free software; you can redistribute it and/or

trunk/yat/regression/PolynomialWeighted.h

r1275	r1437
8	8	Copyright (C) 2008 Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/AUC.cc

r1275	r1437
6	6	Copyright (C) 2008 Peter Johansson
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/AUC.h

r1275	r1437
9	9	Copyright (C) 2008 Peter Johansson
10	10
11		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	11	This file is part of the yat library, http://dev.thep.lu.se/yat
12	12
13	13	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/Averager.cc

r1297	r1437
6	6	Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/Averager.h

r1295	r1437
9	9	Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
10	10
11		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	11	This file is part of the yat library, http://dev.thep.lu.se/yat
12	12
13	13	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/AveragerPair.cc

r1295	r1437
6	6	Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/AveragerPair.h

r1295	r1437
9	9	Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
10	10
11		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	11	This file is part of the yat library, http://dev.thep.lu.se/yat
12	12
13	13	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/AveragerPairWeighted.cc

r1275	r1437
6	6	Copyright (C) 2008 Peter Johansson
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/AveragerPairWeighted.h

r1275	r1437
9	9	Copyright (C) 2008 Peter Johansson
10	10
11		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	11	This file is part of the yat library, http://dev.thep.lu.se/yat
12	12
13	13	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/AveragerWeighted.cc

r1275	r1437
7	7	Copyright (C) 2008 Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/AveragerWeighted.h

r1275	r1437
10	10	Copyright (C) 2008 Peter Johansson
11	11
12		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	12	This file is part of the yat library, http://dev.thep.lu.se/yat
13	13
14	14	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/EuclideanDistance.h

r1275	r1437
8	8	Copyright (C) 2008 Peter Johansson, Markus Ringnér
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/Fisher.cc

r1275	r1437
7	7	Copyright (C) 2008 Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/Fisher.h

r1275	r1437
9	9	Copyright (C) 2008 Peter Johansson
10	10
11		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	11	This file is part of the yat library, http://dev.thep.lu.se/yat
12	12
13	13	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/FoldChange.cc

r1275	r1437
6	6	Copyright (C) 2008 Peter Johansson
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/FoldChange.h

r1275	r1437
9	9	Copyright (C) 2008 Peter Johansson
10	10
11		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	11	This file is part of the yat library, http://dev.thep.lu.se/yat
12	12
13	13	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/Histogram.cc

r1275	r1437
8	8	Copyright (C) 2008 Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/Histogram.h

r1275	r1437
11	11	Copyright (C) 2008 Peter Johansson
12	12
13		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	13	This file is part of the yat library, http://dev.thep.lu.se/yat
14	14
15	15	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/KolmogorovSmirnov.cc

r1199	r1437
4	4	Copyright (C) 2008 Peter Johansson
5	5
6		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	6	This file is part of the yat library, http://dev.thep.lu.se/yat
7	7
8	8	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/KolmogorovSmirnov.h

r1202	r1437
7	7	Copyright (C) 2008 Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/Makefile.am

r1324	r1437
7	7	# Copyright (C) 2008 Peter Johansson, Markus Ringnér
8	8	#
9		# This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	# This file is part of the yat library, http://dev.thep.lu.se/yat
10	10	#
11	11	# The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/Pearson.cc

r1275	r1437
6	6	Copyright (C) 2008 Peter Johansson
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/Pearson.h

r1275	r1437
10	10	Copyright (C) 2008 Peter Johansson
11	11
12		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	12	This file is part of the yat library, http://dev.thep.lu.se/yat
13	13
14	14	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/PearsonCorrelation.cc

r1275	r1437
6	6	Copyright (C) 2008 Peter Johansson
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/PearsonCorrelation.h

r1275	r1437
10	10	Copyright (C) 2008 Peter Johansson
11	11
12		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	12	This file is part of the yat library, http://dev.thep.lu.se/yat
13	13
14	14	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/PearsonDistance.h

r1306	r1437
8	8	Copyright (C) 2008 Peter Johansson, Markus Ringnér
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/ROC.cc

r1275	r1437
6	6	Copyright (C) 2008 Peter Johansson
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/ROC.h

-                      r1271
+                      r1437
   Copyright (C) 2005, 2006, 2007, 2008 Jari Häkkinen, Peter Johansson
   This file is part of the yat library, http://trac.thep.lu.se/yat
+  This file is part of the yat library, http://dev.thep.lu.se/yat
   The yat library is free software; you can redistribute it and/or
 …
     /**
        Adding a data value to ROC.
+       \see add(T &o, ForwardIterator first, ForwardIterator last,
+       const classifier::Target &target)
     */
     void add(double value, bool target, double weight=1.0);

trunk/yat/statistics/SAMScore.cc

r1275	r1437
5	5	Copyright (C) 2008 Peter Johansson
6	6
7		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	7	This file is part of the yat library, http://dev.thep.lu.se/yat
8	8
9	9	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/SAMScore.h

r1275	r1437
8	8	Copyright (C) 2008 Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/SNRScore.cc

r1275	r1437
5	5	Copyright (C) 2008 Peter Johansson
6	6
7		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	7	This file is part of the yat library, http://dev.thep.lu.se/yat
8	8
9	9	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/SNRScore.h

r1275	r1437
8	8	Copyright (C) 2008 Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/Score.cc

r1275	r1437
7	7	Copyright (C) 2008 Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/Score.h

r1275	r1437
10	10	Copyright (C) 2008 Peter Johansson
11	11
12		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	12	This file is part of the yat library, http://dev.thep.lu.se/yat
13	13
14	14	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/VectorFunction.cc

r1275	r1437
5	5	Copyright (C) 2008 Peter Johansson
6	6
7		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	7	This file is part of the yat library, http://dev.thep.lu.se/yat
8	8
9	9	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/VectorFunction.h

r1275	r1437
7	7	Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/WilcoxonFoldChange.cc

r1315	r1437
6	6	Copyright (C) 2008 Peter Johansson
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/WilcoxonFoldChange.h

r1315	r1437
9	9	Copyright (C) 2008 Peter Johansson
10	10
11		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	11	This file is part of the yat library, http://dev.thep.lu.se/yat
12	12
13	13	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/tScore.cc

r1275	r1437
8	8	Copyright (C) 2008 Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/tScore.h

r1275	r1437
10	10	Copyright (C) 2008 Peter Johansson
11	11
12		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	12	This file is part of the yat library, http://dev.thep.lu.se/yat
13	13
14	14	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/tTest.cc

r1275	r1437
7	7	Copyright (C) 2007 Jari Häkkinen, Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/tTest.h

r1275	r1437
10	10	Copyright (C) 2008 Peter Johansson
11	11
12		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	12	This file is part of the yat library, http://dev.thep.lu.se/yat
13	13
14	14	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/utility.cc

r1287	r1437
7	7	Copyright (C) 2008 Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/statistics/utility.h

r1404	r1437
11	11	Copyright (C) 2008 Peter Johansson
12	12
13		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	13	This file is part of the yat library, http://dev.thep.lu.se/yat
14	14
15	15	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/Alignment.cc

r1275	r1437
8	8	Copyright (C) 2008 Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/Alignment.h

r1275	r1437
11	11	Copyright (C) 2008 Peter Johansson
12	12
13		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	13	This file is part of the yat library, http://dev.thep.lu.se/yat
14	14
15	15	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/ColumnStream.cc

r1275	r1437
4	4	Copyright (C) 2007 Jari Häkkinen, Peter Johansson
5	5
6		This file is part of svndigest, http://~~trac~~.thep.lu.se/svndigest
	6	This file is part of svndigest, http://dev.thep.lu.se/svndigest
7	7
8	8	svndigest is free software; you can redistribute it and/or modify it

trunk/yat/utility/ColumnStream.h

r1275	r1437
7	7	Copyright (C) 2007 Jari Häkkinen, Peter Johansson
8	8
9		This file is part of svndigest, http://~~trac~~.thep.lu.se/svndigest
	9	This file is part of svndigest, http://dev.thep.lu.se/svndigest
10	10
11	11	svndigest is free software; you can redistribute it and/or modify it

trunk/yat/utility/CommandLine.cc

r1426	r1437
5	5	Copyright (C) 2008 Peter Johansson
6	6
7		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	7	This file is part of the yat library, http://dev.thep.lu.se/yat
8	8
9	9	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/CommandLine.h

-                      r1275
+                      r1437
   Copyright (C) 2008 Peter Johansson
   This file is part of the yat library, http://trac.thep.lu.se/yat
+  This file is part of the yat library, http://dev.thep.lu.se/yat
   The yat library is free software; you can redistribute it and/or
 …
+     }
      catch (cmd_error& e){
+       if (version.present()){
+         std::cout << cmd.program_name() << " 1.0\n"
+                   << "Copyright (C) 2007 Peter Johansson\n\n"
+                   << "This is free software see the source for copying "
+                   << "conditions. There is NO\nwarranty; not even for "
+                   << "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\n";
+         exit(0);
+       }
        std::cout << e.what() << std::endl;
        return 1;
+     }
-     if (version.present()){
-       std::cout << cmd.program_name() << " 1.0\n"
-                 << "Copyright (C) 2007 Peter Johansson\n\n"
-                 << "This is free software see the source for copying "
-                 << "conditions. There is NO\nwarranty; not even for "
-                 << "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\n";
-       exit(0);
+     }
      ...
      \endcode
 …
   /**
      \brief CommandLine output operator
+     A typical output may look like this
+     \verbatim
+     Available options are:
+     -h, --help      display this help and exit
+     -v, --verbose   explain what is being done
+     \endverbatim
+     The output starts with a descriptive line such as "Available
+     options are:" (default) that can be set in constructor. Then follows the
+     options described in the order they were added to
+     Commandline. Each Option is described according to
+     Option::print(void) function.
+     \see OptionHelp
   */
   std::ostream& operator<<(std::ostream&, const CommandLine&);

trunk/yat/utility/Container2DIterator.h

r1374	r1437
8	8	Copyright (C) 2008 Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/Exception.h

r1275	r1437
8	8	Copyright (C) 2008 Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/FileUtil.cc

-                      r1261
+                      r1437
   Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
   This file is part of the yat library, http://trac.thep.lu.se/yat
+  This file is part of the yat library, http://dev.thep.lu.se/yat
   The yat library is free software; you can redistribute it and/or
 …
 #include <iostream>
 #include <stdexcept>
+#include <sstream>
 #include <string>
 …
             break;
           case 'd':
             struct stat nodestat;
             stat(tryme.c_str(),&nodestat);
+            struct stat64 nodestat;
+            stat64(tryme.c_str(),&nodestat);
             if (!S_ISDIR(nodestat.st_mode))
               ok = false;
 …
   bool FileUtil::exists(void) const
+  {
+    struct stat statt;
+    if ( stat(path_.c_str(),&statt) && (errno!=ENOENT) )
+      throw IO_error(std::string("stat(2) call failed with errno: "+errno));
+    struct stat64 statt;
+    if ( stat64(path_.c_str(),&statt) && (errno!=ENOENT) ) {
+      std::stringstream ss;
+      ss << "stat64(2) call failed with errno: " << errno;
+      throw IO_error(ss.str());
+    }
     if (errno) {
       errno = 0; // don't leave errno in state of failure

trunk/yat/utility/FileUtil.h

r1275	r1437
11	11	Copyright (C) 2008 Peter Johansson
12	12
13		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	13	This file is part of the yat library, http://dev.thep.lu.se/yat
14	14
15	15	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/Index.cc

r1361	r1437
4	4	Copyright (C) 2008 Peter Johansson
5	5
6		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	6	This file is part of the yat library, http://dev.thep.lu.se/yat
7	7
8	8	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/Index.h

r1134	r1437
7	7	Copyright (C) 2008 Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/IteratorPolicy.h

r1145	r1437
7	7	Copyright (C) 2008 Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/Makefile.am

r1410	r1437
6	6	# Copyright (C) 2008 Peter Johansson
7	7	#
8		# This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	# This file is part of the yat library, http://dev.thep.lu.se/yat
9	9	#
10	10	# The yat library is free software; you can redistribute it and/or

trunk/yat/utility/Matrix.cc

r1313	r1437
7	7	Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/Matrix.h

-                      r1320
+                      r1437
   Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
   This file is part of the yat library, http://trac.thep.lu.se/yat
+  This file is part of the yat library, http://dev.thep.lu.se/yat
   The yat library is free software; you can redistribute it and/or
 …
      The two matrices must have the same size.
      \throw GSL_error if either index is out of bounds.
+     \throw GSL_error if sizes are not equal.
   */
   void swap(Matrix&, Matrix&);

trunk/yat/utility/NNI.cc

r1275	r1437
8	8	Copyright (C) 2008 Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/NNI.h

r1275	r1437
8	8	Copyright (C) 2005, 2006, 2007, 2008 Jari Häkkinen, Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/Option.cc

r1275	r1437
5	5	Copyright (C) 2008 Peter Johansson
6	6
7		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	7	This file is part of the yat library, http://dev.thep.lu.se/yat
8	8
9	9	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/Option.h

-                      r1275
+                      r1437
   Copyright (C) 2008 Peter Johansson
   This file is part of the yat library, http://trac.thep.lu.se/yat
+  This file is part of the yat library, http://dev.thep.lu.se/yat
   The yat library is free software; you can redistribute it and/or
 …
     /**
        \brief print help output
+       This function calls the four virtual private functions print1,
+       print2, print3, and print4. This allows an inherited class to
+       implement one (or several) of these functions and keep the
+       default output of the others. The default behavior is that:
+       - print1 prints the short name, '-h', as short_name(void) const
+       - print2 prints the long name, '--help', as long_name(void) const
+       - print3 is empty
+       - print4 prints the description as description(void) const.
      */
     std::string print(void);

trunk/yat/utility/OptionArg.h

r1275	r1437
8	8	Copyright (C) 2008 Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/OptionFile.cc

r1275	r1437
5	5	Copyright (C) 2008 Peter Johansson
6	6
7		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	7	This file is part of the yat library, http://dev.thep.lu.se/yat
8	8
9	9	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/OptionFile.h

r1275	r1437
8	8	Copyright (C) 2008 Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/OptionHelp.cc

r1275	r1437
4	4	Copyright (C) 2007 Jari Häkkinen, Peter Johansson
5	5
6		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	6	This file is part of the yat library, http://dev.thep.lu.se/yat
7	7
8	8	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/OptionHelp.h

-                      r1275
+                      r1437
   Copyright (C) 2008 Peter Johansson
   This file is part of the yat library, http://trac.thep.lu.se/yat
+  This file is part of the yat library, http://dev.thep.lu.se/yat
   The yat library is free software; you can redistribute it and/or
 …
      When this option is found in parsing of commandline, it displays
+     a help output exits.
+     a help output and exits. A typical output looks like:
+     \verbatim
+     Usage: foo [OPTION]...
+     SYNOPSIS
+     Available options are:
+     -h, --help      display this help and exit
+     -v, --verbose   explain what is being done
+     Some extra information explaining something.
+     \endverbatim
+     The output consist of four blocks. The first block can be
+     modified with usage(void) function. The second is block is
+     typically a one-liner explaining the application and can be
+     modified with the synopsis(void) function. The third block
+     contain the description of the different options, see
+     operator<<(std::ostream&, const CommandLine&) for further
+     details. The last block can be modified with post_arguments(void)
+     function.
    */
   class OptionHelp : public OptionSwitch

trunk/yat/utility/OptionInFile.cc

r1014	r1437
4	4	Copyright (C) 2008 Peter Johansson
5	5
6		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	6	This file is part of the yat library, http://dev.thep.lu.se/yat
7	7
8	8	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/OptionInFile.h

r1014	r1437
7	7	Copyright (C) 2008 Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/OptionOutFile.cc

r1014	r1437
4	4	Copyright (C) 2008 Peter Johansson
5	5
6		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	6	This file is part of the yat library, http://dev.thep.lu.se/yat
7	7
8	8	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/OptionOutFile.h

r1014	r1437
7	7	Copyright (C) 2008 Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/OptionSwitch.cc

r1275	r1437
4	4	Copyright (C) 2007 Jari Häkkinen, Peter Johansson
5	5
6		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	6	This file is part of the yat library, http://dev.thep.lu.se/yat
7	7
8	8	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/OptionSwitch.h

r1275	r1437
7	7	Copyright (C) 2007 Jari Häkkinen, Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/PCA.cc

r1275	r1437
8	8	Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/PCA.h

r1275	r1437
12	12	Copyright (C) 2008 Peter Johansson
13	13
14		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	14	This file is part of the yat library, http://dev.thep.lu.se/yat
15	15
16	16	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/SVD.cc

r1275	r1437
9	9	Copyright (C) 2008 Peter Johansson
10	10
11		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	11	This file is part of the yat library, http://dev.thep.lu.se/yat
12	12
13	13	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/SVD.h

r1275	r1437
12	12	Copyright (C) 2008 Peter Johansson
13	13
14		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	14	This file is part of the yat library, http://dev.thep.lu.se/yat
15	15
16	16	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/SmartPtr.h

r1275	r1437
7	7	Copyright (C) 2008 Jari Häkkinen, Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/StrideIterator.h

r1390	r1437
8	8	Copyright (C) 2008 Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/TypeInfo.cc

r1275	r1437
4	4	Copyright (C) 2007 Jari Häkkinen, Peter Johansson
5	5
6		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	6	This file is part of the yat library, http://dev.thep.lu.se/yat
7	7
8	8	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/TypeInfo.h

-                      r1275
+                      r1437
 /*
   Copyright (C) 2007 Jari Häkkinen, Peter Johansson
+  Copyright (C) 2008 Peter Johansson
   This file is part of the yat library, http://trac.thep.lu.se/yat
+  This file is part of the yat library, http://dev.thep.lu.se/yat
   The yat library is free software; you can redistribute it and/or
 …
   /**
      \brief Based on operators == and <
+     \brief Based on operator <
    */
   bool operator>(const TypeInfo&, const TypeInfo&);
   /**
      \brief Based on operators == and <
+     \brief Based on operator <=
    */
   bool operator>=(const TypeInfo&, const TypeInfo&);

trunk/yat/utility/Vector.cc

r1314	r1437
7	7	Copyright (C) 2008 Jari Häkkinen, Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/Vector.h

r1275	r1437
12	12	Copyright (C) 2008 Jari Häkkinen, Peter Johansson
13	13
14		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	14	This file is part of the yat library, http://dev.thep.lu.se/yat
15	15
16	16	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/VectorBase.cc

r1275	r1437
7	7	Copyright (C) 2008 Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/trac/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/trac/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/VectorBase.h

-                      r1275
+                      r1437
   Copyright (C) 2008 Peter Johansson
   This file is part of the yat library, http://trac.thep.lu.se/trac/yat
+  This file is part of the yat library, http://dev.thep.lu.se/trac/yat
   The yat library is free software; you can redistribute it and/or
 …
   /**
      \brief The output operator for the VectorBase class.
+  */
+  std::ostream& operator<<(std::ostream&, const VectorBase&);
+     Elements in VectorBase \a v are sent to ostream \a s and
+     separated with the fill character of stream \a s, s.fill(). If
+     you, for example, want to print the VectorBase \a v with the
+     elements separated by a ':', you do so by:
+     \verbatim
+     s << setfill(':') << v;
+     \endverbatim
+  */
+  std::ostream& operator<<(std::ostream& s, const VectorBase& v);
 }}} // of namespace utility, yat, and theplu

trunk/yat/utility/VectorConstView.cc

r1275	r1437
7	7	Copyright (C) 2008 Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/trac/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/trac/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/VectorConstView.h

r1275	r1437
12	12	Copyright (C) 2008 Peter Johansson
13	13
14		This file is part of the yat library, http://~~trac~~.thep.lu.se/trac/yat
	14	This file is part of the yat library, http://dev.thep.lu.se/trac/yat
15	15
16	16	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/VectorMutable.cc

r1275	r1437
7	7	Copyright (C) 2008 Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/trac/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/trac/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/VectorMutable.h

r1275	r1437
12	12	Copyright (C) 2008 Peter Johansson
13	13
14		This file is part of the yat library, http://~~trac~~.thep.lu.se/trac/yat
	14	This file is part of the yat library, http://dev.thep.lu.se/trac/yat
15	15
16	16	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/VectorView.cc

r1275	r1437
7	7	Copyright (C) 2008 Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/trac/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/trac/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/VectorView.h

r1275	r1437
12	12	Copyright (C) 2008 Peter Johansson
13	13
14		This file is part of the yat library, http://~~trac~~.thep.lu.se/trac/yat
	14	This file is part of the yat library, http://dev.thep.lu.se/trac/yat
15	15
16	16	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/WeNNI.cc

r1275	r1437
8	8	Copyright (C) 2008 Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/WeNNI.h

r1275	r1437
11	11	Copyright (C) 2008 Peter Johansson
12	12
13		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	13	This file is part of the yat library, http://dev.thep.lu.se/yat
14	14
15	15	The yat library is free software; you can redistribute it

trunk/yat/utility/iterator_traits.h

r1382	r1437
8	8	Copyright (C) 2008 Peter Johansson, Markus Ringnér
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/kNNI.cc

r1275	r1437
8	8	Copyright (C) 2008 Peter Johansson
9	9
10		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	10	This file is part of the yat library, http://dev.thep.lu.se/yat
11	11
12	12	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/kNNI.h

r1275	r1437
11	11	Copyright (C) 2008 Peter Johansson
12	12
13		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	13	This file is part of the yat library, http://dev.thep.lu.se/yat
14	14
15	15	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/stl_utility.cc

r1275	r1437
6	6	Copyright (C) 2007 Jari Häkkinen, Peter Johansson
7	7
8		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	8	This file is part of the yat library, http://dev.thep.lu.se/yat
9	9
10	10	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/stl_utility.h

r1403	r1437
10	10	Copyright (C) 2008 Peter Johansson
11	11
12		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	12	This file is part of the yat library, http://dev.thep.lu.se/yat
13	13
14	14	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/utility.cc

r1432	r1437
5	5	Copyright (C) 2007 Jari Häkkinen, Peter Johansson
6	6
7		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	7	This file is part of the yat library, http://dev.thep.lu.se/yat
8	8
9	9	The yat library is free software; you can redistribute it and/or

trunk/yat/utility/utility.h

-                      r1432
+                      r1437
   Copyright (C) 2008 Peter Johansson
   This file is part of the yat library, http://trac.thep.lu.se/yat
+  This file is part of the yat library, http://dev.thep.lu.se/yat
   The yat library is free software; you can redistribute it and/or
 …
 ///
+#include <limits>
 #include <string>
 #include <stdexcept>

trunk/yat/utility/yat_assert.h

r1275	r1437
7	7	Copyright (C) 2008 Peter Johansson
8	8
9		This file is part of the yat library, http://~~trac~~.thep.lu.se/yat
	9	This file is part of the yat library, http://dev.thep.lu.se/yat
10	10
11	11	The yat library is free software; you can redistribute it and/or

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