bpp-phyl-omics-2.2.0/genIncludes.sh000775 001750 001750 00000001231 12372454317 020646 0ustar00jdutheiljdutheil000000 000000 #! /bin/bash createGeneric() { echo "-- Creating generic include file: $1.all" #Make sure we run into subdirectories first: dirs=() for file in "$1"/* do if [ -d "$file" ] then # Recursion: dirs+=( "$file" ) fi done for dir in ${dirs[@]} do createGeneric $dir done #Now list all files, including newly created .all files: if [ -f $1.all ] then rm $1.all fi dir=`basename $1` for file in "$1"/* do if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] ) then file=`basename $file` echo "#include \"$dir/$file\"" >> $1.all fi done; } createGeneric $1 bpp-phyl-omics-2.2.0/src/CMakeLists.txt000664 001750 001750 00000003600 12411254450 021366 0ustar00jdutheiljdutheil000000 000000 # CMake script for Bio++ Phylo(gen)-omics Library # Author: Sylvain Gaillard and Julien Dutheil # Created: 08/11/2012 # File list SET(CPP_FILES Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.cpp Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp ) SET(H_FILES Bpp/Seq/Io/Maf/AbstractDistanceEstimationMafIterator.h Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.h Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.h Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.h Bpp/Seq/Io/Maf/AbstractPhylogenyReconstructionMafIterator.h Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.h Bpp/Seq/Io/Maf/TreeManipulationMafIterators.h Bpp/Seq/Io/Maf/OutputTreeMafIterator.h Bpp/Seq/Io/Maf/CountClustersMafStatistics.h ) # Build the static lib ADD_LIBRARY(bppphylomics-static STATIC ${CPP_FILES}) SET_TARGET_PROPERTIES(bppphylomics-static PROPERTIES OUTPUT_NAME bpp-phyl-omics CLEAN_DIRECT_OUTPUT 1 ) TARGET_LINK_LIBRARIES(bppphylomics-static ${LIBS}) # Build the shared lib ADD_LIBRARY(bppphylomics-shared SHARED ${CPP_FILES}) SET_TARGET_PROPERTIES(bppphylomics-shared PROPERTIES OUTPUT_NAME bpp-phyl-omics CLEAN_DIRECT_OUTPUT 1 VERSION ${BPPPHYLOMICS_VERSION} SOVERSION ${BPPPHYLOMICS_VERSION_MAJOR} ) TARGET_LINK_LIBRARIES(bppphylomics-shared ${LIBS}) # Install libs INSTALL(TARGETS bppphylomics-static bppphylomics-shared DESTINATION lib${LIB_SUFFIX}) # Install headers INSTALL(DIRECTORY Bpp/ DESTINATION include/Bpp FILES_MATCHING PATTERN "*.h") INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${CMAKE_SOURCE_DIR}/genIncludes.sh ${CMAKE_PREFIX_PATH}/include/Bpp)") bpp-phyl-omics-2.2.0/src/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.h000664 001750 001750 00000021321 12411254450 031066 0ustar00jdutheiljdutheil000000 000000 // // File: MaximumLikelihoodModelFitMafStatistics.h // Created by: Julien Dutheil // Created on: Mar 25 2014 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to test the homogeneity of the substitution process of a given alignment. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ #ifndef _MAXIMUMLIKELIHOODMODELFITMAFSTATISTICS_H_ #define _MAXIMUMLIKELIHOODMODELFITMAFSTATISTICS_H_ #include #include //From bpp-phyl: #include #include #include #include #include //From bpp-core #include namespace bpp { /** * @brief Fit a substitution model. * * All nucleotide substitution models and rate distributions are supported. * Only time-homogeneous models are allowed though. */ class MaximumLikelihoodModelFitMafStatistics: public AbstractMafStatistics { private: std::auto_ptr model_; std::auto_ptr modelSet_; //Only used in case of non-stationary model. std::auto_ptr rDist_; std::auto_ptr rootFreqs_; std::string treePropertyIn_; std::auto_ptr tree_; std::vector parametersOut_; bool reestimateBrLen_; double propGapsToKeep_; //Exclude sites with too many gaps bool gapsAsUnresolved_; //For most models, should be yes as they do not allow for gap characters ParameterList initParameters_; ParameterList fixedParameters_; public: /** * @brief Build a new distance estimation maf mafstat, based on the DistanceEstimation class. * * A tree must be associated to each block before this analysis can be run. * * @param model The substitution model. * @param rDist The distribution of rates. * @param rootFreqs Root frequencies for non-stationary model. If set to 0, then a stationary model is assumed. * @param treePropertyIn The name of the property where the input tree is stored for each block. * @param parametersOut Parameters to output. * @param fixedParameters Parameter which should not be estimated but fixed to the given value instead. * @param reestimateBrLen If the branch length from the tree should be reestimated (otherwise kept as is). * @param propGapsToKeep The maximum gapfrequency in a site to include it in the analysis. * @param gapsAsUnresolved Tell if gap characters should be considered as unresolved states. In ost cases it should be set to true, as very few substitution models consider gaps as genuine states. */ MaximumLikelihoodModelFitMafStatistics( SubstitutionModel* model, DiscreteDistribution* rDist, NucleotideFrequenciesSet* rootFreqs, const std::string& treePropertyIn, const std::vector& parametersOut, const ParameterList& fixedParameters, bool reestimateBrLen = true, double propGapsToKeep = 0, bool gapsAsUnresolved = true): AbstractMafStatistics(), model_(model), modelSet_(0), rDist_(rDist), rootFreqs_(rootFreqs), treePropertyIn_(treePropertyIn), tree_(0), parametersOut_(parametersOut), reestimateBrLen_(reestimateBrLen), propGapsToKeep_(propGapsToKeep), gapsAsUnresolved_(gapsAsUnresolved), initParameters_(), fixedParameters_(fixedParameters) { if (!rootFreqs) init_(); //Otherwise we do not initialize parameters as the tree might change for each block. //We therefore have to initialize once for each block. } /** * @brief Build a new distance estimation maf mafstat, based on the DistanceEstimation class. * * This analysis use the same input tree for all blocks. * * @param model The substitution model. * @param rDist The distribution of rates. * @param rootFreqs Root frequencies for non-stationary model. If set to 0, then a stationary model is assumed. * @param tree The tree to use for fitting the model. * @param parametersOut Parameters to output. * @param fixedParameters Parameter which should not be estimated but fixed to the given value instead. * @param reestimateBrLen If the branch length from the tree should be reestimated (otherwise kept as is). * @param propGapsToKeep The maximum gapfrequency in a site to include it in the analysis. * @param gapsAsUnresolved Tell if gap characters should be considered as unresolved states. In ost cases it should be set to true, as very few substitution models consider gaps as genuine states. */ MaximumLikelihoodModelFitMafStatistics( SubstitutionModel* model, DiscreteDistribution* rDist, NucleotideFrequenciesSet* rootFreqs, const Tree* tree, const std::vector& parametersOut, const ParameterList& fixedParameters, bool reestimateBrLen = true, double propGapsToKeep = 0, bool gapsAsUnresolved = true): AbstractMafStatistics(), model_(model), modelSet_(0), rDist_(rDist), rootFreqs_(rootFreqs), treePropertyIn_(NO_PROPERTY), tree_(0), parametersOut_(parametersOut), reestimateBrLen_(reestimateBrLen), propGapsToKeep_(propGapsToKeep), gapsAsUnresolved_(gapsAsUnresolved), initParameters_(), fixedParameters_(fixedParameters) { if (rootFreqs) modelSet_.reset(SubstitutionModelSetTools::createHomogeneousModelSet(model->clone(), rootFreqs->clone(), tree)); init_(); } private: MaximumLikelihoodModelFitMafStatistics(const MaximumLikelihoodModelFitMafStatistics& mafstat): AbstractMafStatistics(), model_(0), modelSet_(0), rDist_(0), rootFreqs_(0), treePropertyIn_(mafstat.treePropertyIn_), tree_(0), parametersOut_(mafstat.parametersOut_), reestimateBrLen_(mafstat.reestimateBrLen_), propGapsToKeep_(mafstat.propGapsToKeep_), gapsAsUnresolved_(mafstat.gapsAsUnresolved_), initParameters_(mafstat.initParameters_), fixedParameters_(mafstat.fixedParameters_) {} MaximumLikelihoodModelFitMafStatistics& operator=(const MaximumLikelihoodModelFitMafStatistics& mafstat) { model_.reset(); modelSet_.reset(); rDist_.reset(); rootFreqs_.reset(); treePropertyIn_ = mafstat.treePropertyIn_; tree_.reset(); parametersOut_ = mafstat.parametersOut_; reestimateBrLen_ = mafstat.reestimateBrLen_; propGapsToKeep_ = mafstat.propGapsToKeep_; gapsAsUnresolved_ = mafstat.gapsAsUnresolved_; initParameters_ = mafstat.initParameters_; fixedParameters_ = mafstat.fixedParameters_; return *this; } public: std::string getShortName() const { return "MLModelFit"; } std::string getFullName() const { return "Maximum Likelihood Model Fitting"; } void compute(const MafBlock& block); std::vector getSupportedTags() const { std::vector tags; tags.push_back("NbIterations"); tags.insert(tags.end(), parametersOut_.begin(), parametersOut_.end()); return tags; } static const std::string NO_PROPERTY; private: void init_(); }; } //end of namespace bpp. #endif //_MAXIMUMLIKELIHOODDISTANCEESTIMATIONMAFSTATISTICS_H_ bpp-phyl-omics-2.2.0/src/Bpp/Seq/Io/Maf/CountClustersMafStatistics.h000664 001750 001750 00000006040 12372454317 026651 0ustar00jdutheiljdutheil000000 000000 // // File: CountClustersMafStatistics.h // Created by: Julien Dutheil // Created on: Jul 24 2012 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to test the homogeneity of the substitution process of a given alignment. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ #ifndef _COUNTCLUSTERSMAFSTATISTICS_H_ #define _COUNTCLUSTERSMAFSTATISTICS_H_ #include //From bpp-phyl: #include //From the STL: #include namespace bpp { /** * @brief Count the number of sequence cluster, given a certain threshold. * This requires that a phylogenetic tree was previously computed. */ class CountClustersMafStatistics: public AbstractMafStatisticsSimple { private: std::string treeProperty_; double threshold_; public: CountClustersMafStatistics(const std::string& property, double threshold): AbstractMafStatisticsSimple("NbClusters"), treeProperty_(property), threshold_(threshold) {} public: void setTreeProperty(const std::string& property) { treeProperty_ = property; } const std::string& getTreeProperty() const { return treeProperty_; } std::string getShortName() const { return "CountClusters(" + TextTools::toString(threshold_) + ")"; } std::string getFullName() const { return "Number of sequence clusters with divergence <= " + TextTools::toString(threshold_) + "."; } void compute(const MafBlock& block); std::string getPropertyName() const { return "CountClusters"; } private: unsigned int getNumberOfClusters_(const Node* node, std::map& heights); }; } //end of namespace bpp. #endif //_COUNTCLUSTERSMAFSTATISTICS_H_ bpp-phyl-omics-2.2.0/src/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp000664 001750 001750 00000007074 12372454317 027501 0ustar00jdutheiljdutheil000000 000000 // // File: TreeManipulationMafIterators.cpp // Created by: Julien Dutheil // Created on: Jul 24 2012 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to test the homogeneity of the substitution process of a given alignment. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ #include "TreeManipulationMafIterators.h" using namespace bpp; using namespace std; MafBlock* TreeManipulationMafIterator::analyseCurrentBlock_() throw (Exception) { currentBlock_ = iterator_->nextBlock(); if (currentBlock_) { if (!currentBlock_->hasProperty(treePropertyRead_)) throw Exception("TreeManipulationMafIterator::analyseCurrentBlock_(). No property available for " + treePropertyRead_); try { TreeTemplate* tree = new TreeTemplate(dynamic_cast(currentBlock_->getProperty(treePropertyRead_))); manipulateTree_(tree); currentBlock_->setProperty(treePropertyWrite_, tree); } catch (bad_cast& e) { throw Exception("TreeManipulationMafIterator::analyseCurrentBlock_(). A property was found for '" + treePropertyRead_ + "' but does not appear to contain a phylogenetic tree."); } } return currentBlock_; } void NewOutgroupMafIterator::manipulateTree_(TreeTemplate* tree) throw (Exception) { vector leaves = tree->getLeaves(); Node* outgroup = 0; bool outgroupFound = false; for (size_t i = 0; i < leaves.size() && !outgroupFound; ++i) { string species, chr; MafSequence::splitNameIntoSpeciesAndChromosome(leaves[i]->getName(), species, chr); if (species == outgroupSpecies_) { outgroup = leaves[i]; outgroupFound = true; } } if (!outgroupFound) throw Exception("NewOutgroupTreeMafIterator::analyseCurrentBlock_(). No ougroup species was found in the attached tree."); tree->newOutGroup(outgroup); } void DropSpeciesMafIterator::manipulateTree_(TreeTemplate* tree) throw (Exception) { vector leaves = tree->getLeaves(); for (size_t i = 0; i < leaves.size(); ++i) { string species, chr; MafSequence::splitNameIntoSpeciesAndChromosome(leaves[i]->getName(), species, chr); if (species == species_) { TreeTemplateTools::dropSubtree(*tree, leaves[i]); } } } bpp-phyl-omics-2.2.0/src/Bpp/Seq/Io/Maf/OutputTreeMafIterator.h000664 001750 001750 00000006625 12372454317 025624 0ustar00jdutheiljdutheil000000 000000 // // File: OutputTreeMafIterator.h // Created by: Julien Dutheil // Created on: Jul 24 2012 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to test the homogeneity of the substitution process of a given alignment. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ #ifndef _OUTPUTTREEMAFITERATOR_H_ #define _OUTPUTTREEMAFITERATOR_H_ #include //From bpp-phyl: #include #include /** * @mainpage * * @par * The bpp-phyl-omics library contains 'omics' phylogenetic tools and classes. * * As for Bio++ version 2.1.0, these consist of bpp::MafIterator classes allowing to reconstruct phylogenies from a genome alignment. * More tools are expected to developped in the incoming versions. */ namespace bpp { /** * @brief This iterator print an attached tree to a newick file. */ class OutputTreeMafIterator: public AbstractFilterMafIterator { private: std::ostream* output_; std::string treeProperty_; Newick writer_; public: OutputTreeMafIterator(MafIterator* iterator, std::ostream* out, const std::string treeProperty) : AbstractFilterMafIterator(iterator), output_(out), treeProperty_(treeProperty), writer_() {} private: OutputTreeMafIterator(const OutputTreeMafIterator& iterator) : AbstractFilterMafIterator(0), output_(iterator.output_), treeProperty_(iterator.treeProperty_), writer_() {} OutputTreeMafIterator& operator=(const OutputTreeMafIterator& iterator) { output_ = iterator.output_; treeProperty_ = iterator.treeProperty_; writer_ = iterator.writer_; return *this; } public: MafBlock* analyseCurrentBlock_() throw (Exception) { currentBlock_ = iterator_->nextBlock(); if (output_ && currentBlock_) writeBlock(*output_, *currentBlock_); return currentBlock_; } private: void writeBlock(std::ostream& out, const MafBlock& block) const; }; } //end of namespace bpp. #endif //_OUTPUTTREEMAFITERATOR_H_ bpp-phyl-omics-2.2.0/src/Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.cpp000664 001750 001750 00000011453 12411254450 031426 0ustar00jdutheiljdutheil000000 000000 // // File: MaximumLikelihoodModelFitMafStatistics.cpp // Created by: Julien Dutheil // Created on: Mar 25 2014 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to test the homogeneity of the substitution process of a given alignment. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ #include "MaximumLikelihoodModelFitMafStatistics.h" //From bpp-seq: #include //From bpp-phyl: #include #include #include #include using namespace bpp; using namespace std; const string MaximumLikelihoodModelFitMafStatistics::NO_PROPERTY = "RESERVED_NOPROPERTY"; void MaximumLikelihoodModelFitMafStatistics::compute(const MafBlock& block) { //First we get the alignment: auto_ptr sites(SiteContainerTools::removeGapSites(block.getAlignment(), propGapsToKeep_)); if (gapsAsUnresolved_) SiteContainerTools::changeGapsToUnknownCharacters(*sites); //Second we get the tree: const Tree* tree = 0; if (!tree_.get()) { //No default tree is given, we try to retrieve one from the block: if (!block.hasProperty(treePropertyIn_)) throw Exception("MaximumLikelihoodModelFitMafIterator::fitModelBlock. No property available for " + treePropertyIn_); try { tree = &(dynamic_cast(block.getProperty(treePropertyIn_))); if (tree->isRooted()) throw Exception("MaximumLikelihoodModelFitMafIterator::fitModelBlock. Tree must be unrooted."); } catch (bad_cast& e) { throw Exception("MaximumLikelihoodModelFitMafIterator::fitModelBlock. A property was found for '" + treePropertyIn_ + "' but does not appear to contain a phylogenetic tree."); } } else { tree = tree_.get(); } //We build a new TreeLikelihood object: auto_ptr tl; if (rootFreqs_.get()) { modelSet_.reset(SubstitutionModelSetTools::createHomogeneousModelSet(model_->clone(), rootFreqs_->clone(), tree)); tl.reset(new RNonHomogeneousTreeLikelihood(*tree, *sites, modelSet_.get(), rDist_.get(), false, true, false)); //Initialize: if (initParameters_.size() == 0) init_(); //so far, even if tree changed, parameter names are supposingly the same. This might not be true in some complex cases... } else { tl.reset(new RHomogeneousTreeLikelihood(*tree, *sites, model_.get(), rDist_.get(), false, false, true)); } tl->initialize(); tl->setParameters(fixedParameters_); //We optimize parameters: unsigned int nbIt = OptimizationTools::optimizeNumericalParameters2(tl.get(), initParameters_, 0, 0.000001, 10000, 0, 0, false, false, 0); //And we save interesting parameter values: result_.setValue("NbIterations", static_cast(nbIt)); for (size_t i = 0;i < parametersOut_.size(); ++i) { result_.setValue(parametersOut_[i], tl->getParameterValue(parametersOut_[i])); } } void MaximumLikelihoodModelFitMafStatistics::init_() { if (rootFreqs_.get()) { initParameters_.addParameters(modelSet_->getIndependentParameters()); } else { initParameters_.addParameters(model_->getIndependentParameters()); } initParameters_.addParameters(rDist_->getIndependentParameters()); //Remove from initParameters the ones to consider fixed: initParameters_.deleteParameters(fixedParameters_.getParameterNames()); } bpp-phyl-omics-2.2.0/src/Bpp/Seq/Io/Maf/CountClustersMafStatistics.cpp000664 001750 001750 00000006136 12411254450 027200 0ustar00jdutheiljdutheil000000 000000 // // File: MafIterators.cpp // Created by: Julien Dutheil // Created on: Jul 24 2012 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to test the homogeneity of the substitution process of a given alignment. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ #include "CountClustersMafStatistics.h" //From bpp-seq: #include //From bpp-phyl: #include using namespace bpp; using namespace std; unsigned int CountClustersMafStatistics::getNumberOfClusters_(const Node* node, map& heights) { unsigned int nClust = 0; double h = heights[node]; if (h < threshold_) { nClust++; } else { for (int i = 0; i < static_cast(node->getNumberOfSons()); ++i) { nClust += getNumberOfClusters_((*node)[i], heights); } } return nClust; } void CountClustersMafStatistics::compute(const MafBlock& block) { if (!block.hasProperty(treeProperty_)) throw Exception("CountClustersMafStatistics::compute. No property available for " + treeProperty_); try { TreeTemplate tree(dynamic_cast(block.getProperty(treeProperty_))); if (!tree.isRooted()) throw Exception("CountClustersMafStatistics::compute. Cluster count only works with a rooted tree."); //Compute all tree heights: map heights; TreeTemplateTools::getHeights(*tree.getRootNode(), heights); unsigned int nClust = getNumberOfClusters_(tree.getRootNode(), heights); result_.setValue("NbClusters", nClust); } catch (bad_cast& e) { throw Exception("CountClustersMafStatistics::compute. A property was found for '" + treeProperty_ + "' but does not appear to contain a phylogenetic tree."); } } bpp-phyl-omics-2.2.0/src/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp000664 001750 001750 00000005377 12372454317 033374 0ustar00jdutheiljdutheil000000 000000 // // File: DistanceBasedPhylogenyReconstructionMafIterator.cpp // Created by: Julien Dutheil // Created on: Jul 24 2012 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to test the homogeneity of the substitution process of a given alignment. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ #include "DistanceBasedPhylogenyReconstructionMafIterator.h" #include using namespace bpp; using namespace std; Tree* DistanceBasedPhylogenyReconstructionMafIterator::buildTreeForBlock(const MafBlock& block) throw (Exception) { //First get the distance matrix for this block: if (!block.hasProperty(distanceProperty_)) throw Exception("DistanceBasedPhylogenyReconstructionMafIterator::buildTreeForBlock. No property available for " + distanceProperty_); try { const DistanceMatrix& dist = dynamic_cast(block.getProperty(distanceProperty_)); builder_->setDistanceMatrix(dist); builder_->computeTree(); Tree* tree = builder_->getTree(); if (!tree) throw Exception("DistanceBasedPhylogenyReconstructionMafIterator::buildTreeForBlock. Tree reconstruction failed!"); return tree; } catch (bad_cast& e) { throw Exception("DistanceBasedPhylogenyReconstructionMafIterator::buildTreeForBlock. A property was found for '" + distanceProperty_ + "' but does not appear to contain a distance matrix."); } } bpp-phyl-omics-2.2.0/src/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.h000664 001750 001750 00000007467 12372454317 027154 0ustar00jdutheiljdutheil000000 000000 // // File: TreeManipulationMafIterators.h // Created by: Julien Dutheil // Created on: Jul 24 2012 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to test the homogeneity of the substitution process of a given alignment. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ #ifndef _TREEMANIPULATIONMAFITERATOR_H_ #define _TREEMANIPULATIONMAFITERATOR_H_ #include //From bpp-phyl: #include namespace bpp { /** * @brief This iterator root associated trees according to an outgroup sequence. */ class TreeManipulationMafIterator: public AbstractFilterMafIterator { private: std::string treePropertyRead_; std::string treePropertyWrite_; public: //Write can be the same as read. TreeManipulationMafIterator(MafIterator* iterator, const std::string& treePropertyRead, const std::string& treePropertyWrite) : AbstractFilterMafIterator(iterator), treePropertyRead_(treePropertyRead), treePropertyWrite_(treePropertyWrite) {} public: MafBlock* analyseCurrentBlock_() throw (Exception); protected: virtual void manipulateTree_(TreeTemplate* tree) throw (Exception) = 0; }; /** * @brief This iterator root associated trees according to an outgroup sequence. */ class NewOutgroupMafIterator: public TreeManipulationMafIterator { private: std::string outgroupSpecies_; public: //Write can be the same as read. NewOutgroupMafIterator(MafIterator* iterator, const std::string& treePropertyRead, const std::string& treePropertyWrite, const std::string& outgroupSpecies) : TreeManipulationMafIterator(iterator, treePropertyRead, treePropertyWrite), outgroupSpecies_(outgroupSpecies) {} private: void manipulateTree_(TreeTemplate* tree) throw (Exception); }; /** * @brief This iterator removes leaves of a certain species in an attached tree. */ class DropSpeciesMafIterator: public TreeManipulationMafIterator { private: std::string species_; public: //Write can be the same as read. DropSpeciesMafIterator(MafIterator* iterator, const std::string& treePropertyRead, const std::string& treePropertyWrite, const std::string& species) : TreeManipulationMafIterator(iterator, treePropertyRead, treePropertyWrite), species_(species) {} private: void manipulateTree_(TreeTemplate* tree) throw (Exception); }; } //end of namespace bpp. #endif //_TREEMANIPULATIONMAFITERATOR_H_ bpp-phyl-omics-2.2.0/src/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.h000664 001750 001750 00000011144 12411254450 032613 0ustar00jdutheiljdutheil000000 000000 // // File: MaximumLikelihoodDistanceEstimationMafIterators.h // Created by: Julien Dutheil // Created on: Nov 13 2012 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to test the homogeneity of the substitution process of a given alignment. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ #ifndef _MAXIMUMLIKELIHOODDISTANCEESTIMATIONMAFITERATOR_H_ #define _MAXIMUMLIKELIHOODDISTANCEESTIMATIONMAFITERATOR_H_ #include "AbstractDistanceEstimationMafIterator.h" //From bpp-phyl: #include namespace bpp { /** * @brief Compute A simple distance using observed counts. */ class MaximumLikelihoodDistanceEstimationMafIterator: public AbstractDistanceEstimationMafIterator { private: std::auto_ptr distEst_; double propGapsToKeep_; //Exclude sites with too many gaps bool gapsAsUnresolved_; //For most models, should be yes as they do not allow for gap characters std::string paramOpt_; public: /** * @brief Build a new distance estimation maf iterator, based on the DistanceEstimation class. * * @see DistanceEstimation * @param iterator The input iterator. * @param distEst A DistanceEstimation object, initialized with an appropriate substitution model. * @param propGapsToKeep The maximum gapfrequency in a site to include it in the analysis. * @param gapsAsUnresolved Tell if gap characters should be considered as unresolved states. In ost cases it should be set to true, as very few substitution models consider gaps as genuine states. * @param paramOpt Tell if substitution model parameters should be optimized in a pairwise manner or not. See OptimizationTools::estimateDistanceMatrix for more details. * @param verbose Tell if some information should be output in the default message stream. */ MaximumLikelihoodDistanceEstimationMafIterator(MafIterator* iterator, DistanceEstimation* distEst, double propGapsToKeep = 0, bool gapsAsUnresolved = true, const string& paramOpt = OptimizationTools::DISTANCEMETHOD_INIT, bool verbose = true): AbstractDistanceEstimationMafIterator(iterator), distEst_(distEst), propGapsToKeep_(propGapsToKeep), gapsAsUnresolved_(gapsAsUnresolved), paramOpt_(paramOpt) { setVerbose(verbose); distEst_->setVerbose(verbose ? 3 : 0); } private: MaximumLikelihoodDistanceEstimationMafIterator(const MaximumLikelihoodDistanceEstimationMafIterator& iterator): AbstractDistanceEstimationMafIterator(0), distEst_(0), propGapsToKeep_(iterator.propGapsToKeep_), gapsAsUnresolved_(iterator.gapsAsUnresolved_), paramOpt_(iterator.paramOpt_) {} MaximumLikelihoodDistanceEstimationMafIterator& operator=(const MaximumLikelihoodDistanceEstimationMafIterator& iterator) { distEst_.reset(); propGapsToKeep_ = iterator.propGapsToKeep_; gapsAsUnresolved_ = iterator.gapsAsUnresolved_; paramOpt_ = iterator.paramOpt_; return *this; } public: std::string getPropertyName() const { return "MLDistance"; } DistanceMatrix* estimateDistanceMatrixForBlock(const MafBlock& block); }; } //end of namespace bpp. #endif //_MAXIMUMLIKELIHOODDISTANCEESTIMATIONMAFITERATOR_H_ bpp-phyl-omics-2.2.0/src/Bpp/Seq/Io/Maf/OutputTreeMafIterator.cpp000664 001750 001750 00000004511 12372454317 026147 0ustar00jdutheiljdutheil000000 000000 // // File: OutputTreeMafIterator.cpp // Created by: Julien Dutheil // Created on: Jul 24 2012 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to test the homogeneity of the substitution process of a given alignment. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ #include "OutputTreeMafIterator.h" using namespace bpp; using namespace std; void OutputTreeMafIterator::writeBlock(std::ostream& out, const MafBlock& block) const { //First get the tree for this block: if (!block.hasProperty(treeProperty_)) throw Exception("OutputTreeAlignmentMafIterator::writeBlock. No property available for " + treeProperty_); try { const Tree& tree = dynamic_cast(block.getProperty(treeProperty_)); writer_.write(tree, out); } catch (bad_cast& e) { throw Exception("OutputTreeAlignmentMafIterator::writeBlock. A property was found for '" + treeProperty_ + "' but does not appear to contain a phylogenetic tree."); } } bpp-phyl-omics-2.2.0/src/Bpp/Seq/Io/Maf/AbstractDistanceEstimationMafIterator.h000664 001750 001750 00000006040 12411254450 030734 0ustar00jdutheiljdutheil000000 000000 // // File: AbstractDistanceEstimationMafIterator.h // Created by: Julien Dutheil // Created on: Jul 24 2012 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to test the homogeneity of the substitution process of a given alignment. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ #ifndef _ABSTRACTDISTANCEESTIMATIONMAFITERATOR_H_ #define _ABSTRACTDISTANCEESTIMATIONMAFITERATOR_H_ #include #include #include #include #include #include namespace bpp { /** * @brief Partial implementation for distance estimation iterator. * * This iterator calls a distance reconstruction method (to be implemented by the derivated class) * and store the resulting distance matrix as an associated block property for the block, * before forwarding it. */ class AbstractDistanceEstimationMafIterator: public AbstractFilterMafIterator { public: AbstractDistanceEstimationMafIterator(MafIterator* iterator): AbstractFilterMafIterator(iterator) {} private: MafBlock* analyseCurrentBlock_() throw (Exception) { MafBlock* block = iterator_->nextBlock(); if (!block) return 0; auto_ptr dist(estimateDistanceMatrixForBlock(*block)); block->setProperty(getPropertyName(), dist.release()); return block; } public: virtual std::string getPropertyName() const = 0; virtual DistanceMatrix* estimateDistanceMatrixForBlock(const MafBlock& block) = 0; }; } //end of namespace bpp. #endif // _ABSTRACTDISTANCEESTIMATIONMAFITERATOR_H_ bpp-phyl-omics-2.2.0/src/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp000664 001750 001750 00000004043 12372454317 030627 0ustar00jdutheiljdutheil000000 000000 // // File: CountDistanceEstimationMafIterators.cpp // Created by: Julien Dutheil // Created on: Jul 24 2012 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to test the homogeneity of the substitution process of a given alignment. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ #include "CountDistanceEstimationMafIterator.h" #include using namespace bpp; DistanceMatrix* CountDistanceEstimationMafIterator::estimateDistanceMatrixForBlock(const MafBlock& block) { DistanceMatrix* dist = SiteContainerTools::computeSimilarityMatrix(block.getAlignment(), true, gapOption_, unresolvedAsGap_); return dist; } bpp-phyl-omics-2.2.0/src/Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.h000664 001750 001750 00000005760 12372454317 030303 0ustar00jdutheiljdutheil000000 000000 // // File: CountDistanceEstimationMafIterators.h // Created by: Julien Dutheil // Created on: Jul 24 2012 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to test the homogeneity of the substitution process of a given alignment. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ #ifndef _COUNTDISTANCEESTIMATIONMAFITERATOR_H_ #define _COUNTDISTANCEESTIMATIONMAFITERATOR_H_ #include "AbstractDistanceEstimationMafIterator.h" namespace bpp { /** * @brief Compute A simple distance using observed counts. */ class CountDistanceEstimationMafIterator: public AbstractDistanceEstimationMafIterator { private: std::string gapOption_; bool unresolvedAsGap_; public: /** * @brief Build a new distance estimation maf iterator, based on the SiteContainerTools::computeSimilarityMatrix method. * * @see SiteContainerTools * @param iterator The input iterator. * @param gapOption How to deal with gaps. Option forawarded to the computeSimilarityMatrix method. * @param unresolvedAsGap Tell if unresolved characters should be considered as gaps. Option forawarded to the computeSimilarityMatrix method. */ CountDistanceEstimationMafIterator(MafIterator* iterator, const std::string& gapOption, bool unresolvedAsGap): AbstractDistanceEstimationMafIterator(iterator), gapOption_(gapOption), unresolvedAsGap_(unresolvedAsGap) {} public: std::string getPropertyName() const { return "CountDistance"; } DistanceMatrix* estimateDistanceMatrixForBlock(const MafBlock& block); }; } //end of namespace bpp. #endif //_COUNTDISTANCEESTIMATIONMAFITERATOR_H_ bpp-phyl-omics-2.2.0/src/Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.cpp000664 001750 001750 00000004615 12411254450 033153 0ustar00jdutheiljdutheil000000 000000 // // File: MaximumLikelihoodDistanceEstimationMafIterators.cpp // Created by: Julien Dutheil // Created on: Nov 13 2012 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to test the homogeneity of the substitution process of a given alignment. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ #include "MaximumLikelihoodDistanceEstimationMafIterator.h" //From bpp-seq: #include using namespace bpp; DistanceMatrix* MaximumLikelihoodDistanceEstimationMafIterator::estimateDistanceMatrixForBlock(const MafBlock& block) { //First we get the alignment: auto_ptr sites(SiteContainerTools::removeGapSites(block.getAlignment(), propGapsToKeep_)); if (gapsAsUnresolved_) SiteContainerTools::changeGapsToUnknownCharacters(*sites); //Set the data and fit the matrix: distEst_->setData(sites.get()); ParameterList p; auto_ptr mat(OptimizationTools::estimateDistanceMatrix(*distEst_, p, paramOpt_, verbose_)); return mat.release(); } bpp-phyl-omics-2.2.0/src/Bpp/Seq/Io/Maf/AbstractPhylogenyReconstructionMafIterator.h000664 001750 001750 00000005607 12372454317 032107 0ustar00jdutheiljdutheil000000 000000 // // File: AbstractPhylogenyReconstructionMafIterators.h // Created by: Julien Dutheil // Created on: Jul 24 2012 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to test the homogeneity of the substitution process of a given alignment. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ #ifndef _ABSTRACTPHYLOGENYRECONSTRUCTIONMAFITERATOR_H_ #define _ABSTRACTPHYLOGENYRECONSTRUCTIONMAFITERATOR_H_ #include #include namespace bpp { /** * @brief Partial implementation for phylogeny reconstruction iterator. * * This iterator calls a tree reconstruction method (to be implemented by the derivated class) * and store the resulting tree as an associated block property for the block, * before forwarding it. */ class AbstractPhylogenyReconstructionMafIterator: public AbstractFilterMafIterator { public: AbstractPhylogenyReconstructionMafIterator(MafIterator* iterator): AbstractFilterMafIterator(iterator) {} virtual ~AbstractPhylogenyReconstructionMafIterator() {} private: MafBlock* analyseCurrentBlock_() throw (Exception) { MafBlock* block = iterator_->nextBlock(); if (!block) return 0; Tree* tree = buildTreeForBlock(*block); block->setProperty(getPropertyName(), tree); return block; } public: virtual std::string getPropertyName() const = 0; virtual Tree* buildTreeForBlock(const MafBlock& block) = 0; }; } //end of namespace #endif //_ABSTRACTPHYLOGENYRECONSTRUCTIONMAFITERATOR_H_ bpp-phyl-omics-2.2.0/src/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.h000664 001750 001750 00000006460 12372454317 033033 0ustar00jdutheiljdutheil000000 000000 // // File: DistanceBasedPhylogenyReconstructionMafIterators.h // Created by: Julien Dutheil // Created on: Jul 24 2012 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to test the homogeneity of the substitution process of a given alignment. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ #ifndef _DISTANCEBASEDPHYLOGENYRECONSTRUCTIONMAFITERATOR_H_ #define _DISTANCEBASEDPHYLOGENYRECONSTRUCTIONMAFITERATOR_H_ #include "AbstractPhylogenyReconstructionMafIterator.h" #include namespace bpp { /** * @brief Implementation for distance-based phylogeny reconstruction iterator. */ class DistanceBasedPhylogenyReconstructionMafIterator: public AbstractPhylogenyReconstructionMafIterator { private: std::string distanceProperty_; std::auto_ptr builder_; public: DistanceBasedPhylogenyReconstructionMafIterator(MafIterator* iterator, DistanceMethod* method, const std::string& property): AbstractPhylogenyReconstructionMafIterator(iterator), distanceProperty_(property), builder_(method) {} private: DistanceBasedPhylogenyReconstructionMafIterator(const DistanceBasedPhylogenyReconstructionMafIterator& it): AbstractPhylogenyReconstructionMafIterator(0), distanceProperty_(it.distanceProperty_), builder_() {} DistanceBasedPhylogenyReconstructionMafIterator& operator=(const DistanceBasedPhylogenyReconstructionMafIterator& it) { distanceProperty_ = it.distanceProperty_; return *this; } public: void setDistanceProperty(const std::string& property) { distanceProperty_ = property; } const std::string& getDistanceProperty() const { return distanceProperty_; } std::string getPropertyName() const { return builder_->getName(); } Tree* buildTreeForBlock(const MafBlock& block) throw (Exception); }; } //end of namespace bpp. #endif //_DISTANCEBASEDPHYLOGENYRECONSTRUCTIONMAFITERATOR_H_ bpp-phyl-omics-2.2.0/INSTALL.txt000664 001750 001750 00000000700 12372454317 017716 0ustar00jdutheiljdutheil000000 000000 This software needs cmake >= 2.6 to build. After installing cmake, run it with the following command: cmake -DCMAKE_INSTALL_PREFIX=[where to install, for instance /usr/local or $HOME/.local] . If available, you can also use ccmake instead of cmake for a more user-friendly interface. Then compile and install the software with make install You may also consider installing and using the software checkinstall for easier system administration. bpp-phyl-omics-2.2.0/bpp-phyl-omics.spec000664 001750 001750 00000011717 12411254454 021572 0ustar00jdutheiljdutheil000000 000000 %define _basename bpp-phyl-omics %define _version 2.2.0 %define _release 1 %define _prefix /usr URL: http://biopp.univ-montp2.fr/ Name: %{_basename} Version: %{_version} Release: %{_release} License: CECILL-2.0 Vendor: The Bio++ Project Source: http://biopp.univ-montp2.fr/repos/sources/%{_basename}-%{_version}.tar.gz Summary: Bio++ Sequence library: genomics components Group: Development/Libraries/C and C++ Requires: bpp-core = %{_version} Requires: bpp-seq = %{_version} Requires: bpp-phyl = %{_version} Requires: bpp-seq-omics = %{_version} BuildRoot: %{_builddir}/%{_basename}-root BuildRequires: cmake >= 2.6.0 BuildRequires: gcc-c++ >= 4.0.0 BuildRequires: libbpp-core2 = %{_version} BuildRequires: libbpp-core-devel = %{_version} BuildRequires: libbpp-seq9 = %{_version} BuildRequires: libbpp-seq-devel = %{_version} BuildRequires: libbpp-phyl9 = %{_version} BuildRequires: libbpp-phyl-devel = %{_version} BuildRequires: libbpp-seq-omics1 = %{_version} BuildRequires: libbpp-seq-omics-devel = %{_version} AutoReq: yes AutoProv: yes %description This library contains the genomics components of the Bio++ phylogenetics library. It is part of the Bio++ project. %package -n libbpp-phyl-omics1 Summary: Bio++ Phylogenetics library: genomics components Group: Development/Libraries/C and C++ %description -n libbpp-phyl-omics1 This library contains the genomics components of the Bio++ phylogenetics library. It is part of the Bio++ project. %package -n libbpp-phyl-omics-devel Summary: Bio++ Phylogenetics library: genomics components Group: Development/Libraries/C and C++ Requires: libbpp-phyl-omics1 = %{_version} Requires: libbpp-seq9 = %{_version} Requires: libbpp-seq-devel = %{_version} Requires: libbpp-core2 = %{_version} Requires: libbpp-core-devel = %{_version} Requires: libbpp-phyl9 = %{_version} Requires: libbpp-phyl-devel = %{_version} Requires: libbpp-seq-omics1 = %{_version} Requires: libbpp-seq-omics-devel = %{_version} %description -n libbpp-phyl-omics-devel The libbpp-phyl-omics-devel package contains the header files and static libraries for building applications which use %{_basename}. %prep %setup -q %build CFLAGS="$RPM_OPT_FLAGS" CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=%{_prefix} -DBUILD_TESTING=OFF" if [ %{_lib} == 'lib64' ] ; then CMAKE_FLAGS="$CMAKE_FLAGS -DLIB_SUFFIX=64" fi cmake $CMAKE_FLAGS . make %install make DESTDIR=$RPM_BUILD_ROOT install %clean rm -rf $RPM_BUILD_ROOT %post -n libbpp-phyl-omics1 -p /sbin/ldconfig %post -n libbpp-phyl-omics-devel createGeneric() { echo "-- Creating generic include file: $1.all" #Make sure we run into subdirectories first: dirs=() for file in "$1"/* do if [ -d "$file" ] then # Recursion: dirs+=( "$file" ) fi done for dir in ${dirs[@]} do createGeneric $dir done #Now list all files, including newly created .all files: if [ -f $1.all ] then rm $1.all fi dir=`basename $1` for file in "$1"/* do if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] ) then file=`basename $file` echo "#include \"$dir/$file\"" >> $1.all fi done; } # Actualize .all files createGeneric %{_prefix}/include/Bpp exit 0 %preun -n libbpp-phyl-omics-devel removeGeneric() { if [ -f $1.all ] then echo "-- Remove generic include file: $1.all" rm $1.all fi for file in "$1"/* do if [ -d "$file" ] then # Recursion: removeGeneric $file fi done } # Actualize .all files removeGeneric %{_prefix}/include/Bpp exit 0 %postun -n libbpp-phyl-omics1 -p /sbin/ldconfig %postun -n libbpp-phyl-omics-devel createGeneric() { echo "-- Creating generic include file: $1.all" #Make sure we run into subdirectories first: dirs=() for file in "$1"/* do if [ -d "$file" ] then # Recursion: dirs+=( "$file" ) fi done for dir in ${dirs[@]} do createGeneric $dir done #Now list all files, including newly created .all files: if [ -f $1.all ] then rm $1.all fi dir=`basename $1` for file in "$1"/* do if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] ) then file=`basename $file` echo "#include \"$dir/$file\"" >> $1.all fi done; } # Actualize .all files createGeneric %{_prefix}/include/Bpp exit 0 %files -n libbpp-phyl-omics1 %defattr(-,root,root) %doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog %{_prefix}/%{_lib}/lib*.so.* %files -n libbpp-phyl-omics-devel %defattr(-,root,root) %doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog %{_prefix}/%{_lib}/lib*.so %{_prefix}/%{_lib}/lib*.a %{_prefix}/include/* %changelog * Fri Sep 26 2014 Julien Dutheil 2.2.0-1 - Added model fitting and parameter estimations. * Thu Mar 07 2013 Julien Dutheil 2.1.0-1 - Initial release. Contains tools to build phylogenies along a genome alignment (distance methods only for now). * Tue Nov 06 2012 Julien Dutheil 2.0.3-1 - First draft of the spec file. bpp-phyl-omics-2.2.0/COPYING.txt000664 001750 001750 00000051140 12372454317 017724 0ustar00jdutheiljdutheil000000 000000 CeCILL FREE SOFTWARE LICENSE AGREEMENT Notice This Agreement is a Free Software license agreement that is the result of discussions between its authors in order to ensure compliance with the two main principles guiding its drafting: * firstly, compliance with the principles governing the distribution of Free Software: access to source code, broad rights granted to users, * secondly, the election of a governing law, French law, with which it is conformant, both as regards the law of torts and intellectual property law, and the protection that it offers to both authors and holders of the economic rights over software. The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[logiciel] L[ibre]) license are: Commissariat à l'Energie Atomique - CEA, a public scientific, technical and industrial establishment, having its principal place of business at 31-33 rue de la Fédération, 75752 Paris cedex 15, France. Centre National de la Recherche Scientifique - CNRS, a public scientific and technological establishment, having its principal place of business at 3 rue Michel-Ange 75794 Paris cedex 16, France. Institut National de Recherche en Informatique et en Automatique - INRIA, a public scientific and technological establishment, having its principal place of business at Domaine de Voluceau, Rocquencourt, BP 105, 78153 Le Chesnay cedex, France. Preamble The purpose of this Free Software license agreement is to grant users the right to modify and redistribute the software governed by this license within the framework of an open source distribution model. The exercising of these rights is conditional upon certain obligations for users so as to preserve this status for all subsequent redistributions. In consideration of access to the source code and the rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors only have limited liability. In this respect, the risks associated with loading, using, modifying and/or developing or reproducing the software by the user are brought to the user's attention, given its Free Software status, which may make it complicated to use, with the result that its use is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the Software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions of security. This Agreement may be freely reproduced and published, provided it is not altered, and that no provisions are either added or removed herefrom. This Agreement may apply to any or all software for which the holder of the economic rights decides to submit the use thereof to its provisions. Article 1 - DEFINITIONS For the purpose of this Agreement, when the following expressions commence with a capital letter, they shall have the following meaning: Agreement: means this license agreement, and its possible subsequent versions and annexes. Software: means the software in its Object Code and/or Source Code form and, where applicable, its documentation, "as is" when the Licensee accepts the Agreement. 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Otherwise one should specify the include paths that # are normally passed to the compiler using the -I flag. STRIP_FROM_INC_PATH = ./src/ # If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter # (but less readable) file names. This can be useful if your file system # doesn't support long names like on DOS, Mac, or CD-ROM. SHORT_NAMES = NO # If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen # will interpret the first line (until the first dot) of a JavaDoc-style # comment as the brief description. If set to NO, the JavaDoc # comments will behave just like regular Qt-style comments # (thus requiring an explicit @brief command for a brief description.) JAVADOC_AUTOBRIEF = NO # If the QT_AUTOBRIEF tag is set to YES then Doxygen will # interpret the first line (until the first dot) of a Qt-style # comment as the brief description. If set to NO, the comments # will behave just like regular Qt-style comments (thus requiring # an explicit \brief command for a brief description.) QT_AUTOBRIEF = NO # The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen # treat a multi-line C++ special comment block (i.e. a block of //! or /// # comments) as a brief description. This used to be the default behaviour. # The new default is to treat a multi-line C++ comment block as a detailed # description. Set this tag to YES if you prefer the old behaviour instead. MULTILINE_CPP_IS_BRIEF = NO # If the INHERIT_DOCS tag is set to YES (the default) then an undocumented # member inherits the documentation from any documented member that it # re-implements. INHERIT_DOCS = YES # If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce # a new page for each member. If set to NO, the documentation of a member will # be part of the file/class/namespace that contains it. SEPARATE_MEMBER_PAGES = NO # The TAB_SIZE tag can be used to set the number of spaces in a tab. # Doxygen uses this value to replace tabs by spaces in code fragments. TAB_SIZE = 2 # This tag can be used to specify a number of aliases that acts # as commands in the documentation. An alias has the form "name=value". # For example adding "sideeffect=\par Side Effects:\n" will allow you to # put the command \sideeffect (or @sideeffect) in the documentation, which # will result in a user-defined paragraph with heading "Side Effects:". # You can put \n's in the value part of an alias to insert newlines. ALIASES = # This tag can be used to specify a number of word-keyword mappings (TCL only). # A mapping has the form "name=value". For example adding # "class=itcl::class" will allow you to use the command class in the # itcl::class meaning. TCL_SUBST = # Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C # sources only. Doxygen will then generate output that is more tailored for C. # For instance, some of the names that are used will be different. The list # of all members will be omitted, etc. OPTIMIZE_OUTPUT_FOR_C = NO # Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java # sources only. Doxygen will then generate output that is more tailored for # Java. For instance, namespaces will be presented as packages, qualified # scopes will look different, etc. OPTIMIZE_OUTPUT_JAVA = NO # Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran # sources only. Doxygen will then generate output that is more tailored for # Fortran. OPTIMIZE_FOR_FORTRAN = NO # Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL # sources. Doxygen will then generate output that is tailored for # VHDL. OPTIMIZE_OUTPUT_VHDL = NO # Doxygen selects the parser to use depending on the extension of the files it # parses. With this tag you can assign which parser to use for a given # extension. Doxygen has a built-in mapping, but you can override or extend it # using this tag. The format is ext=language, where ext is a file extension, # and language is one of the parsers supported by doxygen: IDL, Java, # Javascript, CSharp, C, C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, # C++. For instance to make doxygen treat .inc files as Fortran files (default # is PHP), and .f files as C (default is Fortran), use: inc=Fortran f=C. Note # that for custom extensions you also need to set FILE_PATTERNS otherwise the # files are not read by doxygen. EXTENSION_MAPPING = # If MARKDOWN_SUPPORT is enabled (the default) then doxygen pre-processes all # comments according to the Markdown format, which allows for more readable # documentation. See http://daringfireball.net/projects/markdown/ for details. # The output of markdown processing is further processed by doxygen, so you # can mix doxygen, HTML, and XML commands with Markdown formatting. # Disable only in case of backward compatibilities issues. MARKDOWN_SUPPORT = YES # When enabled doxygen tries to link words that correspond to documented classes, # or namespaces to their corresponding documentation. Such a link can be # prevented in individual cases by by putting a % sign in front of the word or # globally by setting AUTOLINK_SUPPORT to NO. AUTOLINK_SUPPORT = YES # If you use STL classes (i.e. std::string, std::vector, etc.) but do not want # to include (a tag file for) the STL sources as input, then you should # set this tag to YES in order to let doxygen match functions declarations and # definitions whose arguments contain STL classes (e.g. func(std::string); v.s. # func(std::string) {}). This also makes the inheritance and collaboration # diagrams that involve STL classes more complete and accurate. BUILTIN_STL_SUPPORT = YES # If you use Microsoft's C++/CLI language, you should set this option to YES to # enable parsing support. CPP_CLI_SUPPORT = NO # Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. # Doxygen will parse them like normal C++ but will assume all classes use public # instead of private inheritance when no explicit protection keyword is present. SIP_SUPPORT = NO # For Microsoft's IDL there are propget and propput attributes to indicate # getter and setter methods for a property. Setting this option to YES (the # default) will make doxygen replace the get and set methods by a property in # the documentation. This will only work if the methods are indeed getting or # setting a simple type. If this is not the case, or you want to show the # methods anyway, you should set this option to NO. IDL_PROPERTY_SUPPORT = YES # If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC # tag is set to YES, then doxygen will reuse the documentation of the first # member in the group (if any) for the other members of the group. By default # all members of a group must be documented explicitly. DISTRIBUTE_GROUP_DOC = NO # Set the SUBGROUPING tag to YES (the default) to allow class member groups of # the same type (for instance a group of public functions) to be put as a # subgroup of that type (e.g. under the Public Functions section). Set it to # NO to prevent subgrouping. Alternatively, this can be done per class using # the \nosubgrouping command. SUBGROUPING = YES # When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and # unions are shown inside the group in which they are included (e.g. using # @ingroup) instead of on a separate page (for HTML and Man pages) or # section (for LaTeX and RTF). INLINE_GROUPED_CLASSES = NO # When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and # unions with only public data fields or simple typedef fields will be shown # inline in the documentation of the scope in which they are defined (i.e. file, # namespace, or group documentation), provided this scope is documented. If set # to NO (the default), structs, classes, and unions are shown on a separate # page (for HTML and Man pages) or section (for LaTeX and RTF). INLINE_SIMPLE_STRUCTS = NO # When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum # is documented as struct, union, or enum with the name of the typedef. So # typedef struct TypeS {} TypeT, will appear in the documentation as a struct # with name TypeT. When disabled the typedef will appear as a member of a file, # namespace, or class. And the struct will be named TypeS. This can typically # be useful for C code in case the coding convention dictates that all compound # types are typedef'ed and only the typedef is referenced, never the tag name. TYPEDEF_HIDES_STRUCT = NO # The SYMBOL_CACHE_SIZE determines the size of the internal cache use to # determine which symbols to keep in memory and which to flush to disk. # When the cache is full, less often used symbols will be written to disk. # For small to medium size projects (<1000 input files) the default value is # probably good enough. For larger projects a too small cache size can cause # doxygen to be busy swapping symbols to and from disk most of the time # causing a significant performance penalty. # If the system has enough physical memory increasing the cache will improve the # performance by keeping more symbols in memory. Note that the value works on # a logarithmic scale so increasing the size by one will roughly double the # memory usage. The cache size is given by this formula: # 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0, # corresponding to a cache size of 2^16 = 65536 symbols. SYMBOL_CACHE_SIZE = 0 # Similar to the SYMBOL_CACHE_SIZE the size of the symbol lookup cache can be # set using LOOKUP_CACHE_SIZE. This cache is used to resolve symbols given # their name and scope. Since this can be an expensive process and often the # same symbol appear multiple times in the code, doxygen keeps a cache of # pre-resolved symbols. If the cache is too small doxygen will become slower. # If the cache is too large, memory is wasted. The cache size is given by this # formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range is 0..9, the default is 0, # corresponding to a cache size of 2^16 = 65536 symbols. LOOKUP_CACHE_SIZE = 0 #--------------------------------------------------------------------------- # Build related configuration options #--------------------------------------------------------------------------- # If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in # documentation are documented, even if no documentation was available. # Private class members and static file members will be hidden unless # the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES EXTRACT_ALL = YES # If the EXTRACT_PRIVATE tag is set to YES all private members of a class # will be included in the documentation. EXTRACT_PRIVATE = YES # If the EXTRACT_PACKAGE tag is set to YES all members with package or internal # scope will be included in the documentation. EXTRACT_PACKAGE = NO # If the EXTRACT_STATIC tag is set to YES all static members of a file # will be included in the documentation. EXTRACT_STATIC = YES # If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) # defined locally in source files will be included in the documentation. # If set to NO only classes defined in header files are included. EXTRACT_LOCAL_CLASSES = YES # This flag is only useful for Objective-C code. When set to YES local # methods, which are defined in the implementation section but not in # the interface are included in the documentation. # If set to NO (the default) only methods in the interface are included. EXTRACT_LOCAL_METHODS = NO # If this flag is set to YES, the members of anonymous namespaces will be # extracted and appear in the documentation as a namespace called # 'anonymous_namespace{file}', where file will be replaced with the base # name of the file that contains the anonymous namespace. By default # anonymous namespaces are hidden. EXTRACT_ANON_NSPACES = NO # If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all # undocumented members of documented classes, files or namespaces. # If set to NO (the default) these members will be included in the # various overviews, but no documentation section is generated. # This option has no effect if EXTRACT_ALL is enabled. HIDE_UNDOC_MEMBERS = NO # If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all # undocumented classes that are normally visible in the class hierarchy. # If set to NO (the default) these classes will be included in the various # overviews. This option has no effect if EXTRACT_ALL is enabled. HIDE_UNDOC_CLASSES = NO # If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all # friend (class|struct|union) declarations. # If set to NO (the default) these declarations will be included in the # documentation. HIDE_FRIEND_COMPOUNDS = NO # If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any # documentation blocks found inside the body of a function. # If set to NO (the default) these blocks will be appended to the # function's detailed documentation block. HIDE_IN_BODY_DOCS = NO # The INTERNAL_DOCS tag determines if documentation # that is typed after a \internal command is included. If the tag is set # to NO (the default) then the documentation will be excluded. # Set it to YES to include the internal documentation. INTERNAL_DOCS = NO # If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate # file names in lower-case letters. If set to YES upper-case letters are also # allowed. This is useful if you have classes or files whose names only differ # in case and if your file system supports case sensitive file names. Windows # and Mac users are advised to set this option to NO. CASE_SENSE_NAMES = YES # If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen # will show members with their full class and namespace scopes in the # documentation. If set to YES the scope will be hidden. HIDE_SCOPE_NAMES = NO # If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen # will put a list of the files that are included by a file in the documentation # of that file. SHOW_INCLUDE_FILES = YES # If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen # will list include files with double quotes in the documentation # rather than with sharp brackets. FORCE_LOCAL_INCLUDES = NO # If the INLINE_INFO tag is set to YES (the default) then a tag [inline] # is inserted in the documentation for inline members. INLINE_INFO = YES # If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen # will sort the (detailed) documentation of file and class members # alphabetically by member name. If set to NO the members will appear in # declaration order. SORT_MEMBER_DOCS = YES # If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the # brief documentation of file, namespace and class members alphabetically # by member name. If set to NO (the default) the members will appear in # declaration order. SORT_BRIEF_DOCS = NO # If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen # will sort the (brief and detailed) documentation of class members so that # constructors and destructors are listed first. If set to NO (the default) # the constructors will appear in the respective orders defined by # SORT_MEMBER_DOCS and SORT_BRIEF_DOCS. # This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO # and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO. SORT_MEMBERS_CTORS_1ST = NO # If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the # hierarchy of group names into alphabetical order. If set to NO (the default) # the group names will appear in their defined order. SORT_GROUP_NAMES = NO # If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be # sorted by fully-qualified names, including namespaces. If set to # NO (the default), the class list will be sorted only by class name, # not including the namespace part. # Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. # Note: This option applies only to the class list, not to the # alphabetical list. SORT_BY_SCOPE_NAME = NO # If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to # do proper type resolution of all parameters of a function it will reject a # match between the prototype and the implementation of a member function even # if there is only one candidate or it is obvious which candidate to choose # by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen # will still accept a match between prototype and implementation in such cases. STRICT_PROTO_MATCHING = NO # The GENERATE_TODOLIST tag can be used to enable (YES) or # disable (NO) the todo list. This list is created by putting \todo # commands in the documentation. GENERATE_TODOLIST = YES # The GENERATE_TESTLIST tag can be used to enable (YES) or # disable (NO) the test list. This list is created by putting \test # commands in the documentation. GENERATE_TESTLIST = NO # The GENERATE_BUGLIST tag can be used to enable (YES) or # disable (NO) the bug list. This list is created by putting \bug # commands in the documentation. GENERATE_BUGLIST = NO # The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or # disable (NO) the deprecated list. This list is created by putting # \deprecated commands in the documentation. GENERATE_DEPRECATEDLIST= YES # The ENABLED_SECTIONS tag can be used to enable conditional # documentation sections, marked by \if section-label ... \endif # and \cond section-label ... \endcond blocks. ENABLED_SECTIONS = # The MAX_INITIALIZER_LINES tag determines the maximum number of lines # the initial value of a variable or macro consists of for it to appear in # the documentation. If the initializer consists of more lines than specified # here it will be hidden. Use a value of 0 to hide initializers completely. # The appearance of the initializer of individual variables and macros in the # documentation can be controlled using \showinitializer or \hideinitializer # command in the documentation regardless of this setting. MAX_INITIALIZER_LINES = 30 # Set the SHOW_USED_FILES tag to NO to disable the list of files generated # at the bottom of the documentation of classes and structs. If set to YES the # list will mention the files that were used to generate the documentation. SHOW_USED_FILES = YES # Set the SHOW_FILES tag to NO to disable the generation of the Files page. # This will remove the Files entry from the Quick Index and from the # Folder Tree View (if specified). The default is YES. SHOW_FILES = YES # Set the SHOW_NAMESPACES tag to NO to disable the generation of the # Namespaces page. This will remove the Namespaces entry from the Quick Index # and from the Folder Tree View (if specified). The default is YES. SHOW_NAMESPACES = YES # The FILE_VERSION_FILTER tag can be used to specify a program or script that # doxygen should invoke to get the current version for each file (typically from # the version control system). Doxygen will invoke the program by executing (via # popen()) the command , where is the value of # the FILE_VERSION_FILTER tag, and is the name of an input file # provided by doxygen. Whatever the program writes to standard output # is used as the file version. See the manual for examples. FILE_VERSION_FILTER = # The LAYOUT_FILE tag can be used to specify a layout file which will be parsed # by doxygen. The layout file controls the global structure of the generated # output files in an output format independent way. To create the layout file # that represents doxygen's defaults, run doxygen with the -l option. # You can optionally specify a file name after the option, if omitted # DoxygenLayout.xml will be used as the name of the layout file. LAYOUT_FILE = # The CITE_BIB_FILES tag can be used to specify one or more bib files # containing the references data. This must be a list of .bib files. The # .bib extension is automatically appended if omitted. Using this command # requires the bibtex tool to be installed. See also # http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style # of the bibliography can be controlled using LATEX_BIB_STYLE. To use this # feature you need bibtex and perl available in the search path. Do not use # file names with spaces, bibtex cannot handle them. CITE_BIB_FILES = #--------------------------------------------------------------------------- # configuration options related to warning and progress messages #--------------------------------------------------------------------------- # The QUIET tag can be used to turn on/off the messages that are generated # by doxygen. Possible values are YES and NO. If left blank NO is used. QUIET = NO # The WARNINGS tag can be used to turn on/off the warning messages that are # generated by doxygen. Possible values are YES and NO. If left blank # NO is used. WARNINGS = YES # If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings # for undocumented members. If EXTRACT_ALL is set to YES then this flag will # automatically be disabled. WARN_IF_UNDOCUMENTED = YES # If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for # potential errors in the documentation, such as not documenting some # parameters in a documented function, or documenting parameters that # don't exist or using markup commands wrongly. WARN_IF_DOC_ERROR = YES # The WARN_NO_PARAMDOC option can be enabled to get warnings for # functions that are documented, but have no documentation for their parameters # or return value. If set to NO (the default) doxygen will only warn about # wrong or incomplete parameter documentation, but not about the absence of # documentation. WARN_NO_PARAMDOC = NO # The WARN_FORMAT tag determines the format of the warning messages that # doxygen can produce. The string should contain the $file, $line, and $text # tags, which will be replaced by the file and line number from which the # warning originated and the warning text. Optionally the format may contain # $version, which will be replaced by the version of the file (if it could # be obtained via FILE_VERSION_FILTER) WARN_FORMAT = "$file:$line: $text" # The WARN_LOGFILE tag can be used to specify a file to which warning # and error messages should be written. If left blank the output is written # to stderr. WARN_LOGFILE = #--------------------------------------------------------------------------- # configuration options related to the input files #--------------------------------------------------------------------------- # The INPUT tag can be used to specify the files and/or directories that contain # documented source files. You may enter file names like "myfile.cpp" or # directories like "/usr/src/myproject". Separate the files or directories # with spaces. INPUT = src # This tag can be used to specify the character encoding of the source files # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is # also the default input encoding. Doxygen uses libiconv (or the iconv built # into libc) for the transcoding. See http://www.gnu.org/software/libiconv for # the list of possible encodings. INPUT_ENCODING = UTF-8 # If the value of the INPUT tag contains directories, you can use the # FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp # and *.h) to filter out the source-files in the directories. If left # blank the following patterns are tested: # *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh # *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py # *.f90 *.f *.for *.vhd *.vhdl FILE_PATTERNS = *.h \ *.cpp # The RECURSIVE tag can be used to turn specify whether or not subdirectories # should be searched for input files as well. Possible values are YES and NO. # If left blank NO is used. RECURSIVE = YES # The EXCLUDE tag can be used to specify files and/or directories that should be # excluded from the INPUT source files. This way you can easily exclude a # subdirectory from a directory tree whose root is specified with the INPUT tag. # Note that relative paths are relative to the directory from which doxygen is # run. EXCLUDE = # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or # directories that are symbolic links (a Unix file system feature) are excluded # from the input. EXCLUDE_SYMLINKS = NO # If the value of the INPUT tag contains directories, you can use the # EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude # certain files from those directories. Note that the wildcards are matched # against the file with absolute path, so to exclude all test directories # for example use the pattern */test/* EXCLUDE_PATTERNS = # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names # (namespaces, classes, functions, etc.) that should be excluded from the # output. The symbol name can be a fully qualified name, a word, or if the # wildcard * is used, a substring. Examples: ANamespace, AClass, # AClass::ANamespace, ANamespace::*Test EXCLUDE_SYMBOLS = # The EXAMPLE_PATH tag can be used to specify one or more files or # directories that contain example code fragments that are included (see # the \include command). EXAMPLE_PATH = # If the value of the EXAMPLE_PATH tag contains directories, you can use the # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp # and *.h) to filter out the source-files in the directories. If left # blank all files are included. EXAMPLE_PATTERNS = # If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be # searched for input files to be used with the \include or \dontinclude # commands irrespective of the value of the RECURSIVE tag. # Possible values are YES and NO. If left blank NO is used. EXAMPLE_RECURSIVE = NO # The IMAGE_PATH tag can be used to specify one or more files or # directories that contain image that are included in the documentation (see # the \image command). IMAGE_PATH = # The INPUT_FILTER tag can be used to specify a program that doxygen should # invoke to filter for each input file. Doxygen will invoke the filter program # by executing (via popen()) the command , where # is the value of the INPUT_FILTER tag, and is the name of an # input file. Doxygen will then use the output that the filter program writes # to standard output. If FILTER_PATTERNS is specified, this tag will be # ignored. INPUT_FILTER = # The FILTER_PATTERNS tag can be used to specify filters on a per file pattern # basis. Doxygen will compare the file name with each pattern and apply the # filter if there is a match. The filters are a list of the form: # pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further # info on how filters are used. If FILTER_PATTERNS is empty or if # non of the patterns match the file name, INPUT_FILTER is applied. FILTER_PATTERNS = # If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using # INPUT_FILTER) will be used to filter the input files when producing source # files to browse (i.e. when SOURCE_BROWSER is set to YES). FILTER_SOURCE_FILES = NO # The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file # pattern. A pattern will override the setting for FILTER_PATTERN (if any) # and it is also possible to disable source filtering for a specific pattern # using *.ext= (so without naming a filter). This option only has effect when # FILTER_SOURCE_FILES is enabled. FILTER_SOURCE_PATTERNS = # If the USE_MD_FILE_AS_MAINPAGE tag refers to the name of a markdown file that # is part of the input, its contents will be placed on the main page (index.html). # This can be useful if you have a project on for instance GitHub and want reuse # the introduction page also for the doxygen output. USE_MDFILE_AS_MAINPAGE = #--------------------------------------------------------------------------- # configuration options related to source browsing #--------------------------------------------------------------------------- # If the SOURCE_BROWSER tag is set to YES then a list of source files will # be generated. Documented entities will be cross-referenced with these sources. # Note: To get rid of all source code in the generated output, make sure also # VERBATIM_HEADERS is set to NO. SOURCE_BROWSER = YES # Setting the INLINE_SOURCES tag to YES will include the body # of functions and classes directly in the documentation. INLINE_SOURCES = NO # Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct # doxygen to hide any special comment blocks from generated source code # fragments. Normal C, C++ and Fortran comments will always remain visible. STRIP_CODE_COMMENTS = YES # If the REFERENCED_BY_RELATION tag is set to YES # then for each documented function all documented # functions referencing it will be listed. REFERENCED_BY_RELATION = YES # If the REFERENCES_RELATION tag is set to YES # then for each documented function all documented entities # called/used by that function will be listed. REFERENCES_RELATION = YES # If the REFERENCES_LINK_SOURCE tag is set to YES (the default) # and SOURCE_BROWSER tag is set to YES, then the hyperlinks from # functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will # link to the source code. Otherwise they will link to the documentation. REFERENCES_LINK_SOURCE = YES # If the USE_HTAGS tag is set to YES then the references to source code # will point to the HTML generated by the htags(1) tool instead of doxygen # built-in source browser. The htags tool is part of GNU's global source # tagging system (see http://www.gnu.org/software/global/global.html). You # will need version 4.8.6 or higher. USE_HTAGS = NO # If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen # will generate a verbatim copy of the header file for each class for # which an include is specified. Set to NO to disable this. VERBATIM_HEADERS = YES #--------------------------------------------------------------------------- # configuration options related to the alphabetical class index #--------------------------------------------------------------------------- # If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index # of all compounds will be generated. Enable this if the project # contains a lot of classes, structs, unions or interfaces. ALPHABETICAL_INDEX = NO # If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then # the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns # in which this list will be split (can be a number in the range [1..20]) COLS_IN_ALPHA_INDEX = 5 # In case all classes in a project start with a common prefix, all # classes will be put under the same header in the alphabetical index. # The IGNORE_PREFIX tag can be used to specify one or more prefixes that # should be ignored while generating the index headers. IGNORE_PREFIX = #--------------------------------------------------------------------------- # configuration options related to the HTML output #--------------------------------------------------------------------------- # If the GENERATE_HTML tag is set to YES (the default) Doxygen will # generate HTML output. GENERATE_HTML = YES # The HTML_OUTPUT tag is used to specify where the HTML docs will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `html' will be used as the default path. HTML_OUTPUT = html # The HTML_FILE_EXTENSION tag can be used to specify the file extension for # each generated HTML page (for example: .htm,.php,.asp). If it is left blank # doxygen will generate files with .html extension. HTML_FILE_EXTENSION = .html # The HTML_HEADER tag can be used to specify a personal HTML header for # each generated HTML page. If it is left blank doxygen will generate a # standard header. Note that when using a custom header you are responsible # for the proper inclusion of any scripts and style sheets that doxygen # needs, which is dependent on the configuration options used. # It is advised to generate a default header using "doxygen -w html # header.html footer.html stylesheet.css YourConfigFile" and then modify # that header. Note that the header is subject to change so you typically # have to redo this when upgrading to a newer version of doxygen or when # changing the value of configuration settings such as GENERATE_TREEVIEW! HTML_HEADER = # The HTML_FOOTER tag can be used to specify a personal HTML footer for # each generated HTML page. If it is left blank doxygen will generate a # standard footer. HTML_FOOTER = # The HTML_STYLESHEET tag can be used to specify a user-defined cascading # style sheet that is used by each HTML page. It can be used to # fine-tune the look of the HTML output. If left blank doxygen will # generate a default style sheet. Note that it is recommended to use # HTML_EXTRA_STYLESHEET instead of this one, as it is more robust and this # tag will in the future become obsolete. HTML_STYLESHEET = # The HTML_EXTRA_STYLESHEET tag can be used to specify an additional # user-defined cascading style sheet that is included after the standard # style sheets created by doxygen. Using this option one can overrule # certain style aspects. This is preferred over using HTML_STYLESHEET # since it does not replace the standard style sheet and is therefor more # robust against future updates. Doxygen will copy the style sheet file to # the output directory. HTML_EXTRA_STYLESHEET = # The HTML_EXTRA_FILES tag can be used to specify one or more extra images or # other source files which should be copied to the HTML output directory. Note # that these files will be copied to the base HTML output directory. Use the # $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these # files. In the HTML_STYLESHEET file, use the file name only. Also note that # the files will be copied as-is; there are no commands or markers available. HTML_EXTRA_FILES = # The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. # Doxygen will adjust the colors in the style sheet and background images # according to this color. Hue is specified as an angle on a colorwheel, # see http://en.wikipedia.org/wiki/Hue for more information. # For instance the value 0 represents red, 60 is yellow, 120 is green, # 180 is cyan, 240 is blue, 300 purple, and 360 is red again. # The allowed range is 0 to 359. HTML_COLORSTYLE_HUE = 220 # The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of # the colors in the HTML output. For a value of 0 the output will use # grayscales only. A value of 255 will produce the most vivid colors. HTML_COLORSTYLE_SAT = 100 # The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to # the luminance component of the colors in the HTML output. Values below # 100 gradually make the output lighter, whereas values above 100 make # the output darker. The value divided by 100 is the actual gamma applied, # so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2, # and 100 does not change the gamma. HTML_COLORSTYLE_GAMMA = 80 # If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML # page will contain the date and time when the page was generated. Setting # this to NO can help when comparing the output of multiple runs. HTML_TIMESTAMP = YES # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML # documentation will contain sections that can be hidden and shown after the # page has loaded. HTML_DYNAMIC_SECTIONS = YES # With HTML_INDEX_NUM_ENTRIES one can control the preferred number of # entries shown in the various tree structured indices initially; the user # can expand and collapse entries dynamically later on. Doxygen will expand # the tree to such a level that at most the specified number of entries are # visible (unless a fully collapsed tree already exceeds this amount). # So setting the number of entries 1 will produce a full collapsed tree by # default. 0 is a special value representing an infinite number of entries # and will result in a full expanded tree by default. HTML_INDEX_NUM_ENTRIES = 100 # If the GENERATE_DOCSET tag is set to YES, additional index files # will be generated that can be used as input for Apple's Xcode 3 # integrated development environment, introduced with OSX 10.5 (Leopard). # To create a documentation set, doxygen will generate a Makefile in the # HTML output directory. Running make will produce the docset in that # directory and running "make install" will install the docset in # ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find # it at startup. # See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html # for more information. GENERATE_DOCSET = YES # When GENERATE_DOCSET tag is set to YES, this tag determines the name of the # feed. A documentation feed provides an umbrella under which multiple # documentation sets from a single provider (such as a company or product suite) # can be grouped. DOCSET_FEEDNAME = "Bio++ Phylogenetics Library - Omics components" # When GENERATE_DOCSET tag is set to YES, this tag specifies a string that # should uniquely identify the documentation set bundle. This should be a # reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen # will append .docset to the name. DOCSET_BUNDLE_ID = bpp.phyl.omics # When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely # identify the documentation publisher. This should be a reverse domain-name # style string, e.g. com.mycompany.MyDocSet.documentation. DOCSET_PUBLISHER_ID = org.doxygen.Publisher # The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher. DOCSET_PUBLISHER_NAME = Publisher # If the GENERATE_HTMLHELP tag is set to YES, additional index files # will be generated that can be used as input for tools like the # Microsoft HTML help workshop to generate a compiled HTML help file (.chm) # of the generated HTML documentation. GENERATE_HTMLHELP = NO # If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can # be used to specify the file name of the resulting .chm file. You # can add a path in front of the file if the result should not be # written to the html output directory. CHM_FILE = # If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can # be used to specify the location (absolute path including file name) of # the HTML help compiler (hhc.exe). If non-empty doxygen will try to run # the HTML help compiler on the generated index.hhp. HHC_LOCATION = # If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag # controls if a separate .chi index file is generated (YES) or that # it should be included in the master .chm file (NO). GENERATE_CHI = NO # If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING # is used to encode HtmlHelp index (hhk), content (hhc) and project file # content. CHM_INDEX_ENCODING = # If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag # controls whether a binary table of contents is generated (YES) or a # normal table of contents (NO) in the .chm file. BINARY_TOC = NO # The TOC_EXPAND flag can be set to YES to add extra items for group members # to the contents of the HTML help documentation and to the tree view. TOC_EXPAND = NO # If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and # QHP_VIRTUAL_FOLDER are set, an additional index file will be generated # that can be used as input for Qt's qhelpgenerator to generate a # Qt Compressed Help (.qch) of the generated HTML documentation. GENERATE_QHP = NO # If the QHG_LOCATION tag is specified, the QCH_FILE tag can # be used to specify the file name of the resulting .qch file. # The path specified is relative to the HTML output folder. QCH_FILE = # The QHP_NAMESPACE tag specifies the namespace to use when generating # Qt Help Project output. For more information please see # http://doc.trolltech.com/qthelpproject.html#namespace QHP_NAMESPACE = org.doxygen.Project # The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating # Qt Help Project output. For more information please see # http://doc.trolltech.com/qthelpproject.html#virtual-folders QHP_VIRTUAL_FOLDER = doc # If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to # add. For more information please see # http://doc.trolltech.com/qthelpproject.html#custom-filters QHP_CUST_FILTER_NAME = # The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the # custom filter to add. For more information please see # # Qt Help Project / Custom Filters. QHP_CUST_FILTER_ATTRS = # The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this # project's # filter section matches. # # Qt Help Project / Filter Attributes. QHP_SECT_FILTER_ATTRS = # If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can # be used to specify the location of Qt's qhelpgenerator. # If non-empty doxygen will try to run qhelpgenerator on the generated # .qhp file. QHG_LOCATION = # If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files # will be generated, which together with the HTML files, form an Eclipse help # plugin. To install this plugin and make it available under the help contents # menu in Eclipse, the contents of the directory containing the HTML and XML # files needs to be copied into the plugins directory of eclipse. The name of # the directory within the plugins directory should be the same as # the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before # the help appears. GENERATE_ECLIPSEHELP = NO # A unique identifier for the eclipse help plugin. When installing the plugin # the directory name containing the HTML and XML files should also have # this name. ECLIPSE_DOC_ID = org.doxygen.Project # The DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) # at top of each HTML page. The value NO (the default) enables the index and # the value YES disables it. Since the tabs have the same information as the # navigation tree you can set this option to NO if you already set # GENERATE_TREEVIEW to YES. DISABLE_INDEX = NO # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index # structure should be generated to display hierarchical information. # If the tag value is set to YES, a side panel will be generated # containing a tree-like index structure (just like the one that # is generated for HTML Help). For this to work a browser that supports # JavaScript, DHTML, CSS and frames is required (i.e. any modern browser). # Windows users are probably better off using the HTML help feature. # Since the tree basically has the same information as the tab index you # could consider to set DISABLE_INDEX to NO when enabling this option. GENERATE_TREEVIEW = YES # The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values # (range [0,1..20]) that doxygen will group on one line in the generated HTML # documentation. Note that a value of 0 will completely suppress the enum # values from appearing in the overview section. ENUM_VALUES_PER_LINE = 4 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be # used to set the initial width (in pixels) of the frame in which the tree # is shown. TREEVIEW_WIDTH = 250 # When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open # links to external symbols imported via tag files in a separate window. EXT_LINKS_IN_WINDOW = NO # Use this tag to change the font size of Latex formulas included # as images in the HTML documentation. The default is 10. Note that # when you change the font size after a successful doxygen run you need # to manually remove any form_*.png images from the HTML output directory # to force them to be regenerated. FORMULA_FONTSIZE = 10 # Use the FORMULA_TRANPARENT tag to determine whether or not the images # generated for formulas are transparent PNGs. Transparent PNGs are # not supported properly for IE 6.0, but are supported on all modern browsers. # Note that when changing this option you need to delete any form_*.png files # in the HTML output before the changes have effect. FORMULA_TRANSPARENT = YES # Enable the USE_MATHJAX option to render LaTeX formulas using MathJax # (see http://www.mathjax.org) which uses client side Javascript for the # rendering instead of using prerendered bitmaps. Use this if you do not # have LaTeX installed or if you want to formulas look prettier in the HTML # output. When enabled you may also need to install MathJax separately and # configure the path to it using the MATHJAX_RELPATH option. USE_MATHJAX = NO # When MathJax is enabled you can set the default output format to be used for # thA MathJax output. Supported types are HTML-CSS, NativeMML (i.e. MathML) and # SVG. The default value is HTML-CSS, which is slower, but has the best # compatibility. MATHJAX_FORMAT = HTML-CSS # When MathJax is enabled you need to specify the location relative to the # HTML output directory using the MATHJAX_RELPATH option. The destination # directory should contain the MathJax.js script. For instance, if the mathjax # directory is located at the same level as the HTML output directory, then # MATHJAX_RELPATH should be ../mathjax. The default value points to # the MathJax Content Delivery Network so you can quickly see the result without # installing MathJax. However, it is strongly recommended to install a local # copy of MathJax from http://www.mathjax.org before deployment. MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest # The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension # names that should be enabled during MathJax rendering. MATHJAX_EXTENSIONS = # When the SEARCHENGINE tag is enabled doxygen will generate a search box # for the HTML output. The underlying search engine uses javascript # and DHTML and should work on any modern browser. Note that when using # HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets # (GENERATE_DOCSET) there is already a search function so this one should # typically be disabled. For large projects the javascript based search engine # can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution. SEARCHENGINE = YES # When the SERVER_BASED_SEARCH tag is enabled the search engine will be # implemented using a web server instead of a web client using Javascript. # There are two flavours of web server based search depending on the # EXTERNAL_SEARCH setting. When disabled, doxygen will generate a PHP script for # searching and an index file used by the script. When EXTERNAL_SEARCH is # enabled the indexing and searching needs to be provided by external tools. # See the manual for details. SERVER_BASED_SEARCH = NO # When EXTERNAL_SEARCH is enabled doxygen will no longer generate the PHP # script for searching. Instead the search results are written to an XML file # which needs to be processed by an external indexer. Doxygen will invoke an # external search engine pointed to by the SEARCHENGINE_URL option to obtain # the search results. Doxygen ships with an example indexer (doxyindexer) and # search engine (doxysearch.cgi) which are based on the open source search engine # library Xapian. See the manual for configuration details. EXTERNAL_SEARCH = NO # The SEARCHENGINE_URL should point to a search engine hosted by a web server # which will returned the search results when EXTERNAL_SEARCH is enabled. # Doxygen ships with an example search engine (doxysearch) which is based on # the open source search engine library Xapian. See the manual for configuration # details. SEARCHENGINE_URL = # When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed # search data is written to a file for indexing by an external tool. With the # SEARCHDATA_FILE tag the name of this file can be specified. SEARCHDATA_FILE = searchdata.xml # When SERVER_BASED_SEARCH AND EXTERNAL_SEARCH are both enabled the # EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is # useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple # projects and redirect the results back to the right project. EXTERNAL_SEARCH_ID = # The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen # projects other than the one defined by this configuration file, but that are # all added to the same external search index. Each project needs to have a # unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id # of to a relative location where the documentation can be found. # The format is: EXTRA_SEARCH_MAPPINGS = id1=loc1 id2=loc2 ... EXTRA_SEARCH_MAPPINGS = #--------------------------------------------------------------------------- # configuration options related to the LaTeX output #--------------------------------------------------------------------------- # If the GENERATE_LATEX tag is set to YES (the default) Doxygen will # generate Latex output. GENERATE_LATEX = NO # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `latex' will be used as the default path. LATEX_OUTPUT = latex # The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be # invoked. If left blank `latex' will be used as the default command name. # Note that when enabling USE_PDFLATEX this option is only used for # generating bitmaps for formulas in the HTML output, but not in the # Makefile that is written to the output directory. LATEX_CMD_NAME = latex # The MAKEINDEX_CMD_NAME tag can be used to specify the command name to # generate index for LaTeX. If left blank `makeindex' will be used as the # default command name. MAKEINDEX_CMD_NAME = makeindex # If the COMPACT_LATEX tag is set to YES Doxygen generates more compact # LaTeX documents. This may be useful for small projects and may help to # save some trees in general. COMPACT_LATEX = NO # The PAPER_TYPE tag can be used to set the paper type that is used # by the printer. Possible values are: a4, letter, legal and # executive. If left blank a4wide will be used. PAPER_TYPE = a4wide # The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX # packages that should be included in the LaTeX output. EXTRA_PACKAGES = amsmath # The LATEX_HEADER tag can be used to specify a personal LaTeX header for # the generated latex document. The header should contain everything until # the first chapter. If it is left blank doxygen will generate a # standard header. Notice: only use this tag if you know what you are doing! LATEX_HEADER = # The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for # the generated latex document. The footer should contain everything after # the last chapter. If it is left blank doxygen will generate a # standard footer. Notice: only use this tag if you know what you are doing! LATEX_FOOTER = # The LATEX_EXTRA_FILES tag can be used to specify one or more extra images # or other source files which should be copied to the LaTeX output directory. # Note that the files will be copied as-is; there are no commands or markers # available. LATEX_EXTRA_FILES = # If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated # is prepared for conversion to pdf (using ps2pdf). The pdf file will # contain links (just like the HTML output) instead of page references # This makes the output suitable for online browsing using a pdf viewer. PDF_HYPERLINKS = NO # If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of # plain latex in the generated Makefile. Set this option to YES to get a # higher quality PDF documentation. USE_PDFLATEX = YES # If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. # command to the generated LaTeX files. This will instruct LaTeX to keep # running if errors occur, instead of asking the user for help. # This option is also used when generating formulas in HTML. LATEX_BATCHMODE = NO # If LATEX_HIDE_INDICES is set to YES then doxygen will not # include the index chapters (such as File Index, Compound Index, etc.) # in the output. LATEX_HIDE_INDICES = NO # If LATEX_SOURCE_CODE is set to YES then doxygen will include # source code with syntax highlighting in the LaTeX output. # Note that which sources are shown also depends on other settings # such as SOURCE_BROWSER. LATEX_SOURCE_CODE = NO # The LATEX_BIB_STYLE tag can be used to specify the style to use for the # bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See # http://en.wikipedia.org/wiki/BibTeX for more info. LATEX_BIB_STYLE = plain #--------------------------------------------------------------------------- # configuration options related to the RTF output #--------------------------------------------------------------------------- # If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output # The RTF output is optimized for Word 97 and may not look very pretty with # other RTF readers or editors. GENERATE_RTF = NO # The RTF_OUTPUT tag is used to specify where the RTF docs will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `rtf' will be used as the default path. RTF_OUTPUT = rtf # If the COMPACT_RTF tag is set to YES Doxygen generates more compact # RTF documents. This may be useful for small projects and may help to # save some trees in general. COMPACT_RTF = NO # If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated # will contain hyperlink fields. The RTF file will # contain links (just like the HTML output) instead of page references. # This makes the output suitable for online browsing using WORD or other # programs which support those fields. # Note: wordpad (write) and others do not support links. RTF_HYPERLINKS = NO # Load style sheet definitions from file. Syntax is similar to doxygen's # config file, i.e. a series of assignments. You only have to provide # replacements, missing definitions are set to their default value. RTF_STYLESHEET_FILE = # Set optional variables used in the generation of an rtf document. # Syntax is similar to doxygen's config file. RTF_EXTENSIONS_FILE = #--------------------------------------------------------------------------- # configuration options related to the man page output #--------------------------------------------------------------------------- # If the GENERATE_MAN tag is set to YES (the default) Doxygen will # generate man pages GENERATE_MAN = NO # The MAN_OUTPUT tag is used to specify where the man pages will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `man' will be used as the default path. MAN_OUTPUT = man # The MAN_EXTENSION tag determines the extension that is added to # the generated man pages (default is the subroutine's section .3) MAN_EXTENSION = .3 # If the MAN_LINKS tag is set to YES and Doxygen generates man output, # then it will generate one additional man file for each entity # documented in the real man page(s). These additional files # only source the real man page, but without them the man command # would be unable to find the correct page. The default is NO. MAN_LINKS = NO #--------------------------------------------------------------------------- # configuration options related to the XML output #--------------------------------------------------------------------------- # If the GENERATE_XML tag is set to YES Doxygen will # generate an XML file that captures the structure of # the code including all documentation. GENERATE_XML = NO # The XML_OUTPUT tag is used to specify where the XML pages will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `xml' will be used as the default path. XML_OUTPUT = xml # The XML_SCHEMA tag can be used to specify an XML schema, # which can be used by a validating XML parser to check the # syntax of the XML files. XML_SCHEMA = # The XML_DTD tag can be used to specify an XML DTD, # which can be used by a validating XML parser to check the # syntax of the XML files. XML_DTD = # If the XML_PROGRAMLISTING tag is set to YES Doxygen will # dump the program listings (including syntax highlighting # and cross-referencing information) to the XML output. Note that # enabling this will significantly increase the size of the XML output. XML_PROGRAMLISTING = YES #--------------------------------------------------------------------------- # configuration options related to the DOCBOOK output #--------------------------------------------------------------------------- # If the GENERATE_DOCBOOK tag is set to YES Doxygen will generate DOCBOOK files # that can be used to generate PDF. GENERATE_DOCBOOK = NO # The DOCBOOK_OUTPUT tag is used to specify where the DOCBOOK pages will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be put in # front of it. If left blank docbook will be used as the default path. DOCBOOK_OUTPUT = docbook #--------------------------------------------------------------------------- # configuration options for the AutoGen Definitions output #--------------------------------------------------------------------------- # If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will # generate an AutoGen Definitions (see autogen.sf.net) file # that captures the structure of the code including all # documentation. Note that this feature is still experimental # and incomplete at the moment. GENERATE_AUTOGEN_DEF = NO #--------------------------------------------------------------------------- # configuration options related to the Perl module output #--------------------------------------------------------------------------- # If the GENERATE_PERLMOD tag is set to YES Doxygen will # generate a Perl module file that captures the structure of # the code including all documentation. Note that this # feature is still experimental and incomplete at the # moment. GENERATE_PERLMOD = NO # If the PERLMOD_LATEX tag is set to YES Doxygen will generate # the necessary Makefile rules, Perl scripts and LaTeX code to be able # to generate PDF and DVI output from the Perl module output. PERLMOD_LATEX = NO # If the PERLMOD_PRETTY tag is set to YES the Perl module output will be # nicely formatted so it can be parsed by a human reader. This is useful # if you want to understand what is going on. On the other hand, if this # tag is set to NO the size of the Perl module output will be much smaller # and Perl will parse it just the same. PERLMOD_PRETTY = YES # The names of the make variables in the generated doxyrules.make file # are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. # This is useful so different doxyrules.make files included by the same # Makefile don't overwrite each other's variables. PERLMOD_MAKEVAR_PREFIX = #--------------------------------------------------------------------------- # Configuration options related to the preprocessor #--------------------------------------------------------------------------- # If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will # evaluate all C-preprocessor directives found in the sources and include # files. ENABLE_PREPROCESSING = YES # If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro # names in the source code. If set to NO (the default) only conditional # compilation will be performed. Macro expansion can be done in a controlled # way by setting EXPAND_ONLY_PREDEF to YES. MACRO_EXPANSION = NO # If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES # then the macro expansion is limited to the macros specified with the # PREDEFINED and EXPAND_AS_DEFINED tags. EXPAND_ONLY_PREDEF = NO # If the SEARCH_INCLUDES tag is set to YES (the default) the includes files # pointed to by INCLUDE_PATH will be searched when a #include is found. SEARCH_INCLUDES = YES # The INCLUDE_PATH tag can be used to specify one or more directories that # contain include files that are not input files but should be processed by # the preprocessor. INCLUDE_PATH = # You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard # patterns (like *.h and *.hpp) to filter out the header-files in the # directories. If left blank, the patterns specified with FILE_PATTERNS will # be used. INCLUDE_FILE_PATTERNS = # The PREDEFINED tag can be used to specify one or more macro names that # are defined before the preprocessor is started (similar to the -D option of # gcc). The argument of the tag is a list of macros of the form: name # or name=definition (no spaces). If the definition and the = are # omitted =1 is assumed. To prevent a macro definition from being # undefined via #undef or recursively expanded use the := operator # instead of the = operator. PREDEFINED = # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then # this tag can be used to specify a list of macro names that should be expanded. # The macro definition that is found in the sources will be used. # Use the PREDEFINED tag if you want to use a different macro definition that # overrules the definition found in the source code. EXPAND_AS_DEFINED = # If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then # doxygen's preprocessor will remove all references to function-like macros # that are alone on a line, have an all uppercase name, and do not end with a # semicolon, because these will confuse the parser if not removed. SKIP_FUNCTION_MACROS = YES #--------------------------------------------------------------------------- # Configuration::additions related to external references #--------------------------------------------------------------------------- # The TAGFILES option can be used to specify one or more tagfiles. For each # tag file the location of the external documentation should be added. The # format of a tag file without this location is as follows: # TAGFILES = file1 file2 ... # Adding location for the tag files is done as follows: # TAGFILES = file1=loc1 "file2 = loc2" ... # where "loc1" and "loc2" can be relative or absolute paths # or URLs. Note that each tag file must have a unique name (where the name does # NOT include the path). If a tag file is not located in the directory in which # doxygen is run, you must also specify the path to the tagfile here. TAGFILES = ../bpp-core/BppCore.tag=../../bpp-core/html/ \ ../bpp-seq/BppSeq.tag=../../bpp-seq/html/ \ ../bpp-phyl/BppPhyl.tag=../../bpp-phyl/html/ \ ../bpp-seq-omics/BppSeqOmics.tag=../../bpp-seq-omics/html/ # When a file name is specified after GENERATE_TAGFILE, doxygen will create # a tag file that is based on the input files it reads. GENERATE_TAGFILE = BppPhylOmics.tag # If the ALLEXTERNALS tag is set to YES all external classes will be listed # in the class index. If set to NO only the inherited external classes # will be listed. ALLEXTERNALS = NO # If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed # in the modules index. If set to NO, only the current project's groups will # be listed. EXTERNAL_GROUPS = YES # If the EXTERNAL_PAGES tag is set to YES all external pages will be listed # in the related pages index. If set to NO, only the current project's # pages will be listed. EXTERNAL_PAGES = YES # The PERL_PATH should be the absolute path and name of the perl script # interpreter (i.e. the result of `which perl'). PERL_PATH = /usr/bin/perl #--------------------------------------------------------------------------- # Configuration options related to the dot tool #--------------------------------------------------------------------------- # If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will # generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base # or super classes. Setting the tag to NO turns the diagrams off. Note that # this option also works with HAVE_DOT disabled, but it is recommended to # install and use dot, since it yields more powerful graphs. CLASS_DIAGRAMS = YES # You can define message sequence charts within doxygen comments using the \msc # command. Doxygen will then run the mscgen tool (see # http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the # documentation. 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DOT_FONTPATH = # If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen # will generate a graph for each documented class showing the direct and # indirect inheritance relations. Setting this tag to YES will force the # CLASS_DIAGRAMS tag to NO. CLASS_GRAPH = YES # If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen # will generate a graph for each documented class showing the direct and # indirect implementation dependencies (inheritance, containment, and # class references variables) of the class with other documented classes. COLLABORATION_GRAPH = YES # If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen # will generate a graph for groups, showing the direct groups dependencies GROUP_GRAPHS = YES # If the UML_LOOK tag is set to YES doxygen will generate inheritance and # collaboration diagrams in a style similar to the OMG's Unified Modeling # Language. 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So in most cases it will be better to enable caller # graphs for selected functions only using the \callergraph command. CALLER_GRAPH = NO # If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen # will generate a graphical hierarchy of all classes instead of a textual one. GRAPHICAL_HIERARCHY = YES # If the DIRECTORY_GRAPH and HAVE_DOT tags are set to YES # then doxygen will show the dependencies a directory has on other directories # in a graphical way. The dependency relations are determined by the #include # relations between the files in the directories. DIRECTORY_GRAPH = YES # The DOT_IMAGE_FORMAT tag can be used to set the image format of the images # generated by dot. Possible values are svg, png, jpg, or gif. # If left blank png will be used. If you choose svg you need to set # HTML_FILE_EXTENSION to xhtml in order to make the SVG files # visible in IE 9+ (other browsers do not have this requirement). DOT_IMAGE_FORMAT = png # If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to # enable generation of interactive SVG images that allow zooming and panning. # Note that this requires a modern browser other than Internet Explorer. # Tested and working are Firefox, Chrome, Safari, and Opera. For IE 9+ you # need to set HTML_FILE_EXTENSION to xhtml in order to make the SVG files # visible. Older versions of IE do not have SVG support. INTERACTIVE_SVG = NO # The tag DOT_PATH can be used to specify the path where the dot tool can be # found. If left blank, it is assumed the dot tool can be found in the path. DOT_PATH = # The DOTFILE_DIRS tag can be used to specify one or more directories that # contain dot files that are included in the documentation (see the # \dotfile command). DOTFILE_DIRS = # The MSCFILE_DIRS tag can be used to specify one or more directories that # contain msc files that are included in the documentation (see the # \mscfile command). MSCFILE_DIRS = # The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of # nodes that will be shown in the graph. If the number of nodes in a graph # becomes larger than this value, doxygen will truncate the graph, which is # visualized by representing a node as a red box. Note that doxygen if the # number of direct children of the root node in a graph is already larger than # DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note # that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH. DOT_GRAPH_MAX_NODES = 50 # The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the # graphs generated by dot. A depth value of 3 means that only nodes reachable # from the root by following a path via at most 3 edges will be shown. Nodes # that lay further from the root node will be omitted. Note that setting this # option to 1 or 2 may greatly reduce the computation time needed for large # code bases. Also note that the size of a graph can be further restricted by # DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction. MAX_DOT_GRAPH_DEPTH = 0 # Set the DOT_TRANSPARENT tag to YES to generate images with a transparent # background. This is disabled by default, because dot on Windows does not # seem to support this out of the box. Warning: Depending on the platform used, # enabling this option may lead to badly anti-aliased labels on the edges of # a graph (i.e. they become hard to read). DOT_TRANSPARENT = NO # Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output # files in one run (i.e. multiple -o and -T options on the command line). This # makes dot run faster, but since only newer versions of dot (>1.8.10) # support this, this feature is disabled by default. DOT_MULTI_TARGETS = YES # If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will # generate a legend page explaining the meaning of the various boxes and # arrows in the dot generated graphs. GENERATE_LEGEND = YES # If the DOT_CLEANUP tag is set to YES (the default) Doxygen will # remove the intermediate dot files that are used to generate # the various graphs. DOT_CLEANUP = YES bpp-phyl-omics-2.2.0/debian/rules000775 001750 001750 00000005405 12372454317 020360 0ustar00jdutheiljdutheil000000 000000 #!/usr/bin/make -f # -*- makefile -*- # Sample debian/rules that uses debhelper. # This file was originally written by Joey Hess and Craig Small. # As a special exception, when this file is copied by dh-make into a # dh-make output file, you may use that output file without restriction. # This special exception was added by Craig Small in version 0.37 of dh-make. # 24/01/10 Modification for use with CMake by Julien Dutheil. # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 # These are used for cross-compiling and for saving the configure script # from having to guess our platform (since we know it already) DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE) DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE) CFLAGS = -Wall -g ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) CFLAGS += -O0 else CFLAGS += -O2 endif # shared library versions version=`ls src/lib*.so.* | \ awk '{if (match($$0,/[0-9]+\.[0-9]+\.[0-9]+$$/)) print substr($$0,RSTART)}'` major=`ls src/lib*.so.* | \ awk '{if (match($$0,/\.so\.[0-9]+$$/)) print substr($$0,RSTART+4)}'` configure: cmake -DCMAKE_INSTALL_PREFIX=/usr -DBUILD_TESTING=OFF . config.status: configure dh_testdir build: build-arch build-indep build-arch: build-stamp build-indep: build-stamp build-stamp: config.status dh_testdir # Add here commands to compile the package. $(MAKE) touch $@ clean: dh_testdir dh_testroot # Add here commands to clean up after the build process. [ ! -f Makefile ] || $(MAKE) clean; [ ! -f Makefile ] || rm Makefile; [ ! -f src/Makefile ] || rm src/Makefile; [ ! -f test/Makefile ] || rm test/Makefile; rm -f config.sub config.guess rm -f build-stamp rm -f CMakeCache.txt rm -f *.cmake rm -f src/*.cmake rm -f test/*.cmake rm -rf CMakeFiles rm -rf src/CMakeFiles rm -rf test/CMakeFiles rm -rf _CPack_Packages rm -rf Testing rm -f DartConfiguration.tcl dh_clean install: build dh_testdir dh_testroot dh_prep dh_installdirs # Add here commands to install the package into debian/tmp $(MAKE) DESTDIR=$(CURDIR)/debian/tmp install # Build architecture-independent files here. binary-indep: build install # We have nothing to do by default. # Build architecture-dependent files here. binary-arch: build install dh_testdir dh_testroot dh_installchangelogs ChangeLog dh_installdocs dh_installexamples dh_install # dh_installmenu # dh_installdebconf # dh_installlogrotate # dh_installemacsen # dh_installpam # dh_installmime # dh_installinit # dh_installcron # dh_installinfo dh_installman dh_link dh_strip dh_compress dh_fixperms # dh_perl # dh_python dh_makeshlibs dh_installdeb dh_shlibdeps dh_gencontrol dh_md5sums dh_builddeb binary: binary-indep binary-arch .PHONY: build clean binary-indep binary-arch binary install bpp-phyl-omics-2.2.0/debian/libbpp-phyl-omics-dev.install000664 001750 001750 00000000116 12372454317 024770 0ustar00jdutheiljdutheil000000 000000 debian/tmp/usr/include/* debian/tmp/usr/lib/lib*.a debian/tmp/usr/lib/lib*.so bpp-phyl-omics-2.2.0/debian/compat000664 001750 001750 00000000002 12372454317 020472 0ustar00jdutheiljdutheil000000 000000 5 bpp-phyl-omics-2.2.0/debian/copyright000664 001750 001750 00000005641 12411254454 021227 0ustar00jdutheiljdutheil000000 000000 This package was debianized by Julien Dutheil on Fri, 26 Sep 2014 14:00:00 +0100. It was downloaded from Upstream Author: Julien Dutheil Copyright: Copyright (C) 2014 Bio++ Development Team License: This package 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. This package 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 package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL'. The Debian packaging is (C) 2014, Julien Dutheil and is licensed under the GPL, see above. The provided software is distributed under the CeCILL license: This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. The complete text of the license may be found here: http://www.cecill.info/licences/Licence_CeCILL_V2-en.html bpp-phyl-omics-2.2.0/debian/libbpp-phyl-omics1.install000664 001750 001750 00000000035 12372454317 024275 0ustar00jdutheiljdutheil000000 000000 debian/tmp/usr/lib/lib*.so.* bpp-phyl-omics-2.2.0/debian/source/format000664 001750 001750 00000000014 12372454317 022002 0ustar00jdutheiljdutheil000000 000000 3.0 (quilt) bpp-phyl-omics-2.2.0/debian/changelog000664 001750 001750 00000001133 12411254454 021136 0ustar00jdutheiljdutheil000000 000000 libbpp-phyl-omics (2.2.0-1) unstable; urgency=low * Added model fitting and parameter estimations. -- Julien Dutheil Fri, 26 Sep 2014 14:00:00 +0100 libbpp-phyl-omics (2.1.0-1) unstable; urgency=low * Contain tools to apply phylogenetic method along a genome alignment. Only distance methods are implemented for now. -- Julien Dutheil Wed, 06 Mar 2013 14:34:00 +0100 libbpp-phyl-omics (2.0.3-1) unstable; urgency=low * Initial release. -- Julien Dutheil Tue, 06 Nov 2012 14:05:00 +0100 bpp-phyl-omics-2.2.0/debian/postinst000775 001750 001750 00000002062 12372454317 021105 0ustar00jdutheiljdutheil000000 000000 #! /bin/bash # Abort if any command returns an error value set -e createGeneric() { echo "-- Creating generic include file: $1.all" #Make sure we run into subdirectories first: dirs=() for file in "$1"/* do if [ -d "$file" ] then # Recursion: dirs+=( "$file" ) fi done for dir in ${dirs[@]} do createGeneric $dir done #Now list all files, including newly created .all files: if [ -f $1.all ] then rm $1.all fi dir=`basename $1` for file in "$1"/* do if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] ) then file=`basename $file` echo "#include \"$dir/$file\"" >> $1.all fi done; } case "$1" in configure) # Actualize .all files createGeneric /usr/include/Bpp ;; abort-upgrade|abort-remove|abort-deconfigure) echo "$1" ;; *) echo "postinst called with unknown argument \`\$1'" >&2 exit 0 ;; esac # dh_installdeb will replace this with shell code automatically # generated by other debhelper scripts. #DEBHELPER# exit 0 bpp-phyl-omics-2.2.0/debian/postrm000775 001750 001750 00000002171 12372454317 020547 0ustar00jdutheiljdutheil000000 000000 #! /bin/bash # Abort if any command returns an error value set -e createGeneric() { echo "-- Creating generic include file: $1.all" #Make sure we run into subdirectories first: dirs=() for file in "$1"/* do if [ -d "$file" ] then # Recursion: dirs+=( "$file" ) fi done for dir in ${dirs[@]} do createGeneric $dir done #Now list all files, including newly created .all files: if [ -f $1.all ] then rm $1.all fi dir=`basename $1` for file in "$1"/* do if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] ) then file=`basename $file` echo "#include \"$dir/$file\"" >> $1.all fi done; } case "$1" in remove) # Automatically added by dh_makeshlibs ldconfig # Actualize .all files createGeneric /usr/include/Bpp ;; purge|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear) echo $1 ;; *) echo "postrm called with unknown argument \`\$1'" >&2 exit 0 ;; esac # dh_installdeb will replace this with shell code automatically # generated by other debhelper scripts. #DEBHELPER# exit 0 bpp-phyl-omics-2.2.0/debian/control000664 001750 001750 00000001622 12411254454 020672 0ustar00jdutheiljdutheil000000 000000 Source: libbpp-phyl-omics Section: libs Priority: optional Maintainer: Loic Dachary Uploaders: Julien Dutheil Build-Depends: debhelper (>= 5), cmake (>= 2.6), libbpp-phyl-dev (>= 2.2.0), libbpp-seq-omics-dev (>= 2.2.0) Standards-Version: 3.9.4 Package: libbpp-phyl-omics-dev Section: libdevel Architecture: any Depends: libbpp-phyl-omics1 (= ${binary:Version}), ${misc:Depends}, libbpp-phyl-dev (>= 2.2.0), libbpp-seq-omics-dev (>= 2.2.0) Description: Bio++ Phylogenetics library: genomics components. Contains the Bio++ sequence classes dedicated to phylogenomics. Package: libbpp-phyl-omics1 Section: libs Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, libbpp-phyl9 (>= 2.2.0), libbpp-seq-omics1 (>= 2.2.0) Description: Bio++ Phylogenetics library: genomics components. Contains the Bio++ sequence classes dedicated to phylogenomics. bpp-phyl-omics-2.2.0/debian/prerm000775 001750 001750 00000001217 12372454317 020350 0ustar00jdutheiljdutheil000000 000000 #! /bin/bash # Abort if any command returns an error value set -e removeGeneric() { if [ -f $1.all ] then echo "-- Remove generic include file: $1.all" rm $1.all fi for file in "$1"/* do if [ -d "$file" ] then # Recursion: removeGeneric $file fi done } case "$1" in remove|upgrade|deconfigure) # Actualize .all files removeGeneric /usr/include/Bpp ;; failed-upgrade) echo "$1" ;; *) echo "prerm called with unknown argument \`$1'" >&2 exit 1 ;; esac # dh_installdeb will replace this with shell code automatically # generated by other debhelper scripts. #DEBHELPER# exit 0 bpp-phyl-omics-2.2.0/CMakeLists.txt000664 001750 001750 00000015076 12411254454 020615 0ustar00jdutheiljdutheil000000 000000 # CMake script for Bio++ Phylo(gen)-Omics library # Author: Sylvain Gaillard and Julien Dutheil # Created: 30/07/2012 # Global parameters CMAKE_MINIMUM_REQUIRED(VERSION 2.6) PROJECT(bpp-phyl-omics CXX) IF(NOT CMAKE_BUILD_TYPE) SET(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE) ENDIF(NOT CMAKE_BUILD_TYPE) SET(CMAKE_CXX_FLAGS "-Wall -Weffc++ -Wshadow -Wconversion") IF(NOT NO_VIRTUAL_COV) SET(NO_VIRTUAL_COV FALSE CACHE BOOL "Disable covariant return type with virtual inheritance, for compilers that do not support it." FORCE) ENDIF(NOT NO_VIRTUAL_COV) IF(NO_VIRTUAL_COV) MESSAGE("-- Covariant return with virtual inheritance disabled.") SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DNO_VIRTUAL_COV=1") ENDIF(NO_VIRTUAL_COV) IF(NOT NO_DEP_CHECK) SET(NO_DEP_CHECK FALSE CACHE BOOL "Disable dependencies check for building distribution only." FORCE) ENDIF(NOT NO_DEP_CHECK) IF(NO_DEP_CHECK) MESSAGE("-- Dependencies checking disabled. Only distribution can be built.") ELSE(NO_DEP_CHECK) # Libtool-like version number # CURRENT:REVISION:AGE => file.so.(C-A).A.R # current: The most recent interface number that this library implements. # revision: The implementation number of the current interface. # age: The difference between the newest and oldest interfaces that this # library implements. # In other words, the library implements all the interface numbers in the # range from number current - age to current. SET(BPPPHYLOMICS_VERSION_CURRENT "1") SET(BPPPHYLOMICS_VERSION_REVISION "0") SET(BPPPHYLOMICS_VERSION_AGE "0") # Effective version number computation math(EXPR BPPPHYLOMICS_VERSION_MAJOR "${BPPPHYLOMICS_VERSION_CURRENT} - ${BPPPHYLOMICS_VERSION_AGE}") SET(BPPPHYLOMICS_VERSION_MINOR ${BPPPHYLOMICS_VERSION_AGE}) SET(BPPPHYLOMICS_VERSION_PATCH ${BPPPHYLOMICS_VERSION_REVISION}) SET(BPPPHYLOMICS_VERSION "${BPPPHYLOMICS_VERSION_MAJOR}.${BPPPHYLOMICS_VERSION_MINOR}.${BPPPHYLOMICS_VERSION_PATCH}") # Set the CMAKE_PREFIX_PATH for the find_library fonction when using non # standard install location IF(CMAKE_INSTALL_PREFIX) SET(CMAKE_PREFIX_PATH "${CMAKE_INSTALL_PREFIX}" ${CMAKE_PREFIX_PATH}) ENDIF(CMAKE_INSTALL_PREFIX) MACRO(IMPROVED_FIND_LIBRARY OUTPUT_LIBS lib_name include_to_find) #start: FIND_PATH(${lib_name}_INCLUDE_DIR ${include_to_find} ) SET(${lib_name}_NAMES ${lib_name} ${lib_name}lib ${lib_name}dll) FIND_LIBRARY(${lib_name}_LIBRARY NAMES ${${lib_name}_NAMES} PATH_SUFFIXES lib${LIB_SUFFIX}) IF(${lib_name}_LIBRARY) MESSAGE("-- Library ${lib_name} found here:") MESSAGE(" includes : ${${lib_name}_INCLUDE_DIR}") MESSAGE(" libraries: ${${lib_name}_LIBRARY}") ELSE(${lib_name}_LIBRARY) MESSAGE(FATAL_ERROR "${lib_name} required but not found.") ENDIF(${lib_name}_LIBRARY) #add the dependency: INCLUDE_DIRECTORIES(${${lib_name}_INCLUDE_DIR}) SET(${OUTPUT_LIBS} ${${OUTPUT_LIBS}} ${${lib_name}_LIBRARY}) ENDMACRO(IMPROVED_FIND_LIBRARY) #Find the Bio++ libraries: IMPROVED_FIND_LIBRARY(LIBS bpp-core Bpp/Clonable.h) IMPROVED_FIND_LIBRARY(LIBS bpp-seq Bpp/Seq/Alphabet/Alphabet.h) IMPROVED_FIND_LIBRARY(LIBS bpp-seq-omics Bpp/Seq/Feature/SequenceFeature.h) IMPROVED_FIND_LIBRARY(LIBS bpp-phyl Bpp/Phyl/Tree.h) # Subdirectories ADD_SUBDIRECTORY(src) # Doxygen FIND_PACKAGE(Doxygen) IF (DOXYGEN_FOUND) ADD_CUSTOM_TARGET (apidoc cp Doxyfile ${CMAKE_BINARY_DIR}/Doxyfile-build COMMAND echo "OUTPUT_DIRECTORY=${CMAKE_BINARY_DIR}" >> ${CMAKE_BINARY_DIR}/Doxyfile-build COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_BINARY_DIR}/Doxyfile-build WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}) ADD_CUSTOM_TARGET (apidoc-stable cp Doxyfile ${CMAKE_BINARY_DIR}/Doxyfile-stable COMMAND echo "OUTPUT_DIRECTORY=${CMAKE_BINARY_DIR}" >> ${CMAKE_BINARY_DIR}/Doxyfile-stable COMMAND echo "HTML_HEADER=header.html" >> ${CMAKE_BINARY_DIR}/Doxyfile-stable COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_BINARY_DIR}/Doxyfile-stable WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}) ENDIF (DOXYGEN_FOUND) ENDIF(NO_DEP_CHECK) # Packager SET(CPACK_PACKAGE_NAME "libbpp-phyl-omics") SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team") SET(CPACK_PACKAGE_VERSION "2.2.0") SET(CPACK_PACKAGE_VERSION_MAJOR "2") SET(CPACK_PACKAGE_VERSION_MINOR "2") SET(CPACK_PACKAGE_VERSION_PATCH "0") SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Phylogen-Omics library") SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt") SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt") SET(CPACK_RESOURCE_FILE_INSTALL "${CMAKE_SOURCE_DIR}/INSTALL.txt") SET(CPACK_SOURCE_GENERATOR "TGZ") SET(CPACK_SOURCE_IGNORE_FILES "CMakeFiles" "Makefile" "_CPack_Packages" "CMakeCache.txt" ".*\\\\.cmake" ".*\\\\.git" ".*\\\\.gz" ".*\\\\.deb" ".*\\\\.rpm" ".*\\\\.dmg" ".*\\\\..*\\\\.swp" "src/\\\\..*" "src/libbpp*" "debian/tmp" "debian/libbpp.*/" "debian/libbpp.*\\\\.so.*" "debian/libbpp.*\\\\.a" "debian/libbpp.*\\\\.substvars" "debian/libbpp.*\\\\.debhelper" "debian/debhelper\\\\.log" "html" "PhylOmics.tag" "Testing" "build-stamp" "install_manifest.txt" "DartConfiguration.tcl" ${CPACK_SOURCE_IGNORE_FILES} ) IF (MACOS) SET(CPACK_GENERATOR "Bundle") ENDIF() SET(CPACK_SOURCE_PACKAGE_FILE_NAME "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}") SET(CPACK_DEBSOURCE_PACKAGE_FILE_NAME "lib${CMAKE_PROJECT_NAME}_${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}.orig") INCLUDE(CPack) #This adds the 'dist' target ADD_CUSTOM_TARGET(dist COMMAND ${CMAKE_MAKE_PROGRAM} package_source) # 'clean' is not (yet) a first class target. However, we need to clean the directories before building the sources: IF("${CMAKE_GENERATOR}" MATCHES "Make") ADD_CUSTOM_TARGET(make_clean COMMAND ${CMAKE_MAKE_PROGRAM} clean WORKING_DIRECTORY ${CMAKE_CURRENT_DIR} ) ADD_DEPENDENCIES(dist make_clean) ENDIF() IF(NOT NO_DEP_CHECK) IF (UNIX) #This creates deb packages: ADD_CUSTOM_TARGET(origdist COMMAND cp ${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz ../${CPACK_DEBSOURCE_PACKAGE_FILE_NAME}.tar.gz) ADD_DEPENDENCIES(origdist dist) ADD_CUSTOM_TARGET(deb dpkg-buildpackage -uc -us -i${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz) ADD_DEPENDENCIES(deb origdist) #This creates rpm packages: ADD_CUSTOM_TARGET(rpm rpmbuild -ta ${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz) ADD_DEPENDENCIES(rpm dist) ENDIF() SET(CTEST_UPDATE_TYPE git) SET(UPDATE_COMMAND "git") SET(UPDATE_OPTIONS "") #ENABLE_TESTING() #INCLUDE(CTest) #IF (BUILD_TESTING) # ADD_SUBDIRECTORY(test) #ENDIF(BUILD_TESTING) ENDIF(NOT NO_DEP_CHECK) bpp-phyl-omics-2.2.0/ChangeLog000664 001750 001750 00000000522 12411254454 017615 0ustar00jdutheiljdutheil000000 000000 26/09/14 -*- Version 2.2.0. -*- 04/06/14 Julien Dutheil * Added non-homogeneous model fitting. 12/04/14 Julien Dutheil * Added model fitting and parameter estimation. 07/03/13 -*- Version 2.1.0. -*- 21/01/13 Julien Dutheil * Compiles with -Wconversion *** See bpp-seq-omics ChangeLog for previous changes which might be relevent *** bpp-phyl-omics-2.2.0/AUTHORS.txt000664 001750 001750 00000000326 12372454317 017741 0ustar00jdutheiljdutheil000000 000000 Julien Dutheil Contributed code to Bio++ was enabled thanks to the following institutions and resources: 2010 - ISE-M UMR CNRS 5554 Université Montpellier 2 (Julien Dutheil) bpp-phyl-omics-2.2.0/genIncludes.py000664 001750 001750 00000000675 12372454317 020674 0ustar00jdutheiljdutheil000000 000000 #! /usr/bin/python import os; from os.path import *; import sys; for root, dirs, files in os.walk(sys.argv[1]): print "-- Creating generic include file: " + str(root) + ".all" f = open(str(root) + ".all", 'w') head, tail = split(root) files.sort() for file in files: base, ext = splitext(file) if (ext == ".h") or (ext == ".all"): f.write("#include \"" + tail + "/" + file + "\"\n") f.close()