├── .github
    └── workflows
    │   └── ci.yaml
├── .gitignore
├── .gitmodules
├── .vscode
    └── settings.json
├── .ycm_extra_conf.py
├── CMakeLists.txt
├── CMakeSettings.json
├── CODE_OF_CONDUCT.md
├── FindEigen3.cmake
├── LICENSE
├── README.md
├── alignment
    ├── CMakeLists.txt
    ├── alignment.cpp
    ├── alignment.h
    ├── alignmentpairwise.cpp
    ├── alignmentpairwise.h
    ├── alignmentsummary.cpp
    ├── alignmentsummary.h
    ├── maalignment.cpp
    ├── maalignment.h
    ├── pattern.cpp
    ├── pattern.h
    ├── sequence.cpp
    ├── sequence.h
    ├── sequencechunkstr.cpp
    ├── sequencechunkstr.h
    ├── substitution.cpp
    ├── substitution.h
    ├── superalignment.cpp
    ├── superalignment.h
    ├── superalignmentpairwise.cpp
    ├── superalignmentpairwise.h
    ├── superalignmentpairwiseplen.cpp
    ├── superalignmentpairwiseplen.h
    ├── superalignmentunlinked.cpp
    └── superalignmentunlinked.h
├── booster
    ├── CMakeLists.txt
    ├── Makefile
    ├── bitset_index.c
    ├── bitset_index.h
    ├── booster.c
    ├── booster.h
    ├── externs.h
    ├── hashmap.c
    ├── hashmap.h
    ├── hashtables_bfields.c
    ├── hashtables_bfields.h
    ├── io.c
    ├── io.h
    ├── prng.c
    ├── prng.h
    ├── sort.c
    ├── sort.h
    ├── stats.c
    ├── stats.h
    ├── test.c
    ├── tree.c
    ├── tree.h
    ├── tree_utils.c
    ├── tree_utils.h
    ├── version.c
    └── version.h
├── doc
    ├── html
    │   ├── bc_s.png
    │   ├── bdwn.png
    │   ├── closed.png
    │   ├── doc.png
    │   ├── doxygen.css
    │   ├── doxygen.svg
    │   ├── dynsections.js
    │   ├── folderclosed.png
    │   ├── folderopen.png
    │   ├── index.html
    │   ├── jquery.js
    │   ├── md__r_e_a_d_m_e.html
    │   ├── menu.js
    │   ├── menudata.js
    │   ├── nav_f.png
    │   ├── nav_g.png
    │   ├── nav_h.png
    │   ├── open.png
    │   ├── pages.html
    │   ├── search
    │   │   ├── all_0.html
    │   │   ├── all_0.js
    │   │   ├── close.svg
    │   │   ├── mag_sel.svg
    │   │   ├── nomatches.html
    │   │   ├── pages_0.html
    │   │   ├── pages_0.js
    │   │   ├── search.css
    │   │   ├── search.js
    │   │   ├── search_l.png
    │   │   ├── search_m.png
    │   │   ├── search_r.png
    │   │   └── searchdata.js
    │   ├── splitbar.png
    │   ├── sync_off.png
    │   ├── sync_on.png
    │   ├── tab_a.png
    │   ├── tab_b.png
    │   ├── tab_h.png
    │   ├── tab_s.png
    │   └── tabs.css
    └── latex
    │   ├── Makefile
    │   ├── doxygen.sty
    │   ├── longtable_doxygen.sty
    │   ├── md__r_e_a_d_m_e.tex
    │   ├── refman.tex
    │   └── tabu_doxygen.sty
├── example
    ├── custom_distributions.txt
    ├── example.cf
    ├── example.nex
    ├── example.phy
    ├── models.nex
    └── tree.nwk
├── flake.lock
├── flake.nix
├── gsl
    ├── CMakeLists.txt
    ├── binomial_tpe.cpp
    ├── gauss.cpp
    ├── gaussinv.cpp
    ├── gausspdf.cpp
    ├── gsl_nan.h
    ├── multinomial.cpp
    ├── mygsl.h
    ├── pow_int.cpp
    └── rat_eval.h
├── iqtree.doxy
├── iqtree_config.h.in
├── lbfgsb
    ├── CMakeLists.txt
    ├── lbfgsb_new.cpp
    └── lbfgsb_new.h
├── lib
    ├── libiomp5md.dll
    ├── libomp.a
    ├── libompstatic.a
    ├── pthreadGC2.dll
    ├── pthreadGC2_64.dll
    ├── pthreadVC2.dll
    └── pthreadVC2.lib
├── libmac
    └── libomp.a
├── libmac_m1
    └── libomp.a
├── main
    ├── CMakeLists.txt
    ├── alisim.cpp
    ├── alisim.h
    ├── main.cpp
    ├── phyloanalysis.cpp
    ├── phyloanalysis.h
    ├── phylotesting.cpp
    ├── phylotesting.h
    ├── terraceanalysis.cpp
    ├── terraceanalysis.h
    ├── timetree.cpp
    ├── timetree.h
    ├── treetesting.cpp
    └── treetesting.h
├── model
    ├── CMakeLists.txt
    ├── modelbin.cpp
    ├── modelbin.h
    ├── modelcodon.cpp
    ├── modelcodon.h
    ├── modelcodonempirical.cpp
    ├── modelcodonempirical.h
    ├── modelcodonmixture.cpp
    ├── modelcodonmixture.h
    ├── modelcodonparametric.cpp
    ├── modelcodonparametric.h
    ├── modelcodonsemiempirical.cpp
    ├── modelcodonsemiempirical.h
    ├── modeldna.cpp
    ├── modeldna.h
    ├── modeldnaerror.cpp
    ├── modeldnaerror.h
    ├── modelfactory.cpp
    ├── modelfactory.h
    ├── modelfactorymixlen.cpp
    ├── modelfactorymixlen.h
    ├── modelgtr.cpp
    ├── modelhmm.cpp
    ├── modelhmm.h
    ├── modelhmmgm.cpp
    ├── modelhmmgm.h
    ├── modelhmmtm.cpp
    ├── modelhmmtm.h
    ├── modelliemarkov.cpp
    ├── modelliemarkov.h
    ├── modelmarkov.cpp
    ├── modelmarkov.h
    ├── modelmixture.cpp
    ├── modelmixture.h
    ├── modelmorphology.cpp
    ├── modelmorphology.h
    ├── modelnonrev.cpp
    ├── modelnonrev.h
    ├── modelpomo.cpp
    ├── modelpomo.h
    ├── modelpomomixture.cpp
    ├── modelpomomixture.h
    ├── modelprotein.cpp
    ├── modelprotein.h
    ├── modelset.cpp
    ├── modelset.h
    ├── modelsubst.cpp
    ├── modelsubst.h
    ├── modelunrest.cpp
    ├── modelunrest.h
    ├── partitionmodel.cpp
    ├── partitionmodel.h
    ├── partitionmodelplen.cpp
    ├── partitionmodelplen.h
    ├── ratecontinuousgamma.cpp
    ├── ratecontinuousgamma.h
    ├── ratecontinuousgammainvar.cpp
    ├── ratecontinuousgammainvar.h
    ├── ratefree.cpp
    ├── ratefree.h
    ├── ratefreeinvar.cpp
    ├── ratefreeinvar.h
    ├── rategamma.cpp
    ├── rategamma.h
    ├── rategammainvar.cpp
    ├── rategammainvar.h
    ├── rateheterogeneity.cpp
    ├── rateheterogeneity.h
    ├── rateheterotachy.cpp
    ├── rateheterotachy.h
    ├── rateheterotachyinvar.cpp
    ├── rateheterotachyinvar.h
    ├── rateinvar.cpp
    ├── rateinvar.h
    ├── ratekategory.cpp
    ├── ratekategory.h
    ├── ratemeyerdiscrete.cpp
    ├── ratemeyerdiscrete.h
    ├── ratemeyerhaeseler.cpp
    └── ratemeyerhaeseler.h
├── ncl
    ├── CMakeLists.txt
    ├── ncl.h
    ├── nxsassumptionsblock.cpp
    ├── nxsassumptionsblock.h
    ├── nxsblock.cpp
    ├── nxsblock.h
    ├── nxscharactersblock.cpp
    ├── nxscharactersblock.h
    ├── nxsdatablock.cpp
    ├── nxsdatablock.h
    ├── nxsdefs.h
    ├── nxsdiscretedatum.cpp
    ├── nxsdiscretedatum.h
    ├── nxsdiscretematrix.cpp
    ├── nxsdiscretematrix.h
    ├── nxsdistancedatum.cpp
    ├── nxsdistancedatum.h
    ├── nxsdistancesblock.cpp
    ├── nxsdistancesblock.h
    ├── nxsemptyblock.cpp
    ├── nxsemptyblock.h
    ├── nxsexception.cpp
    ├── nxsexception.h
    ├── nxsindent.h
    ├── nxsreader.cpp
    ├── nxsreader.h
    ├── nxssetreader.cpp
    ├── nxssetreader.h
    ├── nxsstring.cpp
    ├── nxsstring.h
    ├── nxstaxablock.cpp
    ├── nxstaxablock.h
    ├── nxstoken.cpp
    ├── nxstoken.h
    ├── nxstreesblock.cpp
    └── nxstreesblock.h
├── nclextra
    ├── CMakeLists.txt
    ├── modelsblock.cpp
    ├── modelsblock.h
    ├── mpdablock.cpp
    ├── mpdablock.h
    ├── msetsblock.cpp
    ├── msetsblock.h
    ├── msplitsblock.cpp
    ├── msplitsblock.h
    └── myreader.h
├── nn
    ├── CMakeLists.txt
    ├── neuralnetwork.cpp
    └── neuralnetwork.h
├── nn_models
    ├── lanfear_alpha_lstm.onnx
    └── resnet_modelfinder.onnx
├── obsolete
    ├── gss.cpp
    ├── gss.h
    ├── guidedbootstrap.cpp
    ├── guidedbootstrap.h
    ├── ngs.cpp
    ├── ngs.h
    ├── parsmultistate.cpp
    └── parsmultistate.h
├── onnxruntimeConfig.cmake
├── pda
    ├── CMakeLists.txt
    ├── circularnetwork.cpp
    ├── circularnetwork.h
    ├── ecopd.cpp
    ├── ecopd.h
    ├── ecopdmtreeset.cpp
    ├── ecopdmtreeset.h
    ├── graph.cpp
    ├── graph.h
    ├── greedy.cpp
    ├── greedy.h
    ├── gurobiwrapper.cpp
    ├── gurobiwrapper.h
    ├── hashsplitset.cpp
    ├── hashsplitset.h
    ├── lpwrapper.c
    ├── lpwrapper.h
    ├── pdnetwork.cpp
    ├── pdnetwork.h
    ├── pdtree.cpp
    ├── pdtree.h
    ├── pdtreeset.cpp
    ├── pdtreeset.h
    ├── pruning.cpp
    ├── pruning.h
    ├── split.cpp
    ├── split.h
    ├── splitgraph.cpp
    ├── splitgraph.h
    ├── splitset.cpp
    └── splitset.h
├── phylo-yaml
    ├── CMakeLists.txt
    ├── statespace.cpp
    └── statespace.h
├── pll
    ├── CMakeLists.txt
    ├── alignment.c
    ├── avxLikelihood.c
    ├── bipartitionList.c
    ├── cycle.h
    ├── errcodes.h
    ├── evaluateGenericSpecial.c
    ├── evaluatePartialGenericSpecial.c
    ├── fastDNAparsimony.c
    ├── genericParallelization.c
    ├── genericParallelization.h
    ├── globalVariables.h
    ├── hardware.c
    ├── hardware.h
    ├── hash.c
    ├── hash.h
    ├── lexer.c
    ├── lexer.h
    ├── makenewzGenericSpecial.c
    ├── mem_alloc.c
    ├── mem_alloc.h
    ├── mic_native.h
    ├── mic_native_aa.c
    ├── mic_native_dna.c
    ├── models.c
    ├── newick.c
    ├── newick.h
    ├── newviewGenericSpecial.c
    ├── optimizeModel.c
    ├── parsePartition.c
    ├── parsePartition.h
    ├── parsimony.c
    ├── pll.h
    ├── pllInternal.h
    ├── pthread.h
    ├── queue.c
    ├── queue.h
    ├── randomTree.c
    ├── recom.c
    ├── restartHashTable.c
    ├── sched.h
    ├── searchAlgo.c
    ├── semaphore.h
    ├── ssort.c
    ├── stack.c
    ├── stack.h
    ├── systypes.h
    ├── topologies.c
    ├── trash.c
    ├── treeIO.c
    ├── treeIO.h
    └── utils.c
├── simulator
    ├── CMakeLists.txt
    ├── alisimulator.cpp
    ├── alisimulator.h
    ├── alisimulatorheterogeneity.cpp
    ├── alisimulatorheterogeneity.h
    ├── alisimulatorheterogeneityinvar.cpp
    ├── alisimulatorheterogeneityinvar.h
    ├── alisimulatorinvar.cpp
    └── alisimulatorinvar.h
├── sprng
    ├── CMakeLists.txt
    ├── README
    ├── checkid.c
    ├── interface.h
    ├── lcg64.c
    ├── makeseed.c
    ├── memory.c
    ├── memory.h
    ├── primelist-lcg64.h
    ├── primes-lcg64.c
    ├── primes-lcg64.h
    ├── sprng.h
    ├── store.c
    └── store.h
├── terrace
    ├── CMakeLists.txt
    ├── README.md
    ├── presenceabsencematrix.cpp
    ├── presenceabsencematrix.hpp
    ├── terrace.cpp
    ├── terrace.hpp
    ├── terracenode.cpp
    ├── terracenode.hpp
    ├── terracetree.cpp
    └── terracetree.hpp
├── terracetphast
    ├── CMakeLists.txt
    ├── terracetphast.cpp
    └── terracetphast.h
├── terraphast
    ├── .gitattributes
    ├── .gitignore
    ├── AUTHORS
    ├── CMakeLists.txt
    ├── LICENSE
    ├── README.md
    ├── app
    │   └── app.cpp
    ├── appveyor.yml
    ├── c_include
    │   └── terraces
    │   │   └── terraces.h
    ├── c_lib
    │   └── terraces.cpp
    ├── catch
    │   ├── LICENSE.txt
    │   └── catch.hpp
    ├── cmake
    │   └── FindGMP.cmake
    ├── documentation
    │   ├── Changelog.md
    │   ├── Dependencies.md
    │   └── walkthrough.md
    ├── doxygen.conf
    ├── include
    │   └── terraces
    │   │   ├── advanced.hpp
    │   │   ├── bigint.hpp
    │   │   ├── bitmatrix.hpp
    │   │   ├── clamped_uint.hpp
    │   │   ├── constraints.hpp
    │   │   ├── definitions.hpp
    │   │   ├── errors.hpp
    │   │   ├── parser.hpp
    │   │   ├── rooting.hpp
    │   │   ├── simple.hpp
    │   │   ├── subtree_extraction.hpp
    │   │   └── trees.hpp
    ├── lib
    │   ├── advanced.cpp
    │   ├── bigint.cpp
    │   ├── bipartitions.cpp
    │   ├── bipartitions.hpp
    │   ├── bitmatrix.cpp
    │   ├── bits.hpp
    │   ├── bitvector.hpp
    │   ├── cl
    │   │   └── intrinsics.hpp
    │   ├── clamped_uint.cpp
    │   ├── constraints.cpp
    │   ├── constraints_impl.hpp
    │   ├── errors.cpp
    │   ├── gcc_clang
    │   │   └── intrinsics.hpp
    │   ├── intel
    │   │   └── intrinsics.hpp
    │   ├── io_utils.hpp
    │   ├── multitree.cpp
    │   ├── multitree.hpp
    │   ├── multitree_impl.hpp
    │   ├── multitree_iterator.cpp
    │   ├── multitree_iterator.hpp
    │   ├── nodes.cpp
    │   ├── parser.cpp
    │   ├── ranked_bitvector.hpp
    │   ├── rooting.cpp
    │   ├── simple.cpp
    │   ├── small_bipartition.hpp
    │   ├── stack_allocator.hpp
    │   ├── subtree_extraction.cpp
    │   ├── subtree_extraction_impl.hpp
    │   ├── supertree_enumerator.hpp
    │   ├── supertree_helpers.cpp
    │   ├── supertree_helpers.hpp
    │   ├── supertree_variants.hpp
    │   ├── supertree_variants_debug.hpp
    │   ├── supertree_variants_multitree.hpp
    │   ├── trees.cpp
    │   ├── trees_impl.hpp
    │   ├── union_find.cpp
    │   ├── union_find.hpp
    │   ├── union_find_debug.hpp
    │   ├── utils.hpp
    │   ├── validation.cpp
    │   └── validation.hpp
    ├── scripts
    │   ├── build_appveyor.bat
    │   ├── format.sh
    │   ├── pre-commit
    │   ├── setup_workspace.sh
    │   └── setup_workspace_windows.sh
    ├── test
    │   ├── advanced.cpp
    │   ├── bipartitions.cpp
    │   ├── bitmatrix.cpp
    │   ├── bits.cpp
    │   ├── bitvector.cpp
    │   ├── c_api.cpp
    │   ├── clamped_uint.cpp
    │   ├── compile_test.cpp
    │   ├── constraints.cpp
    │   ├── fast_set.cpp
    │   ├── integration.cpp
    │   ├── main.cc
    │   ├── multitree_iterator.cpp
    │   ├── parser.cpp
    │   ├── rooting.cpp
    │   ├── simple.cpp
    │   ├── small_bipartition.cpp
    │   ├── stack_allocator.cpp
    │   ├── subtree_extraction.cpp
    │   ├── supertree.cpp
    │   ├── trees.cpp
    │   ├── union_find.cpp
    │   ├── util.cpp
    │   └── validation.cpp
    └── tools
    │   ├── isomorphic.cpp
    │   ├── nwk_to_dot.cpp
    │   ├── reroot.cpp
    │   ├── site_gen.cpp
    │   ├── subtree.cpp
    │   ├── tree_gen.cpp
    │   ├── validated_run.cpp
    │   └── verbose_run.cpp
├── test_scripts
    ├── README
    ├── compile.sh
    ├── gen_test_standard.py
    ├── gen_test_webserver.py
    ├── iqtree2.h
    ├── jobmanager.py
    ├── linux_universal.sh
    ├── make_linux_universal.sh
    ├── make_universal.sh
    ├── run_tests.sh
    ├── submit_jobs.sh
    ├── test_configs.txt
    ├── test_data
    │   ├── d59_8.nex
    │   ├── d59_8.phy
    │   ├── example.nex
    │   ├── example.phy
    │   └── prot_M126_27_269.phy
    └── unify-static-libs.sh
├── tree
    ├── CMakeLists.txt
    ├── candidateset.cpp
    ├── candidateset.h
    ├── constrainttree.cpp
    ├── constrainttree.h
    ├── discordance.cpp
    ├── genomenode.cpp
    ├── genomenode.h
    ├── genometree.cpp
    ├── genometree.h
    ├── iqtree.cpp
    ├── iqtree.h
    ├── iqtreemix.cpp
    ├── iqtreemix.h
    ├── iqtreemixhmm.cpp
    ├── iqtreemixhmm.h
    ├── matree.cpp
    ├── matree.h
    ├── memslot.cpp
    ├── memslot.h
    ├── mexttree.cpp
    ├── mexttree.h
    ├── mtree.cpp
    ├── mtree.h
    ├── mtreeset.cpp
    ├── mtreeset.h
    ├── ncbitree.cpp
    ├── ncbitree.h
    ├── node.cpp
    ├── node.h
    ├── parstree.cpp
    ├── parstree.h
    ├── phylohmm.cpp
    ├── phylohmm.h
    ├── phylokernel.h
    ├── phylokernelavx512.cpp
    ├── phylokernelfma.cpp
    ├── phylokernelmixrate.h
    ├── phylokernelmixture.h
    ├── phylokernelnew.h
    ├── phylokernelnonrev.cpp
    ├── phylokernelnonrev.h
    ├── phylokernelsafe.h
    ├── phylokernelsitemodel.cpp
    ├── phylokernelsitemodel.h
    ├── phylokernelsse.cpp
    ├── phylonode.cpp
    ├── phylonode.h
    ├── phylonodemixlen.cpp
    ├── phylonodemixlen.h
    ├── phylosuperhmm.cpp
    ├── phylosuperhmm.h
    ├── phylosupertree.cpp
    ├── phylosupertree.h
    ├── phylosupertreeplen.cpp
    ├── phylosupertreeplen.h
    ├── phylosupertreeunlinked.cpp
    ├── phylosupertreeunlinked.h
    ├── phylotree.cpp
    ├── phylotree.h
    ├── phylotreeavx.cpp
    ├── phylotreeeigen.cpp
    ├── phylotreemixlen.cpp
    ├── phylotreemixlen.h
    ├── phylotreepars.cpp
    ├── phylotreesse.cpp
    ├── quartet.cpp
    ├── supernode.cpp
    ├── supernode.h
    ├── tinatree.cpp
    ├── tinatree.h
    ├── upperbounds.cpp
    └── upperbounds.h
├── utils
    ├── CMakeLists.txt
    ├── MPIHelper.cpp
    ├── MPIHelper.h
    ├── ObjectStream.cpp
    ├── ObjectStream.h
    ├── TreeCollection.cpp
    ├── TreeCollection.h
    ├── bionj.cpp
    ├── bionj2.cpp
    ├── bionj2.h
    ├── checkpoint.cpp
    ├── checkpoint.h
    ├── decenttree.cpp
    ├── eigendecomposition.cpp
    ├── eigendecomposition.h
    ├── gzstream.cpp
    ├── gzstream.h
    ├── hammingdistance.h
    ├── heapsort.h
    ├── operatingsystem.cpp
    ├── operatingsystem.h
    ├── optimization.cpp
    ├── optimization.h
    ├── pllnni.cpp
    ├── pllnni.h
    ├── progress.cpp
    ├── progress.h
    ├── sse2neon.h
    ├── starttree.cpp
    ├── starttree.h
    ├── stoprule.cpp
    ├── stoprule.h
    ├── timeutil.h
    ├── tools.cpp
    └── tools.h
├── vectorclass
    ├── CMakeLists.txt
    ├── changelog.txt
    ├── instrset.h
    ├── instrset_detect.cpp
    ├── license.txt
    ├── vectorclass.h
    ├── vectorf128.h
    ├── vectorf256.h
    ├── vectorf256e.h
    ├── vectorf512.h
    ├── vectorf512e.h
    ├── vectorf64.h
    ├── vectori128.h
    ├── vectori256.h
    ├── vectori256e.h
    ├── vectori512.h
    ├── vectori512e.h
    ├── vectormath_common.h
    ├── vectormath_exp.h
    ├── vectormath_hyp.h
    ├── vectormath_lib.h
    └── vectormath_trig.h
├── whtest
    ├── CMakeLists.txt
    ├── eigen.c
    ├── eigen.h
    ├── eigen_sym.c
    ├── eigen_sym.h
    ├── random.c
    ├── random.h
    ├── weisslambda.c
    ├── weisslambda_sub.c
    ├── weisslambda_sub.h
    ├── whtest.c
    ├── whtest.h
    ├── whtest_sub.c
    ├── whtest_sub.h
    ├── whtest_wrapper.cpp
    ├── whtest_wrapper.h
    └── whtools.h
├── yaml-cpp
    ├── CMakeLists.txt
    ├── CONTRIBUTING.md
    ├── LICENSE
    ├── README.md
    ├── include
    │   └── yaml-cpp
    │   │   ├── anchor.h
    │   │   ├── binary.h
    │   │   ├── contrib
    │   │       ├── anchordict.h
    │   │       └── graphbuilder.h
    │   │   ├── dll.h
    │   │   ├── emitfromevents.h
    │   │   ├── emitter.h
    │   │   ├── emitterdef.h
    │   │   ├── emittermanip.h
    │   │   ├── emitterstyle.h
    │   │   ├── eventhandler.h
    │   │   ├── exceptions.h
    │   │   ├── mark.h
    │   │   ├── node
    │   │       ├── convert.h
    │   │       ├── detail
    │   │       │   ├── bool_type.h
    │   │       │   ├── impl.h
    │   │       │   ├── iterator.h
    │   │       │   ├── iterator_fwd.h
    │   │       │   ├── memory.h
    │   │       │   ├── node.h
    │   │       │   ├── node_data.h
    │   │       │   ├── node_iterator.h
    │   │       │   └── node_ref.h
    │   │       ├── emit.h
    │   │       ├── impl.h
    │   │       ├── iterator.h
    │   │       ├── node.h
    │   │       ├── parse.h
    │   │       ├── ptr.h
    │   │       └── type.h
    │   │   ├── noncopyable.h
    │   │   ├── null.h
    │   │   ├── ostream_wrapper.h
    │   │   ├── parser.h
    │   │   ├── stlemitter.h
    │   │   ├── traits.h
    │   │   └── yaml.h
    ├── install.txt
    ├── src
    │   ├── binary.cpp
    │   ├── collectionstack.h
    │   ├── contrib
    │   │   ├── graphbuilder.cpp
    │   │   ├── graphbuilderadapter.cpp
    │   │   ├── graphbuilderadapter.h
    │   │   ├── yaml-cpp.natvis
    │   │   └── yaml-cpp.natvis.md
    │   ├── convert.cpp
    │   ├── directives.cpp
    │   ├── directives.h
    │   ├── emit.cpp
    │   ├── emitfromevents.cpp
    │   ├── emitter.cpp
    │   ├── emitterstate.cpp
    │   ├── emitterstate.h
    │   ├── emitterutils.cpp
    │   ├── emitterutils.h
    │   ├── exceptions.cpp
    │   ├── exp.cpp
    │   ├── exp.h
    │   ├── indentation.h
    │   ├── memory.cpp
    │   ├── node.cpp
    │   ├── node_data.cpp
    │   ├── nodebuilder.cpp
    │   ├── nodebuilder.h
    │   ├── nodeevents.cpp
    │   ├── nodeevents.h
    │   ├── null.cpp
    │   ├── ostream_wrapper.cpp
    │   ├── parse.cpp
    │   ├── parser.cpp
    │   ├── ptr_vector.h
    │   ├── regex_yaml.cpp
    │   ├── regex_yaml.h
    │   ├── regeximpl.h
    │   ├── scanner.cpp
    │   ├── scanner.h
    │   ├── scanscalar.cpp
    │   ├── scanscalar.h
    │   ├── scantag.cpp
    │   ├── scantag.h
    │   ├── scantoken.cpp
    │   ├── setting.h
    │   ├── simplekey.cpp
    │   ├── singledocparser.cpp
    │   ├── singledocparser.h
    │   ├── stream.cpp
    │   ├── stream.h
    │   ├── streamcharsource.h
    │   ├── stringsource.h
    │   ├── tag.cpp
    │   ├── tag.h
    │   └── token.h
    ├── util
    │   ├── CMakeLists.txt
    │   ├── api.cpp
    │   ├── parse.cpp
    │   ├── read.cpp
    │   └── sandbox.cpp
    ├── yaml-cpp-config-version.cmake.in
    ├── yaml-cpp-config.cmake.in
    └── yaml-cpp.pc.cmake
└── zlib-1.2.7
    ├── CMakeLists.txt
    ├── ChangeLog
    ├── FAQ
    ├── INDEX
    ├── Makefile
    ├── Makefile.in
    ├── README
    ├── adler32.c
    ├── amiga
        ├── Makefile.pup
        └── Makefile.sas
    ├── as400
        ├── bndsrc
        ├── compile.clp
        ├── readme.txt
        └── zlib.inc
    ├── compress.c
    ├── configure
    ├── contrib
        ├── README.contrib
        ├── ada
        │   ├── buffer_demo.adb
        │   ├── mtest.adb
        │   ├── read.adb
        │   ├── readme.txt
        │   ├── test.adb
        │   ├── zlib-streams.adb
        │   ├── zlib-streams.ads
        │   ├── zlib-thin.adb
        │   ├── zlib-thin.ads
        │   ├── zlib.adb
        │   ├── zlib.ads
        │   └── zlib.gpr
        ├── amd64
        │   └── amd64-match.S
        ├── asm686
        │   ├── README.686
        │   └── match.S
        ├── blast
        │   ├── Makefile
        │   ├── README
        │   ├── blast.c
        │   ├── blast.h
        │   ├── test.pk
        │   └── test.txt
        ├── delphi
        │   ├── ZLib.pas
        │   ├── ZLibConst.pas
        │   ├── readme.txt
        │   └── zlibd32.mak
        ├── dotzlib
        │   ├── DotZLib.build
        │   ├── DotZLib.chm
        │   ├── DotZLib.sln
        │   ├── DotZLib
        │   │   ├── AssemblyInfo.cs
        │   │   ├── ChecksumImpl.cs
        │   │   ├── CircularBuffer.cs
        │   │   ├── CodecBase.cs
        │   │   ├── Deflater.cs
        │   │   ├── DotZLib.cs
        │   │   ├── DotZLib.csproj
        │   │   ├── GZipStream.cs
        │   │   ├── Inflater.cs
        │   │   └── UnitTests.cs
        │   ├── LICENSE_1_0.txt
        │   └── readme.txt
        ├── gcc_gvmat64
        │   └── gvmat64.S
        ├── infback9
        │   ├── README
        │   ├── infback9.c
        │   ├── infback9.h
        │   ├── inffix9.h
        │   ├── inflate9.h
        │   ├── inftree9.c
        │   └── inftree9.h
        ├── inflate86
        │   ├── inffas86.c
        │   └── inffast.S
        ├── iostream
        │   ├── test.cpp
        │   ├── zfstream.cpp
        │   └── zfstream.h
        ├── iostream2
        │   ├── zstream.h
        │   └── zstream_test.cpp
        ├── iostream3
        │   ├── README
        │   ├── TODO
        │   ├── test.cc
        │   ├── zfstream.cc
        │   └── zfstream.h
        ├── masmx64
        │   ├── bld_ml64.bat
        │   ├── gvmat64.asm
        │   ├── inffas8664.c
        │   ├── inffasx64.asm
        │   └── readme.txt
        ├── masmx86
        │   ├── bld_ml32.bat
        │   ├── inffas32.asm
        │   ├── match686.asm
        │   └── readme.txt
        ├── minizip
        │   ├── Makefile
        │   ├── Makefile.am
        │   ├── MiniZip64_Changes.txt
        │   ├── MiniZip64_info.txt
        │   ├── configure.ac
        │   ├── crypt.h
        │   ├── ioapi.c
        │   ├── ioapi.h
        │   ├── iowin32.c
        │   ├── iowin32.h
        │   ├── make_vms.com
        │   ├── miniunz.c
        │   ├── minizip.c
        │   ├── minizip.pc.in
        │   ├── mztools.c
        │   ├── mztools.h
        │   ├── unzip.c
        │   ├── unzip.h
        │   ├── zip.c
        │   └── zip.h
        ├── pascal
        │   ├── example.pas
        │   ├── readme.txt
        │   ├── zlibd32.mak
        │   └── zlibpas.pas
        ├── puff
        │   ├── Makefile
        │   ├── README
        │   ├── puff.c
        │   ├── puff.h
        │   ├── pufftest.c
        │   └── zeros.raw
        ├── testzlib
        │   ├── testzlib.c
        │   └── testzlib.txt
        ├── untgz
        │   ├── Makefile
        │   ├── Makefile.msc
        │   └── untgz.c
        └── vstudio
        │   ├── readme.txt
        │   ├── vc10
        │       ├── miniunz.vcxproj
        │       ├── miniunz.vcxproj.filters
        │       ├── miniunz.vcxproj.user
        │       ├── minizip.vcxproj
        │       ├── minizip.vcxproj.filters
        │       ├── minizip.vcxproj.user
        │       ├── testzlib.vcxproj
        │       ├── testzlib.vcxproj.filters
        │       ├── testzlib.vcxproj.user
        │       ├── testzlibdll.vcxproj
        │       ├── testzlibdll.vcxproj.filters
        │       ├── testzlibdll.vcxproj.user
        │       ├── zlib.rc
        │       ├── zlibstat.vcxproj
        │       ├── zlibstat.vcxproj.filters
        │       ├── zlibstat.vcxproj.user
        │       ├── zlibvc.def
        │       ├── zlibvc.sln
        │       ├── zlibvc.vcxproj
        │       ├── zlibvc.vcxproj.filters
        │       └── zlibvc.vcxproj.user
        │   └── vc9
        │       ├── miniunz.vcproj
        │       ├── minizip.vcproj
        │       ├── testzlib.vcproj
        │       ├── testzlibdll.vcproj
        │       ├── zlib.rc
        │       ├── zlibstat.vcproj
        │       ├── zlibvc.def
        │       ├── zlibvc.sln
        │       └── zlibvc.vcproj
    ├── crc32.c
    ├── crc32.h
    ├── deflate.c
    ├── deflate.h
    ├── doc
        ├── algorithm.txt
        ├── rfc1950.txt
        ├── rfc1951.txt
        ├── rfc1952.txt
        └── txtvsbin.txt
    ├── examples
        ├── README.examples
        ├── enough.c
        ├── fitblk.c
        ├── gun.c
        ├── gzappend.c
        ├── gzjoin.c
        ├── gzlog.c
        ├── gzlog.h
        ├── zlib_how.html
        ├── zpipe.c
        └── zran.c
    ├── gzclose.c
    ├── gzguts.h
    ├── gzlib.c
    ├── gzread.c
    ├── gzwrite.c
    ├── infback.c
    ├── inffast.c
    ├── inffast.h
    ├── inffixed.h
    ├── inflate.c
    ├── inflate.h
    ├── inftrees.c
    ├── inftrees.h
    ├── make_vms.com
    ├── msdos
        ├── Makefile.bor
        ├── Makefile.dj2
        ├── Makefile.emx
        ├── Makefile.msc
        └── Makefile.tc
    ├── nintendods
        ├── Makefile
        └── README
    ├── old
        ├── Makefile.emx
        ├── Makefile.riscos
        ├── README
        ├── descrip.mms
        ├── os2
        │   ├── Makefile.os2
        │   └── zlib.def
        └── visual-basic.txt
    ├── qnx
        └── package.qpg
    ├── test
        ├── example.c
        ├── infcover.c
        └── minigzip.c
    ├── treebuild.xml
    ├── trees.c
    ├── trees.h
    ├── uncompr.c
    ├── watcom
        ├── watcom_f.mak
        └── watcom_l.mak
    ├── win32
        ├── DLL_FAQ.txt
        ├── Makefile.bor
        ├── Makefile.gcc
        ├── Makefile.msc
        ├── README-WIN32.txt
        ├── VisualC.txt
        ├── zlib.def
        └── zlib1.rc
    ├── zconf.h.cmakein
    ├── zconf.h.in
    ├── zconf.h.included
    ├── zlib.3
    ├── zlib.3.pdf
    ├── zlib.h
    ├── zlib.map
    ├── zlib.pc.cmakein
    ├── zlib.pc.in
    ├── zlib2ansi
    ├── zutil.c
    └── zutil.h


/.gitignore:
--------------------------------------------------------------------------------
 1 | *~
 2 | .cproject
 3 | .settings
 4 | .project
 5 | examples
 6 | pll/CMakeFiles/
 7 | pll/Makefile
 8 | pll/cmake_install.cmake
 9 | pll/libpll.a
10 | pll_test/
11 | test_scripts/iqtree_release
12 | test_scripts/iqtree_test
13 | tags
14 | test_scripts/iqtree_test_cmds.txt
15 | pllrepo/
16 | build/
17 | /Default-clang
18 | .idea/
19 | .idea/codeStyleSettings.xml
20 | /GPATH
21 | /GRTAGS
22 | /GTAGS
23 | /.dir-locals.el
24 | /iqtree_config.h
25 | .DS_Store
26 | *.ipch
27 | *.log
28 | /.vs/
29 | example/
30 | sprng/
31 | terraphast/
32 | test_scripts/
33 | vectorclass/
34 | zlib-1.2.7/
35 | /.direnv/
36 | /.envrc
37 | 


--------------------------------------------------------------------------------
/.gitmodules:
--------------------------------------------------------------------------------
1 | [submodule "lsd2"]
2 | 	path = lsd2
3 | 	url = https://github.com/tothuhien/lsd2.git
4 | [submodule "cmaple"]
5 | 	path = cmaple
6 | 	url = https://github.com/trongnhanuit/cmaple.git
7 | 	branch = dev2_2
8 | 


--------------------------------------------------------------------------------
/.vscode/settings.json:
--------------------------------------------------------------------------------
1 | {
2 |     "cmake.configureOnOpen": true
3 | }


--------------------------------------------------------------------------------
/CMakeSettings.json:
--------------------------------------------------------------------------------
 1 | {
 2 |   "configurations": [
 3 |     {
 4 |       "name": "x64-Debug",
 5 |       "generator": "Ninja",
 6 |       "configurationType": "Debug",
 7 |       "inheritEnvironments": [ "clang_cl_x64" ],
 8 |       "buildRoot": "${projectDir}\\out\\build\\${name}",
 9 |       "installRoot": "${projectDir}\\out\\install\\${name}",
10 |       "cmakeCommandArgs": "-DEIGEN3_INCLUDE_DIR=C:\\Projects\\eigen-3.3.7 -DBoost_INCLUDE_DIR=C:\\Projects\\boost_1_73_0\\boost_1_73_0  -DIQTREE_FLAGS=mpi,fma -DMPI_DIR=c:\\Projects\\Microsoft_MPI_10_1_2",
11 |       "buildCommandArgs": "",
12 |       "ctestCommandArgs": "",
13 |       "variables": []
14 |     },
15 |     {
16 |       "name": "x64-Release",
17 |       "generator": "Ninja",
18 |       "configurationType": "RelWithDebInfo",
19 |       "buildRoot": "${projectDir}\\out\\build\\${name}",
20 |       "installRoot": "${projectDir}\\out\\install\\${name}",
21 |       "cmakeCommandArgs": "-DEIGEN3_INCLUDE_DIR=C:\\Projects\\eigen-3.3.7 -DBoost_INCLUDE_DIR=C:\\Projects\\boost_1_73_0\\boost_1_73_0  -DIQTREE_FLAGS=mpi,fma -DMPI_DIR=c:\\Projects\\Microsoft_MPI_10_1_2",
22 |       "buildCommandArgs": "",
23 |       "ctestCommandArgs": "",
24 |       "inheritEnvironments": [ "clang_cl_x64" ],
25 |       "variables": []
26 |     }
27 |   ]
28 | }


--------------------------------------------------------------------------------
/alignment/CMakeLists.txt:
--------------------------------------------------------------------------------
 1 | add_library(alignment
 2 | substitution.h
 3 | substitution.cpp
 4 | pattern.cpp
 5 | pattern.h
 6 | alignment.cpp
 7 | alignment.h
 8 | alignmentpairwise.cpp
 9 | alignmentpairwise.h
10 | alignmentsummary.cpp
11 | alignmentsummary.h
12 | maalignment.cpp
13 | maalignment.h
14 | superalignment.cpp
15 | superalignment.h
16 | superalignmentpairwise.cpp
17 | superalignmentpairwise.h
18 | superalignmentpairwiseplen.cpp
19 | superalignmentpairwiseplen.h
20 | superalignmentunlinked.cpp
21 | superalignmentunlinked.h
22 | sequence.cpp
23 | sequence.h
24 | sequencechunkstr.cpp
25 | sequencechunkstr.h
26 | )
27 | 
28 | target_link_libraries(alignment simulator ncl gsl model)
29 | 


--------------------------------------------------------------------------------
/alignment/sequence.cpp:
--------------------------------------------------------------------------------
 1 | #include "sequence.h"
 2 | 
 3 | Sequence::Sequence() {
 4 |     nums_children_done_simulation.resize(1);
 5 |     sequence_chunks.resize(1);
 6 |     num_threads_done_simulation = 0;
 7 |     num_threads_reach_barrier = 0;
 8 |     num_gaps = 0;
 9 |     depth = 0;
10 |     insertion_pos = NULL;
11 |     parent = NULL;
12 | }
13 | 
14 | 


--------------------------------------------------------------------------------
/alignment/sequence.h:
--------------------------------------------------------------------------------
 1 | #ifndef SEQUENCE_H
 2 | #define SEQUENCE_H
 3 | 
 4 | #include "utils/tools.h"
 5 | #include "tree/genometree.h"
 6 | 
 7 | using namespace std;
 8 | 
 9 | class Sequence {
10 | public:
11 |     
12 |     /**
13 |     chunks of sequence
14 |     */
15 |    vector<vector<short int>> sequence_chunks;
16 |    
17 |    /**
18 |        number of children which have completed simulating the sequence (for AliSim)
19 |     */
20 |    vector<short int> nums_children_done_simulation;
21 | 
22 |     
23 |     /**
24 |         number of OPENMP threads that completed simulating the sequence (for AliSim)
25 |      */
26 |     short int num_threads_done_simulation;
27 |     
28 |     /**
29 |         number of OPENMP threads reach a barrier
30 |      */
31 |     unsigned short int num_threads_reach_barrier;
32 |     
33 |     /**
34 |         pointer to the position of the insertion event that occurs after simulating sequence at this node
35 |      */
36 |     Insertion* insertion_pos;
37 |     
38 |     /**
39 |         parent node of the current node (only use when simulating Indels with AliSim)
40 |      */
41 |     Node* parent;
42 |     
43 |     /**
44 |         number of gaps in the sequence
45 |      */
46 |     int num_gaps;
47 |     
48 |     /**
49 |         depth of the current node
50 |      */
51 |     int depth;
52 | 
53 |     /**
54 |         constructor
55 |      */
56 |     Sequence();
57 |     
58 |     /**
59 |         deconstructor
60 |      */
61 |     ~Sequence() {
62 |         // do nothing, pointers should be deallocated by other tasks
63 |     }
64 | };
65 | 
66 | #endif
67 | 


--------------------------------------------------------------------------------
/alignment/sequencechunkstr.cpp:
--------------------------------------------------------------------------------
 1 | #include "sequencechunkstr.h"
 2 | 
 3 | SequenceChunkStr::SequenceChunkStr()
 4 | {
 5 |     chunk_status = EMPTY;
 6 |     pos = 0;
 7 |     chunk_str = "";
 8 | }
 9 | 
10 | SequenceChunkStr::~SequenceChunkStr()
11 | {
12 |     string().swap(chunk_str);
13 | }
14 | 


--------------------------------------------------------------------------------
/alignment/sequencechunkstr.h:
--------------------------------------------------------------------------------
 1 | #ifndef SEQUENCECHUNK_H
 2 | #define SEQUENCECHUNK_H
 3 | 
 4 | #include "utils/tools.h"
 5 | 
 6 | /** class storing a chunk of readable sequence waiting in writing queue */
 7 | class SequenceChunkStr {
 8 | public:
 9 |     SEQ_CHUNK_STATUS chunk_status;
10 |     int64_t pos;
11 |     string chunk_str;
12 |     
13 |     /**
14 |         constructor
15 |      */
16 |     SequenceChunkStr();
17 |     
18 |     /**
19 |         deconstructor
20 |      */
21 |     ~SequenceChunkStr();
22 |     
23 | };
24 | 
25 | #endif
26 | 


--------------------------------------------------------------------------------
/alignment/substitution.h:
--------------------------------------------------------------------------------
 1 | #ifndef SUBSTITUTION_H
 2 | #define SUBSTITUTION_H
 3 | 
 4 | #include "alignment.h"
 5 | 
 6 | /** class storing a substition (evolving from one state to another state) at a site */
 7 | class Substitution {
 8 | private:
 9 |     /**
10 |      The old state
11 |      */
12 |     short int old_state;
13 |     
14 |     /**
15 |      The new state
16 |      */
17 |     short int new_state;
18 |     
19 |     /**
20 |      Position where the substitution occurs
21 |      */
22 |     int position;
23 |     
24 |     /**
25 |      Parse a state from readable character(s)
26 |      */
27 |     int parseState(const std::string& old_state_str, Alignment* const aln) const;
28 |     
29 | public:
30 |     /**
31 |      Default constructor
32 |      */
33 |     // Substitution();
34 |     
35 |     /**
36 |      Custom constructor from a string
37 |      */
38 |     Substitution(const std::string& sub_str, Alignment* const aln, const int& seq_length);
39 |     
40 |     /**
41 |      Get the old state
42 |      */
43 |     short int getOldState() const;
44 |     
45 |     /**
46 |      Get the new state
47 |      */
48 |     short int getNewState() const;
49 |     
50 |     /**
51 |      Get the position
52 |      */
53 |     int getPosition() const;
54 | };
55 | 
56 | /** class storing a set of substitions */
57 | class Substitutions: public std::vector<Substitution> {
58 | public:
59 |     /**
60 |      Custom constructor from a string {<Sub>/.../<Sub>}
61 |      */
62 |     Substitutions(const std::string& sub_str, Alignment* const aln, const int& seq_length);
63 | };
64 | 
65 | #endif
66 | 


--------------------------------------------------------------------------------
/alignment/superalignmentpairwiseplen.cpp:
--------------------------------------------------------------------------------
 1 | //
 2 | //  superalignmentpairwiseplen.cpp
 3 | //  iqtree
 4 | //
 5 | //  Created by Olga on 04/05/17.
 6 | //
 7 | //
 8 | 
 9 | #include <stdio.h>
10 | #include "superalignmentpairwiseplen.h"
11 | 
12 | /**********************************************************
13 |  * class SuperAlignmentPairwisePlen
14 |  **********************************************************/
15 | 
16 | SuperAlignmentPairwisePlen::SuperAlignmentPairwisePlen(PhyloSuperTreePlen *atree, int seq1, int seq2)
17 | : SuperAlignmentPairwise((PhyloSuperTree*) atree, seq1, seq2)
18 | {
19 |     part_info = &(atree->part_info);
20 | }
21 | 
22 | double SuperAlignmentPairwisePlen::computeFunction(double value) {
23 |     int part = 0;
24 |     double lh = 0.0;
25 |     for (auto it = partitions.begin(); it != partitions.end(); it++, part++) {
26 |         lh += it->computeFunction(part_info->at(part).part_rate*value);
27 |     }
28 |     return lh;
29 | }
30 | 
31 | void SuperAlignmentPairwisePlen::computeFuncDerv(double value, double &df, double &ddf) {
32 |     int part = 0;
33 |     df = 0.0;
34 |     ddf = 0.0;
35 |     for (auto it = partitions.begin(); it != partitions.end(); it++, part++) {
36 |         double d1, d2;
37 |         it->computeFuncDerv(part_info->at(part).part_rate*value, d1, d2);
38 |         df += part_info->at(part).part_rate*d1;
39 |         ddf += part_info->at(part).part_rate*part_info->at(part).part_rate*d2;
40 |     }
41 | }
42 | 
43 | SuperAlignmentPairwisePlen::~SuperAlignmentPairwisePlen()
44 | {}
45 | 


--------------------------------------------------------------------------------
/booster/CMakeLists.txt:
--------------------------------------------------------------------------------
1 | add_library(booster
2 | bitset_index.c       hashmap.c            io.c                 sort.c               tree_utils.h
3 | bitset_index.h       hashmap.h            io.h                 sort.h               tree.c               
4 | booster.c            hashtables_bfields.c prng.c               stats.c              tree.h
5 | externs.h            hashtables_bfields.h prng.h               stats.h              tree_utils.c
6 | booster.h
7 | )
8 | 
9 | 


--------------------------------------------------------------------------------
/booster/Makefile:
--------------------------------------------------------------------------------
 1 | # Version of booster
 2 | GIT_VERSION := $(shell git describe --abbrev=10 --dirty --always --tags)
 3 | 
 4 | UNAME := $(shell uname)
 5 | 
 6 | CFLAGS = -Wall -g -O3 -DVERSION=\"$(GIT_VERSION)\"
 7 | CFLAGS_OMP = -Wall -g -fopenmp
 8 | 
 9 | # Compiler: gcc
10 | ifeq ($(cross),win32)
11 |         CC = i686-w64-mingw32-gcc
12 | else
13 | 	ifeq ($(cross),win64)
14 | 		CC = x86_64-w64-mingw32-gcc
15 | 	else
16 | 		ifeq ($(cross),linux32)
17 | 			CFLAGS_OMP += -m32
18 | 			CFLAGS += -m32
19 | 		else
20 | 			CC = gcc
21 | 		endif
22 | 	endif
23 | endif
24 | 
25 | ifeq ($(UNAME),Darwin)
26 | 	CFLAGS_OMP += -static-libgcc
27 | #else
28 | #	CFLAGS_OMP += -static
29 | endif
30 | 
31 | LIBS = -lm
32 | OBJS = hashtables_bfields.o  tree.o stats.o prng.o hashmap.o version.o sort.o io.o tree_utils.o bitset_index.o
33 | 
34 | # default target
35 | ALL = booster
36 | 
37 | INSTALL_PATH=$$HOME/bin/
38 | 
39 | all : $(ALL)
40 | 
41 | %.o: %.c %.h
42 | 	$(CC) $(CFLAGS) -c $<
43 | 
44 | # ****
45 | # the "booster" supports. Needs ref tree and bt trees.
46 | # ****
47 | booster: $(OBJS) booster.c
48 | 	$(CC) $(CFLAGS_OMP) -o $@ $^ $(LIBS)
49 | 
50 | 
51 | # ****
52 | # TESTS
53 | # ****
54 | tests: $(OBJS) test.c
55 | 	$(CC) $(CFLAGS) -o $@ $^ $(LIBS)
56 | 
57 | test : tests
58 | 	./tests
59 | 
60 | .PHONY: clean
61 | 
62 | clean:
63 | 	rm -f *~ *.o $(ALL) tests 
64 | 	rm -rf *.dSYM
65 | 
66 | install: all
67 | 	mkdir -p $(INSTALL_PATH)
68 | 	cp $(ALL) $(INSTALL_PATH)
69 | 
70 | uninstall:
71 | 	rm $(addprefix $(INSTALL_PATH),$(ALL))
72 | 


--------------------------------------------------------------------------------
/booster/booster.h:
--------------------------------------------------------------------------------
 1 | 
 2 | /**
 3 |  interface to call booster for transfer bootstrap expectation (TBE)
 4 |  @param input_tree reference tree file
 5 |  @param boot_trees bootstrap trees file
 6 |  @param out_tree output tree
 7 |  @param out_raw_tree output raw tree
 8 |  @param stat_out statistic output file
 9 |  @param num_threads number of threads
10 |  @param quiet 1 to stay quiet, 0 otherwise
11 |  */
12 | int main_booster (const char* input_tree, const char *boot_trees,
13 |                   const char* out_tree, const char* out_raw_tree, const char* stat_out,
14 |                   int quiet);
15 | 


--------------------------------------------------------------------------------
/booster/externs.h:
--------------------------------------------------------------------------------
 1 | /*
 2 | 
 3 | BOOSTER: BOOtstrap Support by TransfER: 
 4 | BOOSTER is an alternative method to compute bootstrap branch supports 
 5 | in large trees. It uses transfer distance between bipartitions, instead
 6 | of perfect match.
 7 | 
 8 | Copyright (C) 2017 Frederic Lemoine, Jean-Baka Domelevo Entfellner, Olivier Gascuel
 9 | 
10 | This program is free software; you can redistribute it and/or
11 | modify it under the terms of the GNU General Public License
12 | as published by the Free Software Foundation; either version 2
13 | of the License, or (at your option) any later version.
14 | 
15 | This program is distributed in the hope that it will be useful,
16 | but WITHOUT ANY WARRANTY; without even the implied warranty of
17 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
18 | GNU General Public License for more details.
19 | 
20 | You should have received a copy of the GNU General Public License
21 | along with this program; if not, write to the Free Software
22 | Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
23 | 
24 | */
25 | extern int ntax; /* this is set in parse_nh, in tree.c */
26 | 


--------------------------------------------------------------------------------
/booster/io.c:
--------------------------------------------------------------------------------
 1 | /*
 2 | 
 3 | BOOSTER: BOOtstrap Support by TransfER: 
 4 | BOOSTER is an alternative method to compute bootstrap branch supports 
 5 | in large trees. It uses transfer distance between bipartitions, instead
 6 | of perfect match.
 7 | 
 8 | Copyright (C) 2017 Frederic Lemoine, Jean-Baka Domelevo Entfellner, Olivier Gascuel
 9 | 
10 | This program is free software; you can redistribute it and/or
11 | modify it under the terms of the GNU General Public License
12 | as published by the Free Software Foundation; either version 2
13 | of the License, or (at your option) any later version.
14 | 
15 | This program is distributed in the hope that it will be useful,
16 | but WITHOUT ANY WARRANTY; without even the implied warranty of
17 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
18 | GNU General Public License for more details.
19 | 
20 | You should have received a copy of the GNU General Public License
21 | along with this program; if not, write to the Free Software
22 | Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
23 | 
24 | */
25 | 
26 | #include "io.h"
27 | 
28 | void Generic_Exit(const char *file, int line, const char *function, int code){
29 |   fprintf(stderr,"\n== Err. in file '%s' (line %d), function '%s'\n",file,line,function);
30 |   exit(code);
31 | }
32 | 


--------------------------------------------------------------------------------
/booster/io.h:
--------------------------------------------------------------------------------
 1 | /*
 2 | 
 3 | BOOSTER: BOOtstrap Support by TransfER: 
 4 | BOOSTER is an alternative method to compute bootstrap branch supports 
 5 | in large trees. It uses transfer distance between bipartitions, instead
 6 | of perfect match.
 7 | 
 8 | Copyright (C) 2017 Frederic Lemoine, Jean-Baka Domelevo Entfellner, Olivier Gascuel
 9 | 
10 | This program is free software; you can redistribute it and/or
11 | modify it under the terms of the GNU General Public License
12 | as published by the Free Software Foundation; either version 2
13 | of the License, or (at your option) any later version.
14 | 
15 | This program is distributed in the hope that it will be useful,
16 | but WITHOUT ANY WARRANTY; without even the implied warranty of
17 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
18 | GNU General Public License for more details.
19 | 
20 | You should have received a copy of the GNU General Public License
21 | along with this program; if not, write to the Free Software
22 | Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
23 | 
24 | */
25 | 
26 | #ifndef _IO_H
27 | #define _IO_H
28 | #include <stdio.h>
29 | #include <stdlib.h>
30 | 
31 | /* Taken from PhyML*/
32 | void Generic_Exit(const char *file, int line, const char *function, int ret_code);
33 | 
34 | #endif
35 | 


--------------------------------------------------------------------------------
/booster/prng.h:
--------------------------------------------------------------------------------
 1 | /*
 2 | 
 3 | BOOSTER: BOOtstrap Support by TransfER: 
 4 | BOOSTER is an alternative method to compute bootstrap branch supports 
 5 | in large trees. It uses transfer distance between bipartitions, instead
 6 | of perfect match.
 7 | 
 8 | Copyright (C) 2017 Frederic Lemoine, Jean-Baka Domelevo Entfellner, Olivier Gascuel
 9 | 
10 | This program is free software; you can redistribute it and/or
11 | modify it under the terms of the GNU General Public License
12 | as published by the Free Software Foundation; either version 2
13 | of the License, or (at your option) any later version.
14 | 
15 | This program is distributed in the hope that it will be useful,
16 | but WITHOUT ANY WARRANTY; without even the implied warranty of
17 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
18 | GNU General Public License for more details.
19 | 
20 | You should have received a copy of the GNU General Public License
21 | along with this program; if not, write to the Free Software
22 | Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
23 | 
24 | */
25 | 
26 | #ifndef PRNG_H_INCLUDED
27 | #define PRNG_H_INCLUDED
28 | 
29 | #include <stddef.h>
30 | 
31 | long prng_seed_time (void);
32 | void prng_seed_bytes (const void *, size_t);
33 | unsigned char prng_get_octet (void);
34 | unsigned char prng_get_byte (void);
35 | void prng_get_bytes (void *, size_t);
36 | unsigned long prng_get_ulong (void);
37 | long prng_get_long (void);
38 | unsigned prng_get_uint (void);
39 | int prng_get_int (void);
40 | double prng_get_double (void);
41 | double prng_get_double_normal (void);
42 | 
43 | #endif /* prng.h */
44 | 


--------------------------------------------------------------------------------
/booster/sort.h:
--------------------------------------------------------------------------------
 1 | /*
 2 | 
 3 | BOOSTER: BOOtstrap Support by TransfER: 
 4 | BOOSTER is an alternative method to compute bootstrap branch supports 
 5 | in large trees. It uses transfer distance between bipartitions, instead
 6 | of perfect match.
 7 | 
 8 | Copyright (C) 2017 Frederic Lemoine, Jean-Baka Domelevo Entfellner, Olivier Gascuel
 9 | 
10 | This program is free software; you can redistribute it and/or
11 | modify it under the terms of the GNU General Public License
12 | as published by the Free Software Foundation; either version 2
13 | of the License, or (at your option) any later version.
14 | 
15 | This program is distributed in the hope that it will be useful,
16 | but WITHOUT ANY WARRANTY; without even the implied warranty of
17 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
18 | GNU General Public License for more details.
19 | 
20 | You should have received a copy of the GNU General Public License
21 | along with this program; if not, write to the Free Software
22 | Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
23 | 
24 | */
25 | 
26 | #define _GNU_SOURCE
27 | #include <stdlib.h>
28 | 
29 | #ifndef _SORT_H
30 | #define _SORT_H
31 | 
32 | int comp_double(const void * elem1, const void * elem2);
33 | int comp_indexes(const void * elem1, const void * elem2, void * other_array);
34 | int comp_indexes_apple(void * other_array, const void * elem1, const void * elem2);
35 | 
36 | void sort_double(double * tab, int size);
37 | void sort_indexes_double(int * indexes, int size, double * values);
38 | 
39 | #endif
40 | 


--------------------------------------------------------------------------------
/booster/version.c:
--------------------------------------------------------------------------------
 1 | /*
 2 | 
 3 | BOOSTER: BOOtstrap Support by TransfER: 
 4 | BOOSTER is an alternative method to compute bootstrap branch supports 
 5 | in large trees. It uses transfer distance between bipartitions, instead
 6 | of perfect match.
 7 | 
 8 | Copyright (C) 2017 Frederic Lemoine, Jean-Baka Domelevo Entfellner, Olivier Gascuel
 9 | 
10 | This program is free software; you can redistribute it and/or
11 | modify it under the terms of the GNU General Public License
12 | as published by the Free Software Foundation; either version 2
13 | of the License, or (at your option) any later version.
14 | 
15 | This program is distributed in the hope that it will be useful,
16 | but WITHOUT ANY WARRANTY; without even the implied warranty of
17 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
18 | GNU General Public License for more details.
19 | 
20 | You should have received a copy of the GNU General Public License
21 | along with this program; if not, write to the Free Software
22 | Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
23 | 
24 | */
25 | 
26 | #include "version.h"
27 | 
28 | void version(FILE *out, char *executable){
29 |   fprintf(out,"%s version %s\n",NAME, VERSION);
30 | }
31 | 
32 | void short_version(FILE *out){
33 |   fprintf(out,"%s : version %s\n",NAME,VERSION);
34 | }
35 | 


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 1 | /*
 2 |  @licstart  The following is the entire license notice for the JavaScript code in this file.
 3 | 
 4 |  The MIT License (MIT)
 5 | 
 6 |  Copyright (C) 1997-2020 by Dimitri van Heesch
 7 | 
 8 |  Permission is hereby granted, free of charge, to any person obtaining a copy of this software
 9 |  and associated documentation files (the "Software"), to deal in the Software without restriction,
10 |  including without limitation the rights to use, copy, modify, merge, publish, distribute,
11 |  sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is
12 |  furnished to do so, subject to the following conditions:
13 | 
14 |  The above copyright notice and this permission notice shall be included in all copies or
15 |  substantial portions of the Software.
16 | 
17 |  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING
18 |  BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
19 |  NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
20 |  DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
21 |  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
22 | 
23 |  @licend  The above is the entire license notice for the JavaScript code in this file
24 | */
25 | var menudata={children:[
26 | {text:"Main Page",url:"index.html"},
27 | {text:"Related Pages",url:"pages.html"}]}
28 | 


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26 | searchResults.Search();
27 | window.addEventListener("message", function(event) {
28 |   if (event.data == "take_focus") {
29 |     var elem = searchResults.NavNext(0);
30 |     if (elem) elem.focus();
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32 | });
33 | /* @license-end */
34 | </script>
35 | </div>
36 | </body>
37 | </html>
38 | 


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2 | [
3 |   ['iq_2dtree_0',['IQ-TREE',['../md__r_e_a_d_m_e.html',1,'']]]
4 | ];
5 | 


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 4 | <meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
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25 | var searchResults = new SearchResults("searchResults");
26 | searchResults.Search();
27 | window.addEventListener("message", function(event) {
28 |   if (event.data == "take_focus") {
29 |     var elem = searchResults.NavNext(0);
30 |     if (elem) elem.focus();
31 |   }
32 | });
33 | /* @license-end */
34 | </script>
35 | </div>
36 | </body>
37 | </html>
38 | 


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/doc/html/search/searchdata.js:
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 1 | var indexSectionsWithContent =
 2 | {
 3 |   0: "i",
 4 |   1: "i"
 5 | };
 6 | 
 7 | var indexSectionNames =
 8 | {
 9 |   0: "all",
10 |   1: "pages"
11 | };
12 | 
13 | var indexSectionLabels =
14 | {
15 |   0: "All",
16 |   1: "Pages"
17 | };
18 | 
19 | 


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/doc/latex/Makefile:
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 1 | LATEX_CMD?=pdflatex
 2 | MKIDX_CMD?=makeindex
 3 | BIBTEX_CMD?=bibtex
 4 | LATEX_COUNT?=8
 5 | MANUAL_FILE?=refman
 6 | 
 7 | all: $(MANUAL_FILE).pdf
 8 | 
 9 | pdf: $(MANUAL_FILE).pdf
10 | 
11 | $(MANUAL_FILE).pdf: clean $(MANUAL_FILE).tex
12 | 	$(LATEX_CMD) $(MANUAL_FILE)
13 | 	$(MKIDX_CMD) $(MANUAL_FILE).idx
14 | 	$(LATEX_CMD) $(MANUAL_FILE)
15 | 	latex_count=$(LATEX_COUNT) ; \
16 | 	while egrep -s 'Rerun (LaTeX|to get cross-references right|to get bibliographical references right)' $(MANUAL_FILE).log && [ $$latex_count -gt 0 ] ;\
17 | 	    do \
18 | 	      echo "Rerunning latex...." ;\
19 | 	      $(LATEX_CMD) $(MANUAL_FILE) ;\
20 | 	      latex_count=`expr $$latex_count - 1` ;\
21 | 	    done
22 | 	$(MKIDX_CMD) $(MANUAL_FILE).idx
23 | 	$(LATEX_CMD) $(MANUAL_FILE)
24 | 
25 | 
26 | clean:
27 | 	rm -f *.ps *.dvi *.aux *.toc *.idx *.ind *.ilg *.log *.out *.brf *.blg *.bbl $(MANUAL_FILE).pdf
28 | 


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/example/custom_distributions.txt:
--------------------------------------------------------------------------------
 1 | F_A 0.363799 0.313203 0.277533 0.24235 0.260252
 2 | F_B 0.321134 0.299891 0.315519 0.269172 0.258165 
 3 | F_C 0.287641 0.309442 0.264017 0.23103
 4 | F_D 0.200087 0.336534 0.337547 0.325379 0.335034 
 5 | F_E 0.306336 0.359459 0.249315 0.388073 
 6 | F_F 0.345694 0.338733 0.305404 0.294181 
 7 | I_A 0.257679 0.417313 0.290922 0.301826 0.292324 0.33887
 8 | I_B 0.179902 0.122071 0.348381 0.33887 0.228999
 9 | I_C 0.377297 0.296036 0.044523 0.262098 0.295087
10 | R_A 10.363799 20.313203 10.277533 5.24235 3.26025
11 | R_B 6.321134 0.299891 10.315519 0.269172 04.258165
12 | R_C 10.287641 8.309442 20.264017 03.23103 04.178778
13 | R_D 9.200087 10.336534 30.337547 03.325379 0.335034
14 | R_E 2.306336 4.359459 0.249315 0.388073 04.296979
15 | R_F 4.345694 06.338733 02.305404 02.294181 04.303477
16 | R_G 3.257679 07.417313 03.290922 04.301826 03.292324
17 | N_A -0.363799 -0.313203 -0.277533 0.24235 -0.260252
18 | N_B 0.321134 -0.299891 -01.315519 -0.269172 -0.258165
19 | N_C 0.287641 -0.309442 0.264017 -0.23103 0.178778


--------------------------------------------------------------------------------
/example/example.nex:
--------------------------------------------------------------------------------
 1 | #nexus
 2 | 
 3 | begin sets;
 4 | 	charset part1 = 1-999\3 2-999\3;
 5 | 	charset part2 = 3-999\3;
 6 | 	charset part3 = 1000-1998;
 7 | 
 8 | 	charpartition mine = HKY:part1, GTR+G:part2, GTR+G: part3;
 9 | end;
10 | 


--------------------------------------------------------------------------------
/example/tree.nwk:
--------------------------------------------------------------------------------
1 | (A:0.3544,(B:0.1905,C:0.1328):0.0998,D:0.0898);


--------------------------------------------------------------------------------
/flake.lock:
--------------------------------------------------------------------------------
 1 | {
 2 |   "nodes": {
 3 |     "flake-utils": {
 4 |       "locked": {
 5 |         "lastModified": 1644229661,
 6 |         "narHash": "sha256-1YdnJAsNy69bpcjuoKdOYQX0YxZBiCYZo4Twxerqv7k=",
 7 |         "owner": "numtide",
 8 |         "repo": "flake-utils",
 9 |         "rev": "3cecb5b042f7f209c56ffd8371b2711a290ec797",
10 |         "type": "github"
11 |       },
12 |       "original": {
13 |         "owner": "numtide",
14 |         "repo": "flake-utils",
15 |         "type": "github"
16 |       }
17 |     },
18 |     "nixpkgs": {
19 |       "locked": {
20 |         "lastModified": 1646051047,
21 |         "narHash": "sha256-XDJGACWVeNs3OAECpx20zegX/YDigHOUZ1nVmCJUeEM=",
22 |         "owner": "NixOS",
23 |         "repo": "nixpkgs",
24 |         "rev": "21968db378c9144f418c1e8e7002316aa8b75776",
25 |         "type": "github"
26 |       },
27 |       "original": {
28 |         "owner": "NixOS",
29 |         "ref": "nixos-unstable-small",
30 |         "repo": "nixpkgs",
31 |         "type": "github"
32 |       }
33 |     },
34 |     "root": {
35 |       "inputs": {
36 |         "flake-utils": "flake-utils",
37 |         "nixpkgs": "nixpkgs"
38 |       }
39 |     }
40 |   },
41 |   "root": "root",
42 |   "version": 7
43 | }
44 | 


--------------------------------------------------------------------------------
/flake.nix:
--------------------------------------------------------------------------------
 1 | {
 2 |   description = "IQ-TREE 2";
 3 | 
 4 |   inputs.flake-utils.url = "github:numtide/flake-utils";
 5 | 
 6 |   inputs.nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable-small";
 7 | 
 8 |   outputs =
 9 |     { self
10 |     , flake-utils
11 |     , nixpkgs
12 |     }:
13 |     flake-utils.lib.eachDefaultSystem (
14 |       system:
15 |       let
16 |         # # For Nixpkgs and the NUR repository, the following two forms are
17 |         # # equivalent because the flake just imports the base directory.
18 |         pkgs = nixpkgs.legacyPackages.${system};
19 |         # pkgs = import nixpkgs {
20 |         #   inherit system;
21 |         #   config = { allowUnfree = true; };
22 |         # };
23 |       in
24 |       {
25 |         devShell = pkgs.mkShell {
26 |           packages = with pkgs; [
27 |             # See https://github.com/NixOS/nixpkgs/issues/59209.
28 |             bashInteractive
29 |           ];
30 |           nativeBuildInputs = with pkgs; [ cmake ];
31 |           buildInputs = with pkgs; [ boost eigen zlib ];
32 | 
33 |           cmakeFlags = [
34 |             "-DIQTREE_FLAGS=omp"
35 |           ];
36 |         };
37 |       }
38 |     );
39 | }
40 | 


--------------------------------------------------------------------------------
/gsl/CMakeLists.txt:
--------------------------------------------------------------------------------
 1 | add_library(gsl
 2 | binomial_tpe.cpp
 3 | multinomial.cpp
 4 | pow_int.cpp
 5 | gauss.cpp
 6 | gaussinv.cpp
 7 | gausspdf.cpp
 8 | mygsl.h
 9 | )
10 | 


--------------------------------------------------------------------------------
/gsl/gausspdf.cpp:
--------------------------------------------------------------------------------
 1 | /* randist/gauss.c
 2 |  * 
 3 |  * Copyright (C) 1996, 1997, 1998, 1999, 2000, 2006, 2007 James Theiler, Brian Gough
 4 |  * Copyright (C) 2006 Charles Karney
 5 |  * 
 6 |  * This program is free software; you can redistribute it and/or modify
 7 |  * it under the terms of the GNU General Public License as published by
 8 |  * the Free Software Foundation; either version 3 of the License, or (at
 9 |  * your option) any later version.
10 |  * 
11 |  * This program is distributed in the hope that it will be useful, but
12 |  * WITHOUT ANY WARRANTY; without even the implied warranty of
13 |  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
14 |  * General Public License for more details.
15 |  * 
16 |  * You should have received a copy of the GNU General Public License
17 |  * along with this program; if not, write to the Free Software
18 |  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
19 |  */
20 | 
21 | //#include <config.h>
22 | #include <math.h>
23 | //#include <gsl/gsl_math.h>
24 | //#include <gsl/gsl_rng.h>
25 | //#include <gsl/gsl_randist.h>
26 | 
27 | double
28 | gsl_ran_gaussian_pdf (const double x, const double sigma)
29 | {
30 |   double u = x / fabs (sigma);
31 |   double p = (1 / (sqrt (2 * 3.14159265358979323846264338327950288) * fabs (sigma))) * exp (-u * u / 2);
32 |   return p;
33 | }
34 | 
35 | double
36 | gsl_ran_ugaussian_pdf (const double x)
37 | {
38 |   return gsl_ran_gaussian_pdf (x, 1.0);
39 | }
40 | 
41 | 


--------------------------------------------------------------------------------
/gsl/gsl_nan.h:
--------------------------------------------------------------------------------
 1 | /* gsl_nan.h
 2 |  * 
 3 |  * Copyright (C) 1996, 1997, 1998, 1999, 2000, 2007 Gerard Jungman, Brian Gough
 4 |  * 
 5 |  * This program is free software; you can redistribute it and/or modify
 6 |  * it under the terms of the GNU General Public License as published by
 7 |  * the Free Software Foundation; either version 3 of the License, or (at
 8 |  * your option) any later version.
 9 |  * 
10 |  * This program is distributed in the hope that it will be useful, but
11 |  * WITHOUT ANY WARRANTY; without even the implied warranty of
12 |  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
13 |  * General Public License for more details.
14 |  * 
15 |  * You should have received a copy of the GNU General Public License
16 |  * along with this program; if not, write to the Free Software
17 |  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
18 |  */
19 | 
20 | #ifndef __GSL_NAN_H__
21 | #define __GSL_NAN_H__
22 | 
23 | #ifdef INFINITY
24 | # define GSL_POSINF INFINITY
25 | # define GSL_NEGINF (-INFINITY)
26 | #elif defined(HUGE_VAL)
27 | # define GSL_POSINF HUGE_VAL
28 | # define GSL_NEGINF (-HUGE_VAL)
29 | #else
30 | # define GSL_POSINF (gsl_posinf())
31 | # define GSL_NEGINF (gsl_neginf())
32 | #endif
33 | 
34 | #ifdef NAN
35 | # define GSL_NAN NAN
36 | #elif defined(INFINITY)
37 | # define GSL_NAN (INFINITY/INFINITY)
38 | #else
39 | # define GSL_NAN (gsl_nan())
40 | #endif
41 | 
42 | #define GSL_POSZERO (+0.0)
43 | #define GSL_NEGZERO (-0.0)
44 | 
45 | #endif /* __GSL_NAN_H__ */
46 | 


--------------------------------------------------------------------------------
/gsl/rat_eval.h:
--------------------------------------------------------------------------------
 1 | static double
 2 | rat_eval (const double a[], const size_t na,
 3 |           const double b[], const size_t nb, const double x)
 4 | {
 5 |   size_t i, j;
 6 |   double u, v, r;
 7 | 
 8 |   u = a[na - 1];
 9 | 
10 |   for (i = na - 1; i > 0; i--)
11 |     {
12 |       u = x * u + a[i - 1];
13 |     }
14 | 
15 |   v = b[nb - 1];
16 | 
17 |   for (j = nb - 1; j > 0; j--)
18 |     {
19 |       v = x * v + b[j - 1];
20 |     }
21 | 
22 |   r = u / v;
23 | 
24 |   return r;
25 | }
26 | 


--------------------------------------------------------------------------------
/iqtree_config.h.in:
--------------------------------------------------------------------------------
 1 | #define iqtree_VERSION_MAJOR @iqtree_VERSION_MAJOR@
 2 | #define iqtree_VERSION_MINOR @iqtree_VERSION_MINOR@
 3 | #define iqtree_VERSION_PATCH "@iqtree_VERSION_PATCH@"
 4 | 
 5 | /* does the platform provide gettimeofday functions? */
 6 | #cmakedefine HAVE_GETTIMEOFDAY
 7 | /* does the platform provide getrusage functions? */
 8 | #cmakedefine HAVE_GETRUSAGE
 9 | /* does the platform provide popen functions? */
10 | /*#cmakedefine HAVE_POPEN*/
11 | /* does the platform provide pclose functions? */
12 | /*#cmakedefine HAVE_PCLOSE*/
13 | /* does the platform provide GlobalMemoryStatusEx functions? */
14 | #cmakedefine HAVE_GLOBALMEMORYSTATUSEX
15 | #cmakedefine HAVE_STRNDUP
16 | #cmakedefine HAVE_STRTOK_R
17 | 
18 | /* does the platform provide backtrace functions? */
19 | #cmakedefine Backtrace_FOUND
20 | 


--------------------------------------------------------------------------------
/lbfgsb/CMakeLists.txt:
--------------------------------------------------------------------------------
1 | add_library(lbfgsb
2 | lbfgsb_new.cpp
3 | )
4 | 


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/lib/libiomp5md.dll:
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/lib/pthreadGC2.dll:
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/lib/pthreadVC2.dll:
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/lib/pthreadVC2.lib:
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/libmac/libomp.a:
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/libmac_m1/libomp.a:
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/main/CMakeLists.txt:
--------------------------------------------------------------------------------
 1 | add_library(main
 2 | main.cpp
 3 | phyloanalysis.cpp
 4 | phyloanalysis.h
 5 | phylotesting.cpp
 6 | phylotesting.h
 7 | treetesting.cpp
 8 | treetesting.h
 9 | timetree.cpp
10 | timetree.h
11 | alisim.cpp
12 | alisim.h
13 | terraceanalysis.cpp
14 | terraceanalysis.h
15 | )
16 | 
17 | if (USE_BOOSTER)
18 |     target_link_libraries(main booster)
19 | endif()
20 | 
21 | if (USE_LSD2)
22 |     target_link_libraries(main lsd2)
23 | endif()
24 | 
25 | if (USE_NN OR USE_OLD_NN)
26 |     target_link_libraries(main nn)
27 | endif()
28 | 
29 | target_link_libraries(main pda whtest vectorclass terrace)
30 | 
31 | if (USE_CMAPLE)
32 | 	target_link_libraries(main maple)
33 | 	
34 |     if (USE_CMAPLE_AA)
35 |         add_library(main-aa
36 |         main.cpp
37 |         phyloanalysis.cpp
38 |         phyloanalysis.h
39 |         phylotesting.cpp
40 |         phylotesting.h
41 |         treetesting.cpp
42 |         treetesting.h
43 |         timetree.cpp
44 |         timetree.h
45 |         alisim.cpp
46 |         alisim.h
47 |         terraceanalysis.cpp
48 |         terraceanalysis.h
49 |         )
50 | 
51 |         if (USE_BOOSTER)
52 |                 target_link_libraries(main-aa booster)
53 |         endif()
54 | 
55 |         if (USE_LSD2)
56 |                 target_link_libraries(main-aa lsd2)
57 |         endif()
58 |         
59 |         target_link_libraries(main-aa pda whtest vectorclass terrace maple-aa)
60 |     endif()
61 | endif()
62 | 


--------------------------------------------------------------------------------
/main/terraceanalysis.h:
--------------------------------------------------------------------------------
 1 | /*
 2 |  *  terraceanalysis.ch
 3 |  *  Interface to work with terraces
 4 |  *  Created on: Sep 10, 2020
 5 |  *      Author: Olga
 6 |  */
 7 | 
 8 | #ifndef terraceanalysis_hpp
 9 | #define terraceanalysis_hpp
10 | 
11 | #include <stdio.h>
12 | #include "utils/tools.h"
13 | #include "terrace/terrace.hpp"
14 | 
15 | /*
16 |  *  Main function for terrace analysis
17 |  */
18 | void runterraceanalysis(Params &params);
19 | 
20 | /*
21 |  * Run terrace check:
22 |  * - check if query trees lie on the same terrace with a representative tree. Naive pairwise comparison of induced partition trees.
23 |  */
24 | void run_terrace_check(Terrace *terrace, Params &params);
25 | 
26 | 
27 | /**
28 |         This is the function that calls generation of terrace trees, when the input data (representative tree and presence-absence matrix are processed already)
29 |  */
30 | void run_generate_trees(Terrace *terrace, Params &params,const int m);
31 | 
32 | /**
33 |         The function is used to read a set of subtrees to be considered as partition trees for terrace analysis
34 |  */
35 | void read_tree_set(const char *infile, bool &is_rooted, vector<TerraceTree*> &subtrees);
36 | 
37 | #endif /* terraceanalysis_hpp */
38 | 


--------------------------------------------------------------------------------
/main/timetree.h:
--------------------------------------------------------------------------------
 1 | /*
 2 |  * Time tree for phylogenetic dating
 3 |  *
 4 |  *  Created on: Apr 4, 2020
 5 |  *      Author: minh
 6 |  */
 7 | 
 8 | #ifndef TIMETREE_H_
 9 | #define TIMETREE_H_
10 | 
11 | #include "tree/phylotree.h"
12 | 
13 | /**
14 |  main function to build time-tree
15 |  @param tree input phylogenetic tree
16 |  */
17 | void doTimeTree(PhyloTree *tree);
18 | 
19 | #endif
20 | 


--------------------------------------------------------------------------------
/model/CMakeLists.txt:
--------------------------------------------------------------------------------
 1 | add_library(model
 2 | modelmarkov.cpp modelmarkov.h
 3 | modelbin.cpp modelbin.h
 4 | modeldna.cpp modeldna.h
 5 | modeldnaerror.cpp modeldnaerror.h
 6 | modelfactory.cpp modelfactory.h
 7 | modelprotein.cpp modelprotein.h
 8 | modelset.cpp modelset.h
 9 | modelsubst.cpp modelsubst.h
10 | partitionmodel.cpp partitionmodel.h
11 | partitionmodelplen.cpp partitionmodelplen.h
12 | rategamma.cpp rategamma.h
13 | rategammainvar.cpp rategammainvar.h
14 | ratecontinuousgamma.cpp ratecontinuousgamma.h
15 | ratecontinuousgammainvar.cpp ratecontinuousgammainvar.h
16 | rateheterogeneity.cpp rateheterogeneity.h
17 | rateinvar.cpp rateinvar.h
18 | ratemeyerdiscrete.cpp ratemeyerdiscrete.h
19 | ratemeyerhaeseler.cpp ratemeyerhaeseler.h
20 | ratekategory.cpp ratekategory.h
21 | ratefree.cpp ratefree.h
22 | ratefreeinvar.cpp ratefreeinvar.h
23 | rateheterotachy.cpp rateheterotachy.h
24 | rateheterotachyinvar.cpp rateheterotachyinvar.h
25 | modelcodon.cpp modelcodon.h
26 | modelmorphology.cpp modelmorphology.h
27 | modelmixture.cpp modelmixture.h
28 | modelunrest.cpp modelunrest.h
29 | modelliemarkov.cpp modelliemarkov.h
30 | modelpomo.cpp modelpomo.h
31 | modelpomomixture.cpp modelpomomixture.h
32 | modelfactorymixlen.cpp modelfactorymixlen.h
33 | modelhmm.cpp modelhmm.h
34 | modelhmmgm.cpp modelhmmgm.h
35 | modelhmmtm.cpp modelhmmtm.h
36 | modelcodonmixture.cpp modelcodonmixture.h
37 | )
38 | 
39 | target_link_libraries(model utils)
40 | 


--------------------------------------------------------------------------------
/model/modelcodonempirical.h:
--------------------------------------------------------------------------------
 1 | /*
 2 |  * modelcodonempirical.h
 3 |  *
 4 |  *  Created on: May 29, 2013
 5 |  *      Author: minh
 6 |  */
 7 | 
 8 | #ifndef MODELCODONEMPIRICAL_H_
 9 | #define MODELCODONEMPIRICAL_H_
10 | 
11 | #include "modelcodon.h"
12 | 
13 | /**
14 |  * empirical codon model (e.g., Kosiol et al. 2007)
15 |  */
16 | class ModelCodonEmpirical: virtual public ModelCodon {
17 | public:
18 | 	/**
19 | 		constructor
20 | 		@param model_name model name, e.g., GY,YN
21 | 		@param freq state frequency type
22 | 		@param tree associated phylogenetic tree
23 | 	*/
24 | 	ModelCodonEmpirical(const char *model_name, string model_params, StateFreqType freq, string freq_params,
25 |     		PhyloTree *tree, bool count_rates = true);
26 | 
27 | 	/**
28 | 	 * destructor
29 | 	 */
30 | 	virtual ~ModelCodonEmpirical();
31 | 
32 | 	/**
33 | 		initialization, called automatically by the constructor, no need to call it
34 | 		@param model_name model name, e.g., JC, HKY.
35 | 		@param freq state frequency type
36 | 	*/
37 | 	virtual void init(const char *model_name, string model_params, StateFreqType freq, string freq_params);
38 | 
39 | 
40 | 	/**
41 | 	 * read codon model from a stream, modying rates and state_freq accordingly
42 | 	 * @param in input stream containing lower triangular matrix of rates, frequencies and list of codons
43 | 	 */
44 | 	void readCodonModel(istream &in);
45 | 
46 | };
47 | 
48 | #endif /* MODELCODONEMPIRICAL_H_ */
49 | 


--------------------------------------------------------------------------------
/model/modelcodonparametric.h:
--------------------------------------------------------------------------------
 1 | /*
 2 |  * modelcodonparametric.h
 3 |  *
 4 |  *  Created on: May 29, 2013
 5 |  *      Author: minh
 6 |  */
 7 | 
 8 | #ifndef MODELCODONPARAMETRIC_H_
 9 | #define MODELCODONPARAMETRIC_H_
10 | 
11 | #include "modelcodon.h"
12 | 
13 | /**
14 |  * parametric codon model (e.g., Goldman-Yang, Muse-Gaut)
15 |  */
16 | class ModelCodonParametric: virtual public ModelCodon {
17 | public:
18 | 	/**
19 | 		constructor
20 | 		@param model_name model name, e.g., GY,YN
21 | 		@param freq state frequency type
22 | 		@param tree associated phylogenetic tree
23 | 	*/
24 | 	ModelCodonParametric(const char *model_name, string model_params, StateFreqType freq, string freq_params,
25 |     		PhyloTree *tree, bool count_rates = true);
26 | 
27 |     /**
28 |      * destructor
29 |      */
30 | 	virtual ~ModelCodonParametric();
31 | 
32 | 	/**
33 | 		initialization, called automatically by the constructor, no need to call it
34 | 		@param model_name model name, e.g., JC, HKY.
35 | 		@param freq state frequency type
36 | 	*/
37 | 	virtual void init(const char *model_name, string model_params, StateFreqType freq, string freq_params);
38 | 
39 | 	/**
40 | 		write information
41 | 		@param out output stream
42 | 	*/
43 | 	virtual void writeInfo(ostream &out);
44 | 
45 | protected:
46 | 
47 | 	/** initialize Muse-Gaut 1994 model */
48 | 	void initMG94();
49 | 
50 | 	/** initialize Goldman-Yang 1994 model (simplified version with 2 parameters omega and kappa */
51 | 	void initGY94();
52 | 
53 | 
54 | };
55 | 
56 | #endif /* MODELCODONPARAMETRIC_H_ */
57 | 


--------------------------------------------------------------------------------
/model/modelcodonsemiempirical.cpp:
--------------------------------------------------------------------------------
 1 | /*
 2 |  * modelcodonsemiempirical.cpp
 3 |  *
 4 |  *  Created on: May 29, 2013
 5 |  *      Author: minh
 6 |  */
 7 | 
 8 | #include "modelcodonsemiempirical.h"
 9 | 
10 | ModelCodonSemiEmpirical::ModelCodonSemiEmpirical(const char *model_name, string model_params,
11 | 		StateFreqType freq, string freq_params, PhyloTree *tree, bool count_rates) :
12 | 		ModelCodon(tree, count_rates)
13 | {
14 | 	init(model_name, model_params, freq, freq_params);
15 | }
16 | 
17 | 
18 | ModelCodonSemiEmpirical::~ModelCodonSemiEmpirical() {
19 | }
20 | 
21 | 
22 | void ModelCodonSemiEmpirical::init(const char *model_name, string model_params, StateFreqType freq, string freq_params) {
23 | 	name = full_name = model_name;
24 | 	size_t pos = name.find('+');
25 | 	ASSERT(pos != string::npos);
26 | 	if (name.substr(0,3) == "ECM") {
27 | 		ModelCodonEmpirical::init(name.substr(0,pos), "", FREQ_USER_DEFINED, "");
28 | 		ModelCodonParametric::init(name.substr(pos), model_params, freq, freq_params);
29 | 	}
30 | 
31 | }
32 | 


--------------------------------------------------------------------------------
/model/modelcodonsemiempirical.h:
--------------------------------------------------------------------------------
 1 | /*
 2 |  * modelcodonsemiempirical.h
 3 |  *
 4 |  *  Created on: May 29, 2013
 5 |  *      Author: minh
 6 |  */
 7 | 
 8 | #ifndef MODELCODONSEMIEMPIRICAL_H_
 9 | #define MODELCODONSEMIEMPIRICAL_H_
10 | 
11 | #include "modelcodonempirical.h"
12 | #include "modelcodonparametric.h"
13 | 
14 | class ModelCodonSemiEmpirical: public ModelCodonEmpirical, public ModelCodonParametric {
15 | public:
16 | 	/**
17 | 		constructor
18 | 		@param model_name model name, e.g., GY,YN
19 | 		@param freq state frequency type
20 | 		@param tree associated phylogenetic tree
21 | 	*/
22 | 	ModelCodonSemiEmpirical(const char *model_name, string model_params, StateFreqType freq, string freq_params,
23 |     		PhyloTree *tree, bool count_rates = true);
24 | 
25 | 
26 | 	/**
27 | 	 * destructor
28 | 	 */
29 | 	virtual ~ModelCodonSemiEmpirical();
30 | 
31 | 	/**
32 | 		initialization, called automatically by the constructor, no need to call it
33 | 		@param model_name model name, e.g., JC, HKY.
34 | 		@param freq state frequency type
35 | 	*/
36 | 	virtual void init(const char *model_name, string model_params, StateFreqType freq, string freq_params);
37 | 
38 | };
39 | 
40 | #endif /* MODELCODONSEMIEMPIRICAL_H_ */
41 | 


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/model/modelfactorymixlen.h:
--------------------------------------------------------------------------------
 1 | /*
 2 |  * modelfactorymixlen.h
 3 |  *
 4 |  *  Created on: Sep 2, 2015
 5 |  *      Author: minh
 6 |  */
 7 | 
 8 | 
 9 | #include "modelfactory.h"
10 | 
11 | class ModelFactoryMixlen : public ModelFactory {
12 | 
13 | public:
14 | 
15 | 	/**
16 | 		constructor
17 | 		create substitution model with possible rate heterogeneity. Create proper class objects
18 | 		for two variables: model and site_rate. It takes the following field of params into account:
19 | 			model_name, num_rate_cats, freq_type, store_trans_matrix
20 | 		@param params program parameters
21 | 		@param tree associated phylogenetic tree
22 | 	*/
23 | 	ModelFactoryMixlen(Params &params, string &model_name, PhyloTree *tree, ModelsBlock *models_block);
24 | 
25 | 	/**
26 | 		optimize model parameters and tree branch lengths
27 | 		@param fixed_len TRUE to fix branch lengths, default is false
28 | 		@return the best likelihood 
29 | 	*/
30 | 	virtual double optimizeParameters(int fixed_len = BRLEN_OPTIMIZE, bool write_info = true,
31 |                                       double logl_epsilon = 0.1, double gradient_epsilon = 0.0001);
32 | 
33 |     /**
34 |         sort classes in ascending order of tree lengths
35 |         @return tree string with sorted branch lengths
36 |     */
37 |     string sortClassesByTreeLength();
38 | 
39 | 
40 |     /**
41 |      * @param brlen_type either BRLEN_OPTIMIZE, BRLEN_FIX or BRLEN_SCALE
42 |      * @return #parameters of the model + # branches
43 |      */
44 |     virtual int getNParameters(int brlen_type);
45 | 
46 | };
47 | 


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/model/modelnonrev.cpp:
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https://raw.githubusercontent.com/iqtree/iqtree3/4c823e9757857e098e99c4aba611748d5c4cc8db/model/modelnonrev.cpp


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/model/modelnonrev.h:
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https://raw.githubusercontent.com/iqtree/iqtree3/4c823e9757857e098e99c4aba611748d5c4cc8db/model/modelnonrev.h


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/model/modelunrest.h:
--------------------------------------------------------------------------------
 1 | /*
 2 |  * modelunrest.h
 3 |  *
 4 |  *  Created on: 24/05/2016
 5 |  *      Author: Michael Woodhams
 6 |  */
 7 | 
 8 | #ifndef MODELUNREST_H_
 9 | #define MODELUNREST_H_
10 | 
11 | #include "modelmarkov.h"
12 | 
13 | class ModelUnrest: public ModelMarkov {
14 | public:
15 | 
16 |     /** constructor */
17 | 	ModelUnrest(PhyloTree *tree, string model_params, StateFreqType freq_type, string freq_params);
18 | 
19 |     /**
20 |      * true if model_name is the name of some known non-reversible model
21 |      */
22 | 	static bool validModelName(string model_name);
23 | 
24 | 	/**
25 | 	 * setup the bounds for joint optimization with BFGS
26 | 	 */
27 | 	virtual void setBounds(double *lower_bound, double *upper_bound, bool *bound_check);
28 |     
29 |     /**
30 |      set the state frequency vector.
31 |      @param state_freq state frequency vector. Assume state_freq has size of num_states
32 |      */
33 |     virtual void setStateFrequency(double *state_freq);
34 | 
35 |     /**
36 |      start structure for checkpointing
37 |      */
38 |     virtual void startCheckpoint();
39 |     
40 |     /**
41 |      save object into the checkpoint
42 |      */
43 |     virtual void saveCheckpoint();
44 |     
45 |     /**
46 |      restore object from the checkpoint
47 |      */
48 |     virtual void restoreCheckpoint();
49 | 
50 | protected:
51 | 	void writeInfo(ostream &out);
52 |     virtual void setRates();
53 | };
54 | 
55 | #endif /* MODELUNREST_H_ */
56 | 


--------------------------------------------------------------------------------
/ncl/CMakeLists.txt:
--------------------------------------------------------------------------------
 1 | add_library(ncl 
 2 | nxsassumptionsblock.cpp
 3 | nxsblock.cpp
 4 | nxscharactersblock.cpp
 5 | nxsdatablock.cpp
 6 | nxsdiscretedatum.cpp
 7 | nxsdiscretematrix.cpp
 8 | nxsdistancedatum.cpp
 9 | nxsdistancesblock.cpp
10 | nxsemptyblock.cpp
11 | nxsexception.cpp
12 | nxsreader.cpp
13 | nxssetreader.cpp
14 | nxsstring.cpp
15 | nxstaxablock.cpp
16 | nxstoken.cpp
17 | nxstreesblock.cpp)
18 | 


--------------------------------------------------------------------------------
/ncl/nxsdatablock.h:
--------------------------------------------------------------------------------
 1 | //	Copyright (C) 1999-2003 Paul O. Lewis
 2 | //
 3 | //	This file is part of NCL (Nexus Class Library) version 2.0.
 4 | //
 5 | //	NCL is free software; you can redistribute it and/or modify
 6 | //	it under the terms of the GNU General Public License as published by
 7 | //	the Free Software Foundation; either version 2 of the License, or
 8 | //	(at your option) any later version.
 9 | //
10 | //	NCL is distributed in the hope that it will be useful,
11 | //	but WITHOUT ANY WARRANTY; without even the implied warranty of
12 | //	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 | //	GNU General Public License for more details.
14 | //
15 | //	You should have received a copy of the GNU General Public License
16 | //	along with NCL; if not, write to the Free Software Foundation, Inc., 
17 | //	59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
18 | //
19 | 
20 | #ifndef NCL_NXSDATABLOCK_H
21 | #define NCL_NXSDATABLOCK_H
22 | 
23 | /*----------------------------------------------------------------------------------------------------------------------
24 | |	This class handles reading and storage for the NEXUS block DATA. It is derived from the NxsCharactersBlock class, 
25 | |	and differs from NxsCharactersBlock only in name and the fact that `newtaxa' is initially true rather than false.
26 | */
27 | class NxsDataBlock
28 |   : public NxsCharactersBlock
29 | 	{
30 | 	public:
31 | 		NxsDataBlock(NxsTaxaBlock *tb, NxsAssumptionsBlock *ab);
32 | 
33 | 		void TransferTo(NxsCharactersBlock &charactersblock);
34 | 		void Reset();
35 | 	};
36 | 
37 | typedef NxsDataBlock DataBlock;
38 | 
39 | #endif
40 | 


--------------------------------------------------------------------------------
/ncl/nxsdistancedatum.cpp:
--------------------------------------------------------------------------------
 1 | //	Copyright (C) 1999-2003 Paul O. Lewis
 2 | //
 3 | //	This file is part of NCL (Nexus Class Library) version 2.0.
 4 | //
 5 | //	NCL is free software; you can redistribute it and/or modify
 6 | //	it under the terms of the GNU General Public License as published by
 7 | //	the Free Software Foundation; either version 2 of the License, or
 8 | //	(at your option) any later version.
 9 | //
10 | //	NCL is distributed in the hope that it will be useful,
11 | //	but WITHOUT ANY WARRANTY; without even the implied warranty of
12 | //	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 | //	GNU General Public License for more details.
14 | //
15 | //	You should have received a copy of the GNU General Public License
16 | //	along with NCL; if not, write to the Free Software Foundation, Inc., 
17 | //	59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
18 | //
19 | 
20 | #include "ncl.h"
21 | 
22 | /*----------------------------------------------------------------------------------------------------------------------
23 | |	Initializes value to 0.0 and missing to true.
24 | */
25 | NxsDistanceDatum::NxsDistanceDatum()
26 | 	{
27 | 	missing	= true;
28 | 	value	= 0.0;
29 | 	}
30 | 
31 | /*----------------------------------------------------------------------------------------------------------------------
32 | |	Does nothing.
33 | */
34 | NxsDistanceDatum::~NxsDistanceDatum()
35 | 	{
36 | 	}
37 | 


--------------------------------------------------------------------------------
/nclextra/CMakeLists.txt:
--------------------------------------------------------------------------------
1 | add_library(nclextra
2 | mpdablock.cpp mpdablock.h
3 | msetsblock.cpp msetsblock.h
4 | msplitsblock.cpp msplitsblock.h
5 | modelsblock.cpp modelsblock.h
6 | )
7 | 


--------------------------------------------------------------------------------
/nn/CMakeLists.txt:
--------------------------------------------------------------------------------
1 | add_library(nn
2 | neuralnetwork.cpp
3 | neuralnetwork.h
4 | )
5 | 
6 | target_link_libraries(nn alignment)
7 | 


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/nn/neuralnetwork.h:
--------------------------------------------------------------------------------
 1 | //
 2 | // Created by tamara on 3/8/21.
 3 | //
 4 | 
 5 | #ifndef IQTREE_NEURALNETWORK_H
 6 | #define IQTREE_NEURALNETWORK_H
 7 | 
 8 | #include <onnxruntime_cxx_api.h>
 9 | #include <alignment/alignment.h>
10 | 
11 | class NeuralNetwork {
12 | public:
13 |     /** constructor */
14 |     NeuralNetwork(Alignment *alignment);
15 | 
16 |     /** destructor */
17 |     virtual ~NeuralNetwork();
18 | 
19 |     double doAlphaInference();
20 |     string doModelInference();
21 | 
22 |     Alignment *alignment;
23 | 
24 | };
25 | 
26 | 
27 | #endif //IQTREE_NEURALNETWORK_H
28 | 


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/nn_models/lanfear_alpha_lstm.onnx:
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1 | version https://git-lfs.github.com/spec/v1
2 | oid sha256:0fe3e55d7cddbd7716c2c22c91acba2900831a056d65a5005b5b1e139aed7260
3 | size 82114237
4 | 


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/nn_models/resnet_modelfinder.onnx:
--------------------------------------------------------------------------------
1 | version https://git-lfs.github.com/spec/v1
2 | oid sha256:990e788b2a5480de1dfbc1cedb2acaed097cd7dec7a91325adb05b524de97ba2
3 | size 107534983
4 | 


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/onnxruntimeConfig.cmake:
--------------------------------------------------------------------------------
 1 | # Custom cmake config file by jcarius to enable find_package(onnxruntime) without modifying LIBRARY_PATH and LD_LIBRARY_PATH
 2 | # Place file at ~/.local/share/cmake/onnxruntime
 3 | # This will define the following variables:
 4 | #   onnxruntime_FOUND        -- True if the system has the onnxruntime library
 5 | #   onnxruntime_INCLUDE_DIRS -- The include directories for onnxruntime
 6 | #   onnxruntime_LIBRARIES    -- Libraries to link against
 7 | #   onnxruntime_CXX_FLAGS    -- Additional (required) compiler flags
 8 | 
 9 | include(FindPackageHandleStandardArgs)
10 | 
11 | # Assume we are in <install-prefix>/share/cmake/onnxruntime/onnxruntimeConfig.cmake
12 | get_filename_component(CMAKE_CURRENT_LIST_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
13 | get_filename_component(onnxruntime_INSTALL_PREFIX "${CMAKE_CURRENT_LIST_DIR}/../../../" ABSOLUTE)
14 | 
15 | set(onnxruntime_INCLUDE_DIRS ${onnxruntime_INSTALL_PREFIX}/include)
16 | set(onnxruntime_LIBRARIES onnxruntime)
17 | set(onnxruntime_CXX_FLAGS "") # no flags needed
18 | 
19 | 
20 | find_library(onnxruntime_LIBRARY onnxruntime
21 |     PATHS "${onnxruntime_INSTALL_PREFIX}/lib"
22 | )
23 | 
24 | add_library(onnxruntime SHARED IMPORTED)
25 | set_property(TARGET onnxruntime PROPERTY IMPORTED_LOCATION "${onnxruntime_LIBRARY}")
26 | set_property(TARGET onnxruntime PROPERTY INTERFACE_INCLUDE_DIRECTORIES "${onnxruntime_INCLUDE_DIRS}")
27 | set_property(TARGET onnxruntime PROPERTY INTERFACE_COMPILE_OPTIONS "${onnxruntime_CXX_FLAGS}")
28 | 
29 | find_package_handle_standard_args(onnxruntime DEFAULT_MSG onnxruntime_LIBRARY onnxruntime_INCLUDE_DIRS)
30 | 


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/pda/CMakeLists.txt:
--------------------------------------------------------------------------------
 1 | add_library(pda
 2 | circularnetwork.cpp circularnetwork.h
 3 | greedy.cpp greedy.h
 4 | gurobiwrapper.cpp gurobiwrapper.h
 5 | hashsplitset.cpp hashsplitset.h
 6 | pdnetwork.cpp pdnetwork.h
 7 | pruning.cpp pruning.h
 8 | split.cpp split.h
 9 | splitgraph.cpp splitgraph.h
10 | splitset.cpp splitset.h
11 | lpwrapper.c lpwrapper.h
12 | ecopd.cpp ecopd.h
13 | graph.cpp graph.h
14 | pdtree.cpp pdtree.h
15 | pdtreeset.cpp pdtreeset.h
16 | ecopdmtreeset.cpp ecopdmtreeset.h
17 | )
18 | 
19 | target_link_libraries(pda nclextra)
20 | 


--------------------------------------------------------------------------------
/pda/ecopdmtreeset.cpp:
--------------------------------------------------------------------------------
 1 | /*
 2 |  * EcoPDmtreeset.cpp
 3 |  *
 4 |  *  Created on: Nov 4, 2013
 5 |  *      Author: olga
 6 |  */
 7 | 
 8 | #include "ecopdmtreeset.h"
 9 | #include "tree/mtreeset.h"
10 | 
11 | EcoPDmtreeset::EcoPDmtreeset() {
12 | }
13 | 
14 | EcoPDmtreeset::~EcoPDmtreeset() {
15 | }
16 | 
17 | EcoPDmtreeset::EcoPDmtreeset(const char *userTreeFile, bool &is_rooted,
18 | 	int burnin, int max_count, const char *tree_weight_file) {
19 | 	initEcoSD(userTreeFile, is_rooted, burnin, max_count, tree_weight_file);
20 | }
21 | 
22 | void EcoPDmtreeset::initEcoSD(const char *userTreeFile, bool &is_rooted, int burnin, int max_count,
23 | 	const char *tree_weight_file, IntVector *weights, bool compressed)
24 | {
25 | 	readTrees(userTreeFile, is_rooted, burnin, max_count, weights, compressed);
26 | 	//checkConsistency();
27 | 
28 | 	if (tree_weight_file)
29 | 		readIntVector(tree_weight_file, burnin, max_count, tree_weights);
30 | /*	else if (!weights)
31 | 		tree_weights.resize(size(), 1);*/
32 | 
33 | 	if (size() != tree_weights.size())
34 | 		outError("Tree file and tree weight file have different number of entries");
35 | 
36 | }
37 | 


--------------------------------------------------------------------------------
/pda/ecopdmtreeset.h:
--------------------------------------------------------------------------------
 1 | /*
 2 |  * EcoPDmtreeset.h
 3 |  *
 4 |  *  Created on: Nov 4, 2013
 5 |  *      Author: olga
 6 |  */
 7 | 
 8 | #ifndef ECOPDMTREESET_H_
 9 | #define ECOPDMTREESET_H_
10 | 
11 | #include "tree/mtreeset.h"
12 | 
13 | class EcoPDmtreeset : public MTreeSet
14 | {
15 | public:
16 | 	EcoPDmtreeset();
17 | 
18 | 	/**
19 | 		constructor, read trees from user file
20 | 		@param userTreeFile the name of the user trees
21 | 		@param is_rooted (IN/OUT) true if tree is rooted
22 | 		@param burnin the number of beginning trees to be discarded
23 | 		@param max_count max number of trees to load
24 | 	*/
25 | 	EcoPDmtreeset(const char *userTreeFile, bool &is_rooted, int burnin, int max_count,
26 | 		const char *tree_weight_file = NULL);
27 | 
28 | 	void initEcoSD(const char *userTreeFile, bool &is_rooted, int burnin, int max_count,
29 | 		const char *tree_weight_file = NULL, IntVector *weights = NULL, bool compressed = false);
30 | 
31 | 
32 | 	virtual ~EcoPDmtreeset();
33 | };
34 | 
35 | #endif /* ECOPDMTREESET_H_ */
36 | 


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/pda/graph.cpp:
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https://raw.githubusercontent.com/iqtree/iqtree3/4c823e9757857e098e99c4aba611748d5c4cc8db/pda/graph.cpp


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/pda/graph.h:
--------------------------------------------------------------------------------
 1 | /*
 2 |  * graph.h
 3 |  *
 4 |  *  Created on: Nov 14, 2013
 5 |  *      Author: olga
 6 |  */
 7 | 
 8 | #include <iostream>
 9 | #include <list>
10 | #include <limits.h>
11 | 
12 | #ifndef GRAPH_H_
13 | #define GRAPH_H_
14 | 
15 | using namespace std;
16 | 
17 | class Graph
18 | {
19 |     int V;    			// No. of vertices
20 |     list<int> *adj;		// Pointer to an array containing adjacency lists
21 |     bool isCyclicUtil(int v, bool visited[], bool *rs);  // used by isCyclic()
22 | 
23 | public:
24 |     Graph(int V);   // Constructor
25 |     void addEdge(int v, int w);   // to add an edge to graph
26 |     bool isCyclic();    // returns true if there is a cycle in this graph
27 | };
28 | 
29 | #endif
30 | 


--------------------------------------------------------------------------------
/phylo-yaml/CMakeLists.txt:
--------------------------------------------------------------------------------
1 | add_library(phyloYAML
2 | statespace.h
3 | statespace.cpp
4 | )
5 | 
6 | target_link_libraries(phyloYAML yaml-cpp)
7 | 


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/pll/hardware.h:
--------------------------------------------------------------------------------
 1 | #ifndef PLL_HARDWARE
 2 | #define PLL_HARDWARE
 3 | 
 4 | /* leaf 1 */
 5 | /* edx */
 6 | #define PLL_HAS_MMX             1 << 23
 7 | #define PLL_HAS_SSE             1 << 25
 8 | #define PLL_HAS_SSE2            1 << 26
 9 | 
10 | /* ecx */
11 | #define PLL_HAS_SSE3            1
12 | #define PLL_HAS_SSSE3           1 <<  9
13 | #define PLL_HAS_FMA             1 << 12
14 | #define PLL_HAS_SSE41           1 << 19
15 | #define PLL_HAS_SSE42           1 << 20
16 | #define PLL_HAS_AVX             1 << 28
17 | 
18 | 
19 | /* leaf 7 */
20 | /* ebx */
21 | #define PLL_HAS_AVX2            1 <<  5
22 | 
23 | /* leaf 0x80000001 */
24 | /* ecx*/
25 | #define PLL_HAS_SSE4A           1 <<  6
26 | #define PLL_HAS_FMA4            1 << 16
27 | 
28 | typedef struct
29 | {
30 |   int has_mmx;
31 |   int has_sse;
32 |   int has_sse2;
33 |   int has_sse3;
34 |   int has_ssse3;
35 |   int has_sse41;
36 |   int has_sse42;
37 |   int has_sse4a;
38 |   int has_avx;
39 |   int has_avx2;
40 |   int has_fma;
41 |   int has_fma4;
42 |   int cpu_sockets;
43 |   int cores;
44 |   char vendor[13];
45 | 
46 | } pllHardwareInfo;
47 | 
48 | #endif
49 | 


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/pll/systypes.h:
--------------------------------------------------------------------------------
 1 | #ifdef WIN32
 2 | #include <direct.h>
 3 | #endif
 4 | 
 5 | #if !defined(WIN32) && !defined(WIN64)
 6 | #include <unistd.h>
 7 | #include <sys/times.h>
 8 | #include <sys/types.h>
 9 | #include <sys/time.h>
10 | #endif
11 | 


--------------------------------------------------------------------------------
/pll/treeIO.h:
--------------------------------------------------------------------------------
 1 | /*
 2 |  * treeIO.h
 3 |  *
 4 |  *  Created on: Nov 22, 2012
 5 |  *      Author: tung
 6 |  */
 7 | 
 8 | /*
 9 | I just put some declarations of the functions that I need here.
10 | Please extend this file. It's important to have a header file.
11 | It make things much easier for the integration with other software.
12 | */
13 | 
14 | #ifndef TREEIO_H_
15 | #define TREEIO_H_
16 | 
17 | #include "pll.h"
18 | 
19 | char *pllTreeToNewick(char *treestr, tree *tr, nodeptr p, pllBoolean printBranchLengths, pllBoolean printNames, pllBoolean printLikelihood,
20 | 		  pllBoolean rellTree, pllBoolean finalPrint, int perGene, pllBoolean branchLabelSupport, pllBoolean printSHSupport);
21 | double getBranchLength(pllInstance *tr, partitionList *pr, int perGene, nodeptr p);
22 | 
23 | #endif /* TREEIO_H_ */
24 | 


--------------------------------------------------------------------------------
/simulator/CMakeLists.txt:
--------------------------------------------------------------------------------
1 | add_library(simulator
2 | alisimulator.cpp alisimulator.h
3 | alisimulatorinvar.cpp alisimulatorinvar.h
4 | alisimulatorheterogeneity.cpp alisimulatorheterogeneity.h
5 | alisimulatorheterogeneityinvar.cpp alisimulatorheterogeneityinvar.h
6 | )
7 | target_link_libraries(simulator alignment ncl gsl model)
8 | 


--------------------------------------------------------------------------------
/sprng/CMakeLists.txt:
--------------------------------------------------------------------------------
1 | add_library(sprng 
2 | lcg64.c
3 | makeseed.c
4 | memory.c
5 | store.c
6 | primes-lcg64.c
7 | checkid.c)
8 | 


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/sprng/README:
--------------------------------------------------------------------------------
1 | The original source files are from the SPRNG (Scalable Pseudo Random 
2 | Number Generator) library package.
3 | 
4 | Mascagni, Michael and Srinivasan, Ashok (2000)
5 |   SPRNG: A Scalable Library for Pseudorandom Number Generation.
6 |   ACM Trans. Math. Software, 26:436-461, DOI: 10.1145/358407.358427
7 | 
8 | 


--------------------------------------------------------------------------------
/sprng/makeseed.c:
--------------------------------------------------------------------------------
 1 | #include <time.h>
 2 | 
 3 | #ifdef __STDC__
 4 | int make_new_seed()
 5 | #else
 6 | int make_new_seed()
 7 | #endif
 8 | {
 9 |   time_t tp;
10 |   struct tm *temp;
11 |   unsigned int temp2, temp3;
12 |   static unsigned int temp4 = 0xe0e1;
13 |   
14 |   time(&tp);
15 |   temp = localtime(&tp);
16 |   
17 |   temp2 = (temp->tm_sec<<26)+(temp->tm_min<<20)+(temp->tm_hour<<15)+
18 |     (temp->tm_mday<<10)+(temp->tm_mon<<6);
19 |   temp3 = (temp->tm_year<<13)+(temp->tm_wday<<10)+(temp->tm_yday<<1)+
20 |     temp->tm_isdst;
21 |   temp2 ^= clock()^temp3;
22 | 
23 |   temp4 = (temp4*0xeeee)%0xffff;
24 |   temp2 ^= temp4<<16;
25 |   temp4 = (temp4*0xaeee)%0xffff;
26 |   temp2 ^= temp4;
27 |   
28 |   temp2 &= 0x7fffffff;
29 | 
30 |   return temp2;
31 | }
32 | 
33 | 
34 | #if 0
35 | main()
36 | {
37 |   printf("%u\n", make_new_seed());
38 | }
39 | #endif
40 | 
41 | 
42 | 


--------------------------------------------------------------------------------
/sprng/memory.c:
--------------------------------------------------------------------------------
 1 | #include <stdio.h>
 2 | #include <stdlib.h>
 3 | 
 4 | #ifdef __STDC__
 5 | void *_mymalloc(long size, int line, char *message)
 6 | #else
 7 | void *_mymalloc(size, line, message)
 8 | long size;
 9 | int line;
10 | char *message;
11 | #endif
12 | {
13 |   char *temp;
14 | 
15 |   if(size == 0)
16 |     return NULL;
17 | 
18 |   temp = (char *) malloc(size);
19 |   
20 |   if(temp == NULL)
21 |     {
22 |       fprintf(stderr,"\nmemory allocation failure in file: %s at line number: %d\n", message, line);
23 |       return NULL;
24 |     }
25 | 
26 |   return (void *) temp;
27 | }
28 | 


--------------------------------------------------------------------------------
/sprng/memory.h:
--------------------------------------------------------------------------------
 1 | #define mymalloc(a) (_mymalloc((a), __LINE__, __FILE__))
 2 | 
 3 | #ifndef ANSI_ARGS
 4 | #ifdef __STDC__
 5 | #define ANSI_ARGS(args) args
 6 | #else
 7 | #define ANSI_ARGS(args) ()
 8 | #endif
 9 | #endif
10 | 
11 | void *_mymalloc ANSI_ARGS((long size, int line, char *message));
12 | 
13 | 


--------------------------------------------------------------------------------
/sprng/primes-lcg64.h:
--------------------------------------------------------------------------------
 1 | #ifndef _primes64_h_
 2 | #define _primes64_h_
 3 | 
 4 | #ifndef ANSI_ARGS
 5 | #ifdef __STDC__
 6 | #define ANSI_ARGS(args) args
 7 | #else
 8 | #define ANSI_ARGS(args) ()
 9 | #endif
10 | #endif
11 | 
12 | int getprime ANSI_ARGS((int need, unsigned int *prime_array, int offset));
13 |  
14 | #define MAXPRIME 3037000501U  /* largest odd # < sqrt(2)*2^31+2 */
15 | #define MINPRIME 55108   /* sqrt(MAXPRIME) */
16 | #define MAXPRIMEOFFSET 146138719U /* Total number of available primes */
17 | 
18 | #endif
19 | 


--------------------------------------------------------------------------------
/sprng/store.h:
--------------------------------------------------------------------------------
 1 | #ifndef _STORE_H
 2 | #define _STORE_H
 3 | 
 4 | /* Numbers are stored with most significant bit first (left most) */
 5 | 
 6 | int store_long(unsigned long l, int nbytes, unsigned char *c);
 7 | int store_longarray(unsigned long *l, int n, int nbytes, unsigned char *c);
 8 | int load_long(unsigned char *c, int nbytes, unsigned long *l);
 9 | int load_longarray(unsigned char *c, int n, int nbytes, unsigned long *l);
10 | int store_int(unsigned int l, int nbytes, unsigned char *c);
11 | int store_intarray(unsigned int *l, int n, int nbytes, unsigned char *c);
12 | int load_int(unsigned char *c, int nbytes, unsigned int *l);
13 | int load_intarray(unsigned char *c, int n, int nbytes, unsigned int *l);
14 | 
15 | 
16 | #ifdef _LONG_LONG
17 | 
18 | int store_longlong(unsigned long long l, int nbytes, unsigned char *c);
19 | int store_longlongarray(unsigned long long *l, int n, int nbytes, unsigned char *c);
20 | int load_longlong(unsigned char *c, int nbytes, unsigned long long *l);
21 | int load_longlongarray(unsigned char *c, int n, int nbytes, unsigned long long *l);
22 | 
23 | #endif /* _LONG_LONG */
24 | 
25 | 
26 | #endif /* _STORE_H */
27 | 
28 | 


--------------------------------------------------------------------------------
/terrace/CMakeLists.txt:
--------------------------------------------------------------------------------
 1 | add_library(terrace
 2 | terracenode.cpp
 3 | terracenode.hpp
 4 | terracetree.cpp
 5 | terracetree.hpp
 6 | presenceabsencematrix.cpp
 7 | presenceabsencematrix.hpp
 8 | terrace.hpp
 9 | terrace.cpp
10 | )
11 | 
12 | target_link_libraries(terrace tree)
13 | 


--------------------------------------------------------------------------------
/terracetphast/CMakeLists.txt:
--------------------------------------------------------------------------------
1 | add_library(terracetphast
2 | terracetphast.cpp
3 | terracetphast.h
4 | )
5 | 
6 | target_link_libraries(terracetphast tree alignment terraphast)
7 | 


--------------------------------------------------------------------------------
/terraphast/.gitattributes:
--------------------------------------------------------------------------------
1 | appveyor.yml eol=crlf
2 | 


--------------------------------------------------------------------------------
/terraphast/.gitignore:
--------------------------------------------------------------------------------
 1 | build
 2 | .idea
 3 | cmake-*
 4 | *.o
 5 | *.user
 6 | .vscode
 7 | .ycm_extra_conf.py
 8 | .ycm_extra_conf.pyc
 9 | callgrind.out.*
10 | *.orig
11 | 


--------------------------------------------------------------------------------
/terraphast/AUTHORS:
--------------------------------------------------------------------------------
 1 | This library was built in a joint effort by
 2 | 
 3 |   Peter Boszoky
 4 |   Tobias Ribizel
 5 |   Fedor Scholz
 6 |   Florian Weber
 7 | 
 8 | The C interface was provided by
 9 | 
10 |   Michael Hamann
11 |   Bui Quang Minh
12 |   Alexandros Stamatakis
13 | 


--------------------------------------------------------------------------------
/terraphast/app/app.cpp:
--------------------------------------------------------------------------------
 1 | #include <bitset>
 2 | #include <chrono>
 3 | #include <fstream>
 4 | #include <iomanip>
 5 | #include <iostream>
 6 | #include <sstream>
 7 | #include <thread>
 8 | 
 9 | #include <terraces/simple.hpp>
10 | 
11 | int main(int argc, char** argv) try {
12 | 	auto tree_file_name = std::string{};
13 | 	auto data_file_name = std::string{};
14 | 	if (argc == 3) {
15 | 		tree_file_name = argv[1];
16 | 		data_file_name = argv[2];
17 | 	} else {
18 | 		std::cerr << "Usage: \n" << argv[0] << " <tree-file> <occurrence file>\n";
19 | 		return 1;
20 | 	}
21 | 	auto trees = std::ostringstream{};
22 | 	const auto terraces_count =
23 | 	        terraces::simple::print_terrace_from_file(tree_file_name, data_file_name, trees);
24 | 
25 | 	std::cout << "There are " << terraces_count
26 | 	          << " trees on the terrace.\n\nThe trees in question are:\n"
27 | 	          << trees.str() << '\n';
28 | } catch (std::exception& e) {
29 | 	std::cerr << "Error: " << e.what() << "\n";
30 | }
31 | 


--------------------------------------------------------------------------------
/terraphast/appveyor.yml:
--------------------------------------------------------------------------------
 1 | version: 1.0.{build}
 2 | configuration: Release
 3 | platform:
 4 | - x64
 5 | - Win32
 6 | clone_depth: 1
 7 | before_build:
 8 | - cmd: 'scripts\build_appveyor.bat'
 9 | build:
10 |   project: terraphast.sln
11 |   parallel: true
12 |   verbosity: minimal
13 | test_script:
14 | - cmd: 'Release\unittests.exe'
15 | 
16 | 


--------------------------------------------------------------------------------
/terraphast/catch/LICENSE.txt:
--------------------------------------------------------------------------------
 1 | Boost Software License - Version 1.0 - August 17th, 2003
 2 | 
 3 | Permission is hereby granted, free of charge, to any person or organization
 4 | obtaining a copy of the software and accompanying documentation covered by
 5 | this license (the "Software") to use, reproduce, display, distribute,
 6 | execute, and transmit the Software, and to prepare derivative works of the
 7 | Software, and to permit third-parties to whom the Software is furnished to
 8 | do so, all subject to the following:
 9 | 
10 | The copyright notices in the Software and this entire statement, including
11 | the above license grant, this restriction and the following disclaimer,
12 | must be included in all copies of the Software, in whole or in part, and
13 | all derivative works of the Software, unless such copies or derivative
14 | works are solely in the form of machine-executable object code generated by
15 | a source language processor.
16 | 
17 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
18 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
19 | FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
20 | SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
21 | FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
22 | ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
23 | DEALINGS IN THE SOFTWARE.
24 | 


--------------------------------------------------------------------------------
/terraphast/cmake/FindGMP.cmake:
--------------------------------------------------------------------------------
 1 | find_path(GMP_INCLUDE_DIR NAMES gmp.h gmpxx.h)
 2 | find_library(GMP_LIBRARIES NAMES gmp libgmp)
 3 | find_library(GMPXX_LIBRARIES NAMES gmpxx libgmpxx )
 4 | 
 5 | include(FindPackageHandleStandardArgs)
 6 | find_package_handle_standard_args(GMP DEFAULT_MSG GMP_INCLUDE_DIR GMP_LIBRARIES GMPXX_LIBRARIES)
 7 | mark_as_advanced(GMP_INCLUDE_DIR GMP_LIBRARIES)
 8 | add_library(gmp INTERFACE IMPORTED)
 9 | set_target_properties(gmp PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${GMP_INCLUDE_DIR})
10 | set_target_properties(gmp PROPERTIES INTERFACE_LINK_LIBRARIES ${GMP_LIBRARIES})
11 | add_library(gmpxx INTERFACE IMPORTED)
12 | set_target_properties(gmpxx PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${GMP_INCLUDE_DIR})
13 | set_target_properties(gmpxx PROPERTIES INTERFACE_LINK_LIBRARIES ${GMPXX_LIBRARIES})


--------------------------------------------------------------------------------
/terraphast/documentation/Changelog.md:
--------------------------------------------------------------------------------
 1 | Since 1st meeting
 2 | =================
 3 | 
 4 | Optimizations
 5 | -------------
 6 | 
 7 | * implement bitvector with rank support
 8 | * use bitvector instead of index vectors for subsets
 9 | * inline lots of often-used methods
10 | * deduplicate constraints
11 | * remap constraints (removing inner nodes from the numbering)
12 | * halved union-find storage by out-of-bounds parent trick
13 | * avoid allocations by reusing old storage
14 | * some micro-optimizations
15 | 
16 | Fixes and Features
17 | ------------------
18 | 
19 | * fast terrace check without traversing the tree to the end
20 | * fixed subtree computation (problematic input data caused an assertion to fail)
21 | * fix counting bug (communication problem)
22 | * don't count incorrectly rooted trees
23 | * extracted all computations to callback methods
24 | * implemented logging + stack state decorators
25 | * implemented isomorphy check
26 | * Visual C++ compatibility checked with appveyor
27 | * extracted intrinsics to stay portable
28 | 


--------------------------------------------------------------------------------
/terraphast/documentation/Dependencies.md:
--------------------------------------------------------------------------------
 1 | 
 2 | Dependencies
 3 | ============
 4 | 
 5 | This library has multiple Dependencies
 6 | 
 7 | 
 8 | Detailed List
 9 | -------------
10 | 
11 | * [Catch](https://github.com/philsquared/Catch). The header `catch.hpp` is supposed to be in the default include-path. The framework is avaiable multiple distros under the name `catch`.
12 | * ...
13 | 
14 | Copyable List for installation
15 | ------------------------------
16 | 
17 | 
18 | ```
19 | catch
20 | ```
21 | 
22 | 


--------------------------------------------------------------------------------
/terraphast/include/terraces/bigint.hpp:
--------------------------------------------------------------------------------
 1 | #ifndef TERRACES_BIGINT_HPP
 2 | #define TERRACES_BIGINT_HPP
 3 | 
 4 | #include "definitions.hpp"
 5 | 
 6 | #ifndef USE_GMP
 7 | #include "clamped_uint.hpp"
 8 | namespace terraces {
 9 | using big_integer = terraces::overflow_except_uint;
10 | }
11 | #else
12 | #include <gmpxx.h>
13 | #include <iosfwd>
14 | namespace terraces {
15 | class big_integer {
16 | 	mpz_class m_value;
17 | 
18 | public:
19 | 	big_integer(index i = 0);
20 | 	big_integer& operator+=(const big_integer& other);
21 | 	big_integer& operator*=(const big_integer& other);
22 | 	bool is_clamped() const;
23 | 	const mpz_class& value() const;
24 | };
25 | bool operator==(const big_integer& a, const big_integer& b);
26 | bool operator!=(const big_integer& a, const big_integer& b);
27 | big_integer operator+(const big_integer& a, const big_integer& b);
28 | big_integer operator*(const big_integer& a, const big_integer& b);
29 | std::ostream& operator<<(std::ostream& stream, const big_integer& val);
30 | } // namespace terraces
31 | #endif
32 | 
33 | #endif // TERRACES_BIGINT_HPP
34 | 


--------------------------------------------------------------------------------
/terraphast/include/terraces/bitmatrix.hpp:
--------------------------------------------------------------------------------
 1 | #ifndef TERRACES_BITMATRIX_HPP
 2 | #define TERRACES_BITMATRIX_HPP
 3 | 
 4 | #include <vector>
 5 | 
 6 | #include "trees.hpp"
 7 | 
 8 | namespace terraces {
 9 | 
10 | /** A (memory-wise) compact bitmatrix. */
11 | class bitmatrix {
12 | public:
13 | 	/** Constructs a bitmatrix with \p rows rows and \p cols columns. */
14 | 	bitmatrix(index rows, index cols);
15 | 
16 | 	/** @returns the number of rows. */
17 | 	index rows() const;
18 | 	/** @returns the number of columns. */
19 | 	index cols() const;
20 | 
21 | 	/** Returns the entry at cordinates (row, col). */
22 | 	bool get(index row, index col) const;
23 | 	/** Sets the entry at coordinates (row, col). */
24 | 	void set(index row, index col, bool val);
25 | 	/** Writes the bit rows \p in1 | \p in2 to row \p out. */
26 | 	void row_or(index in1, index in2, index out);
27 | 
28 | 	/** Returns a bitmatrix containing only the given columns. */
29 | 	bitmatrix get_cols(const std::vector<std::size_t>& cols) const;
30 | 
31 | 	/** Tests for equality with another bitmatrix. */
32 | 	bool operator==(const bitmatrix& other) const;
33 | 	/** Tests for inequality with another bitmatrix. */
34 | 	bool operator!=(const bitmatrix& other) const;
35 | 
36 | private:
37 | 	index m_rows;
38 | 	index m_cols;
39 | 	std::vector<bool> m_vec; // yes, it's evil
40 | };
41 | }
42 | 
43 | #endif // TERRACES_BITMATRIX_HPP
44 | 


--------------------------------------------------------------------------------
/terraphast/include/terraces/clamped_uint.hpp:
--------------------------------------------------------------------------------
 1 | #ifndef TERRACES_CLAMPED_UINT_HPP
 2 | #define TERRACES_CLAMPED_UINT_HPP
 3 | 
 4 | #include "definitions.hpp"
 5 | 
 6 | #include <iosfwd>
 7 | 
 8 | namespace terraces {
 9 | 
10 | template <bool except>
11 | class checked_uint {
12 | 	index m_value;
13 | 
14 | public:
15 | 	checked_uint(index value = 0);
16 | 
17 | 	checked_uint<except>& operator+=(checked_uint<except> other);
18 | 	checked_uint<except>& operator*=(checked_uint<except> other);
19 | 	bool is_clamped() const;
20 | 	index value() const;
21 | };
22 | 
23 | template <bool except>
24 | bool operator==(checked_uint<except> a, checked_uint<except> b);
25 | 
26 | template <bool except>
27 | bool operator!=(checked_uint<except> a, checked_uint<except> b);
28 | 
29 | template <bool except>
30 | checked_uint<except> operator+(checked_uint<except> a, checked_uint<except> b);
31 | 
32 | template <bool except>
33 | checked_uint<except> operator*(checked_uint<except> a, checked_uint<except> b);
34 | 
35 | template <bool except>
36 | std::ostream& operator<<(std::ostream& stream, checked_uint<except> val);
37 | 
38 | using clamped_uint = checked_uint<false>;
39 | using overflow_except_uint = checked_uint<true>;
40 | 
41 | } // namespace terraces
42 | 
43 | #endif // TERRACES_CLAMPED_UINT_HPP
44 | 


--------------------------------------------------------------------------------
/terraphast/include/terraces/definitions.hpp:
--------------------------------------------------------------------------------
 1 | #ifndef DEFINITIONS_HPP
 2 | #define DEFINITIONS_HPP
 3 | 
 4 | #include <limits>
 5 | 
 6 | namespace terraces {
 7 | 
 8 | /** Our index type. */
 9 | using index = std::size_t;
10 | 
11 | /** Index value used to represent a non-index. */
12 | #ifdef CLANG_UNDER_VS
13 | #undef max
14 | #endif
15 | constexpr static auto none = std::numeric_limits<index>::max();
16 | 
17 | } // namespace terraces
18 | 
19 | #endif // DEFINITIONS_HPP
20 | 


--------------------------------------------------------------------------------
/terraphast/include/terraces/rooting.hpp:
--------------------------------------------------------------------------------
 1 | #ifndef TERRACES_ROOTING_HPP
 2 | #define TERRACES_ROOTING_HPP
 3 | 
 4 | #include "trees.hpp"
 5 | 
 6 | namespace terraces {
 7 | 
 8 | /**
 9 |  * Returns the root split of the given tree.
10 |  * The root split is a bitvector of size #leaves that is 1
11 |  * for all leaves in the right subtree of the root node.
12 |  */
13 | std::vector<bool> root_split(const tree& t, index num_leaves);
14 | 
15 | /**
16 |  * Re-roots the given tree in-place.
17 |  * The node at the given \p node_idx will be placed below the new root node.
18 |  */
19 | tree reroot_at_node(const tree& t, index node_idx);
20 | 
21 | /**
22 |  * Re-roots the given tree in-place.
23 |  * The leaf corresponding to the given \p comp_taxon will be placed to the right of the root.
24 |  * child of our new root, with the rest of the tree being the left subtree.
25 |  */
26 | void reroot_at_taxon_inplace(tree& t, index comp_taxon);
27 | 
28 | } // namespace terraces
29 | 
30 | #endif
31 | 


--------------------------------------------------------------------------------
/terraphast/include/terraces/subtree_extraction.hpp:
--------------------------------------------------------------------------------
 1 | #ifndef SUBTREE_EXTRACTION_H
 2 | #define SUBTREE_EXTRACTION_H
 3 | 
 4 | #include <vector>
 5 | 
 6 | #include "bitmatrix.hpp"
 7 | #include "trees.hpp"
 8 | 
 9 | namespace terraces {
10 | 
11 | /**
12 |  * Extracts all (pruned) subtrees from the given input tree and missing data matrix.
13 |  * For every column of the missing data matrix, a corresponding tree is constructed,
14 |  * containing only leaves for which this matrix contains a 1.
15 |  */
16 | std::vector<tree> subtrees(const tree& t, const bitmatrix& occ);
17 | 
18 | } // namespace terraces
19 | 
20 | #endif // SUBTREE_EXTRACTION_H
21 | 


--------------------------------------------------------------------------------
/terraphast/lib/bigint.cpp:
--------------------------------------------------------------------------------
 1 | #include <terraces/bigint.hpp>
 2 | 
 3 | #include <ostream>
 4 | 
 5 | #ifdef USE_GMP
 6 | namespace terraces {
 7 | big_integer::big_integer(index i) : m_value{i} {}
 8 | big_integer& big_integer::operator+=(const big_integer& other) {
 9 | 	m_value += other.m_value;
10 | 	return *this;
11 | }
12 | big_integer& big_integer::operator*=(const big_integer& other) {
13 | 	m_value *= other.m_value;
14 | 	return *this;
15 | }
16 | bool big_integer::is_clamped() const { return false; }
17 | const mpz_class& big_integer::value() const { return m_value; }
18 | 
19 | big_integer operator+(const big_integer& a, const big_integer& b) {
20 | 	big_integer result = a;
21 | 	result += b;
22 | 	return result;
23 | }
24 | 
25 | big_integer operator*(const big_integer& a, const big_integer& b) {
26 | 	big_integer result = a;
27 | 	result *= b;
28 | 	return result;
29 | }
30 | 
31 | bool operator==(const big_integer& a, const big_integer& b) { return a.value() == b.value(); }
32 | 
33 | bool operator!=(const big_integer& a, const big_integer& b) { return !(a == b); }
34 | 
35 | std::ostream& operator<<(std::ostream& stream, const big_integer& val) {
36 | 	return stream << val.value();
37 | }
38 | 
39 | } // namespace terraces
40 | #endif // USE_GMP
41 | 


--------------------------------------------------------------------------------
/terraphast/lib/bitmatrix.cpp:
--------------------------------------------------------------------------------
 1 | #include <terraces/bitmatrix.hpp>
 2 | 
 3 | #include <cassert>
 4 | 
 5 | namespace terraces {
 6 | 
 7 | bitmatrix::bitmatrix(index rows, index cols) : m_rows{rows}, m_cols{cols}, m_vec(rows * cols) {}
 8 | 
 9 | index bitmatrix::rows() const { return m_rows; }
10 | index bitmatrix::cols() const { return m_cols; }
11 | 
12 | bool bitmatrix::get(index row, index col) const {
13 | 	assert(row < m_rows && col < m_cols);
14 | 	return m_vec[row * m_cols + col];
15 | }
16 | 
17 | void bitmatrix::set(index row, index col, bool val) {
18 | 	assert(row < m_rows && col < m_cols);
19 | 	m_vec[row * m_cols + col] = val;
20 | }
21 | 
22 | void bitmatrix::row_or(index in1, index in2, index out) {
23 | 	for (index i = 0; i < cols(); ++i) {
24 | 		set(out, i, get(in1, i) || get(in2, i));
25 | 	}
26 | }
27 | 
28 | bitmatrix bitmatrix::get_cols(const std::vector<std::size_t>& cols) const {
29 | 	assert(cols.size() <= this->cols());
30 | 	auto ret = bitmatrix{rows(), cols.size()};
31 | 	for (auto i = std::size_t{}; i < rows(); ++i) {
32 | 		for (auto j = std::size_t{}; j < cols.size(); ++j) {
33 | 			ret.set(i, j, get(i, cols[j]));
34 | 		}
35 | 	}
36 | 	return ret;
37 | }
38 | 
39 | bool bitmatrix::operator==(const bitmatrix& other) const {
40 | 	return other.rows() == rows() && other.cols() == cols() && other.m_vec == m_vec;
41 | }
42 | 
43 | bool bitmatrix::operator!=(const bitmatrix& other) const { return !(*this == other); }
44 | 
45 | } // namespace terraces
46 | 


--------------------------------------------------------------------------------
/terraphast/lib/bits.hpp:
--------------------------------------------------------------------------------
 1 | #ifndef BITS_HPP
 2 | #define BITS_HPP
 3 | 
 4 | #include <intrinsics.hpp>
 5 | 
 6 | namespace terraces {
 7 | namespace bits {
 8 | 
 9 | static_assert(std::numeric_limits<index>::radix == 2, "Our integers must be of base 2");
10 | constexpr index word_bits = std::numeric_limits<index>::digits;
11 | 
12 | inline index block_index(index i) { return i / word_bits; }
13 | inline index base_index(index block) { return block * word_bits; }
14 | inline index shift_index(index i) { return i % word_bits; }
15 | inline index set_mask(index i) { return index(1) << (i & (word_bits - 1)); }
16 | inline index clear_mask(index i) { return ~set_mask(i); }
17 | inline index prefix_mask(index i) { return set_mask(i) - 1; }
18 | inline index next_bit(index block, index i) { return i + bitscan(block >> shift_index(i)); }
19 | inline index next_bit0(index block, index i) { return i + bitscan(block); }
20 | inline bool has_next_bit(index block, index i) { return (block >> shift_index(i)) != 0; }
21 | inline bool has_next_bit0(index block) { return block != 0; }
22 | inline index partial_popcount(index block, index i) { return popcount(block & prefix_mask(i)); }
23 | 
24 | } // namespace bits
25 | } // namespace terraces
26 | 
27 | #endif // BITS_HPP
28 | 


--------------------------------------------------------------------------------
/terraphast/lib/cl/intrinsics.hpp:
--------------------------------------------------------------------------------
 1 | #include <terraces/definitions.hpp>
 2 | 
 3 | #ifdef _WIN64
 4 | #pragma intrinsic(_BitScanForward64, _BitScanReverse64, __popcnt64)
 5 | #else
 6 | #pragma intrinsic(_BitScanForward, _BitScanReverse, __popcnt)
 7 | #endif
 8 | 
 9 | namespace terraces {
10 | namespace bits {
11 | 
12 | #ifdef _WIN64
13 | inline index popcount(index word) { return (index)__popcnt64(word); }
14 | 
15 | inline index bitscan(index word) {
16 | 	unsigned long idx;
17 | 	_BitScanForward64(&idx, word);
18 | 	return (index)idx;
19 | }
20 | 
21 | inline index rbitscan(index word) {
22 | 	unsigned long idx;
23 | 	_BitScanReverse64(&idx, word);
24 | 	return (index)idx;
25 | }
26 | #else
27 | inline index popcount(index word) { return index(__popcnt(word)); }
28 | 
29 | inline index bitscan(index word) {
30 | 	unsigned long idx;
31 | 	_BitScanForward(&idx, word);
32 | 	return index(idx);
33 | }
34 | 
35 | inline index rbitscan(index word) {
36 | 	unsigned long idx;
37 | 	_BitScanReverse(&idx, word);
38 | 	return index(idx);
39 | }
40 | #endif
41 | 
42 | namespace {
43 | constexpr index max_index = std::numeric_limits<index>::max();
44 | }
45 | 
46 | inline bool add_overflow(index a, index b, index& result) {
47 | 	result = a + b;
48 | 	if (max_index - b < a) {
49 | 		return true;
50 | 	} else {
51 | 		return false;
52 | 	}
53 | }
54 | 
55 | inline bool mul_overflow(index a, index b, index& result) {
56 | 	result = a * b;
57 | 	if (max_index / b < a) {
58 | 		return true;
59 | 	} else {
60 | 		return false;
61 | 	}
62 | }
63 | 
64 | } // namespace bits
65 | } // namespace terraces
66 | 


--------------------------------------------------------------------------------
/terraphast/lib/constraints_impl.hpp:
--------------------------------------------------------------------------------
 1 | #ifndef CONSTRAINTS_IMPL_HPP
 2 | #define CONSTRAINTS_IMPL_HPP
 3 | 
 4 | #include <terraces/constraints.hpp>
 5 | 
 6 | namespace terraces {
 7 | 
 8 | namespace utils {
 9 | template <class T1, class T2>
10 | struct named_output;
11 | }
12 | 
13 | std::ostream& operator<<(std::ostream& stream, utils::named_output<constraints, name_map> output);
14 | 
15 | } // namespace terraces
16 | 
17 | #endif // CONSTRAINTS_IMPL_HPP
18 | 


--------------------------------------------------------------------------------
/terraphast/lib/gcc_clang/intrinsics.hpp:
--------------------------------------------------------------------------------
 1 | #include <terraces/definitions.hpp>
 2 | 
 3 | namespace terraces {
 4 | namespace bits {
 5 | 
 6 | inline index popcount(index word) { return index(__builtin_popcountll(word)); }
 7 | 
 8 | inline index bitscan(index word) { return index(__builtin_ctzll(word)); }
 9 | 
10 | static_assert(sizeof(long long) >= sizeof(index), "intrinsic word sizes incompatible");
11 | 
12 | inline index rbitscan(index word) {
13 | 	return index(std::numeric_limits<long long>::digits - __builtin_clzll(word));
14 | }
15 | 
16 | inline bool add_overflow(index a, index b, index& result) {
17 | 	return __builtin_add_overflow(a, b, &result);
18 | }
19 | 
20 | inline bool mul_overflow(index a, index b, index& result) {
21 | 	return __builtin_mul_overflow(a, b, &result);
22 | }
23 | 
24 | } // namespace bits
25 | } // namespace terraces
26 | 


--------------------------------------------------------------------------------
/terraphast/lib/intel/intrinsics.hpp:
--------------------------------------------------------------------------------
 1 | #include <terraces/definitions.hpp>
 2 | 
 3 | namespace terraces {
 4 | namespace bits {
 5 | 
 6 | #if defined(__LP64__) || defined(_LP64)
 7 | inline index popcount(index word) { return index(_popcnt64(word)); }
 8 | 
 9 | inline index bitscan(index word) {
10 |     unsigned int idx;
11 |     _BitScanForward64(&idx, word);
12 |     return index(idx);
13 | }
14 | 
15 | inline index rbitscan(index word) {
16 |     unsigned int idx;
17 |     _BitScanReverse64(&idx, word);
18 |     return index(idx);
19 | }
20 | #else
21 | inline index popcount(index word) { return index(_popcnt(word)); }
22 | 
23 | inline index bitscan(index word) {
24 |     unsigned int idx;
25 |     _BitScanForward(&idx, word);
26 |     return index(idx);
27 | }
28 | 
29 | inline index rbitscan(index word) {
30 |     unsigned int idx;
31 |     _BitScanReverse(&idx, word);
32 |     return index(idx);
33 | }
34 | #endif
35 | 
36 | namespace {
37 | constexpr index max_index = std::numeric_limits<index>::max();
38 | }
39 | 
40 | inline bool add_overflow(index a, index b, index& result) {
41 |     result = a + b;
42 |     if (max_index - b < a) {
43 |         return true;
44 |     } else {
45 |         return false;
46 |     }
47 | }
48 | 
49 | inline bool mul_overflow(index a, index b, index& result) {
50 |     result = a * b;
51 |     if (max_index / b < a) {
52 |         return true;
53 |     } else {
54 |         return false;
55 |     }
56 | }
57 | 
58 | } // namespace bits
59 | } // namespace terraces
60 | 


--------------------------------------------------------------------------------
/terraphast/lib/nodes.cpp:
--------------------------------------------------------------------------------
 1 | #include <terraces/trees.hpp>
 2 | 
 3 | #include <ostream>
 4 | 
 5 | namespace terraces {
 6 | 
 7 | std::ostream& operator<<(std::ostream& s, const node& n) {
 8 | 	auto print_index = [&s](index i) {
 9 | 		if (i == none) {
10 | 			s << "none";
11 | 		} else {
12 | 			s << i;
13 | 		}
14 | 	};
15 | 	s << '(';
16 | 	print_index(n.data[0]);
17 | 	s << ", ";
18 | 	print_index(n.data[1]);
19 | 	s << ", ";
20 | 	print_index(n.data[2]);
21 | 	s << ')';
22 | 	return s;
23 | }
24 | 
25 | } // namespace terraces
26 | 


--------------------------------------------------------------------------------
/terraphast/lib/subtree_extraction_impl.hpp:
--------------------------------------------------------------------------------
 1 | #ifndef SUBTREE_EXTRACTION_IMPL_HPP
 2 | #define SUBTREE_EXTRACTION_IMPL_HPP
 3 | 
 4 | #include <terraces/subtree_extraction.hpp>
 5 | 
 6 | namespace terraces {
 7 | 
 8 | std::pair<bitmatrix, std::vector<index>> compute_node_occ(const tree& t, const bitmatrix& occ);
 9 | 
10 | index induced_lca(const tree& t, const bitmatrix& node_occ, index column);
11 | 
12 | tree subtree(const tree& t, const bitmatrix& node_occ,
13 |              const std::vector<index>& num_leaves_per_site, index site);
14 | 
15 | } // namespace terraces
16 | 
17 | #endif // SUBTREE_EXTRACTION_IMPL_HPP
18 | 


--------------------------------------------------------------------------------
/terraphast/lib/union_find.hpp:
--------------------------------------------------------------------------------
 1 | #ifndef TERRACES_UNION_FIND_HPP
 2 | #define TERRACES_UNION_FIND_HPP
 3 | 
 4 | #include <algorithm>
 5 | 
 6 | #include <terraces/trees.hpp>
 7 | 
 8 | #include "stack_allocator.hpp"
 9 | 
10 | namespace terraces {
11 | 
12 | class union_find {
13 | public:
14 | 	using value_type = index;
15 | 
16 | private:
17 | 	std::vector<index, utils::stack_allocator<index>> m_parent;
18 | #ifndef NDEBUG
19 | 	bool m_compressed;
20 | #endif // NDEBUG
21 | 
22 | public:
23 | 	union_find(index, utils::stack_allocator<index> a);
24 | 	index find(index);
25 | 	index simple_find(index x) const {
26 | 		assert(m_compressed);
27 | 		return is_representative(x) ? x : m_parent[x];
28 | 	}
29 | 	index size() const { return m_parent.size(); }
30 | 	void compress();
31 | 	void merge(index, index);
32 | 	bool is_representative(index x) const { return m_parent[x] >= m_parent.size(); }
33 | 
34 | 	static union_find make_bipartition(const std::vector<bool>& split,
35 | 	                                   utils::stack_allocator<index> alloc);
36 | };
37 | 
38 | } // namespace terraces
39 | 
40 | #endif // TERRACES_UNION_FIND_HPP
41 | 


--------------------------------------------------------------------------------
/terraphast/lib/utils.hpp:
--------------------------------------------------------------------------------
 1 | 
 2 | #ifndef TERRACES_UTILS_HPP
 3 | #define TERRACES_UTILS_HPP
 4 | 
 5 | #include <cctype>
 6 | #include <iterator>
 7 | #include <utility>
 8 | 
 9 | namespace terraces {
10 | namespace utils {
11 | 
12 | template <class T, class U = T>
13 | T exchange(T& obj, U&& new_value) {
14 | 	T old_value = std::move(obj);
15 | 	obj = std::forward<U>(new_value);
16 | 	return old_value;
17 | }
18 | 
19 | template <typename Iterator>
20 | Iterator skip_ws(Iterator it, Iterator last) {
21 | 	while (it != last and std::isspace(*it)) {
22 | 		++it;
23 | 	}
24 | 	return it;
25 | }
26 | 
27 | template <typename Iterator>
28 | Iterator reverse_skip_ws(Iterator first, Iterator last) {
29 | 	while (first != last) {
30 | 		if (std::isspace(*std::prev(last))) {
31 | 			--last;
32 | 		} else {
33 | 			break;
34 | 		}
35 | 	}
36 | 	return last;
37 | }
38 | 
39 | template <typename Exception, typename... Args>
40 | void ensure(bool b, Args&&... args) {
41 | 	if (not b) {
42 | 		throw Exception{std::forward<Args>(args)...};
43 | 	}
44 | }
45 | 
46 | } // namespace utils
47 | } // namespace terraces
48 | 
49 | #endif // TERRACES_UTILS_HPP
50 | 


--------------------------------------------------------------------------------
/terraphast/lib/validation.hpp:
--------------------------------------------------------------------------------
 1 | #ifndef VALIDATION_HPP
 2 | #define VALIDATION_HPP
 3 | 
 4 | #include <terraces/parser.hpp>
 5 | #include <terraces/trees.hpp>
 6 | 
 7 | #include "bitvector.hpp"
 8 | 
 9 | namespace terraces {
10 | 
11 | bool is_isomorphic_unrooted(const tree& fst, const tree& snd);
12 | 
13 | bool is_isomorphic_rooted(const tree& fst, const tree& snd);
14 | 
15 | std::vector<simple_bitvector> tree_bipartitions(const tree& t);
16 | 
17 | } // namespace terraces
18 | 
19 | #endif // TREE_BIPARTITIONS_HPP
20 | 


--------------------------------------------------------------------------------
/terraphast/scripts/build_appveyor.bat:
--------------------------------------------------------------------------------
1 | IF "%Platform%" == "x64" (
2 |     cmake -G "Visual Studio 14 2015 Win64" -DTERRAPHAST_USE_GMP=OFF -DTERRAPHAST_BUILD_CLIB=OFF .
3 | ) ELSE (
4 |     cmake -G "Visual Studio 14 2015" -DTERRAPHAST_USE_GMP=OFF -DTERRAPHAST_BUILD_CLIB=OFF .
5 | )
6 | 


--------------------------------------------------------------------------------
/terraphast/scripts/format.sh:
--------------------------------------------------------------------------------
 1 | #!/bin/bash
 2 | 
 3 | STYLE="{
 4 | 	\"BasedOnStyle\": \"llvm\",
 5 | 	\"IndentWidth\": 8,
 6 | 	\"TabWidth\": 8,
 7 | 	\"ContinuationIndentWidth\": 8,
 8 | 	\"UseTab\": \"ForIndentation\",
 9 | 	\"BreakBeforeBraces\": \"Attach\",
10 | 	\"AlwaysBreakTemplateDeclarations\": \"true\",
11 | 	\"ColumnLimit\": 100,
12 | 	\"PointerBindsToType\": \"true\",
13 | 	\"AccessModifierOffset\": -8,
14 | 	\"ConstructorInitializerIndentWidth\": 8,
15 | }"
16 | 
17 | MODE=$1
18 | 
19 | function format_file() {
20 | 	if ! diff -u <(cat "$1") <(clang-format -style="$STYLE" $1) &> "/dev/null"; then
21 | 		if [ "$MODE" == "check" ]
22 | 		then
23 | 			exit 1
24 | 		fi
25 | 		echo formatting "$1"
26 | 		clang-format -style="$STYLE" -i "$1"
27 | 	fi
28 | }
29 | 
30 | for FILE in $(find include -iname "*.[hc]pp"); do format_file "$FILE"; done
31 | for FILE in $(find lib     -iname "*.[hc]pp"); do format_file "$FILE"; done
32 | for FILE in $(find app     -iname "*.[hc]pp"); do format_file "$FILE"; done
33 | for FILE in $(find tools   -iname "*.[hc]pp"); do format_file "$FILE"; done
34 | for FILE in $(find test    -iname "*.[hc]pp"); do format_file "$FILE"; done
35 | for FILE in $(find c_include -iname "*.[hc]"); do format_file "$FILE"; done
36 | for FILE in $(find c_lib    -iname "*.[hc]pp"); do format_file "$FILE"; done
37 | 
38 | 
39 | 


--------------------------------------------------------------------------------
/terraphast/scripts/pre-commit:
--------------------------------------------------------------------------------
 1 | #!/bin/bash
 2 | 
 3 | # link this file in your git-hooks, for example with:
 4 | #      ln .git/hooks/pre-commit pre-commit
 5 | 
 6 | if ./scripts/format.sh check
 7 | then
 8 | 	echo "nothing to format"
 9 | else
10 | 	echo "unformatted files, please format and stage again" >&2
11 | 	exit 1
12 | fi
13 | 
14 | if lizard include lib app test &> "/dev/null"; then
15 | 	echo "no overcomplicated functions found"
16 | else
17 | 	echo "lizard-warnings found... aborting" >&2
18 | 	exit 1
19 | fi
20 | 
21 | cd "build/debug" 
22 | if ninja ;then
23 | 	echo "debug-build successfull"
24 | else
25 | 	echo "build-failure... aborting" >&2
26 | 	exit 2
27 | fi
28 | cd "../.."
29 | 
30 | cd "build/debug" 
31 | if ninja test &> "/dev/null";then
32 | 	echo "unit-tests run succesfully"
33 | else
34 | 	echo "unit-tests failed... aborting" >&2
35 | 	exit 2
36 | fi
37 | cd "../.."
38 | 


--------------------------------------------------------------------------------
/terraphast/scripts/setup_workspace.sh:
--------------------------------------------------------------------------------
 1 | #! /bin/bash
 2 | 
 3 | # This script is for when you intend to actually work on the code.
 4 | # Do not use it, if all you want to do is build the library for
 5 | # actual use. If that is what you want, just go through the usual
 6 | # way steps for building a cmake-project.
 7 | 
 8 | ln -s "../../scripts/pre-commit" ".git/hooks/pre-commit"
 9 | 
10 | if command -v "ninja" >/dev/null; then
11 | 	echo "found ninja"
12 | 	BUILD_BACKEND="-GNinja"
13 | else
14 | 	echo "failed to find ninja"
15 | 	BUILD_BACKEND=""
16 | fi
17 | 
18 | CC=$(which clang)
19 | CXX=$(which clang++)
20 | 
21 | mkdir "build"
22 | mkdir "build/release"
23 | mkdir "build/debug"
24 | 
25 | cd "build/release"
26 | CC=$CC CXX=$CXX cmake "-DCMAKE_BUILD_TYPE=Release" "-DDEV_ENVIRONMENT=ON" "-DBUILD_TESTS=ON" "$BUILD_BACKEND"  "../.."
27 | cd "../.."
28 | 
29 | cd "build/debug"
30 | CC=$CC CXX=$CXX cmake "-DCMAKE_BUILD_TYPE=Debug" "-DDEV_ENVIRONMENT=ON" "-DBUILD_TESTS=ON" "$BUILD_BACKEND"  "../.."
31 | cd "../.."
32 | 
33 | 


--------------------------------------------------------------------------------
/terraphast/scripts/setup_workspace_windows.sh:
--------------------------------------------------------------------------------
1 | mkdir build
2 | cd build
3 | cmake "-DBUILD_TESTS=ON" -G "Visual Studio 14 2015 Win64" ..
4 | cd ..
5 | 


--------------------------------------------------------------------------------
/terraphast/test/bipartitions.cpp:
--------------------------------------------------------------------------------
 1 | #include <catch.hpp>
 2 | 
 3 | #include <iostream>
 4 | 
 5 | #include "../lib/bipartitions.hpp"
 6 | #include "../lib/ranked_bitvector.hpp"
 7 | #include "../lib/union_find.hpp"
 8 | 
 9 | namespace terraces {
10 | namespace tests {
11 | 
12 | TEST_CASE("bipartition1", "[bipartition]") {
13 | 	auto fl = utils::free_list{};
14 | 	auto alloc = utils::stack_allocator<index>{fl, 4};
15 | 	union_find u(4, alloc);
16 | 	ranked_bitvector s{4, alloc};
17 | 	s.set(0);
18 | 	s.set(1);
19 | 	s.set(2);
20 | 	s.set(3);
21 | 	s.update_ranks();
22 | 	u.merge(0, 1);
23 | 	u.compress();
24 | 	bipartitions bip_it(s, u, alloc);
25 | 	CHECK(bip_it.end_bip() == 4);
26 | 	CHECK(bip_it.num_bip() == 3);
27 | 	CHECK(bip_it.begin_bip() == 1);
28 | 	auto set = bip_it.get_first_set(1, alloc);
29 | 	CHECK(!set.get(0));
30 | 	CHECK(!set.get(1));
31 | 	CHECK(set.get(2));
32 | 	CHECK(!set.get(3));
33 | 	set = bip_it.get_first_set(2, alloc);
34 | 	CHECK(!set.get(0));
35 | 	CHECK(!set.get(1));
36 | 	CHECK(!set.get(2));
37 | 	CHECK(set.get(3));
38 | 	set = bip_it.get_first_set(3, alloc);
39 | 	CHECK(!set.get(0));
40 | 	CHECK(!set.get(1));
41 | 	CHECK(set.get(2));
42 | 	CHECK(set.get(3));
43 | 	CHECK(bip_it.end_bip() == 4);
44 | 	CHECK(bip_it.num_bip() == 3);
45 | }
46 | 
47 | } // namespace tests
48 | } // namespace terraces
49 | 


--------------------------------------------------------------------------------
/terraphast/test/bitmatrix.cpp:
--------------------------------------------------------------------------------
 1 | #include <catch.hpp>
 2 | 
 3 | #include <terraces/bitmatrix.hpp>
 4 | 
 5 | namespace terraces {
 6 | namespace tests {
 7 | 
 8 | TEST_CASE("bitmatrix-construction", "[bitmatrix]") {
 9 | 	auto mat = bitmatrix{10, 5};
10 | 	CHECK(mat.rows() == 10);
11 | 	CHECK(mat.cols() == 5);
12 | }
13 | 
14 | TEST_CASE("bitmatrix set/get", "[bitmatrix]") {
15 | 	auto mat = bitmatrix{3, 4};
16 | 
17 | 	CHECK(!mat.get(1, 2));
18 | 	mat.set(1, 2, true);
19 | 	CHECK(mat.get(1, 2));
20 | }
21 | 
22 | } // namespace tests
23 | } // namespace terraces
24 | 


--------------------------------------------------------------------------------
/terraphast/test/clamped_uint.cpp:
--------------------------------------------------------------------------------
 1 | #include <catch.hpp>
 2 | 
 3 | #include <terraces/clamped_uint.hpp>
 4 | 
 5 | #include <limits>
 6 | #include <terraces/errors.hpp>
 7 | 
 8 | namespace terraces {
 9 | namespace tests {
10 | 
11 | TEST_CASE("clamped_uint", "[checked_uint]") {
12 | 	auto max = std::numeric_limits<index>::max();
13 | 	CHECK((clamped_uint{10} + clamped_uint{417}).value() == 10 + 417);
14 | 	CHECK((clamped_uint{10} * clamped_uint{417}).value() == 10 * 417);
15 | 	CHECK((clamped_uint{max} + clamped_uint{1}).is_clamped());
16 | 	CHECK((clamped_uint{max} + clamped_uint{1}).value() == max);
17 | 	CHECK((clamped_uint{max / 2} * clamped_uint{3}).is_clamped());
18 | 	CHECK((clamped_uint{max / 2} * clamped_uint{3}).value() == max);
19 | }
20 | 
21 | TEST_CASE("overflow_except_uint", "[checked_uint]") {
22 | 	auto max = std::numeric_limits<index>::max();
23 | 	CHECK((overflow_except_uint{10} + overflow_except_uint{417}).value() == 10 + 417);
24 | 	CHECK((overflow_except_uint{10} * overflow_except_uint{417}).value() == 10 * 417);
25 | 	CHECK_THROWS_AS(overflow_except_uint{max} + overflow_except_uint{1},
26 | 	                terraces::tree_count_overflow_error);
27 | 	CHECK_THROWS_AS(overflow_except_uint{max / 2} * overflow_except_uint{3},
28 | 	                terraces::tree_count_overflow_error);
29 | }
30 | 
31 | } // namespace tests
32 | } // namespace terraces
33 | 


--------------------------------------------------------------------------------
/terraphast/test/fast_set.cpp:
--------------------------------------------------------------------------------
 1 | #include <catch.hpp>
 2 | 
 3 | #include "../lib/ranked_bitvector.hpp"
 4 | 
 5 | namespace terraces {
 6 | namespace tests {
 7 | 
 8 | TEST_CASE("fast_set1", "[fast_set]") {
 9 | 	basic_ranked_bitvector<std::allocator<index>> set{10, {}};
10 | 	for (auto&& el : set) {
11 | 		(void)el;
12 | 		FAIL("element in empty set!");
13 | 	}
14 | 	set.set(4);
15 | 	set.update_ranks();
16 | 	CHECK(*set.begin() == 4);
17 | 	CHECK((++set.begin()) == set.end());
18 | 	CHECK(set.get(4));
19 | 	CHECK(!set.get(5));
20 | 	set.clr(4);
21 | 	set.set(5);
22 | 	set.update_ranks();
23 | 	CHECK(!set.get(4));
24 | 	CHECK(set.get(5));
25 | 	CHECK(*set.begin() == 5);
26 | 	CHECK((++set.begin()) == set.end());
27 | 	set.set(2);
28 | 	set.update_ranks();
29 | 	index count = 0;
30 | 	for (auto&& el : set) {
31 | 		(void)el;
32 | 		++count;
33 | 	}
34 | 	CHECK(count == set.count());
35 | }
36 | 
37 | } // namespace tests
38 | } // namespace terraces
39 | 


--------------------------------------------------------------------------------
/terraphast/test/integration.cpp:
--------------------------------------------------------------------------------
 1 | #include <catch.hpp>
 2 | 
 3 | #include <terraces/advanced.hpp>
 4 | #include <terraces/constraints.hpp>
 5 | #include <terraces/parser.hpp>
 6 | #include <terraces/rooting.hpp>
 7 | #include <terraces/subtree_extraction.hpp>
 8 | namespace terraces {
 9 | 
10 | namespace tests {
11 | 
12 | TEST_CASE("full_run_disjoint", "[rerooting],[tree_extraction],[constraints],[supertree]") {
13 | 	tree t{{none, 1, 2, none}, {0, 3, 4, none},    {0, none, none, 0},
14 | 	       {1, 5, 6, none},    {1, 7, 8, none},    {3, none, none, 1},
15 | 	       {3, none, none, 2}, {4, none, none, 3}, {4, none, none, 4}};
16 | 	bitmatrix b{5, 2};
17 | 	b.set(0, 0, true);
18 | 	b.set(0, 1, true);
19 | 	b.set(1, 1, true);
20 | 	b.set(2, 1, true);
21 | 	b.set(3, 0, true);
22 | 	b.set(4, 0, true);
23 | 	auto ts = subtrees(t, b);
24 | 	auto cs = compute_constraints(ts);
25 | 	auto names = name_map(t.size());
26 | 	index root = 0;
27 | 	CHECK(count_terrace({cs, 5, root}) == 15);
28 | }
29 | 
30 | } // namespace tests
31 | } // namespace terraces
32 | 


--------------------------------------------------------------------------------
/terraphast/test/main.cc:
--------------------------------------------------------------------------------
1 | #define CATCH_CONFIG_MAIN
2 | #include <catch.hpp>
3 | 


--------------------------------------------------------------------------------
/terraphast/test/small_bipartition.cpp:
--------------------------------------------------------------------------------
 1 | #include <catch.hpp>
 2 | 
 3 | #include "../lib/small_bipartition.hpp"
 4 | #include "../lib/validation.hpp"
 5 | 
 6 | namespace terraces {
 7 | namespace tests {
 8 | 
 9 | TEST_CASE("small_bipartition", "[unconstrained]") {
10 | 	small_bipartition bip{0b00101001011100};
11 | 	auto step = [&](index i) {
12 | 		CHECK(bip.is_valid());
13 | 		CHECK(bip.left_mask() == i);
14 | 		bip.next();
15 | 	};
16 | 	CHECK(bip.leftmost_leaf() == 2);
17 | 	CHECK(bip.rightmost_leaf() == 11);
18 | 	CHECK(bip.num_leaves() == 6);
19 | 
20 | 	step(0b00000000000100);
21 | 	step(0b00000000001000);
22 | 	step(0b00000000001100);
23 | 	step(0b00000000010000);
24 | 	step(0b00000000010100);
25 | 	step(0b00000000011000);
26 | 	step(0b00000000011100);
27 | 	step(0b00000001000000);
28 | 	step(0b00000001000100);
29 | 	step(0b00000001001000);
30 | 	step(0b00000001001100);
31 | 	step(0b00000001010000);
32 | 	step(0b00000001010100);
33 | 	step(0b00000001011000);
34 | 	step(0b00000001011100);
35 | 	step(0b00001000000000);
36 | 	step(0b00001000000100);
37 | 	step(0b00001000001000);
38 | 	step(0b00001000001100);
39 | 	step(0b00001000010000);
40 | 	step(0b00001000010100);
41 | 	step(0b00001000011000);
42 | 	step(0b00001000011100);
43 | 	step(0b00001001000000);
44 | 	step(0b00001001000100);
45 | 	step(0b00001001001000);
46 | 	step(0b00001001001100);
47 | 	step(0b00001001010000);
48 | 	step(0b00001001010100);
49 | 	step(0b00001001011000);
50 | 	step(0b00001001011100);
51 | 	CHECK(!bip.is_valid());
52 | }
53 | 
54 | } // namespace tests
55 | } // namespace terraces
56 | 


--------------------------------------------------------------------------------
/terraphast/test/stack_allocator.cpp:
--------------------------------------------------------------------------------
 1 | #include <catch.hpp>
 2 | 
 3 | #include "../lib/stack_allocator.hpp"
 4 | 
 5 | namespace terraces {
 6 | namespace tests {
 7 | 
 8 | TEST_CASE("stack_allocator basic", "[utils][utils::stack_allocator]") {
 9 | 	utils::free_list fl;
10 | 	utils::stack_allocator<int> alloc{fl, 10};
11 | 	std::vector<int, utils::stack_allocator<int>> vec(alloc);
12 | 	CHECK_NOTHROW(vec.reserve(10));
13 | }
14 | 
15 | } // namespace tests
16 | } // namespace terraces
17 | 


--------------------------------------------------------------------------------
/terraphast/tools/nwk_to_dot.cpp:
--------------------------------------------------------------------------------
 1 | #include "../lib/io_utils.hpp"
 2 | #include "../lib/trees_impl.hpp"
 3 | 
 4 | #include <iostream>
 5 | #include <terraces/parser.hpp>
 6 | 
 7 | int main(int argc, char** argv) {
 8 | 	if (argc < 3) {
 9 | 		std::cerr << "Usage: " << argv[0] << " [treefile] [rooted]";
10 | 		return -1;
11 | 	}
12 | 	auto tree = terraces::parse_new_nwk(terraces::utils::read_file_full(argv[1]));
13 | 	bool rooted = bool(std::stoi(argv[2]));
14 | 	terraces::print_tree_dot(tree.tree, tree.names, std::cout, rooted);
15 | }


--------------------------------------------------------------------------------
/terraphast/tools/reroot.cpp:
--------------------------------------------------------------------------------
 1 | #include <fstream>
 2 | #include <iostream>
 3 | 
 4 | #include <terraces/advanced.hpp>
 5 | #include <terraces/parser.hpp>
 6 | #include <terraces/rooting.hpp>
 7 | #include <terraces/trees.hpp>
 8 | 
 9 | int main(int argc, char** argv) try {
10 | 	if (argc != 3) {
11 | 		std::cerr << "Usage: " << argv[0] << " <tree-file> <occurrence file>" << std::endl;
12 | 		return 1;
13 | 	}
14 | 	auto data_file = std::ifstream{argv[2]};
15 | 	const auto data = terraces::parse_bitmatrix(data_file);
16 | 
17 | 	auto tree_file = std::ifstream{argv[1]};
18 | 	auto tree_string = std::string{};
19 | 	std::getline(tree_file, tree_string);
20 | 	auto tree = terraces::parse_nwk(tree_string, data.indices);
21 | 	auto comp_taxon = terraces::find_comprehensive_taxon(data.matrix);
22 | 
23 | 	if (comp_taxon == terraces::none) {
24 | 		std::cerr << "Cannot find a comprehensive taxon for the tree\n";
25 | 		return 1;
26 | 	}
27 | 
28 | 	terraces::reroot_at_taxon_inplace(tree, comp_taxon);
29 | 
30 | 	std::cout << as_newick(tree, data.names);
31 | } catch (std::exception& e) {
32 | 	std::cerr << "Error: " << e.what() << "\n";
33 | }
34 | 


--------------------------------------------------------------------------------
/terraphast/tools/site_gen.cpp:
--------------------------------------------------------------------------------
 1 | #include <iostream>
 2 | #include <random>
 3 | #include <string>
 4 | 
 5 | int main(int argc, char** argv) {
 6 | 	if (argc != 4) {
 7 | 		std::cerr << "Usage: " << argv[0]
 8 | 		          << " <number-of-species> <number-of_sites> <probabilty-of-1>\n";
 9 | 		return 1;
10 | 	}
11 | 	const auto num_species = std::stoul(argv[1]);
12 | 	const auto num_sites = std::stoul(argv[2]);
13 | 	const auto prob = std::stod(argv[3]);
14 | 
15 | 	auto gen = std::default_random_engine{std::random_device{}()};
16 | 	auto dist_p = std::uniform_real_distribution<double>{0.0, 1.0};
17 | 
18 | 	const auto root_species =
19 | 	        std::uniform_int_distribution<unsigned long>{0u, num_species}(gen);
20 | 
21 | 	std::cout << num_species << ' ' << num_sites << '\n';
22 | 	for (auto i = 0ul; i < num_species; ++i) {
23 | 		if (i == root_species) {
24 | 			for (auto j = 0ul; j < num_sites; ++j) {
25 | 				std::cout << "1 ";
26 | 			}
27 | 		} else {
28 | 			for (auto j = 0ul; j < num_sites; ++j) {
29 | 				std::cout << (dist_p(gen) < prob) << ' ';
30 | 			}
31 | 		}
32 | 		std::cout << 's' << i << '\n';
33 | 	}
34 | }
35 | 


--------------------------------------------------------------------------------
/terraphast/tools/subtree.cpp:
--------------------------------------------------------------------------------
 1 | #include <fstream>
 2 | #include <iostream>
 3 | #include <iterator>
 4 | 
 5 | #include <set>
 6 | 
 7 | #include <terraces/parser.hpp>
 8 | #include <terraces/rooting.hpp>
 9 | #include <terraces/subtree_extraction.hpp>
10 | #include <terraces/trees.hpp>
11 | 
12 | int main(int argc, char** argv) try {
13 | 	if (argc != 3) {
14 | 		std::cerr << "Usage: " << argv[0] << " <tree-file> <species-file>" << std::endl;
15 | 		return 1;
16 | 	}
17 | 	auto tree_file = std::ifstream{argv[1]};
18 | 	auto tree_string = std::string{};
19 | 	std::getline(tree_file, tree_string);
20 | 	auto data = terraces::parse_new_nwk(tree_string);
21 | 
22 | 	auto names_file = std::ifstream{argv[2]};
23 | 	std::set<std::string> names;
24 | 	std::copy(std::istream_iterator<std::string>(names_file),
25 | 	          std::istream_iterator<std::string>(), std::inserter(names, names.begin()));
26 | 	terraces::bitmatrix occ{data.tree.size(), 1};
27 | 	for (auto& species_pair : data.indices) {
28 | 		if (names.find(species_pair.first) != names.end()) {
29 | 			occ.set(species_pair.second, 0, true);
30 | 		}
31 | 	}
32 | 	terraces::reroot_at_taxon_inplace(data.tree, data.indices[*names.begin()]);
33 | 	auto subtree = terraces::subtrees(data.tree, occ)[0];
34 | 	std::cout << as_newick(subtree, data.names);
35 | } catch (std::exception& e) {
36 | 	std::cerr << "Error: " << e.what() << "\n";
37 | }
38 | 


--------------------------------------------------------------------------------
/test_scripts/iqtree2.h:
--------------------------------------------------------------------------------
 1 | #ifndef LIBIQTREE2_FUN
 2 | #define LIBIQTREE2_FUN
 3 | 
 4 | #include <string>
 5 | 
 6 | using namespace std;
 7 | 
 8 | // Calculates the RF distance between two trees
 9 | int calculate_RF_distance(const string& tree1, const string& tree2);
10 | 
11 | // Generates a random phylogenetic tree
12 | void generate_random_tree_file(int numtaxa, int seed, string tree_gen_mode, string outfile);
13 | 
14 | // perform phylogenetic analysis on the input alignment file
15 | void phylogenetic_analysis(string& align_file, int ncpus = 1);
16 | 
17 | #endif /* LIBIQTREE2_FUN */
18 | 


--------------------------------------------------------------------------------
/test_scripts/linux_universal.sh:
--------------------------------------------------------------------------------
 1 | #!/bin/bash
 2 | 
 3 | ARCH=$(uname -m)
 4 | BINARY=""
 5 | SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 6 | 
 7 | if [[ "$ARCH" == "x86_64" ]]; then
 8 |     BINARY="iqtree3_intel"
 9 | elif [[ "$ARCH" == "aarch64" ]]; then
10 |     BINARY="iqtree3_arm"
11 | else
12 |     echo "Unsupported architecture: $ARCH"
13 |     exit 1
14 | fi
15 | 
16 | # Run the appropriate binary
17 | exec "${SCRIPT_DIR}/$BINARY" "$@"
18 | 


--------------------------------------------------------------------------------
/test_scripts/make_linux_universal.sh:
--------------------------------------------------------------------------------
 1 | #!/bin/bash
 2 | if [ $# -eq 0 ];
 3 | then
 4 |    echo "Syntax: $0 [*-intel.tar.gz] [*-arm.tar.gz]"
 5 |    exit
 6 | fi
 7 | 
 8 | intelname=`basename $1 .tar.gz`
 9 | armname=`basename $2 .tar.gz`
10 | universalname=`basename $1 -intel.tar.gz`
11 | 
12 | tar -xvf $1
13 | tar -xvf $2
14 | mkdir -p $universalname
15 | mkdir -p $universalname/bin
16 | cp $intelname/*.* $universalname
17 | 
18 | cp $intelname/bin/iqtree3 $universalname/bin/iqtree3_intel
19 | cp $armname/bin/iqtree3 $universalname/bin/iqtree3_arm
20 | 
21 | # Make the final file executable
22 | chmod +x test_scripts/linux_universal.sh
23 | cp test_scripts/linux_universal.sh $universalname/bin/iqtree3
24 | 
25 | 
26 | rm -rf $intelname
27 | rm -rf $armname
28 | 
29 | tar czf $universalname.tar.gz $universalname
30 | 
31 | rm -rf $universalname


--------------------------------------------------------------------------------
/test_scripts/make_universal.sh:
--------------------------------------------------------------------------------
 1 | #!/bin/bash
 2 | if [ $# -eq 0 ];
 3 | then
 4 |    echo "Syntax: $0 [intel.zip] [arm.zip]"
 5 |    exit
 6 | fi
 7 | 
 8 | intelname=`basename $1 .zip`
 9 | armname=`basename $2 .zip`
10 | universalname=`basename $1 -intel.zip`
11 | 
12 | unzip $1
13 | unzip $2
14 | mkdir $universalname
15 | mkdir $universalname/bin
16 | cp $intelname/*.* $universalname
17 | lipo -create -output $universalname/bin/iqtree3 $intelname/bin/iqtree3 $armname/bin/iqtree3
18 | zip -vr $universalname.zip $universalname -x "*.DS_Store"
19 | 


--------------------------------------------------------------------------------
/test_scripts/submit_jobs.sh:
--------------------------------------------------------------------------------
 1 | #!/bin/bash - 
 2 | #===============================================================================
 3 | #
 4 | #          FILE: submit_jobs.sh
 5 | # 
 6 | #         USAGE: ./submit_jobs.sh 
 7 | # 
 8 | #   DESCRIPTION: 
 9 | # 
10 | #       OPTIONS: ---
11 | #  REQUIREMENTS: ---
12 | #          BUGS: ---
13 | #         NOTES: ---
14 | #        AUTHOR: Tung Nguyen 
15 | #  ORGANIZATION: 
16 | #       CREATED: 02/06/2015 02:21:40 PM CET
17 | #      REVISION:  ---
18 | #===============================================================================
19 | 
20 | set -o nounset                              # Treat unset variables as an error
21 | 
22 | if [ $# -ne 4 ]
23 | then
24 |   echo "USAGE: $0 <number_of_threads> <cmd_file> <aln_dir> <out_dir>" 
25 |   exit 1
26 | fi
27 | numThreads=$1
28 | cmd_file=$2
29 | aln_dir=$3
30 | out_dir=$4
31 | 
32 | if [ -d $out_dir ]
33 | then
34 |   rm -rf $out_dir
35 | fi
36 | mkdir $out_dir
37 | cp ${aln_dir}/* $out_dir
38 | cp $cmd_file $out_dir
39 | cd $out_dir
40 | submitCMD="submit2sge -N iqtree_system_test -s $numThreads \"../jobmanager.py -f $cmd_file -c $numThreads\""
41 | #echo "../jobmanager.py -f $cmd_file -c $numThreads" | qsub -V -S /bin/bash -cwd -j y -r y -N iqtree_system_test -l zuseX -l cluster -pe threads 16 -q q.norm@zuse02  
42 | $submitCMD
43 | cd ..
44 | 


--------------------------------------------------------------------------------
/test_scripts/test_configs.txt:
--------------------------------------------------------------------------------
 1 | START_PARTITION_ALN
 2 | example.phy example.nex
 3 | d59_8.phy d59_8.nex
 4 | d69_31.phy d69_31.nex
 5 | END_PARTITION_ALN
 6 | 
 7 | START_SINGLE_ALN
 8 | d59_8.phy
 9 | d69_31.phy
10 | example.phy
11 | prot_M126_27_269.phy
12 | END_SINGLE_ALN
13 | 
14 | START_PARTITION_OPTIONS
15 | -sp
16 | -spp
17 | -spj
18 | END_PARTITION_OPTIONS
19 | 
20 | START_GENERIC_OPTIONS
21 | -m TEST
22 | -m TESTNEW
23 | -m TEST -bb 10000 -alrt 1000 -lbp 1000
24 | -m TESTNEW -bb 10000 -alrt 1000 -lbp 1000
25 | -m TEST -b 100
26 | -m TESTNEW -b 100
27 | END_GENERIC_OPTIONS
28 | 


--------------------------------------------------------------------------------
/test_scripts/test_data/d59_8.nex:
--------------------------------------------------------------------------------
 1 | #nexus
 2 | begin sets;
 3 | charset ndhf1st = 1-2183;
 4 | charset rbcl1st = 2184-3527;
 5 | charset rpoc23rd = 3528-4207;
 6 | charset cprs = 4208-4571;
 7 | charset phyb3rd = 4572-5753;
 8 | charset set5_8S = 5754-5913;
 9 | charset its2 = 5914-6177;
10 | charset gbss13rd = 6178-6951;
11 | end;
12 | 


--------------------------------------------------------------------------------
/test_scripts/test_data/example.nex:
--------------------------------------------------------------------------------
1 | #nexus
2 | begin sets;
3 | charset part1 = 1-100;
4 | charset part2 = 101-384;
5 | end;
6 | 


--------------------------------------------------------------------------------
/test_scripts/unify-static-libs.sh:
--------------------------------------------------------------------------------
 1 | #!/bin/bash
 2 | #
 3 | # Creates one static library from several.
 4 | #
 5 | # Usage: copy all your libs to a single directory and call this script.
 6 | #
 7 | if [[ $# -ne 2 ]]; then
 8 |   echo "Usage: unify-static-libs.sh output-name path-to-libs"
 9 |   exit 2
10 | fi
11 | # Inputs
12 | LIBNAME=$1
13 | LIBSDIR=$2
14 | # Tmp dir
15 | OBJDIR=/tmp/unify-static-libs
16 | # Command to evaluate
17 | cmd="ar -crs $LIBNAME"
18 | mkdir -p ${OBJDIR}
19 | # Extract .o
20 | echo "Extracting objects to ${OBJDIR}..."
21 | for i in ${LIBSDIR}/*.a
22 | do
23 |     echo $i
24 |     mkdir -p ${OBJDIR}/$i
25 |     ar --output ${OBJDIR}/$i -x $i
26 |     cmd="${cmd} ${OBJDIR}/$i/*.o"
27 | done
28 | # Link objects into a single lib
29 | echo "Creating $LIBNAME from objects..."
30 | eval "$cmd"
31 | # ar -crs $LIBNAME $OBJDIR/*.o
32 | # Clean up
33 | # rm -rf ${OBJDIR}
34 | echo "Done."
35 | 


--------------------------------------------------------------------------------
/tree/CMakeLists.txt:
--------------------------------------------------------------------------------
 1 | add_library(tree
 2 | constrainttree.cpp
 3 | constrainttree.h
 4 | candidateset.cpp candidateset.h
 5 | iqtree.cpp
 6 | iqtree.h
 7 | iqtreemix.cpp
 8 | iqtreemix.h
 9 | iqtreemixhmm.cpp
10 | iqtreemixhmm.h
11 | matree.cpp
12 | matree.h
13 | memslot.cpp memslot.h
14 | mexttree.cpp
15 | mexttree.h
16 | mtree.cpp
17 | mtree.h
18 | mtreeset.cpp
19 | mtreeset.h
20 | ncbitree.cpp
21 | ncbitree.h
22 | node.cpp
23 | node.h
24 | genomenode.h
25 | genomenode.cpp
26 | genometree.h
27 | genometree.cpp
28 | phylokernel.h
29 | phylokernelnew.h
30 | phylokernelnonrev.h
31 | phylonode.cpp
32 | phylonode.h
33 | phylonodemixlen.cpp
34 | phylonodemixlen.h
35 | phylosuperhmm.cpp
36 | phylosuperhmm.h
37 | phylosupertree.cpp
38 | phylosupertree.h
39 | phylosupertreeplen.cpp
40 | phylosupertreeplen.h
41 | phylosupertreeunlinked.cpp
42 | phylosupertreeunlinked.h
43 | phylotree.cpp
44 | phylotree.h
45 | phylotreemixlen.cpp
46 | phylotreemixlen.h
47 | phylotreepars.cpp
48 | phylotreesse.cpp
49 | quartet.cpp
50 | supernode.cpp
51 | supernode.h
52 | tinatree.cpp
53 | tinatree.h
54 | parstree.cpp
55 | parstree.h
56 | discordance.cpp
57 | phylohmm.cpp
58 | phylohmm.h
59 | )
60 | 
61 | target_link_libraries(tree pll model alignment)
62 | 


--------------------------------------------------------------------------------
/tree/phylonodemixlen.cpp:
--------------------------------------------------------------------------------
 1 | //
 2 | //  phylonodemixlen.cpp
 3 | //  iqtree
 4 | //
 5 | //  Created by Minh Bui on 24/08/15.
 6 | //
 7 | //
 8 | 
 9 | #include "phylonodemixlen.h"
10 | 
11 | void PhyloNodeMixlen::addNeighbor(Node *node, double length, int id) {
12 | 	neighbors.push_back(new PhyloNeighborMixlen(node, length, id));
13 | }
14 | 
15 | void PhyloNodeMixlen::addNeighbor(Node *node, DoubleVector &length, int id) {
16 | 	if (length.empty())
17 | 		addNeighbor(node, -1.0, id);
18 | 	else if (length.size() == 1)
19 | 		addNeighbor(node, length[0], id);
20 | 	else
21 | 		neighbors.push_back(new PhyloNeighborMixlen(node, length, id));
22 | }
23 | 


--------------------------------------------------------------------------------
/tree/phylotreeeigen.cpp:
--------------------------------------------------------------------------------
 1 | /*
 2 |  * phylotreeeigen.cpp
 3 |  *
 4 |  *  Created on: Sep 15, 2014
 5 |  *      Author: minh
 6 |  */
 7 | 
 8 | 
 9 | 
10 | #include "phylotree.h"
11 | #include "modelgtr.h"
12 | 


--------------------------------------------------------------------------------
/utils/CMakeLists.txt:
--------------------------------------------------------------------------------
 1 | add_library(utils
 2 | eigendecomposition.cpp eigendecomposition.h
 3 | gzstream.cpp gzstream.h
 4 | optimization.cpp optimization.h
 5 | stoprule.cpp stoprule.h
 6 | tools.cpp tools.h
 7 | pllnni.cpp pllnni.h
 8 | checkpoint.cpp checkpoint.h
 9 | MPIHelper.cpp MPIHelper.h
10 | starttree.cpp starttree.h
11 | bionj.cpp bionj2.cpp bionj2.h
12 | progress.cpp progress.h
13 | timeutil.h hammingdistance.h
14 | operatingsystem.cpp operatingsystem.h
15 | heapsort.h
16 | )
17 | 
18 | if(ZLIB_FOUND)
19 |   target_link_libraries(utils ${ZLIB_LIBRARIES})
20 | else(ZLIB_FOUND)
21 |   target_link_libraries(utils zlibstatic)
22 | endif(ZLIB_FOUND)
23 | 
24 | target_link_libraries(utils lbfgsb sprng)
25 | 
26 | ##################################################################
27 | # Whether to build the decenttree executable file (default: ON)
28 | ##################################################################
29 | option(BUILD_DECENTTREE "build decenttree" ON)
30 | 
31 | if(BUILD_DECENTTREE)
32 |   add_executable(decentTree
33 |     decenttree.cpp
34 |     starttree.cpp bionj.cpp bionj2.cpp
35 |     gzstream.cpp progress.cpp operatingsystem.cpp)
36 | endif(BUILD_DECENTTREE)
37 | 
38 | if(ZLIB_FOUND)
39 |   target_link_libraries(decentTree ${ZLIB_LIBRARIES})
40 | else(ZLIB_FOUND)
41 |   target_link_libraries(decentTree zlibstatic)
42 | endif(ZLIB_FOUND)
43 | 
44 | if(CLANG AND WIN32)
45 |   target_link_libraries(decentTree ${PROJECT_SOURCE_DIR}/lib/libiomp5md.dll)
46 | endif()
47 | 


--------------------------------------------------------------------------------
/utils/TreeCollection.h:
--------------------------------------------------------------------------------
 1 | //
 2 | // Created by tung on 6/23/15.
 3 | //
 4 | 
 5 | #ifndef IQTREE_TREECOLLECTION_H
 6 | #define IQTREE_TREECOLLECTION_H
 7 | #include "tree/candidateset.h"
 8 | 
 9 | /**
10 |  *  A container for a set of trees together with their scores
11 |  */
12 | class TreeCollection {
13 | private:
14 |     vector<string> treeStrings;
15 |     vector<double> scores;
16 |     vector<int> sourceProcID;
17 | public:
18 | 
19 |     /**
20 |      *  Constructor
21 |      */
22 |     TreeCollection() {};
23 | 
24 |     TreeCollection(vector<string>& trees, vector<double>& scores, vector<int> &sourceProcID);
25 | 
26 |     void addTrees(TreeCollection &trees);
27 | 
28 |     void addTrees(CandidateSet& candidateTrees);
29 | 
30 | 
31 |     /*
32 |      *  Get i-th tree and its score
33 |     */
34 |     pair<string, double> getTree(int i);
35 | 
36 |     void clear();
37 | 
38 |     void setTreeStrings(const vector<string> treeStrings) {
39 |         TreeCollection::treeStrings = treeStrings;
40 |     }
41 | 
42 |     void setScores(const vector<double> scores) {
43 |         TreeCollection::scores = scores;
44 |     }
45 | 
46 |     size_t getNumTrees();
47 | 
48 |     const vector<string> &getTreeStrings() const {
49 |         return treeStrings;
50 |     }
51 | 
52 |     const vector<double> &getScores() const {
53 |         return scores;
54 |     }
55 | 
56 |     const vector<int> &getSourceProcID() const {
57 |         return sourceProcID;
58 |     }
59 | 
60 | };
61 | 
62 | 
63 | #endif //IQTREE_TREECOLLECTION_H
64 | 


--------------------------------------------------------------------------------
/utils/bionj2.h:
--------------------------------------------------------------------------------
 1 | //
 2 | //  bionj2.h
 3 | //  alignment
 4 | //
 5 | //  Created by James Barbetti on 18/6/20.
 6 | //
 7 | 
 8 | #ifndef bionj2_h
 9 | #define bionj2_h
10 | 
11 | #include <string>
12 | #include <algorithm>
13 | class BIONJ2
14 | {
15 | public:
16 |     void constructTree
17 |         ( const std::string &distanceMatrixFilePath
18 |         , const std::string & newickTreeFilePath);
19 |     void constructTreeRapid
20 |         ( const std::string &distanceMatrixFilePath
21 |         , const std::string & newickTreeFilePath);
22 | };
23 | 
24 | #endif /* bionj2_hpp */
25 | 


--------------------------------------------------------------------------------
/utils/operatingsystem.cpp:
--------------------------------------------------------------------------------
 1 | //
 2 | //  operatingsystem.cpp
 3 | //  alignment
 4 | //
 5 | //  Created by James Barbetti on 29/7/20.
 6 | //
 7 | 
 8 | #include "operatingsystem.h"
 9 | #include <string>
10 | #include <sstream>
11 | #if defined(WIN32) || defined(WIN64)
12 |     #include <io.h> //for _isatty
13 | #else
14 |     #include <unistd.h> //for isatty
15 | #endif
16 | 
17 | std::string getOSName() {
18 |     std::stringstream out;
19 |     #if defined _WIN32 || defined WIN32 || defined WIN64
20 |         out << "Windows";
21 |     #elif defined __APPLE__ || defined __MACH__
22 |         out << "Mac OS X";
23 |     #elif defined __linux__
24 |         out << "Linux";
25 |     #elif defined __unix__ || defined __unix
26 |         out << "Unix";
27 |     #else
28 |         out << "Unknown Platform";
29 |     #endif
30 |     out << " " << 8*sizeof(void*) << "-bit";
31 |     return out.str();
32 | }
33 | 
34 | bool isStandardOutputATerminal() {
35 | #if defined(WIN32) || defined(WIN64)
36 |     return _isatty(fileno(stdout));
37 | #else
38 |     return isatty(fileno(stdout));
39 | #endif
40 | }
41 | 


--------------------------------------------------------------------------------
/utils/operatingsystem.h:
--------------------------------------------------------------------------------
 1 | //
 2 | //  operatingsystem.h
 3 | //  iqtree
 4 | //
 5 | //  Created by James Barbetti on 29/7/20.
 6 | //
 7 | 
 8 | #ifndef operatingsystem_h
 9 | #define operatingsystem_h
10 | 
11 | #include <string>
12 | 
13 | std::string getOSName();
14 | bool isStandardOutputATerminal();
15 | 
16 | #endif /* operatingsystem_h */
17 | 


--------------------------------------------------------------------------------
/utils/progress.h:
--------------------------------------------------------------------------------
 1 | //
 2 | //  progress.hpp
 3 | //  alignment
 4 | //
 5 | //  Created by James Barbetti on 28/7/20.
 6 | //
 7 | 
 8 | #ifndef progress_h
 9 | #define progress_h
10 | 
11 | #include <string>
12 | #include "timeutil.h"
13 | 
14 | class progress_display {
15 | public:
16 |     double startTime;
17 |     double startCPUTime;
18 |     double totalWorkToDo;
19 |     double workDone;             //Amount of work done so far
20 |     std::string taskDescription; //A description of the task
21 |     bool        isDone;          //True if the task has been completed
22 |     std::string workVerb;        //A past tense verb (e.g. sorted)
23 |     std::string workUnitName;    //A singular noun   (e.g. row)
24 |     double lastReportedWork;     //Last reported work done
25 |     double lastReportedTime;     //Last reported wall-clock time
26 |     double lastReportedCPUTime;  //Last reported CPU time
27 |     
28 |     explicit progress_display ( double workToDo, const char* doingWhat=""
29 |                               , const char* verb="", const char* unitName="");
30 |     ~progress_display();
31 |     progress_display& operator += (double incrementalWork);
32 |     progress_display& operator ++ ();
33 |     progress_display& operator =  (double workDoneNow);
34 |     progress_display& hide ();
35 |     progress_display& show ();
36 |     progress_display& done ();
37 |     void reportProgress(double time, double cpu, bool newline);
38 |     static void setProgressDisplay(bool displayIt);
39 |     static bool getProgressDisplay();
40 | };
41 | 
42 | 
43 | #endif /* progress_hpp */
44 | 


--------------------------------------------------------------------------------
/vectorclass/CMakeLists.txt:
--------------------------------------------------------------------------------
 1 | add_library(vectorclass
 2 | instrset_detect.cpp
 3 | instrset.h
 4 | vectorclass.h
 5 | vectorf64.h
 6 | vectorf128.h
 7 | vectorf256.h
 8 | vectorf512.h
 9 | )
10 | 


--------------------------------------------------------------------------------
/vectorclass/vectormath_common.h:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/iqtree/iqtree3/4c823e9757857e098e99c4aba611748d5c4cc8db/vectorclass/vectormath_common.h


--------------------------------------------------------------------------------
/whtest/CMakeLists.txt:
--------------------------------------------------------------------------------
 1 | 
 2 | include_directories("${PROJECT_BINARY_DIR}")
 3 | 
 4 | add_library(whtest 
 5 | eigen.c  
 6 | eigen_sym.c  
 7 | random.c  
 8 | weisslambda.c  
 9 | weisslambda_sub.c  
10 | whtest.c  
11 | whtest_sub.c
12 | whtest_wrapper.cpp whtest_wrapper.h
13 | )
14 | 
15 | #install (TARGETS whtest DESTINATION bin)
16 | #install (FILES  eigen.h  eigen_sym.h  random.h  tools.h  weisslambda_sub.h  whtest.h  whtest_sub.h DESTINATION include)
17 | 


--------------------------------------------------------------------------------
/yaml-cpp/CONTRIBUTING.md:
--------------------------------------------------------------------------------
 1 | # Style
 2 | 
 3 | This project is formatted with [clang-format][fmt] using the style file at the root of the repository. Please run clang-format before sending a pull request.
 4 | 
 5 | In general, try to follow the style of surrounding code. We mostly follow the [Google C++ style guide][cpp-style].
 6 | 
 7 | Commit messages should be in the imperative mood, as described in the [Git contributing file][git-contrib]:
 8 | 
 9 | > Describe your changes in imperative mood, e.g. "make xyzzy do frotz"
10 | > instead of "[This patch] makes xyzzy do frotz" or "[I] changed xyzzy
11 | > to do frotz", as if you are giving orders to the codebase to change
12 | > its behaviour.
13 | 
14 | [fmt]: http://clang.llvm.org/docs/ClangFormat.html
15 | [cpp-style]: https://google.github.io/styleguide/cppguide.html
16 | [git-contrib]: http://git.kernel.org/cgit/git/git.git/tree/Documentation/SubmittingPatches?id=HEAD
17 | 
18 | # Tests
19 | 
20 | Please verify the tests pass by running the target `tests/run_tests`.
21 | 
22 | If you are adding functionality, add tests accordingly.
23 | 
24 | # Pull request process
25 | 
26 | Every pull request undergoes a code review. Unfortunately, github's code review process isn't great, but we'll manage. During the code review, if you make changes, add new commits to the pull request for each change. Once the code review is complete, rebase against the master branch and squash into a single commit.
27 | 


--------------------------------------------------------------------------------
/yaml-cpp/LICENSE:
--------------------------------------------------------------------------------
 1 | Copyright (c) 2008-2015 Jesse Beder.
 2 | 
 3 | Permission is hereby granted, free of charge, to any person obtaining a copy
 4 | of this software and associated documentation files (the "Software"), to deal
 5 | in the Software without restriction, including without limitation the rights
 6 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 7 | copies of the Software, and to permit persons to whom the Software is
 8 | furnished to do so, subject to the following conditions:
 9 | 
10 | The above copyright notice and this permission notice shall be included in
11 | all copies or substantial portions of the Software.
12 | 
13 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
14 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
15 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
16 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
17 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
18 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
19 | THE SOFTWARE.
20 | 


--------------------------------------------------------------------------------
/yaml-cpp/include/yaml-cpp/anchor.h:
--------------------------------------------------------------------------------
 1 | #ifndef ANCHOR_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 2 | #define ANCHOR_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 3 | 
 4 | #if defined(_MSC_VER) ||                                            \
 5 |     (defined(__GNUC__) && (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) || \
 6 |      (__GNUC__ >= 4))  // GCC supports "pragma once" correctly since 3.4
 7 | #pragma once
 8 | #endif
 9 | 
10 | #include <cstddef>
11 | 
12 | namespace YAML {
13 | typedef std::size_t anchor_t;
14 | const anchor_t NullAnchor = 0;
15 | }
16 | 
17 | #endif  // ANCHOR_H_62B23520_7C8E_11DE_8A39_0800200C9A66
18 | 


--------------------------------------------------------------------------------
/yaml-cpp/include/yaml-cpp/contrib/anchordict.h:
--------------------------------------------------------------------------------
 1 | #ifndef ANCHORDICT_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 2 | #define ANCHORDICT_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 3 | 
 4 | #if defined(_MSC_VER) ||                                            \
 5 |     (defined(__GNUC__) && (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) || \
 6 |      (__GNUC__ >= 4))  // GCC supports "pragma once" correctly since 3.4
 7 | #pragma once
 8 | #endif
 9 | 
10 | #include <vector>
11 | 
12 | #include "../anchor.h"
13 | 
14 | namespace YAML {
15 | /**
16 |  * An object that stores and retrieves values correlating to {@link anchor_t}
17 |  * values.
18 |  *
19 |  * <p>Efficient implementation that can make assumptions about how
20 |  * {@code anchor_t} values are assigned by the {@link Parser} class.
21 |  */
22 | template <class T>
23 | class AnchorDict {
24 |  public:
25 |   AnchorDict() : m_data{} {}
26 |   void Register(anchor_t anchor, T value) {
27 |     if (anchor > m_data.size()) {
28 |       m_data.resize(anchor);
29 |     }
30 |     m_data[anchor - 1] = value;
31 |   }
32 | 
33 |   T Get(anchor_t anchor) const { return m_data[anchor - 1]; }
34 | 
35 |  private:
36 |   std::vector<T> m_data;
37 | };
38 | }  // namespace YAML
39 | 
40 | #endif  // ANCHORDICT_H_62B23520_7C8E_11DE_8A39_0800200C9A66
41 | 


--------------------------------------------------------------------------------
/yaml-cpp/include/yaml-cpp/emitterdef.h:
--------------------------------------------------------------------------------
 1 | #ifndef EMITTERDEF_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 2 | #define EMITTERDEF_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 3 | 
 4 | #if defined(_MSC_VER) ||                                            \
 5 |     (defined(__GNUC__) && (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) || \
 6 |      (__GNUC__ >= 4))  // GCC supports "pragma once" correctly since 3.4
 7 | #pragma once
 8 | #endif
 9 | 
10 | namespace YAML {
11 | struct EmitterNodeType {
12 |   enum value { NoType, Property, Scalar, FlowSeq, BlockSeq, FlowMap, BlockMap };
13 | };
14 | }
15 | 
16 | #endif  // EMITTERDEF_H_62B23520_7C8E_11DE_8A39_0800200C9A66
17 | 


--------------------------------------------------------------------------------
/yaml-cpp/include/yaml-cpp/emitterstyle.h:
--------------------------------------------------------------------------------
 1 | #ifndef EMITTERSTYLE_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 2 | #define EMITTERSTYLE_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 3 | 
 4 | #if defined(_MSC_VER) ||                                            \
 5 |     (defined(__GNUC__) && (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) || \
 6 |      (__GNUC__ >= 4))  // GCC supports "pragma once" correctly since 3.4
 7 | #pragma once
 8 | #endif
 9 | 
10 | namespace YAML {
11 | struct EmitterStyle {
12 |   enum value { Default, Block, Flow };
13 | };
14 | }
15 | 
16 | #endif  // EMITTERSTYLE_H_62B23520_7C8E_11DE_8A39_0800200C9A66
17 | 


--------------------------------------------------------------------------------
/yaml-cpp/include/yaml-cpp/mark.h:
--------------------------------------------------------------------------------
 1 | #ifndef MARK_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 2 | #define MARK_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 3 | 
 4 | #if defined(_MSC_VER) ||                                            \
 5 |     (defined(__GNUC__) && (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) || \
 6 |      (__GNUC__ >= 4))  // GCC supports "pragma once" correctly since 3.4
 7 | #pragma once
 8 | #endif
 9 | 
10 | #include "yaml-cpp/dll.h"
11 | 
12 | namespace YAML {
13 | struct YAML_CPP_API Mark {
14 |   Mark() : pos(0), line(0), column(0) {}
15 | 
16 |   static const Mark null_mark() { return Mark(-1, -1, -1); }
17 | 
18 |   bool is_null() const { return pos == -1 && line == -1 && column == -1; }
19 | 
20 |   int pos;
21 |   int line, column;
22 | 
23 |  private:
24 |   Mark(int pos_, int line_, int column_)
25 |       : pos(pos_), line(line_), column(column_) {}
26 | };
27 | }
28 | 
29 | #endif  // MARK_H_62B23520_7C8E_11DE_8A39_0800200C9A66
30 | 


--------------------------------------------------------------------------------
/yaml-cpp/include/yaml-cpp/node/detail/bool_type.h:
--------------------------------------------------------------------------------
 1 | #ifndef NODE_DETAIL_BOOL_TYPE_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 2 | #define NODE_DETAIL_BOOL_TYPE_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 3 | 
 4 | #if defined(_MSC_VER) ||                                            \
 5 |     (defined(__GNUC__) && (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) || \
 6 |      (__GNUC__ >= 4))  // GCC supports "pragma once" correctly since 3.4
 7 | #pragma once
 8 | #endif
 9 | 
10 | namespace YAML {
11 | namespace detail {
12 | struct unspecified_bool {
13 |   struct NOT_ALLOWED;
14 |   static void true_value(NOT_ALLOWED*) {}
15 | };
16 | typedef void (*unspecified_bool_type)(unspecified_bool::NOT_ALLOWED*);
17 | }
18 | }
19 | 
20 | #define YAML_CPP_OPERATOR_BOOL()                                            \
21 |   operator YAML::detail::unspecified_bool_type() const {                    \
22 |     return this->operator!() ? 0                                            \
23 |                              : &YAML::detail::unspecified_bool::true_value; \
24 |   }
25 | 
26 | #endif  // NODE_DETAIL_BOOL_TYPE_H_62B23520_7C8E_11DE_8A39_0800200C9A66
27 | 


--------------------------------------------------------------------------------
/yaml-cpp/include/yaml-cpp/node/detail/iterator_fwd.h:
--------------------------------------------------------------------------------
 1 | #ifndef VALUE_DETAIL_ITERATOR_FWD_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 2 | #define VALUE_DETAIL_ITERATOR_FWD_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 3 | 
 4 | #if defined(_MSC_VER) ||                                            \
 5 |     (defined(__GNUC__) && (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) || \
 6 |      (__GNUC__ >= 4))  // GCC supports "pragma once" correctly since 3.4
 7 | #pragma once
 8 | #endif
 9 | 
10 | #include "yaml-cpp/dll.h"
11 | #include <list>
12 | #include <utility>
13 | #include <vector>
14 | 
15 | namespace YAML {
16 | 
17 | namespace detail {
18 | struct iterator_value;
19 | template <typename V>
20 | class iterator_base;
21 | }
22 | 
23 | typedef detail::iterator_base<detail::iterator_value> iterator;
24 | typedef detail::iterator_base<const detail::iterator_value> const_iterator;
25 | }
26 | 
27 | #endif  // VALUE_DETAIL_ITERATOR_FWD_H_62B23520_7C8E_11DE_8A39_0800200C9A66
28 | 


--------------------------------------------------------------------------------
/yaml-cpp/include/yaml-cpp/node/detail/memory.h:
--------------------------------------------------------------------------------
 1 | #ifndef VALUE_DETAIL_MEMORY_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 2 | #define VALUE_DETAIL_MEMORY_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 3 | 
 4 | #if defined(_MSC_VER) ||                                            \
 5 |     (defined(__GNUC__) && (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) || \
 6 |      (__GNUC__ >= 4))  // GCC supports "pragma once" correctly since 3.4
 7 | #pragma once
 8 | #endif
 9 | 
10 | #include <set>
11 | 
12 | #include "yaml-cpp/dll.h"
13 | #include "yaml-cpp/node/ptr.h"
14 | 
15 | namespace YAML {
16 | namespace detail {
17 | class node;
18 | }  // namespace detail
19 | }  // namespace YAML
20 | 
21 | namespace YAML {
22 | namespace detail {
23 | class YAML_CPP_API memory {
24 |  public:
25 |   memory() : m_nodes{} {}
26 |   node& create_node();
27 |   void merge(const memory& rhs);
28 | 
29 |  private:
30 |   typedef std::set<shared_node> Nodes;
31 |   Nodes m_nodes;
32 | };
33 | 
34 | class YAML_CPP_API memory_holder {
35 |  public:
36 |   memory_holder() : m_pMemory(new memory) {}
37 | 
38 |   node& create_node() { return m_pMemory->create_node(); }
39 |   void merge(memory_holder& rhs);
40 | 
41 |  private:
42 |   shared_memory m_pMemory;
43 | };
44 | }  // namespace detail
45 | }  // namespace YAML
46 | 
47 | #endif  // VALUE_DETAIL_MEMORY_H_62B23520_7C8E_11DE_8A39_0800200C9A66
48 | 


--------------------------------------------------------------------------------
/yaml-cpp/include/yaml-cpp/node/emit.h:
--------------------------------------------------------------------------------
 1 | #ifndef NODE_EMIT_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 2 | #define NODE_EMIT_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 3 | 
 4 | #if defined(_MSC_VER) ||                                            \
 5 |     (defined(__GNUC__) && (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) || \
 6 |      (__GNUC__ >= 4))  // GCC supports "pragma once" correctly since 3.4
 7 | #pragma once
 8 | #endif
 9 | 
10 | #include <string>
11 | #include <iosfwd>
12 | 
13 | #include "yaml-cpp/dll.h"
14 | 
15 | namespace YAML {
16 | class Emitter;
17 | class Node;
18 | 
19 | /**
20 |  * Emits the node to the given {@link Emitter}. If there is an error in writing,
21 |  * {@link Emitter#good} will return false.
22 |  */
23 | YAML_CPP_API Emitter& operator<<(Emitter& out, const Node& node);
24 | 
25 | /** Emits the node to the given output stream. */
26 | YAML_CPP_API std::ostream& operator<<(std::ostream& out, const Node& node);
27 | 
28 | /** Converts the node to a YAML string. */
29 | YAML_CPP_API std::string Dump(const Node& node);
30 | }  // namespace YAML
31 | 
32 | #endif  // NODE_EMIT_H_62B23520_7C8E_11DE_8A39_0800200C9A66
33 | 


--------------------------------------------------------------------------------
/yaml-cpp/include/yaml-cpp/node/iterator.h:
--------------------------------------------------------------------------------
 1 | #ifndef VALUE_ITERATOR_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 2 | #define VALUE_ITERATOR_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 3 | 
 4 | #if defined(_MSC_VER) ||                                            \
 5 |     (defined(__GNUC__) && (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) || \
 6 |      (__GNUC__ >= 4))  // GCC supports "pragma once" correctly since 3.4
 7 | #pragma once
 8 | #endif
 9 | 
10 | #include "yaml-cpp/dll.h"
11 | #include "yaml-cpp/node/node.h"
12 | #include "yaml-cpp/node/detail/iterator_fwd.h"
13 | #include "yaml-cpp/node/detail/iterator.h"
14 | #include <list>
15 | #include <utility>
16 | #include <vector>
17 | 
18 | namespace YAML {
19 | namespace detail {
20 | struct iterator_value : public Node, std::pair<Node, Node> {
21 |   iterator_value() {}
22 |   explicit iterator_value(const Node& rhs)
23 |       : Node(rhs),
24 |         std::pair<Node, Node>(Node(Node::ZombieNode), Node(Node::ZombieNode)) {}
25 |   explicit iterator_value(const Node& key, const Node& value)
26 |       : Node(Node::ZombieNode), std::pair<Node, Node>(key, value) {}
27 | };
28 | }
29 | }
30 | 
31 | #endif  // VALUE_ITERATOR_H_62B23520_7C8E_11DE_8A39_0800200C9A66
32 | 


--------------------------------------------------------------------------------
/yaml-cpp/include/yaml-cpp/node/ptr.h:
--------------------------------------------------------------------------------
 1 | #ifndef VALUE_PTR_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 2 | #define VALUE_PTR_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 3 | 
 4 | #if defined(_MSC_VER) ||                                            \
 5 |     (defined(__GNUC__) && (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) || \
 6 |      (__GNUC__ >= 4))  // GCC supports "pragma once" correctly since 3.4
 7 | #pragma once
 8 | #endif
 9 | 
10 | #include "yaml-cpp/dll.h"
11 | #include <memory>
12 | 
13 | namespace YAML {
14 | namespace detail {
15 | class node;
16 | class node_ref;
17 | class node_data;
18 | class memory;
19 | class memory_holder;
20 | 
21 | typedef std::shared_ptr<node> shared_node;
22 | typedef std::shared_ptr<node_ref> shared_node_ref;
23 | typedef std::shared_ptr<node_data> shared_node_data;
24 | typedef std::shared_ptr<memory_holder> shared_memory_holder;
25 | typedef std::shared_ptr<memory> shared_memory;
26 | }
27 | }
28 | 
29 | #endif  // VALUE_PTR_H_62B23520_7C8E_11DE_8A39_0800200C9A66
30 | 


--------------------------------------------------------------------------------
/yaml-cpp/include/yaml-cpp/node/type.h:
--------------------------------------------------------------------------------
 1 | #ifndef VALUE_TYPE_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 2 | #define VALUE_TYPE_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 3 | 
 4 | #if defined(_MSC_VER) ||                                            \
 5 |     (defined(__GNUC__) && (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) || \
 6 |      (__GNUC__ >= 4))  // GCC supports "pragma once" correctly since 3.4
 7 | #pragma once
 8 | #endif
 9 | 
10 | namespace YAML {
11 | struct NodeType {
12 |   enum value { Undefined, Null, Scalar, Sequence, Map };
13 | };
14 | }
15 | 
16 | #endif  // VALUE_TYPE_H_62B23520_7C8E_11DE_8A39_0800200C9A66
17 | 


--------------------------------------------------------------------------------
/yaml-cpp/include/yaml-cpp/noncopyable.h:
--------------------------------------------------------------------------------
 1 | #ifndef NONCOPYABLE_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 2 | #define NONCOPYABLE_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 3 | 
 4 | #if defined(_MSC_VER) ||                                            \
 5 |     (defined(__GNUC__) && (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) || \
 6 |      (__GNUC__ >= 4))  // GCC supports "pragma once" correctly since 3.4
 7 | #pragma once
 8 | #endif
 9 | 
10 | #include "yaml-cpp/dll.h"
11 | 
12 | namespace YAML {
13 | // this is basically boost::noncopyable
14 | class YAML_CPP_API noncopyable {
15 |  protected:
16 |   noncopyable() {}
17 |   ~noncopyable() {}
18 | 
19 |  private:
20 |   noncopyable(const noncopyable&);
21 |   const noncopyable& operator=(const noncopyable&);
22 | };
23 | }
24 | 
25 | #endif  // NONCOPYABLE_H_62B23520_7C8E_11DE_8A39_0800200C9A66
26 | 


--------------------------------------------------------------------------------
/yaml-cpp/include/yaml-cpp/null.h:
--------------------------------------------------------------------------------
 1 | #ifndef NULL_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 2 | #define NULL_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 3 | 
 4 | #if defined(_MSC_VER) ||                                            \
 5 |     (defined(__GNUC__) && (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) || \
 6 |      (__GNUC__ >= 4))  // GCC supports "pragma once" correctly since 3.4
 7 | #pragma once
 8 | #endif
 9 | 
10 | #include "yaml-cpp/dll.h"
11 | #include <string>
12 | 
13 | namespace YAML {
14 | class Node;
15 | 
16 | struct YAML_CPP_API _Null {};
17 | inline bool operator==(const _Null&, const _Null&) { return true; }
18 | inline bool operator!=(const _Null&, const _Null&) { return false; }
19 | 
20 | YAML_CPP_API bool IsNull(const Node& node);  // old API only
21 | YAML_CPP_API bool IsNullString(const std::string& str);
22 | 
23 | extern YAML_CPP_API _Null Null;
24 | }
25 | 
26 | #endif  // NULL_H_62B23520_7C8E_11DE_8A39_0800200C9A66
27 | 


--------------------------------------------------------------------------------
/yaml-cpp/include/yaml-cpp/yaml.h:
--------------------------------------------------------------------------------
 1 | #ifndef YAML_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 2 | #define YAML_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 3 | 
 4 | #if defined(_MSC_VER) ||                                            \
 5 |     (defined(__GNUC__) && (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) || \
 6 |      (__GNUC__ >= 4))  // GCC supports "pragma once" correctly since 3.4
 7 | #pragma once
 8 | #endif
 9 | 
10 | #include "yaml-cpp/parser.h"
11 | #include "yaml-cpp/emitter.h"
12 | #include "yaml-cpp/emitterstyle.h"
13 | #include "yaml-cpp/stlemitter.h"
14 | #include "yaml-cpp/exceptions.h"
15 | 
16 | #include "yaml-cpp/node/node.h"
17 | #include "yaml-cpp/node/impl.h"
18 | #include "yaml-cpp/node/convert.h"
19 | #include "yaml-cpp/node/iterator.h"
20 | #include "yaml-cpp/node/detail/impl.h"
21 | #include "yaml-cpp/node/parse.h"
22 | #include "yaml-cpp/node/emit.h"
23 | 
24 | #endif  // YAML_H_62B23520_7C8E_11DE_8A39_0800200C9A66
25 | 


--------------------------------------------------------------------------------
/yaml-cpp/install.txt:
--------------------------------------------------------------------------------
 1 | *** With CMake ***
 2 | 
 3 | yaml-cpp uses CMake to support cross-platform building. In a UNIX-like system, the basic steps to build are:
 4 | 
 5 | 1. Download and install CMake (if you don't have root privileges, just install to a local directory, like ~/bin)
 6 | 
 7 | 2. From the source directory, run:
 8 | 
 9 | mkdir build
10 | cd build
11 | cmake ..
12 | 
13 | and then the usual
14 | 
15 | make
16 | make install
17 | 
18 | 3. To clean up, just remove the 'build' directory.
19 | 
20 | *** Without CMake ***
21 | 
22 | If you don't want to use CMake, just add all .cpp files to a makefile. yaml-cpp does not need any special build settings, so no 'configure' file is necessary.
23 | 
24 | (Note: this is pretty tedious. It's sooo much easier to use CMake.)
25 | 


--------------------------------------------------------------------------------
/yaml-cpp/src/collectionstack.h:
--------------------------------------------------------------------------------
 1 | #ifndef COLLECTIONSTACK_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 2 | #define COLLECTIONSTACK_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 3 | 
 4 | #if defined(_MSC_VER) ||                                            \
 5 |     (defined(__GNUC__) && (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) || \
 6 |      (__GNUC__ >= 4))  // GCC supports "pragma once" correctly since 3.4
 7 | #pragma once
 8 | #endif
 9 | 
10 | #include <cassert>
11 | #include <stack>
12 | 
13 | namespace YAML {
14 | struct CollectionType {
15 |   enum value { NoCollection, BlockMap, BlockSeq, FlowMap, FlowSeq, CompactMap };
16 | };
17 | 
18 | class CollectionStack {
19 |  public:
20 |   CollectionStack() : collectionStack{} {}
21 |   CollectionType::value GetCurCollectionType() const {
22 |     if (collectionStack.empty())
23 |       return CollectionType::NoCollection;
24 |     return collectionStack.top();
25 |   }
26 | 
27 |   void PushCollectionType(CollectionType::value type) {
28 |     collectionStack.push(type);
29 |   }
30 |   void PopCollectionType(CollectionType::value type) {
31 |     assert(type == GetCurCollectionType());
32 |     (void)type;
33 |     collectionStack.pop();
34 |   }
35 | 
36 |  private:
37 |   std::stack<CollectionType::value> collectionStack;
38 | };
39 | }  // namespace YAML
40 | 
41 | #endif  // COLLECTIONSTACK_H_62B23520_7C8E_11DE_8A39_0800200C9A66
42 | 


--------------------------------------------------------------------------------
/yaml-cpp/src/contrib/graphbuilder.cpp:
--------------------------------------------------------------------------------
 1 | #include "graphbuilderadapter.h"
 2 | 
 3 | #include "yaml-cpp/parser.h"  // IWYU pragma: keep
 4 | 
 5 | namespace YAML {
 6 | class GraphBuilderInterface;
 7 | 
 8 | void* BuildGraphOfNextDocument(Parser& parser,
 9 |                                GraphBuilderInterface& graphBuilder) {
10 |   GraphBuilderAdapter eventHandler(graphBuilder);
11 |   if (parser.HandleNextDocument(eventHandler)) {
12 |     return eventHandler.RootNode();
13 |   } else {
14 |     return nullptr;
15 |   }
16 | }
17 | }
18 | 


--------------------------------------------------------------------------------
/yaml-cpp/src/contrib/yaml-cpp.natvis.md:
--------------------------------------------------------------------------------
 1 | # MSVC debugger visualizer for YAML::Node
 2 | 
 3 | ## How to use
 4 | Add yaml-cpp.natvis to your Visual C++ project like any other source file.  It will be included in the debug information, and improve debugger display on YAML::Node and contained types. 
 5 | 
 6 | ## Compatibility and Troubleshooting
 7 | 
 8 | This has been tested for MSVC 2017. It is expected to be compatible with VS 2015 and VS 2019. If you have any problems, you can open an issue here: https://github.com/peterchen-cp/yaml-cpp-natvis
 9 | 
10 | 


--------------------------------------------------------------------------------
/yaml-cpp/src/directives.cpp:
--------------------------------------------------------------------------------
 1 | #include "directives.h"
 2 | 
 3 | namespace YAML {
 4 | Directives::Directives() : version{true, 1, 2}, tags{} {}
 5 | 
 6 | const std::string Directives::TranslateTagHandle(
 7 |     const std::string& handle) const {
 8 |   std::map<std::string, std::string>::const_iterator it = tags.find(handle);
 9 |   if (it == tags.end()) {
10 |     if (handle == "!!")
11 |       return "tag:yaml.org,2002:";
12 |     return handle;
13 |   }
14 | 
15 |   return it->second;
16 | }
17 | }  // namespace YAML
18 | 


--------------------------------------------------------------------------------
/yaml-cpp/src/directives.h:
--------------------------------------------------------------------------------
 1 | #ifndef DIRECTIVES_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 2 | #define DIRECTIVES_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 3 | 
 4 | #if defined(_MSC_VER) ||                                            \
 5 |     (defined(__GNUC__) && (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) || \
 6 |      (__GNUC__ >= 4))  // GCC supports "pragma once" correctly since 3.4
 7 | #pragma once
 8 | #endif
 9 | 
10 | #include <string>
11 | #include <map>
12 | 
13 | namespace YAML {
14 | struct Version {
15 |   bool isDefault;
16 |   int major, minor;
17 | };
18 | 
19 | struct Directives {
20 |   Directives();
21 | 
22 |   const std::string TranslateTagHandle(const std::string& handle) const;
23 | 
24 |   Version version;
25 |   std::map<std::string, std::string> tags;
26 | };
27 | }
28 | 
29 | #endif  // DIRECTIVES_H_62B23520_7C8E_11DE_8A39_0800200C9A66
30 | 


--------------------------------------------------------------------------------
/yaml-cpp/src/emit.cpp:
--------------------------------------------------------------------------------
 1 | #include "yaml-cpp/node/emit.h"
 2 | #include "yaml-cpp/emitfromevents.h"
 3 | #include "yaml-cpp/emitter.h"
 4 | #include "nodeevents.h"
 5 | 
 6 | namespace YAML {
 7 | Emitter& operator<<(Emitter& out, const Node& node) {
 8 |   EmitFromEvents emitFromEvents(out);
 9 |   NodeEvents events(node);
10 |   events.Emit(emitFromEvents);
11 |   return out;
12 | }
13 | 
14 | std::ostream& operator<<(std::ostream& out, const Node& node) {
15 |   Emitter emitter(out);
16 |   emitter << node;
17 |   return out;
18 | }
19 | 
20 | std::string Dump(const Node& node) {
21 |   Emitter emitter;
22 |   emitter << node;
23 |   return emitter.c_str();
24 | }
25 | }  // namespace YAML
26 | 


--------------------------------------------------------------------------------
/yaml-cpp/src/exceptions.cpp:
--------------------------------------------------------------------------------
 1 | #include "yaml-cpp/exceptions.h"
 2 | 
 3 | // This is here for compatibility with older versions of Visual Studio
 4 | // which don't support noexcept
 5 | #if defined(_MSC_VER) && _MSC_VER < 1900
 6 |     #define YAML_CPP_NOEXCEPT _NOEXCEPT
 7 | #else
 8 |     #define YAML_CPP_NOEXCEPT noexcept
 9 | #endif
10 | 
11 | namespace YAML {
12 | 
13 | // These destructors are defined out-of-line so the vtable is only emitted once.
14 | Exception::~Exception() YAML_CPP_NOEXCEPT {}
15 | ParserException::~ParserException() YAML_CPP_NOEXCEPT {}
16 | RepresentationException::~RepresentationException() YAML_CPP_NOEXCEPT {}
17 | InvalidScalar::~InvalidScalar() YAML_CPP_NOEXCEPT {}
18 | KeyNotFound::~KeyNotFound() YAML_CPP_NOEXCEPT {}
19 | InvalidNode::~InvalidNode() YAML_CPP_NOEXCEPT {}
20 | BadConversion::~BadConversion() YAML_CPP_NOEXCEPT {}
21 | BadDereference::~BadDereference() YAML_CPP_NOEXCEPT {}
22 | BadSubscript::~BadSubscript() YAML_CPP_NOEXCEPT {}
23 | BadPushback::~BadPushback() YAML_CPP_NOEXCEPT {}
24 | BadInsert::~BadInsert() YAML_CPP_NOEXCEPT {}
25 | EmitterException::~EmitterException() YAML_CPP_NOEXCEPT {}
26 | BadFile::~BadFile() YAML_CPP_NOEXCEPT {}
27 | }
28 | 
29 | #undef YAML_CPP_NOEXCEPT
30 | 
31 | 
32 | 


--------------------------------------------------------------------------------
/yaml-cpp/src/indentation.h:
--------------------------------------------------------------------------------
 1 | #ifndef INDENTATION_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 2 | #define INDENTATION_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 3 | 
 4 | #if defined(_MSC_VER) ||                                            \
 5 |     (defined(__GNUC__) && (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) || \
 6 |      (__GNUC__ >= 4))  // GCC supports "pragma once" correctly since 3.4
 7 | #pragma once
 8 | #endif
 9 | 
10 | #include <iostream>
11 | #include <cstddef>
12 | 
13 | #include "yaml-cpp/ostream_wrapper.h"
14 | 
15 | namespace YAML {
16 | struct Indentation {
17 |   Indentation(std::size_t n_) : n(n_) {}
18 |   std::size_t n;
19 | };
20 | 
21 | inline ostream_wrapper& operator<<(ostream_wrapper& out,
22 |                                    const Indentation& indent) {
23 |   for (std::size_t i = 0; i < indent.n; i++)
24 |     out << ' ';
25 |   return out;
26 | }
27 | 
28 | struct IndentTo {
29 |   IndentTo(std::size_t n_) : n(n_) {}
30 |   std::size_t n;
31 | };
32 | 
33 | inline ostream_wrapper& operator<<(ostream_wrapper& out,
34 |                                    const IndentTo& indent) {
35 |   while (out.col() < indent.n)
36 |     out << ' ';
37 |   return out;
38 | }
39 | }
40 | 
41 | #endif  // INDENTATION_H_62B23520_7C8E_11DE_8A39_0800200C9A66
42 | 


--------------------------------------------------------------------------------
/yaml-cpp/src/memory.cpp:
--------------------------------------------------------------------------------
 1 | #include "yaml-cpp/node/detail/memory.h"
 2 | #include "yaml-cpp/node/detail/node.h"  // IWYU pragma: keep
 3 | #include "yaml-cpp/node/ptr.h"
 4 | 
 5 | namespace YAML {
 6 | namespace detail {
 7 | 
 8 | void memory_holder::merge(memory_holder& rhs) {
 9 |   if (m_pMemory == rhs.m_pMemory)
10 |     return;
11 | 
12 |   m_pMemory->merge(*rhs.m_pMemory);
13 |   rhs.m_pMemory = m_pMemory;
14 | }
15 | 
16 | node& memory::create_node() {
17 |   shared_node pNode(new node);
18 |   m_nodes.insert(pNode);
19 |   return *pNode;
20 | }
21 | 
22 | void memory::merge(const memory& rhs) {
23 |   m_nodes.insert(rhs.m_nodes.begin(), rhs.m_nodes.end());
24 | }
25 | }
26 | }
27 | 


--------------------------------------------------------------------------------
/yaml-cpp/src/node.cpp:
--------------------------------------------------------------------------------
 1 | #include "yaml-cpp/node/node.h"
 2 | #include "nodebuilder.h"
 3 | #include "nodeevents.h"
 4 | 
 5 | namespace YAML {
 6 | Node Clone(const Node& node) {
 7 |   NodeEvents events(node);
 8 |   NodeBuilder builder;
 9 |   events.Emit(builder);
10 |   return builder.Root();
11 | }
12 | }
13 | 


--------------------------------------------------------------------------------
/yaml-cpp/src/null.cpp:
--------------------------------------------------------------------------------
 1 | #include "yaml-cpp/null.h"
 2 | 
 3 | namespace YAML {
 4 | _Null Null;
 5 | 
 6 | bool IsNullString(const std::string& str) {
 7 |   return str.empty() || str == "~" || str == "null" || str == "Null" ||
 8 |          str == "NULL";
 9 | }
10 | }
11 | 


--------------------------------------------------------------------------------
/yaml-cpp/src/ptr_vector.h:
--------------------------------------------------------------------------------
 1 | #ifndef PTR_VECTOR_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 2 | #define PTR_VECTOR_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 3 | 
 4 | #if defined(_MSC_VER) ||                                            \
 5 |     (defined(__GNUC__) && (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) || \
 6 |      (__GNUC__ >= 4))  // GCC supports "pragma once" correctly since 3.4
 7 | #pragma once
 8 | #endif
 9 | 
10 | #include <cstddef>
11 | #include <cstdlib>
12 | #include <memory>
13 | #include <vector>
14 | 
15 | namespace YAML {
16 | 
17 | // TODO: This class is no longer needed
18 | template <typename T>
19 | class ptr_vector {
20 |  public:
21 |   ptr_vector() : m_data{} {}
22 |   ptr_vector(const ptr_vector&) = delete;
23 |   ptr_vector(ptr_vector&&) = default;
24 |   ptr_vector& operator=(const ptr_vector&) = delete;
25 |   ptr_vector& operator=(ptr_vector&&) = default;
26 | 
27 |   void clear() { m_data.clear(); }
28 | 
29 |   std::size_t size() const { return m_data.size(); }
30 |   bool empty() const { return m_data.empty(); }
31 | 
32 |   void push_back(std::unique_ptr<T>&& t) { m_data.push_back(std::move(t)); }
33 |   T& operator[](std::size_t i) { return *m_data[i]; }
34 |   const T& operator[](std::size_t i) const { return *m_data[i]; }
35 | 
36 |   T& back() { return *(m_data.back().get()); }
37 | 
38 |   const T& back() const { return *(m_data.back().get()); }
39 | 
40 |  private:
41 |   std::vector<std::unique_ptr<T>> m_data;
42 | };
43 | }  // namespace YAML
44 | 
45 | #endif  // PTR_VECTOR_H_62B23520_7C8E_11DE_8A39_0800200C9A66
46 | 


--------------------------------------------------------------------------------
/yaml-cpp/src/regex_yaml.cpp:
--------------------------------------------------------------------------------
 1 | #include "regex_yaml.h"
 2 | 
 3 | namespace YAML {
 4 | // constructors
 5 | 
 6 | RegEx::RegEx(REGEX_OP op) : m_op(op), m_a(0), m_z(0), m_params{} {}
 7 | RegEx::RegEx() : RegEx(REGEX_EMPTY) {}
 8 | 
 9 | RegEx::RegEx(char ch) : m_op(REGEX_MATCH), m_a(ch), m_z(0), m_params{} {}
10 | 
11 | RegEx::RegEx(char a, char z) : m_op(REGEX_RANGE), m_a(a), m_z(z), m_params{} {}
12 | 
13 | RegEx::RegEx(const std::string& str, REGEX_OP op)
14 |     : m_op(op), m_a(0), m_z(0), m_params(str.begin(), str.end()) {}
15 | 
16 | // combination constructors
17 | RegEx operator!(const RegEx& ex) {
18 |   RegEx ret(REGEX_NOT);
19 |   ret.m_params.push_back(ex);
20 |   return ret;
21 | }
22 | 
23 | RegEx operator|(const RegEx& ex1, const RegEx& ex2) {
24 |   RegEx ret(REGEX_OR);
25 |   ret.m_params.push_back(ex1);
26 |   ret.m_params.push_back(ex2);
27 |   return ret;
28 | }
29 | 
30 | RegEx operator&(const RegEx& ex1, const RegEx& ex2) {
31 |   RegEx ret(REGEX_AND);
32 |   ret.m_params.push_back(ex1);
33 |   ret.m_params.push_back(ex2);
34 |   return ret;
35 | }
36 | 
37 | RegEx operator+(const RegEx& ex1, const RegEx& ex2) {
38 |   RegEx ret(REGEX_SEQ);
39 |   ret.m_params.push_back(ex1);
40 |   ret.m_params.push_back(ex2);
41 |   return ret;
42 | }
43 | }  // namespace YAML
44 | 


--------------------------------------------------------------------------------
/yaml-cpp/src/scantag.h:
--------------------------------------------------------------------------------
 1 | #ifndef SCANTAG_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 2 | #define SCANTAG_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 3 | 
 4 | #if defined(_MSC_VER) ||                                            \
 5 |     (defined(__GNUC__) && (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) || \
 6 |      (__GNUC__ >= 4))  // GCC supports "pragma once" correctly since 3.4
 7 | #pragma once
 8 | #endif
 9 | 
10 | #include <string>
11 | #include "stream.h"
12 | 
13 | namespace YAML {
14 | const std::string ScanVerbatimTag(Stream& INPUT);
15 | const std::string ScanTagHandle(Stream& INPUT, bool& canBeHandle);
16 | const std::string ScanTagSuffix(Stream& INPUT);
17 | }
18 | 
19 | #endif  // SCANTAG_H_62B23520_7C8E_11DE_8A39_0800200C9A66
20 | 


--------------------------------------------------------------------------------
/yaml-cpp/src/stringsource.h:
--------------------------------------------------------------------------------
 1 | #ifndef STRINGSOURCE_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 2 | #define STRINGSOURCE_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 3 | 
 4 | #if defined(_MSC_VER) ||                                            \
 5 |     (defined(__GNUC__) && (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) || \
 6 |      (__GNUC__ >= 4))  // GCC supports "pragma once" correctly since 3.4
 7 | #pragma once
 8 | #endif
 9 | 
10 | #include <cstddef>
11 | 
12 | namespace YAML {
13 | class StringCharSource {
14 |  public:
15 |   StringCharSource(const char* str, std::size_t size)
16 |       : m_str(str), m_size(size), m_offset(0) {}
17 | 
18 |   operator bool() const { return m_offset < m_size; }
19 |   char operator[](std::size_t i) const { return m_str[m_offset + i]; }
20 |   bool operator!() const { return !static_cast<bool>(*this); }
21 | 
22 |   const StringCharSource operator+(int i) const {
23 |     StringCharSource source(*this);
24 |     if (static_cast<int>(source.m_offset) + i >= 0)
25 |       source.m_offset += i;
26 |     else
27 |       source.m_offset = 0;
28 |     return source;
29 |   }
30 | 
31 |   StringCharSource& operator++() {
32 |     ++m_offset;
33 |     return *this;
34 |   }
35 | 
36 |   StringCharSource& operator+=(std::size_t offset) {
37 |     m_offset += offset;
38 |     return *this;
39 |   }
40 | 
41 |  private:
42 |   const char* m_str;
43 |   std::size_t m_size;
44 |   std::size_t m_offset;
45 | };
46 | }
47 | 
48 | #endif  // STRINGSOURCE_H_62B23520_7C8E_11DE_8A39_0800200C9A66
49 | 


--------------------------------------------------------------------------------
/yaml-cpp/src/tag.cpp:
--------------------------------------------------------------------------------
 1 | #include <cassert>
 2 | #include <stdexcept>
 3 | 
 4 | #include "directives.h"  // IWYU pragma: keep
 5 | #include "tag.h"
 6 | #include "token.h"
 7 | 
 8 | namespace YAML {
 9 | Tag::Tag(const Token& token)
10 |     : type(static_cast<TYPE>(token.data)), handle{}, value{} {
11 |   switch (type) {
12 |     case VERBATIM:
13 |       value = token.value;
14 |       break;
15 |     case PRIMARY_HANDLE:
16 |       value = token.value;
17 |       break;
18 |     case SECONDARY_HANDLE:
19 |       value = token.value;
20 |       break;
21 |     case NAMED_HANDLE:
22 |       handle = token.value;
23 |       value = token.params[0];
24 |       break;
25 |     case NON_SPECIFIC:
26 |       break;
27 |     default:
28 |       assert(false);
29 |   }
30 | }
31 | 
32 | const std::string Tag::Translate(const Directives& directives) {
33 |   switch (type) {
34 |     case VERBATIM:
35 |       return value;
36 |     case PRIMARY_HANDLE:
37 |       return directives.TranslateTagHandle("!") + value;
38 |     case SECONDARY_HANDLE:
39 |       return directives.TranslateTagHandle("!!") + value;
40 |     case NAMED_HANDLE:
41 |       return directives.TranslateTagHandle("!" + handle + "!") + value;
42 |     case NON_SPECIFIC:
43 |       // TODO:
44 |       return "!";
45 |     default:
46 |       assert(false);
47 |   }
48 |   throw std::runtime_error("yaml-cpp: internal error, bad tag type");
49 | }
50 | }  // namespace YAML
51 | 


--------------------------------------------------------------------------------
/yaml-cpp/src/tag.h:
--------------------------------------------------------------------------------
 1 | #ifndef TAG_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 2 | #define TAG_H_62B23520_7C8E_11DE_8A39_0800200C9A66
 3 | 
 4 | #if defined(_MSC_VER) ||                                            \
 5 |     (defined(__GNUC__) && (__GNUC__ == 3 && __GNUC_MINOR__ >= 4) || \
 6 |      (__GNUC__ >= 4))  // GCC supports "pragma once" correctly since 3.4
 7 | #pragma once
 8 | #endif
 9 | 
10 | #include <string>
11 | 
12 | namespace YAML {
13 | struct Directives;
14 | struct Token;
15 | 
16 | struct Tag {
17 |   enum TYPE {
18 |     VERBATIM,
19 |     PRIMARY_HANDLE,
20 |     SECONDARY_HANDLE,
21 |     NAMED_HANDLE,
22 |     NON_SPECIFIC
23 |   };
24 | 
25 |   Tag(const Token& token);
26 |   const std::string Translate(const Directives& directives);
27 | 
28 |   TYPE type;
29 |   std::string handle, value;
30 | };
31 | }
32 | 
33 | #endif  // TAG_H_62B23520_7C8E_11DE_8A39_0800200C9A66
34 | 


--------------------------------------------------------------------------------
/yaml-cpp/util/CMakeLists.txt:
--------------------------------------------------------------------------------
 1 | cmake_minimum_required(VERSION 3.5)
 2 | 
 3 | add_sources(parse.cpp)
 4 | add_executable(parse parse.cpp)
 5 | target_link_libraries(parse yaml-cpp)
 6 | 
 7 | add_sources(sandbox.cpp)
 8 | add_executable(sandbox sandbox.cpp)
 9 | target_link_libraries(sandbox yaml-cpp)
10 | 
11 | add_sources(read.cpp)
12 | add_executable(read read.cpp)
13 | target_link_libraries(read yaml-cpp)
14 | 
15 | 


--------------------------------------------------------------------------------
/yaml-cpp/util/sandbox.cpp:
--------------------------------------------------------------------------------
 1 | #include <iostream>
 2 | 
 3 | #include "yaml-cpp/emitterstyle.h"
 4 | #include "yaml-cpp/eventhandler.h"
 5 | #include "yaml-cpp/yaml.h"  // IWYU pragma: keep
 6 | 
 7 | class NullEventHandler : public YAML::EventHandler {
 8 |  public:
 9 |   typedef YAML::Mark Mark;
10 |   typedef YAML::anchor_t anchor_t;
11 | 
12 |   NullEventHandler() {}
13 | 
14 |   virtual void OnDocumentStart(const Mark&) {}
15 |   virtual void OnDocumentEnd() {}
16 |   virtual void OnNull(const Mark&, anchor_t) {}
17 |   virtual void OnAlias(const Mark&, anchor_t) {}
18 |   virtual void OnScalar(const Mark&, const std::string&, anchor_t,
19 |                         const std::string&) {}
20 |   virtual void OnSequenceStart(const Mark&, const std::string&, anchor_t,
21 |                                YAML::EmitterStyle::value style) {}
22 |   virtual void OnSequenceEnd() {}
23 |   virtual void OnMapStart(const Mark&, const std::string&, anchor_t,
24 |                           YAML::EmitterStyle::value style) {}
25 |   virtual void OnMapEnd() {}
26 | };
27 | 
28 | int main() {
29 |   YAML::Node root;
30 | 
31 |   for (;;) {
32 |     YAML::Node node;
33 |     root = node;
34 |   }
35 |   return 0;
36 | }
37 | 


--------------------------------------------------------------------------------
/yaml-cpp/yaml-cpp-config-version.cmake.in:
--------------------------------------------------------------------------------
 1 | set(PACKAGE_VERSION "@YAML_CPP_VERSION@")
 2 | 
 3 | # Check whether the requested PACKAGE_FIND_VERSION is compatible
 4 | if("${PACKAGE_VERSION}" VERSION_LESS "${PACKAGE_FIND_VERSION}")
 5 | 	set(PACKAGE_VERSION_COMPATIBLE FALSE)
 6 | else()
 7 | 	set(PACKAGE_VERSION_COMPATIBLE TRUE)
 8 | 	if ("${PACKAGE_VERSION}" VERSION_EQUAL "${PACKAGE_FIND_VERSION}")
 9 | 		set(PACKAGE_VERSION_EXACT TRUE)
10 | 	endif()
11 | endif()
12 | 


--------------------------------------------------------------------------------
/yaml-cpp/yaml-cpp-config.cmake.in:
--------------------------------------------------------------------------------
 1 | # - Config file for the yaml-cpp package
 2 | # It defines the following variables
 3 | #  YAML_CPP_INCLUDE_DIR - include directory
 4 | #  YAML_CPP_LIBRARIES    - libraries to link against
 5 | 
 6 | # Compute paths
 7 | get_filename_component(YAML_CPP_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
 8 | set(YAML_CPP_INCLUDE_DIR "@CONFIG_INCLUDE_DIRS@")
 9 | 
10 | # Our library dependencies (contains definitions for IMPORTED targets)
11 | include("${YAML_CPP_CMAKE_DIR}/yaml-cpp-targets.cmake")
12 | 
13 | # These are IMPORTED targets created by yaml-cpp-targets.cmake
14 | set(YAML_CPP_LIBRARIES "@EXPORT_TARGETS@")
15 | 


--------------------------------------------------------------------------------
/yaml-cpp/yaml-cpp.pc.cmake:
--------------------------------------------------------------------------------
 1 | prefix=@CMAKE_INSTALL_PREFIX@
 2 | exec_prefix=${prefix}
 3 | includedir=${prefix}/@INCLUDE_INSTALL_ROOT_DIR@
 4 | libdir=${exec_prefix}/@LIB_INSTALL_DIR@
 5 | 
 6 | Name: Yaml-cpp
 7 | Description: A YAML parser and emitter for C++
 8 | Version: @YAML_CPP_VERSION@
 9 | Requires:
10 | Libs: -L${libdir} -lyaml-cpp
11 | Cflags: -I${includedir}
12 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/ChangeLog:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/iqtree/iqtree3/4c823e9757857e098e99c4aba611748d5c4cc8db/zlib-1.2.7/ChangeLog


--------------------------------------------------------------------------------
/zlib-1.2.7/Makefile:
--------------------------------------------------------------------------------
1 | all:
2 | 	-@echo "Please use ./configure first.  Thank you."
3 | 
4 | distclean:
5 | 	make -f Makefile.in distclean
6 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/README.contrib:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/iqtree/iqtree3/4c823e9757857e098e99c4aba611748d5c4cc8db/zlib-1.2.7/contrib/README.contrib


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/ada/zlib.gpr:
--------------------------------------------------------------------------------
 1 | project Zlib is
 2 | 
 3 |    for Languages use ("Ada");
 4 |    for Source_Dirs use (".");
 5 |    for Object_Dir use ".";
 6 |    for Main use ("test.adb", "mtest.adb", "read.adb", "buffer_demo");
 7 | 
 8 |    package Compiler is
 9 |       for Default_Switches ("ada") use ("-gnatwcfilopru", "-gnatVcdfimorst", "-gnatyabcefhiklmnoprst");
10 |    end Compiler;
11 | 
12 |    package Linker is
13 |       for Default_Switches ("ada") use ("-lz");
14 |    end Linker;
15 | 
16 |    package Builder is
17 |       for Default_Switches ("ada") use ("-s", "-gnatQ");
18 |    end Builder;
19 | 
20 | end Zlib;
21 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/blast/Makefile:
--------------------------------------------------------------------------------
1 | blast: blast.c blast.h
2 | 	cc -DTEST -o blast blast.c
3 | 
4 | test: blast
5 | 	blast < test.pk | cmp - test.txt
6 | 
7 | clean:
8 | 	rm -f blast blast.o
9 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/blast/README:
--------------------------------------------------------------------------------
1 | Read blast.h for purpose and usage.
2 | 
3 | Mark Adler
4 | madler@alumni.caltech.edu
5 | 


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/zlib-1.2.7/contrib/blast/test.pk:
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https://raw.githubusercontent.com/iqtree/iqtree3/4c823e9757857e098e99c4aba611748d5c4cc8db/zlib-1.2.7/contrib/blast/test.pk


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/zlib-1.2.7/contrib/blast/test.txt:
--------------------------------------------------------------------------------
1 | AIAIAIAIAIAIA


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/zlib-1.2.7/contrib/delphi/ZLibConst.pas:
--------------------------------------------------------------------------------
 1 | unit ZLibConst;
 2 | 
 3 | interface
 4 | 
 5 | resourcestring
 6 |   sTargetBufferTooSmall = 'ZLib error: target buffer may be too small';
 7 |   sInvalidStreamOp = 'Invalid stream operation';
 8 | 
 9 | implementation
10 | 
11 | end.
12 | 


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/zlib-1.2.7/contrib/dotzlib/DotZLib.build:
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 1 | <?xml version="1.0" encoding="utf-8" ?>
 2 | <project name="DotZLib" default="build" basedir="./DotZLib">
 3 | 	<description>A .Net wrapper library around ZLib1.dll</description>
 4 | 
 5 | 	<property name="nunit.location" value="c:/program files/NUnit V2.1/bin" />
 6 | 	<property name="build.root" value="bin" />
 7 | 
 8 | 	<property name="debug" value="true" />
 9 | 	<property name="nunit" value="true" />
10 | 
11 | 	<property name="build.folder" value="${build.root}/debug/" if="${debug}" />
12 | 	<property name="build.folder" value="${build.root}/release/" unless="${debug}" />
13 | 
14 | 	<target name="clean" description="Remove all generated files">
15 | 		<delete dir="${build.root}" failonerror="false" />
16 | 	</target>
17 | 
18 | 	<target name="build" description="compiles the source code">
19 | 
20 | 		<mkdir dir="${build.folder}" />
21 | 		<csc target="library" output="${build.folder}DotZLib.dll" debug="${debug}">
22 | 			<references basedir="${nunit.location}">
23 | 				<includes if="${nunit}" name="nunit.framework.dll" />
24 | 			</references>
25 | 			<sources>
26 | 				<includes name="*.cs" />
27 | 				<excludes name="UnitTests.cs" unless="${nunit}" />
28 | 			</sources>
29 | 			<arg value="/d:nunit" if="${nunit}" />
30 | 		</csc>
31 | 	</target>
32 | 
33 | </project>


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/zlib-1.2.7/contrib/dotzlib/DotZLib.chm:
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https://raw.githubusercontent.com/iqtree/iqtree3/4c823e9757857e098e99c4aba611748d5c4cc8db/zlib-1.2.7/contrib/dotzlib/DotZLib.chm


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/zlib-1.2.7/contrib/dotzlib/DotZLib.sln:
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 1 | Microsoft Visual Studio Solution File, Format Version 8.00
 2 | Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "DotZLib", "DotZLib\DotZLib.csproj", "{BB1EE0B1-1808-46CB-B786-949D91117FC5}"
 3 | 	ProjectSection(ProjectDependencies) = postProject
 4 | 	EndProjectSection
 5 | EndProject
 6 | Global
 7 | 	GlobalSection(SolutionConfiguration) = preSolution
 8 | 		Debug = Debug
 9 | 		Release = Release
10 | 	EndGlobalSection
11 | 	GlobalSection(ProjectConfiguration) = postSolution
12 | 		{BB1EE0B1-1808-46CB-B786-949D91117FC5}.Debug.ActiveCfg = Debug|.NET
13 | 		{BB1EE0B1-1808-46CB-B786-949D91117FC5}.Debug.Build.0 = Debug|.NET
14 | 		{BB1EE0B1-1808-46CB-B786-949D91117FC5}.Release.ActiveCfg = Release|.NET
15 | 		{BB1EE0B1-1808-46CB-B786-949D91117FC5}.Release.Build.0 = Release|.NET
16 | 	EndGlobalSection
17 | 	GlobalSection(ExtensibilityGlobals) = postSolution
18 | 	EndGlobalSection
19 | 	GlobalSection(ExtensibilityAddIns) = postSolution
20 | 	EndGlobalSection
21 | EndGlobal
22 | 


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/zlib-1.2.7/contrib/dotzlib/DotZLib/ChecksumImpl.cs:
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/zlib-1.2.7/contrib/dotzlib/DotZLib/CodecBase.cs:
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/zlib-1.2.7/contrib/dotzlib/DotZLib/UnitTests.cs:
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/zlib-1.2.7/contrib/dotzlib/LICENSE_1_0.txt:
--------------------------------------------------------------------------------
 1 | Boost Software License - Version 1.0 - August 17th, 2003
 2 | 
 3 | Permission is hereby granted, free of charge, to any person or organization
 4 | obtaining a copy of the software and accompanying documentation covered by
 5 | this license (the "Software") to use, reproduce, display, distribute,
 6 | execute, and transmit the Software, and to prepare derivative works of the
 7 | Software, and to permit third-parties to whom the Software is furnished to
 8 | do so, all subject to the following:
 9 | 
10 | The copyright notices in the Software and this entire statement, including
11 | the above license grant, this restriction and the following disclaimer,
12 | must be included in all copies of the Software, in whole or in part, and
13 | all derivative works of the Software, unless such copies or derivative
14 | works are solely in the form of machine-executable object code generated by
15 | a source language processor.
16 | 
17 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
18 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
19 | FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
20 | SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
21 | FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
22 | ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
23 | DEALINGS IN THE SOFTWARE.


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/infback9/README:
--------------------------------------------------------------------------------
1 | See infback9.h for what this is and how to use it.
2 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/iostream/test.cpp:
--------------------------------------------------------------------------------
 1 | 
 2 | #include "zfstream.h"
 3 | 
 4 | int main() {
 5 | 
 6 |   // Construct a stream object with this filebuffer.  Anything sent
 7 |   // to this stream will go to standard out.
 8 |   gzofstream os( 1, ios::out );
 9 | 
10 |   // This text is getting compressed and sent to stdout.
11 |   // To prove this, run 'test | zcat'.
12 |   os << "Hello, Mommy" << endl;
13 | 
14 |   os << setcompressionlevel( Z_NO_COMPRESSION );
15 |   os << "hello, hello, hi, ho!" << endl;
16 | 
17 |   setcompressionlevel( os, Z_DEFAULT_COMPRESSION )
18 |     << "I'm compressing again" << endl;
19 | 
20 |   os.close();
21 | 
22 |   return 0;
23 | 
24 | }
25 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/iostream2/zstream_test.cpp:
--------------------------------------------------------------------------------
 1 | #include "zstream.h"
 2 | #include <math.h>
 3 | #include <stdlib.h>
 4 | #include <iomanip.h>
 5 | 
 6 | void main() {
 7 |     char h[256] = "Hello";
 8 |     char* g = "Goodbye";
 9 |     ozstream out("temp.gz");
10 |     out < "This works well" < h < g;
11 |     out.close();
12 | 
13 |     izstream in("temp.gz"); // read it back
14 |     char *x = read_string(in), *y = new char[256], z[256];
15 |     in > y > z;
16 |     in.close();
17 |     cout << x << endl << y << endl << z << endl;
18 | 
19 |     out.open("temp.gz"); // try ascii output; zcat temp.gz to see the results
20 |     out << setw(50) << setfill('#') << setprecision(20) << x << endl << y << endl << z << endl;
21 |     out << z << endl << y << endl << x << endl;
22 |     out << 1.1234567890123456789 << endl;
23 | 
24 |     delete[] x; delete[] y;
25 | }
26 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/iostream3/TODO:
--------------------------------------------------------------------------------
 1 | Possible upgrades to gzfilebuf:
 2 | 
 3 | - The ability to do putback (e.g. putbackfail)
 4 | 
 5 | - The ability to seek (zlib supports this, but could be slow/tricky)
 6 | 
 7 | - Simultaneous read/write access (does it make sense?)
 8 | 
 9 | - Support for ios_base::ate open mode
10 | 
11 | - Locale support?
12 | 
13 | - Check public interface to see which calls give problems
14 |   (due to dependence on library internals)
15 | 
16 | - Override operator<<(ostream&, gzfilebuf*) to allow direct copying
17 |   of stream buffer to stream ( i.e. os << is.rdbuf(); )
18 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/masmx64/bld_ml64.bat:
--------------------------------------------------------------------------------
1 | ml64.exe /Flinffasx64 /c /Zi inffasx64.asm
2 | ml64.exe /Flgvmat64   /c /Zi gvmat64.asm
3 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/masmx64/readme.txt:
--------------------------------------------------------------------------------
 1 | Summary
 2 | -------
 3 | This directory contains ASM implementations of the functions
 4 | longest_match() and inflate_fast(), for 64 bits x86 (both AMD64 and Intel EM64t),
 5 | for use with Microsoft Macro Assembler (x64) for AMD64 and Microsoft C++ 64 bits.
 6 | 
 7 | gvmat64.asm is written by Gilles Vollant (2005), by using Brian Raiter 686/32 bits
 8 |    assembly optimized version from Jean-loup Gailly original longest_match function
 9 | 
10 | inffasx64.asm and inffas8664.c were written by Chris Anderson, by optimizing
11 |    original function from Mark Adler
12 | 
13 | Use instructions
14 | ----------------
15 | Assemble the .asm files using MASM and put the object files into the zlib source
16 | directory.  You can also get object files here:
17 | 
18 |      http://www.winimage.com/zLibDll/zlib124_masm_obj.zip
19 | 
20 | define ASMV and ASMINF in your project. Include inffas8664.c in your source tree,
21 | and inffasx64.obj and gvmat64.obj as object to link.
22 | 
23 | 
24 | Build instructions
25 | ------------------
26 | run bld_64.bat with Microsoft Macro Assembler (x64) for AMD64 (ml64.exe)
27 | 
28 | ml64.exe is given with Visual Studio 2005, Windows 2003 server DDK
29 | 
30 | You can get Windows 2003 server DDK with ml64 and cl for AMD64 from
31 |   http://www.microsoft.com/whdc/devtools/ddk/default.mspx for low price)
32 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/masmx86/bld_ml32.bat:
--------------------------------------------------------------------------------
1 | ml /coff /Zi /c /Flmatch686.lst match686.asm
2 | ml /coff /Zi /c /Flinffas32.lst inffas32.asm
3 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/masmx86/readme.txt:
--------------------------------------------------------------------------------
 1 | 
 2 | Summary
 3 | -------
 4 | This directory contains ASM implementations of the functions
 5 | longest_match() and inflate_fast().
 6 | 
 7 | 
 8 | Use instructions
 9 | ----------------
10 | Assemble using MASM, and copy the object files into the zlib source
11 | directory, then run the appropriate makefile, as suggested below.  You can
12 | donwload MASM from here:
13 | 
14 |     http://www.microsoft.com/downloads/details.aspx?displaylang=en&FamilyID=7a1c9da0-0510-44a2-b042-7ef370530c64
15 | 
16 | You can also get objects files here:
17 | 
18 |     http://www.winimage.com/zLibDll/zlib124_masm_obj.zip
19 | 
20 | Build instructions
21 | ------------------
22 | * With Microsoft C and MASM:
23 | nmake -f win32/Makefile.msc LOC="-DASMV -DASMINF" OBJA="match686.obj inffas32.obj"
24 | 
25 | * With Borland C and TASM:
26 | make -f win32/Makefile.bor LOCAL_ZLIB="-DASMV -DASMINF" OBJA="match686.obj inffas32.obj" OBJPA="+match686c.obj+match686.obj+inffas32.obj"
27 | 
28 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/minizip/Makefile:
--------------------------------------------------------------------------------
 1 | CC=cc
 2 | CFLAGS=-O -I../..
 3 | 
 4 | UNZ_OBJS = miniunz.o unzip.o ioapi.o ../../libz.a
 5 | ZIP_OBJS = minizip.o zip.o   ioapi.o ../../libz.a
 6 | 
 7 | .c.o:
 8 | 	$(CC) -c $(CFLAGS) $*.c
 9 | 
10 | all: miniunz minizip
11 | 
12 | miniunz:  $(UNZ_OBJS)
13 | 	$(CC) $(CFLAGS) -o $@ $(UNZ_OBJS)
14 | 
15 | minizip:  $(ZIP_OBJS)
16 | 	$(CC) $(CFLAGS) -o $@ $(ZIP_OBJS)
17 | 
18 | test:	miniunz minizip
19 | 	./minizip test readme.txt
20 | 	./miniunz -l test.zip
21 | 	mv readme.txt readme.old
22 | 	./miniunz test.zip
23 | 
24 | clean:
25 | 	/bin/rm -f *.o *~ minizip miniunz
26 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/minizip/Makefile.am:
--------------------------------------------------------------------------------
 1 | lib_LTLIBRARIES = libminizip.la
 2 | 
 3 | if COND_DEMOS
 4 | bin_PROGRAMS = miniunzip minizip
 5 | endif
 6 | 
 7 | zlib_top_srcdir = $(top_srcdir)/../..
 8 | zlib_top_builddir = $(top_builddir)/../..
 9 | 
10 | AM_CPPFLAGS = -I$(zlib_top_srcdir)
11 | AM_LDFLAGS = -L$(zlib_top_builddir)
12 | 
13 | if WIN32
14 | iowin32_src = iowin32.c
15 | iowin32_h = iowin32.h
16 | endif
17 | 
18 | libminizip_la_SOURCES = \
19 | 	ioapi.c \
20 | 	mztools.c \
21 | 	unzip.c \
22 | 	zip.c \
23 | 	${iowin32_src}
24 | 
25 | libminizip_la_LDFLAGS = $(AM_LDFLAGS) -version-info 1:0:0 -lz
26 | 
27 | minizip_includedir = $(includedir)/minizip
28 | minizip_include_HEADERS = \
29 | 	crypt.h \
30 | 	ioapi.h \
31 | 	mztools.h \
32 | 	unzip.h \
33 | 	zip.h \
34 | 	${iowin32_h}
35 | 
36 | pkgconfigdir = $(libdir)/pkgconfig
37 | pkgconfig_DATA = minizip.pc
38 | 
39 | EXTRA_PROGRAMS = miniunzip minizip
40 | 
41 | miniunzip_SOURCES = miniunz.c
42 | miniunzip_LDADD = libminizip.la
43 | 
44 | minizip_SOURCES = minizip.c
45 | minizip_LDADD = libminizip.la -lz
46 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/minizip/MiniZip64_Changes.txt:
--------------------------------------------------------------------------------
1 | 
2 | MiniZip 1.1 was derrived from MiniZip at version 1.01f
3 | 
4 | Change in 1.0 (Okt 2009)
5 |  - **TODO - Add history**
6 | 
7 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/minizip/configure.ac:
--------------------------------------------------------------------------------
 1 | #                                               -*- Autoconf -*-
 2 | # Process this file with autoconf to produce a configure script.
 3 | 
 4 | AC_INIT([minizip], [1.2.7], [bugzilla.redhat.com])
 5 | AC_CONFIG_SRCDIR([minizip.c])
 6 | AM_INIT_AUTOMAKE([foreign])
 7 | LT_INIT
 8 | 
 9 | AC_MSG_CHECKING([whether to build example programs])
10 | AC_ARG_ENABLE([demos], AC_HELP_STRING([--enable-demos], [build example programs]))
11 | AM_CONDITIONAL([COND_DEMOS], [test "$enable_demos" = yes])
12 | if test "$enable_demos" = yes
13 | then
14 | 	AC_MSG_RESULT([yes])
15 | else
16 | 	AC_MSG_RESULT([no])
17 | fi
18 | 
19 | case "${host}" in
20 | 	*-mingw* | mingw*)
21 | 		WIN32="yes"
22 | 		;;
23 | 	*)
24 | 		;;
25 | esac
26 | AM_CONDITIONAL([WIN32], [test "${WIN32}" = "yes"])
27 | 
28 | 
29 | AC_SUBST([HAVE_UNISTD_H], [0])
30 | AC_CHECK_HEADER([unistd.h], [HAVE_UNISTD_H=1], [])
31 | AC_CONFIG_FILES([Makefile minizip.pc])
32 | AC_OUTPUT
33 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/minizip/iowin32.h:
--------------------------------------------------------------------------------
 1 | /* iowin32.h -- IO base function header for compress/uncompress .zip
 2 |      Version 1.1, February 14h, 2010
 3 |      part of the MiniZip project - ( http://www.winimage.com/zLibDll/minizip.html )
 4 | 
 5 |          Copyright (C) 1998-2010 Gilles Vollant (minizip) ( http://www.winimage.com/zLibDll/minizip.html )
 6 | 
 7 |          Modifications for Zip64 support
 8 |          Copyright (C) 2009-2010 Mathias Svensson ( http://result42.com )
 9 | 
10 |          For more info read MiniZip_info.txt
11 | 
12 | */
13 | 
14 | #include <windows.h>
15 | 
16 | 
17 | #ifdef __cplusplus
18 | extern "C" {
19 | #endif
20 | 
21 | void fill_win32_filefunc OF((zlib_filefunc_def* pzlib_filefunc_def));
22 | void fill_win32_filefunc64 OF((zlib_filefunc64_def* pzlib_filefunc_def));
23 | void fill_win32_filefunc64A OF((zlib_filefunc64_def* pzlib_filefunc_def));
24 | void fill_win32_filefunc64W OF((zlib_filefunc64_def* pzlib_filefunc_def));
25 | 
26 | #ifdef __cplusplus
27 | }
28 | #endif
29 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/minizip/make_vms.com:
--------------------------------------------------------------------------------
 1 | $ if f$search("ioapi.h_orig") .eqs. "" then copy ioapi.h ioapi.h_orig
 2 | $ open/write zdef vmsdefs.h
 3 | $ copy sys$input: zdef
 4 | $ deck
 5 | #define unix
 6 | #define fill_zlib_filefunc64_32_def_from_filefunc32 fillzffunc64from
 7 | #define Write_Zip64EndOfCentralDirectoryLocator Write_Zip64EoDLocator
 8 | #define Write_Zip64EndOfCentralDirectoryRecord Write_Zip64EoDRecord
 9 | #define Write_EndOfCentralDirectoryRecord Write_EoDRecord
10 | $ eod
11 | $ close zdef
12 | $ copy vmsdefs.h,ioapi.h_orig ioapi.h
13 | $ cc/include=[--]/prefix=all ioapi.c
14 | $ cc/include=[--]/prefix=all miniunz.c
15 | $ cc/include=[--]/prefix=all unzip.c
16 | $ cc/include=[--]/prefix=all minizip.c
17 | $ cc/include=[--]/prefix=all zip.c
18 | $ link miniunz,unzip,ioapi,[--]libz.olb/lib
19 | $ link minizip,zip,ioapi,[--]libz.olb/lib
20 | $ mcr []minizip test minizip_info.txt
21 | $ mcr []miniunz -l test.zip
22 | $ rename minizip_info.txt; minizip_info.txt_old
23 | $ mcr []miniunz test.zip
24 | $ delete test.zip;*
25 | $exit
26 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/minizip/minizip.pc.in:
--------------------------------------------------------------------------------
 1 | prefix=@prefix@
 2 | exec_prefix=@exec_prefix@
 3 | libdir=@libdir@
 4 | includedir=@includedir@/minizip
 5 | 
 6 | Name: minizip
 7 | Description: Minizip zip file manipulation library
 8 | Requires:
 9 | Version: @PACKAGE_VERSION@
10 | Libs: -L${libdir} -lminizip
11 | Libs.private: -lz
12 | Cflags: -I${includedir}
13 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/minizip/mztools.h:
--------------------------------------------------------------------------------
 1 | /*
 2 |   Additional tools for Minizip
 3 |   Code: Xavier Roche '2004
 4 |   License: Same as ZLIB (www.gzip.org)
 5 | */
 6 | 
 7 | #ifndef _zip_tools_H
 8 | #define _zip_tools_H
 9 | 
10 | #ifdef __cplusplus
11 | extern "C" {
12 | #endif
13 | 
14 | #ifndef _ZLIB_H
15 | #include "zlib.h"
16 | #endif
17 | 
18 | #include "unzip.h"
19 | 
20 | /* Repair a ZIP file (missing central directory)
21 |    file: file to recover
22 |    fileOut: output file after recovery
23 |    fileOutTmp: temporary file name used for recovery
24 | */
25 | extern int ZEXPORT unzRepair(const char* file,
26 |                              const char* fileOut,
27 |                              const char* fileOutTmp,
28 |                              uLong* nRecovered,
29 |                              uLong* bytesRecovered);
30 | 
31 | 
32 | #ifdef __cplusplus
33 | }
34 | #endif
35 | 
36 | 
37 | #endif
38 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/puff/puff.h:
--------------------------------------------------------------------------------
 1 | /* puff.h
 2 |   Copyright (C) 2002-2010 Mark Adler, all rights reserved
 3 |   version 2.2, 25 Apr 2010
 4 | 
 5 |   This software is provided 'as-is', without any express or implied
 6 |   warranty.  In no event will the author be held liable for any damages
 7 |   arising from the use of this software.
 8 | 
 9 |   Permission is granted to anyone to use this software for any purpose,
10 |   including commercial applications, and to alter it and redistribute it
11 |   freely, subject to the following restrictions:
12 | 
13 |   1. The origin of this software must not be misrepresented; you must not
14 |      claim that you wrote the original software. If you use this software
15 |      in a product, an acknowledgment in the product documentation would be
16 |      appreciated but is not required.
17 |   2. Altered source versions must be plainly marked as such, and must not be
18 |      misrepresented as being the original software.
19 |   3. This notice may not be removed or altered from any source distribution.
20 | 
21 |   Mark Adler    madler@alumni.caltech.edu
22 |  */
23 | 
24 | 
25 | /*
26 |  * See puff.c for purpose and usage.
27 |  */
28 | #ifndef NIL
29 | #  define NIL ((unsigned char *)0)      /* for no output option */
30 | #endif
31 | 
32 | int puff(unsigned char *dest,           /* pointer to destination pointer */
33 |          unsigned long *destlen,        /* amount of output space */
34 |          const unsigned char *source,   /* pointer to source data pointer */
35 |          unsigned long *sourcelen);     /* amount of input available */
36 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/puff/zeros.raw:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/iqtree/iqtree3/4c823e9757857e098e99c4aba611748d5c4cc8db/zlib-1.2.7/contrib/puff/zeros.raw


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/testzlib/testzlib.txt:
--------------------------------------------------------------------------------
 1 | To build testzLib with Visual Studio 2005:
 2 | 
 3 | copy to a directory file from :
 4 | - root of zLib tree
 5 | - contrib/testzlib
 6 | - contrib/masmx86
 7 | - contrib/masmx64
 8 | - contrib/vstudio/vc7
 9 | 
10 | and open testzlib8.sln


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/untgz/Makefile:
--------------------------------------------------------------------------------
 1 | CC=cc
 2 | CFLAGS=-g
 3 | 
 4 | untgz: untgz.o ../../libz.a
 5 | 	$(CC) $(CFLAGS) -o untgz untgz.o -L../.. -lz
 6 | 
 7 | untgz.o: untgz.c ../../zlib.h
 8 | 	$(CC) $(CFLAGS) -c -I../.. untgz.c
 9 | 
10 | ../../libz.a:
11 | 	cd ../..; ./configure; make
12 | 
13 | clean:
14 | 	rm -f untgz untgz.o *~
15 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/untgz/Makefile.msc:
--------------------------------------------------------------------------------
 1 | CC=cl
 2 | CFLAGS=-MD
 3 | 
 4 | untgz.exe: untgz.obj ..\..\zlib.lib
 5 | 	$(CC) $(CFLAGS) untgz.obj ..\..\zlib.lib
 6 | 
 7 | untgz.obj: untgz.c ..\..\zlib.h
 8 | 	$(CC) $(CFLAGS) -c -I..\.. untgz.c
 9 | 
10 | ..\..\zlib.lib:
11 | 	cd ..\..
12 | 	$(MAKE) -f win32\makefile.msc
13 | 	cd contrib\untgz
14 | 
15 | clean:
16 | 	-del untgz.obj
17 | 	-del untgz.exe
18 | 


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/zlib-1.2.7/contrib/vstudio/vc10/miniunz.vcxproj.filters:
--------------------------------------------------------------------------------
 1 | <?xml version="1.0" encoding="utf-8"?>
 2 | <Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
 3 |   <ItemGroup>
 4 |     <Filter Include="Source Files">
 5 |       <UniqueIdentifier>{048af943-022b-4db6-beeb-a54c34774ee2}</UniqueIdentifier>
 6 |       <Extensions>cpp;c;cxx;def;odl;idl;hpj;bat;asm</Extensions>
 7 |     </Filter>
 8 |     <Filter Include="Header Files">
 9 |       <UniqueIdentifier>{c1d600d2-888f-4aea-b73e-8b0dd9befa0c}</UniqueIdentifier>
10 |       <Extensions>h;hpp;hxx;hm;inl;inc</Extensions>
11 |     </Filter>
12 |     <Filter Include="Resource Files">
13 |       <UniqueIdentifier>{0844199a-966b-4f19-81db-1e0125e141b9}</UniqueIdentifier>
14 |       <Extensions>rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe</Extensions>
15 |     </Filter>
16 |   </ItemGroup>
17 |   <ItemGroup>
18 |     <ClCompile Include="..\..\minizip\miniunz.c">
19 |       <Filter>Source Files</Filter>
20 |     </ClCompile>
21 |   </ItemGroup>
22 | </Project>


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/vstudio/vc10/miniunz.vcxproj.user:
--------------------------------------------------------------------------------
1 | <?xml version="1.0" encoding="utf-8"?>
2 | <Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
3 | </Project>


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/vstudio/vc10/minizip.vcxproj.filters:
--------------------------------------------------------------------------------
 1 | <?xml version="1.0" encoding="utf-8"?>
 2 | <Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
 3 |   <ItemGroup>
 4 |     <Filter Include="Source Files">
 5 |       <UniqueIdentifier>{c0419b40-bf50-40da-b153-ff74215b79de}</UniqueIdentifier>
 6 |       <Extensions>cpp;c;cxx;def;odl;idl;hpj;bat;asm</Extensions>
 7 |     </Filter>
 8 |     <Filter Include="Header Files">
 9 |       <UniqueIdentifier>{bb87b070-735b-478e-92ce-7383abb2f36c}</UniqueIdentifier>
10 |       <Extensions>h;hpp;hxx;hm;inl;inc</Extensions>
11 |     </Filter>
12 |     <Filter Include="Resource Files">
13 |       <UniqueIdentifier>{f46ab6a6-548f-43cb-ae96-681abb5bd5db}</UniqueIdentifier>
14 |       <Extensions>rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe</Extensions>
15 |     </Filter>
16 |   </ItemGroup>
17 |   <ItemGroup>
18 |     <ClCompile Include="..\..\minizip\minizip.c">
19 |       <Filter>Source Files</Filter>
20 |     </ClCompile>
21 |   </ItemGroup>
22 | </Project>


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/vstudio/vc10/minizip.vcxproj.user:
--------------------------------------------------------------------------------
1 | <?xml version="1.0" encoding="utf-8"?>
2 | <Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
3 | </Project>


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/vstudio/vc10/testzlib.vcxproj.user:
--------------------------------------------------------------------------------
1 | <?xml version="1.0" encoding="utf-8"?>
2 | <Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
3 | </Project>


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/vstudio/vc10/testzlibdll.vcxproj.filters:
--------------------------------------------------------------------------------
 1 | <?xml version="1.0" encoding="utf-8"?>
 2 | <Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
 3 |   <ItemGroup>
 4 |     <Filter Include="Source Files">
 5 |       <UniqueIdentifier>{fa61a89f-93fc-4c89-b29e-36224b7592f4}</UniqueIdentifier>
 6 |       <Extensions>cpp;c;cxx;def;odl;idl;hpj;bat;asm</Extensions>
 7 |     </Filter>
 8 |     <Filter Include="Header Files">
 9 |       <UniqueIdentifier>{d4b85da0-2ba2-4934-b57f-e2584e3848ee}</UniqueIdentifier>
10 |       <Extensions>h;hpp;hxx;hm;inl;inc</Extensions>
11 |     </Filter>
12 |     <Filter Include="Resource Files">
13 |       <UniqueIdentifier>{e573e075-00bd-4a7d-bd67-a8cc9bfc5aca}</UniqueIdentifier>
14 |       <Extensions>rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe</Extensions>
15 |     </Filter>
16 |   </ItemGroup>
17 |   <ItemGroup>
18 |     <ClCompile Include="..\..\testzlib\testzlib.c">
19 |       <Filter>Source Files</Filter>
20 |     </ClCompile>
21 |   </ItemGroup>
22 | </Project>


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/zlib-1.2.7/contrib/vstudio/vc10/testzlibdll.vcxproj.user:
--------------------------------------------------------------------------------
1 | <?xml version="1.0" encoding="utf-8"?>
2 | <Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
3 | </Project>


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/vstudio/vc10/zlib.rc:
--------------------------------------------------------------------------------
 1 | #include <windows.h>
 2 | 
 3 | #define IDR_VERSION1  1
 4 | IDR_VERSION1	VERSIONINFO	MOVEABLE IMPURE LOADONCALL DISCARDABLE
 5 |   FILEVERSION	 1.2.7,0
 6 |   PRODUCTVERSION 1.2.7,0
 7 |   FILEFLAGSMASK	VS_FFI_FILEFLAGSMASK
 8 |   FILEFLAGS	0
 9 |   FILEOS	VOS_DOS_WINDOWS32
10 |   FILETYPE	VFT_DLL
11 |   FILESUBTYPE	0	// not used
12 | BEGIN
13 |   BLOCK "StringFileInfo"
14 |   BEGIN
15 |     BLOCK "040904E4"
16 |     //language ID = U.S. English, char set = Windows, Multilingual
17 | 
18 |     BEGIN
19 |       VALUE "FileDescription", "zlib data compression and ZIP file I/O library\0"
20 |       VALUE "FileVersion",	"1.2.7\0"
21 |       VALUE "InternalName",	"zlib\0"
22 |       VALUE "OriginalFilename",	"zlib.dll\0"
23 |       VALUE "ProductName",	"ZLib.DLL\0"
24 |       VALUE "Comments","DLL support by Alessandro Iacopetti & Gilles Vollant\0"
25 |       VALUE "LegalCopyright", "(C) 1995-2012 Jean-loup Gailly & Mark Adler\0"
26 |     END
27 |   END
28 |   BLOCK "VarFileInfo"
29 |   BEGIN
30 |     VALUE "Translation", 0x0409, 1252
31 |   END
32 | END
33 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/vstudio/vc10/zlibstat.vcxproj.user:
--------------------------------------------------------------------------------
1 | <?xml version="1.0" encoding="utf-8"?>
2 | <Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
3 | </Project>


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/vstudio/vc10/zlibvc.vcxproj.user:
--------------------------------------------------------------------------------
1 | <?xml version="1.0" encoding="utf-8"?>
2 | <Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
3 | </Project>


--------------------------------------------------------------------------------
/zlib-1.2.7/contrib/vstudio/vc9/zlib.rc:
--------------------------------------------------------------------------------
 1 | #include <windows.h>
 2 | 
 3 | #define IDR_VERSION1  1
 4 | IDR_VERSION1	VERSIONINFO	MOVEABLE IMPURE LOADONCALL DISCARDABLE
 5 |   FILEVERSION	 1.2.7,0
 6 |   PRODUCTVERSION 1.2.7,0
 7 |   FILEFLAGSMASK	VS_FFI_FILEFLAGSMASK
 8 |   FILEFLAGS	0
 9 |   FILEOS	VOS_DOS_WINDOWS32
10 |   FILETYPE	VFT_DLL
11 |   FILESUBTYPE	0	// not used
12 | BEGIN
13 |   BLOCK "StringFileInfo"
14 |   BEGIN
15 |     BLOCK "040904E4"
16 |     //language ID = U.S. English, char set = Windows, Multilingual
17 | 
18 |     BEGIN
19 |       VALUE "FileDescription", "zlib data compression and ZIP file I/O library\0"
20 |       VALUE "FileVersion",	"1.2.7\0"
21 |       VALUE "InternalName",	"zlib\0"
22 |       VALUE "OriginalFilename",	"zlib.dll\0"
23 |       VALUE "ProductName",	"ZLib.DLL\0"
24 |       VALUE "Comments","DLL support by Alessandro Iacopetti & Gilles Vollant\0"
25 |       VALUE "LegalCopyright", "(C) 1995-2012 Jean-loup Gailly & Mark Adler\0"
26 |     END
27 |   END
28 |   BLOCK "VarFileInfo"
29 |   BEGIN
30 |     VALUE "Translation", 0x0409, 1252
31 |   END
32 | END
33 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/gzclose.c:
--------------------------------------------------------------------------------
 1 | /* gzclose.c -- zlib gzclose() function
 2 |  * Copyright (C) 2004, 2010 Mark Adler
 3 |  * For conditions of distribution and use, see copyright notice in zlib.h
 4 |  */
 5 | 
 6 | #include "gzguts.h"
 7 | 
 8 | /* gzclose() is in a separate file so that it is linked in only if it is used.
 9 |    That way the other gzclose functions can be used instead to avoid linking in
10 |    unneeded compression or decompression routines. */
11 | int ZEXPORT gzclose(file)
12 |     gzFile file;
13 | {
14 | #ifndef NO_GZCOMPRESS
15 |     gz_statep state;
16 | 
17 |     if (file == NULL)
18 |         return Z_STREAM_ERROR;
19 |     state = (gz_statep)file;
20 | 
21 |     return state->mode == GZ_READ ? gzclose_r(file) : gzclose_w(file);
22 | #else
23 |     return gzclose_r(file);
24 | #endif
25 | }
26 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/inffast.h:
--------------------------------------------------------------------------------
 1 | /* inffast.h -- header to use inffast.c
 2 |  * Copyright (C) 1995-2003, 2010 Mark Adler
 3 |  * For conditions of distribution and use, see copyright notice in zlib.h
 4 |  */
 5 | 
 6 | /* WARNING: this file should *not* be used by applications. It is
 7 |    part of the implementation of the compression library and is
 8 |    subject to change. Applications should only use zlib.h.
 9 |  */
10 | 
11 | void ZLIB_INTERNAL inflate_fast OF((z_streamp strm, unsigned start));
12 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/nintendods/README:
--------------------------------------------------------------------------------
1 | This Makefile requires devkitARM (http://www.devkitpro.org/category/devkitarm/) and works inside "contrib/nds". It is based on a devkitARM template.
2 | 
3 | Eduardo Costa <eduardo.m.costa@gmail.com>
4 | January 3, 2009
5 | 
6 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/old/README:
--------------------------------------------------------------------------------
1 | This directory contains files that have not been updated for zlib 1.2.x
2 | 
3 | (Volunteers are encouraged to help clean this up.  Thanks.)
4 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/old/os2/zlib.def:
--------------------------------------------------------------------------------
 1 | ;
 2 | ; Slightly modified version of ../nt/zlib.dnt :-)
 3 | ;
 4 | 
 5 | LIBRARY		Z
 6 | DESCRIPTION	"Zlib compression library for OS/2"
 7 | CODE		PRELOAD MOVEABLE DISCARDABLE
 8 | DATA		PRELOAD MOVEABLE MULTIPLE
 9 | 
10 | EXPORTS
11 |     adler32
12 |     compress
13 |     crc32
14 |     deflate
15 |     deflateCopy
16 |     deflateEnd
17 |     deflateInit2_
18 |     deflateInit_
19 |     deflateParams
20 |     deflateReset
21 |     deflateSetDictionary
22 |     gzclose
23 |     gzdopen
24 |     gzerror
25 |     gzflush
26 |     gzopen
27 |     gzread
28 |     gzwrite
29 |     inflate
30 |     inflateEnd
31 |     inflateInit2_
32 |     inflateInit_
33 |     inflateReset
34 |     inflateSetDictionary
35 |     inflateSync
36 |     uncompress
37 |     zlibVersion
38 |     gzprintf
39 |     gzputc
40 |     gzgetc
41 |     gzseek
42 |     gzrewind
43 |     gztell
44 |     gzeof
45 |     gzsetparams
46 |     zError
47 |     inflateSyncPoint
48 |     get_crc_table
49 |     compress2
50 |     gzputs
51 |     gzgets
52 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/watcom/watcom_l.mak:
--------------------------------------------------------------------------------
 1 | # Makefile for zlib
 2 | # OpenWatcom large model
 3 | # Last updated: 28-Dec-2005
 4 | 
 5 | # To use, do "wmake -f watcom_l.mak"
 6 | 
 7 | C_SOURCE =  adler32.c  compress.c crc32.c   deflate.c    &
 8 | 	    gzclose.c  gzlib.c    gzread.c  gzwrite.c    &
 9 |             infback.c  inffast.c  inflate.c inftrees.c   &
10 |             trees.c    uncompr.c  zutil.c
11 | 
12 | OBJS =      adler32.obj  compress.obj crc32.obj   deflate.obj    &
13 | 	    gzclose.obj  gzlib.obj    gzread.obj  gzwrite.obj    &
14 |             infback.obj  inffast.obj  inflate.obj inftrees.obj   &
15 |             trees.obj    uncompr.obj  zutil.obj
16 | 
17 | CC       = wcc
18 | LINKER   = wcl
19 | CFLAGS   = -zq -ml -s -bt=dos -oilrtfm -fr=nul -wx
20 | ZLIB_LIB = zlib_l.lib
21 | 
22 | .C.OBJ:
23 |         $(CC) $(CFLAGS) $[@
24 | 
25 | all: $(ZLIB_LIB) example.exe minigzip.exe
26 | 
27 | $(ZLIB_LIB): $(OBJS)
28 | 	wlib -b -c $(ZLIB_LIB) -+adler32.obj  -+compress.obj -+crc32.obj
29 | 	wlib -b -c $(ZLIB_LIB) -+gzclose.obj  -+gzlib.obj    -+gzread.obj   -+gzwrite.obj
30 |         wlib -b -c $(ZLIB_LIB) -+deflate.obj  -+infback.obj
31 |         wlib -b -c $(ZLIB_LIB) -+inffast.obj  -+inflate.obj  -+inftrees.obj
32 |         wlib -b -c $(ZLIB_LIB) -+trees.obj    -+uncompr.obj  -+zutil.obj
33 | 
34 | example.exe: $(ZLIB_LIB) example.obj
35 | 	$(LINKER) -fe=example.exe example.obj $(ZLIB_LIB)
36 | 
37 | minigzip.exe: $(ZLIB_LIB) minigzip.obj
38 | 	$(LINKER) -fe=minigzip.exe minigzip.obj $(ZLIB_LIB)
39 | 
40 | clean: .SYMBOLIC
41 |           del *.obj
42 |           del $(ZLIB_LIB)
43 |           @echo Cleaning done
44 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/win32/VisualC.txt:
--------------------------------------------------------------------------------
1 | 
2 | To build zlib using the Microsoft Visual C++ environment,
3 | use the appropriate project from the projects/ directory.
4 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/win32/zlib1.rc:
--------------------------------------------------------------------------------
 1 | #include <winver.h>
 2 | #include "../zlib.h"
 3 | 
 4 | #ifdef GCC_WINDRES
 5 | VS_VERSION_INFO		VERSIONINFO
 6 | #else
 7 | VS_VERSION_INFO		VERSIONINFO	MOVEABLE IMPURE LOADONCALL DISCARDABLE
 8 | #endif
 9 |   FILEVERSION		ZLIB_VER_MAJOR,ZLIB_VER_MINOR,ZLIB_VER_REVISION,0
10 |   PRODUCTVERSION	ZLIB_VER_MAJOR,ZLIB_VER_MINOR,ZLIB_VER_REVISION,0
11 |   FILEFLAGSMASK		VS_FFI_FILEFLAGSMASK
12 | #ifdef _DEBUG
13 |   FILEFLAGS		1
14 | #else
15 |   FILEFLAGS		0
16 | #endif
17 |   FILEOS		VOS__WINDOWS32
18 |   FILETYPE		VFT_DLL
19 |   FILESUBTYPE		0	// not used
20 | BEGIN
21 |   BLOCK "StringFileInfo"
22 |   BEGIN
23 |     BLOCK "040904E4"
24 |     //language ID = U.S. English, char set = Windows, Multilingual
25 |     BEGIN
26 |       VALUE "FileDescription",	"zlib data compression library\0"
27 |       VALUE "FileVersion",	ZLIB_VERSION "\0"
28 |       VALUE "InternalName",	"zlib1.dll\0"
29 |       VALUE "LegalCopyright",	"(C) 1995-2006 Jean-loup Gailly & Mark Adler\0"
30 |       VALUE "OriginalFilename",	"zlib1.dll\0"
31 |       VALUE "ProductName",	"zlib\0"
32 |       VALUE "ProductVersion",	ZLIB_VERSION "\0"
33 |       VALUE "Comments",		"For more information visit http://www.zlib.net/\0"
34 |     END
35 |   END
36 |   BLOCK "VarFileInfo"
37 |   BEGIN
38 |     VALUE "Translation", 0x0409, 1252
39 |   END
40 | END
41 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/zlib.3.pdf:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/iqtree/iqtree3/4c823e9757857e098e99c4aba611748d5c4cc8db/zlib-1.2.7/zlib.3.pdf


--------------------------------------------------------------------------------
/zlib-1.2.7/zlib.map:
--------------------------------------------------------------------------------
 1 | ZLIB_1.2.0 {
 2 |   global:
 3 |     compressBound;
 4 |     deflateBound;
 5 |     inflateBack;
 6 |     inflateBackEnd;
 7 |     inflateBackInit_;
 8 |     inflateCopy;
 9 |   local:
10 |     deflate_copyright;
11 |     inflate_copyright;
12 |     inflate_fast;
13 |     inflate_table;
14 |     zcalloc;
15 |     zcfree;
16 |     z_errmsg;
17 |     gz_error;
18 |     gz_intmax;
19 |     _*;
20 | };
21 | 
22 | ZLIB_1.2.0.2 {
23 |     gzclearerr;
24 |     gzungetc;
25 |     zlibCompileFlags;
26 | } ZLIB_1.2.0;
27 | 
28 | ZLIB_1.2.0.8 {
29 |     deflatePrime;
30 | } ZLIB_1.2.0.2;
31 | 
32 | ZLIB_1.2.2 {
33 |     adler32_combine;
34 |     crc32_combine;
35 |     deflateSetHeader;
36 |     inflateGetHeader;
37 | } ZLIB_1.2.0.8;
38 | 
39 | ZLIB_1.2.2.3 {
40 |     deflateTune;
41 |     gzdirect;
42 | } ZLIB_1.2.2;
43 | 
44 | ZLIB_1.2.2.4 {
45 |     inflatePrime;
46 | } ZLIB_1.2.2.3;
47 | 
48 | ZLIB_1.2.3.3 {
49 |     adler32_combine64;
50 |     crc32_combine64;
51 |     gzopen64;
52 |     gzseek64;
53 |     gztell64;
54 |     inflateUndermine;
55 | } ZLIB_1.2.2.4;
56 | 
57 | ZLIB_1.2.3.4 {
58 |     inflateReset2;
59 |     inflateMark;
60 | } ZLIB_1.2.3.3;
61 | 
62 | ZLIB_1.2.3.5 {
63 |     gzbuffer;
64 |     gzoffset;
65 |     gzoffset64;
66 |     gzclose_r;
67 |     gzclose_w;
68 | } ZLIB_1.2.3.4;
69 | 
70 | ZLIB_1.2.5.1 {
71 |     deflatePending;
72 | } ZLIB_1.2.3.5;
73 | 
74 | ZLIB_1.2.5.2 {
75 |     deflateResetKeep;
76 |     gzgetc_;
77 |     inflateResetKeep;
78 | } ZLIB_1.2.5.1;
79 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/zlib.pc.cmakein:
--------------------------------------------------------------------------------
 1 | prefix=@CMAKE_INSTALL_PREFIX@
 2 | exec_prefix=@CMAKE_INSTALL_PREFIX@
 3 | libdir=@INSTALL_LIB_DIR@
 4 | sharedlibdir=@INSTALL_LIB_DIR@
 5 | includedir=@INSTALL_INC_DIR@
 6 | 
 7 | Name: zlib
 8 | Description: zlib compression library
 9 | Version: @VERSION@
10 | 
11 | Requires:
12 | Libs: -L${libdir} -L${sharedlibdir} -lz
13 | Cflags: -I${includedir}
14 | 


--------------------------------------------------------------------------------
/zlib-1.2.7/zlib.pc.in:
--------------------------------------------------------------------------------
 1 | prefix=@prefix@
 2 | exec_prefix=@exec_prefix@
 3 | libdir=@libdir@
 4 | sharedlibdir=@sharedlibdir@
 5 | includedir=@includedir@
 6 | 
 7 | Name: zlib
 8 | Description: zlib compression library
 9 | Version: @VERSION@
10 | 
11 | Requires:
12 | Libs: -L${libdir} -L${sharedlibdir} -lz
13 | Cflags: -I${includedir}
14 | 


--------------------------------------------------------------------------------