├── ._to_be_removed_travis.yml
├── .github
└── workflows
│ ├── cibuildwheel.yml
│ └── ubuntu.yml
├── .gitignore
├── .gitmodules
├── .readthedocs.yml
├── CMakeLists.txt
├── Doxyfile
├── LICENSE
├── MANIFEST.in
├── README.md
├── README.rst
├── ThirdParty
├── CLI
│ └── CLI11.hpp
├── TBB
│ ├── bin
│ │ ├── tbbvars.csh
│ │ └── tbbvars.sh
│ ├── include
│ │ ├── index.html
│ │ ├── serial
│ │ │ └── tbb
│ │ │ │ ├── parallel_for.h
│ │ │ │ └── tbb_annotate.h
│ │ └── tbb
│ │ │ ├── aggregator.h
│ │ │ ├── aligned_space.h
│ │ │ ├── atomic.h
│ │ │ ├── blocked_range.h
│ │ │ ├── blocked_range2d.h
│ │ │ ├── blocked_range3d.h
│ │ │ ├── blocked_rangeNd.h
│ │ │ ├── cache_aligned_allocator.h
│ │ │ ├── combinable.h
│ │ │ ├── compat
│ │ │ ├── condition_variable
│ │ │ ├── ppl.h
│ │ │ ├── thread
│ │ │ └── tuple
│ │ │ ├── concurrent_hash_map.h
│ │ │ ├── concurrent_lru_cache.h
│ │ │ ├── concurrent_priority_queue.h
│ │ │ ├── concurrent_queue.h
│ │ │ ├── concurrent_unordered_map.h
│ │ │ ├── concurrent_unordered_set.h
│ │ │ ├── concurrent_vector.h
│ │ │ ├── critical_section.h
│ │ │ ├── enumerable_thread_specific.h
│ │ │ ├── flow_graph.h
│ │ │ ├── flow_graph_abstractions.h
│ │ │ ├── flow_graph_opencl_node.h
│ │ │ ├── gfx_factory.h
│ │ │ ├── global_control.h
│ │ │ ├── index.html
│ │ │ ├── internal
│ │ │ ├── _aggregator_impl.h
│ │ │ ├── _concurrent_queue_impl.h
│ │ │ ├── _concurrent_unordered_impl.h
│ │ │ ├── _flow_graph_async_msg_impl.h
│ │ │ ├── _flow_graph_body_impl.h
│ │ │ ├── _flow_graph_cache_impl.h
│ │ │ ├── _flow_graph_impl.h
│ │ │ ├── _flow_graph_indexer_impl.h
│ │ │ ├── _flow_graph_item_buffer_impl.h
│ │ │ ├── _flow_graph_join_impl.h
│ │ │ ├── _flow_graph_node_impl.h
│ │ │ ├── _flow_graph_streaming_node.h
│ │ │ ├── _flow_graph_tagged_buffer_impl.h
│ │ │ ├── _flow_graph_trace_impl.h
│ │ │ ├── _flow_graph_types_impl.h
│ │ │ ├── _mutex_padding.h
│ │ │ ├── _range_iterator.h
│ │ │ ├── _tbb_hash_compare_impl.h
│ │ │ ├── _tbb_strings.h
│ │ │ ├── _tbb_trace_impl.h
│ │ │ ├── _tbb_windef.h
│ │ │ ├── _template_helpers.h
│ │ │ ├── _x86_eliding_mutex_impl.h
│ │ │ └── _x86_rtm_rw_mutex_impl.h
│ │ │ ├── machine
│ │ │ ├── gcc_arm.h
│ │ │ ├── gcc_generic.h
│ │ │ ├── gcc_ia32_common.h
│ │ │ ├── gcc_itsx.h
│ │ │ ├── ibm_aix51.h
│ │ │ ├── icc_generic.h
│ │ │ ├── linux_common.h
│ │ │ ├── linux_ia32.h
│ │ │ ├── linux_ia64.h
│ │ │ ├── linux_intel64.h
│ │ │ ├── mac_ppc.h
│ │ │ ├── macos_common.h
│ │ │ ├── mic_common.h
│ │ │ ├── msvc_armv7.h
│ │ │ ├── msvc_ia32_common.h
│ │ │ ├── sunos_sparc.h
│ │ │ ├── windows_api.h
│ │ │ ├── windows_ia32.h
│ │ │ └── windows_intel64.h
│ │ │ ├── memory_pool.h
│ │ │ ├── mutex.h
│ │ │ ├── null_mutex.h
│ │ │ ├── null_rw_mutex.h
│ │ │ ├── parallel_do.h
│ │ │ ├── parallel_for.h
│ │ │ ├── parallel_for_each.h
│ │ │ ├── parallel_invoke.h
│ │ │ ├── parallel_reduce.h
│ │ │ ├── parallel_scan.h
│ │ │ ├── parallel_sort.h
│ │ │ ├── parallel_while.h
│ │ │ ├── partitioner.h
│ │ │ ├── pipeline.h
│ │ │ ├── queuing_mutex.h
│ │ │ ├── queuing_rw_mutex.h
│ │ │ ├── reader_writer_lock.h
│ │ │ ├── recursive_mutex.h
│ │ │ ├── runtime_loader.h
│ │ │ ├── scalable_allocator.h
│ │ │ ├── spin_mutex.h
│ │ │ ├── spin_rw_mutex.h
│ │ │ ├── task.h
│ │ │ ├── task_arena.h
│ │ │ ├── task_group.h
│ │ │ ├── task_scheduler_init.h
│ │ │ ├── task_scheduler_observer.h
│ │ │ ├── tbb.h
│ │ │ ├── tbb_allocator.h
│ │ │ ├── tbb_config.h
│ │ │ ├── tbb_disable_exceptions.h
│ │ │ ├── tbb_exception.h
│ │ │ ├── tbb_machine.h
│ │ │ ├── tbb_profiling.h
│ │ │ ├── tbb_stddef.h
│ │ │ ├── tbb_thread.h
│ │ │ ├── tbbmalloc_proxy.h
│ │ │ └── tick_count.h
│ └── lib
│ │ └── intel64
│ │ └── gcc4.7
│ │ ├── libtbb.so
│ │ ├── libtbb.so.2
│ │ ├── libtbb_debug.so
│ │ ├── libtbb_debug.so.2
│ │ ├── libtbb_preview.so
│ │ ├── libtbb_preview.so.2
│ │ ├── libtbb_preview_debug.so
│ │ ├── libtbb_preview_debug.so.2
│ │ ├── libtbbmalloc.so
│ │ ├── libtbbmalloc.so.2
│ │ ├── libtbbmalloc_debug.so
│ │ ├── libtbbmalloc_debug.so.2
│ │ ├── libtbbmalloc_proxy.so
│ │ ├── libtbbmalloc_proxy.so.2
│ │ ├── libtbbmalloc_proxy_debug.so
│ │ └── libtbbmalloc_proxy_debug.so.2
├── catch.hpp
├── json
│ └── json.hpp
├── ntCard
│ ├── .gitignore
│ ├── CITATION.bib
│ ├── ChangeLog
│ ├── Common
│ │ ├── Fcontrol.cpp
│ │ ├── Fcontrol.h
│ │ ├── SignalHandler.cpp
│ │ ├── SignalHandler.h
│ │ ├── StringUtil.h
│ │ ├── Uncompress.cpp
│ │ ├── Uncompress.h
│ │ ├── ntHashIterator.hpp
│ │ └── nthash.hpp
│ ├── LICENSE
│ ├── Makefile.am
│ ├── README.md
│ ├── autogen.sh
│ ├── configure.ac
│ ├── include
│ │ └── ntcard.hpp
│ ├── libntcard.cpp
│ └── nthll.cpp
└── sdsl-lite
│ ├── .gitignore
│ ├── .gitmodules
│ ├── .travis.yml
│ ├── CMakeLists.txt
│ ├── CMakeModules
│ ├── AppendCompilerFlags.cmake
│ ├── CheckSSE4_2.cmake
│ ├── FindCxaDemangle.cmake
│ ├── check_mode_ti.cpp
│ └── cmake_uninstall.cmake.in
│ ├── COPYING
│ ├── Make.helper.cmake
│ ├── README.md
│ ├── VERSION
│ ├── benchmark
│ ├── Make.download
│ ├── README.md
│ ├── basic_functions.R
│ ├── data
│ │ └── .gitignore
│ ├── document_retrieval
│ │ ├── Makefile
│ │ ├── README.md
│ │ ├── bin
│ │ │ └── .gitignore
│ │ ├── dic.config
│ │ ├── dic
│ │ │ └── .gitignore
│ │ ├── index.config
│ │ ├── index_int.config
│ │ ├── indexes
│ │ │ └── .gitignore
│ │ ├── info
│ │ │ └── .gitignore
│ │ ├── pattern
│ │ │ └── .gitignore
│ │ ├── pattern_length.config
│ │ ├── pattern_length_int.config
│ │ ├── results
│ │ │ └── .gitignore
│ │ ├── src
│ │ │ ├── build_idx.cpp
│ │ │ ├── doc_list_index.hpp
│ │ │ ├── doc_list_index_greedy.hpp
│ │ │ ├── doc_list_index_qprobing.hpp
│ │ │ ├── doc_list_index_sada.hpp
│ │ │ ├── doc_list_index_sort.hpp
│ │ │ ├── gen_pattern.cpp
│ │ │ ├── query_idx.cpp
│ │ │ ├── size_of_idx.cpp
│ │ │ └── word_pat2char_pat.cpp
│ │ ├── test_case.config
│ │ ├── test_case_int.config
│ │ └── visualize
│ │ │ ├── .gitignore
│ │ │ ├── Makefile
│ │ │ ├── doc_re_time.tex
│ │ │ ├── index-filter.config
│ │ │ ├── index-filter_int.config
│ │ │ └── runtime.R
│ ├── indexing_count
│ │ ├── Makefile
│ │ ├── README.md
│ │ ├── bin
│ │ │ └── .gitignore
│ │ ├── compile_options.config
│ │ ├── index.config
│ │ ├── indexes
│ │ │ └── .gitignore
│ │ ├── info
│ │ │ └── .gitignore
│ │ ├── pattern
│ │ │ └── .gitignore
│ │ ├── results
│ │ │ └── .gitignore
│ │ ├── src
│ │ │ ├── build_index_sdsl.cpp
│ │ │ ├── genpatterns.c
│ │ │ ├── info.cpp
│ │ │ ├── interface.h
│ │ │ └── run_queries_sdsl.cpp
│ │ ├── test_case.config
│ │ └── visualize
│ │ │ ├── .gitignore
│ │ │ ├── Makefile
│ │ │ ├── count-footer.tex
│ │ │ ├── count-header.tex
│ │ │ ├── count.R
│ │ │ └── index-filter.config
│ ├── indexing_extract
│ │ ├── Makefile
│ │ ├── README.md
│ │ ├── bin
│ │ │ └── .gitignore
│ │ ├── index.config
│ │ ├── indexes
│ │ │ └── .gitignore
│ │ ├── info
│ │ │ └── .gitignore
│ │ ├── intervals
│ │ │ └── .gitignore
│ │ ├── results
│ │ │ └── .gitignore
│ │ ├── sample.config
│ │ ├── src
│ │ │ ├── build_index_sdsl.cpp
│ │ │ ├── genintervals.c
│ │ │ ├── info.cpp
│ │ │ ├── interface.h
│ │ │ └── run_queries_sdsl.cpp
│ │ ├── test_case.config
│ │ └── visualize
│ │ │ ├── .gitignore
│ │ │ ├── Makefile
│ │ │ ├── extract.R
│ │ │ ├── extract.tex
│ │ │ └── index-filter.config
│ ├── indexing_locate
│ │ ├── Makefile
│ │ ├── README.md
│ │ ├── bin
│ │ │ └── .gitignore
│ │ ├── index.config
│ │ ├── indexes
│ │ │ └── .gitignore
│ │ ├── info
│ │ │ └── .gitignore
│ │ ├── pattern
│ │ │ └── .gitignore
│ │ ├── results
│ │ │ └── .gitignore
│ │ ├── sample.config
│ │ ├── src
│ │ │ ├── build_index_sdsl.cpp
│ │ │ ├── info.cpp
│ │ │ ├── interface.h
│ │ │ ├── pattern_random.cpp
│ │ │ └── run_queries_sdsl.cpp
│ │ ├── test_case.config
│ │ └── visualize
│ │ │ ├── .gitignore
│ │ │ ├── Makefile
│ │ │ ├── index-filter.config
│ │ │ ├── locate.R
│ │ │ └── locate.tex
│ ├── k2_trees
│ │ ├── Makefile
│ │ ├── README.md
│ │ ├── bin
│ │ │ └── .gitignore
│ │ ├── compile_options.config
│ │ ├── k2tree.config
│ │ ├── results
│ │ │ └── .gitignore
│ │ ├── src
│ │ │ ├── gen_k2t.cpp
│ │ │ └── k2_time_and_space.cpp
│ │ ├── test_case.config
│ │ └── visualize
│ │ │ ├── .gitignore
│ │ │ ├── Makefile
│ │ │ ├── k2-footer.tex
│ │ │ ├── k2-header.tex
│ │ │ └── k2.R
│ ├── lcp
│ │ ├── .gitignore
│ │ ├── Makefile
│ │ ├── README.md
│ │ ├── bin
│ │ │ └── .gitignore
│ │ ├── compile_options.config
│ │ ├── lcp.config
│ │ ├── results
│ │ │ └── .gitignore
│ │ ├── src
│ │ │ ├── .gitignore
│ │ │ ├── create_lcp.cpp
│ │ │ └── create_sa_bwt.cpp
│ │ ├── test_case.config
│ │ └── visualize
│ │ │ ├── .gitignore
│ │ │ ├── Makefile
│ │ │ ├── lcp-footer.tex
│ │ │ ├── lcp-header.tex
│ │ │ └── lcp.R
│ ├── rrr_vector
│ │ ├── Makefile
│ │ ├── README.md
│ │ ├── bin
│ │ │ └── .gitignore
│ │ ├── block_size.config
│ │ ├── compile_options.config
│ │ ├── results
│ │ │ └── .gitignore
│ │ ├── src
│ │ │ ├── generate_rnd_bitvector.cpp
│ │ │ └── rrr_time_and_space.cpp
│ │ ├── test_case.config
│ │ └── visualize
│ │ │ ├── .gitignore
│ │ │ ├── Makefile
│ │ │ ├── rrr-footer.tex
│ │ │ ├── rrr-header.tex
│ │ │ └── rrr.R
│ ├── self_delimiting_codes
│ │ ├── Makefile
│ │ ├── README.md
│ │ ├── bin
│ │ │ └── .gitignore
│ │ ├── compile_options.config
│ │ ├── results
│ │ │ └── .gitignore
│ │ ├── src
│ │ │ └── sdc_benchmark.cpp
│ │ ├── test_case.config
│ │ ├── vectors.config
│ │ └── visualize
│ │ │ ├── Makefile
│ │ │ ├── self_delimiting_codes.tex
│ │ │ └── testcase.tex
│ ├── suffix_trees
│ │ ├── Makefile
│ │ ├── README.md
│ │ ├── bin
│ │ │ └── .gitignore
│ │ ├── compile_options.config
│ │ ├── index.config
│ │ ├── index_int.config
│ │ ├── indexes
│ │ │ └── .gitignore
│ │ ├── results
│ │ │ └── .gitignore
│ │ ├── src
│ │ │ ├── build_cst.cpp
│ │ │ ├── depth_stats.cpp
│ │ │ └── time_and_space_cst.cpp
│ │ ├── stats
│ │ │ └── .gitignore
│ │ ├── test_case.config
│ │ ├── test_case_int.config
│ │ └── visualize
│ │ │ ├── .gitignore
│ │ │ ├── Makefile
│ │ │ ├── graph_data.R
│ │ │ ├── output
│ │ │ └── .gitignore
│ │ │ ├── suffix_trees.R
│ │ │ └── suffix_trees.tex
│ ├── tmp
│ │ └── .gitignore
│ └── wavelet_trees
│ │ ├── Makefile
│ │ ├── README.md
│ │ ├── bin
│ │ └── .gitignore
│ │ ├── compile_options.config
│ │ ├── results
│ │ └── .gitignore
│ │ ├── src
│ │ ├── gen_bwt.cpp
│ │ └── wt_time_and_space.cpp
│ │ ├── test_case.config
│ │ ├── visualize
│ │ ├── .gitignore
│ │ ├── Makefile
│ │ ├── wt-footer.tex
│ │ ├── wt-header.tex
│ │ └── wt.R
│ │ └── wt.config
│ ├── build
│ ├── .gitignore
│ ├── build.sh
│ └── clean.sh
│ ├── examples
│ ├── .gitignore
│ ├── Makefile
│ ├── bit-vector.cpp
│ ├── c++11-initializer-list.cpp
│ ├── construct-in-memory.cpp
│ ├── csa-alphabet-strategy.cpp
│ ├── cst-bfs-iterator.cpp
│ ├── cst-node-child-iterator.cpp
│ ├── fm-index.cpp
│ ├── fm-rmq-index.cpp
│ ├── hugepages.cpp
│ ├── int-vector-buffer-iterator.cpp
│ ├── int-vector-buffer.cpp
│ ├── int-vector-entry.cpp
│ ├── int-vector-mapper.cpp
│ ├── intersect.cpp
│ ├── isa_access.cpp
│ ├── k2_treap_in_mem.cpp
│ ├── louds-tree.cpp
│ ├── memory-visualization.cpp
│ ├── node_iterator.cpp
│ ├── print_wt.cpp
│ ├── range-minimum-queries.cpp
│ ├── sa-construct-space-efficient.cpp
│ ├── sa-int-construct-from-file.cpp
│ ├── sd_vector_benchmark.cpp
│ ├── standalone_lcp.cpp
│ ├── storage-visualization.cpp
│ ├── store_to_file.cpp
│ ├── text-statistics.cpp
│ ├── uint64-array2int_vector.cpp
│ ├── write_structure.cpp
│ └── wt_ap.cpp
│ ├── external
│ ├── CMakeLists.txt
│ ├── d3
│ │ ├── LICENSE
│ │ └── d3.min.js
│ └── libdivsufsort
│ │ ├── .gitignore
│ │ ├── CHANGELOG.md
│ │ ├── CMakeLists.txt
│ │ ├── CMakeModules
│ │ ├── AppendCompilerFlags.cmake
│ │ ├── CheckFunctionKeywords.cmake
│ │ ├── CheckLFS.cmake
│ │ ├── ProjectCPack.cmake
│ │ └── cmake_uninstall.cmake.in
│ │ ├── LICENSE
│ │ ├── README.md
│ │ ├── VERSION.cmake
│ │ ├── examples
│ │ ├── CMakeLists.txt
│ │ ├── bwt.c
│ │ ├── mksary.c
│ │ ├── sasearch.c
│ │ ├── suftest.c
│ │ └── unbwt.c
│ │ ├── include
│ │ ├── CMakeLists.txt
│ │ ├── config.h.cmake
│ │ ├── divsufsort.h.cmake
│ │ ├── divsufsort_private.h
│ │ └── lfs.h.cmake
│ │ ├── lib
│ │ ├── CMakeLists.txt
│ │ ├── divsufsort.c
│ │ ├── sssort.c
│ │ ├── trsort.c
│ │ └── utils.c
│ │ └── pkgconfig
│ │ ├── CMakeLists.txt
│ │ └── libdivsufsort.pc.cmake
│ ├── extras
│ ├── Doxyfile.in
│ ├── README.md
│ ├── cheatsheet
│ │ ├── .gitignore
│ │ ├── Makefile
│ │ ├── hyperendnotes.sty
│ │ ├── sdsl-cheatsheet.tex
│ │ └── viz.pdf
│ ├── literature.bib
│ ├── pre-commit
│ ├── resources
│ │ └── space-vis.png
│ ├── sdsl.gdb
│ ├── sdsl.natvis
│ └── sdsl_definitions.sty
│ ├── include
│ ├── CMakeLists.txt
│ └── sdsl
│ │ ├── .gitignore
│ │ ├── CMakeLists.txt
│ │ ├── bit_vector_il.hpp
│ │ ├── bit_vectors.hpp
│ │ ├── bits.hpp
│ │ ├── bp_support.hpp
│ │ ├── bp_support_algorithm.hpp
│ │ ├── bp_support_g.hpp
│ │ ├── bp_support_gg.hpp
│ │ ├── bp_support_sada.hpp
│ │ ├── coder.hpp
│ │ ├── coder_comma.hpp
│ │ ├── coder_elias_delta.hpp
│ │ ├── coder_elias_gamma.hpp
│ │ ├── coder_fibonacci.hpp
│ │ ├── config.hpp
│ │ ├── construct.hpp
│ │ ├── construct_bwt.hpp
│ │ ├── construct_config.hpp
│ │ ├── construct_isa.hpp
│ │ ├── construct_lcp.hpp
│ │ ├── construct_lcp_helper.hpp
│ │ ├── construct_sa.hpp
│ │ ├── construct_sa_se.hpp
│ │ ├── csa_alphabet_strategy.hpp
│ │ ├── csa_bitcompressed.hpp
│ │ ├── csa_sada.hpp
│ │ ├── csa_sampling_strategy.hpp
│ │ ├── csa_wt.hpp
│ │ ├── cst_fully.hpp
│ │ ├── cst_iterators.hpp
│ │ ├── cst_sada.hpp
│ │ ├── cst_sct3.hpp
│ │ ├── dac_vector.hpp
│ │ ├── enc_vector.hpp
│ │ ├── fast_cache.hpp
│ │ ├── hyb_vector.hpp
│ │ ├── int_vector.hpp
│ │ ├── int_vector_buffer.hpp
│ │ ├── int_vector_io_wrappers.hpp
│ │ ├── int_vector_mapper.hpp
│ │ ├── inv_perm_support.hpp
│ │ ├── io.hpp
│ │ ├── iterators.hpp
│ │ ├── k2_treap.hpp
│ │ ├── k2_treap_algorithm.hpp
│ │ ├── k2_treap_helper.hpp
│ │ ├── k2_tree.hpp
│ │ ├── k2_tree_helper.hpp
│ │ ├── lcp.hpp
│ │ ├── lcp_bitcompressed.hpp
│ │ ├── lcp_byte.hpp
│ │ ├── lcp_dac.hpp
│ │ ├── lcp_support_sada.hpp
│ │ ├── lcp_support_tree.hpp
│ │ ├── lcp_support_tree2.hpp
│ │ ├── lcp_vlc.hpp
│ │ ├── lcp_wt.hpp
│ │ ├── louds_tree.hpp
│ │ ├── memory_management.hpp
│ │ ├── nearest_neighbour_dictionary.hpp
│ │ ├── nn_dict_dynamic.hpp
│ │ ├── qsufsort.hpp
│ │ ├── ram_filebuf.hpp
│ │ ├── ram_fs.hpp
│ │ ├── rank_support.hpp
│ │ ├── rank_support_scan.hpp
│ │ ├── rank_support_v.hpp
│ │ ├── rank_support_v5.hpp
│ │ ├── raster_img.hpp
│ │ ├── rmq_succinct_sada.hpp
│ │ ├── rmq_succinct_sct.hpp
│ │ ├── rmq_support.hpp
│ │ ├── rmq_support_sparse_table.hpp
│ │ ├── rrr_helper.hpp
│ │ ├── rrr_vector.hpp
│ │ ├── rrr_vector_15.hpp
│ │ ├── sd_vector.hpp
│ │ ├── sdsl_concepts.hpp
│ │ ├── select_support.hpp
│ │ ├── select_support_mcl.hpp
│ │ ├── select_support_scan.hpp
│ │ ├── sfstream.hpp
│ │ ├── sorted_int_stack.hpp
│ │ ├── sorted_multi_stack_support.hpp
│ │ ├── sorted_stack_support.hpp
│ │ ├── structure_tree.hpp
│ │ ├── suffix_array_algorithm.hpp
│ │ ├── suffix_array_helper.hpp
│ │ ├── suffix_arrays.hpp
│ │ ├── suffix_tree_algorithm.hpp
│ │ ├── suffix_tree_helper.hpp
│ │ ├── suffix_trees.hpp
│ │ ├── uint128_t.hpp
│ │ ├── uint256_t.hpp
│ │ ├── uintx_t.hpp
│ │ ├── util.hpp
│ │ ├── vectors.hpp
│ │ ├── vlc_vector.hpp
│ │ ├── wavelet_trees.hpp
│ │ ├── wm_int.hpp
│ │ ├── wt_algorithm.hpp
│ │ ├── wt_ap.hpp
│ │ ├── wt_blcd.hpp
│ │ ├── wt_gmr.hpp
│ │ ├── wt_helper.hpp
│ │ ├── wt_huff.hpp
│ │ ├── wt_hutu.hpp
│ │ ├── wt_int.hpp
│ │ ├── wt_pc.hpp
│ │ └── wt_rlmn.hpp
│ ├── install.bat
│ ├── install.sh
│ ├── lib
│ ├── .gitignore
│ ├── CMakeLists.txt
│ ├── bits.cpp
│ ├── bp_support_algorithm.cpp
│ ├── coder_elias_delta.cpp
│ ├── coder_elias_gamma.cpp
│ ├── coder_fibonacci.cpp
│ ├── config.cpp
│ ├── construct_config.cpp
│ ├── construct_isa.cpp
│ ├── construct_lcp.cpp
│ ├── construct_lcp_helper.cpp
│ ├── construct_sa.cpp
│ ├── construct_sa_se.cpp
│ ├── csa_alphabet_strategy.cpp
│ ├── io.cpp
│ ├── lcp_support_tree.cpp
│ ├── louds_tree.cpp
│ ├── memory_management.cpp
│ ├── nn_dict_dynamic.cpp
│ ├── ram_filebuf.cpp
│ ├── ram_fs.cpp
│ ├── rrr_vector_15.cpp
│ ├── sd_vector.cpp
│ ├── sfstream.cpp
│ ├── structure_tree.cpp.cmake
│ ├── uint128_t.cpp
│ ├── uint256_t.cpp
│ ├── util.cpp
│ └── wt_helper.cpp
│ ├── sdsl-lite.pc.cmake
│ ├── test
│ ├── .gitignore
│ ├── CMakeLists.txt
│ ├── README.md
│ ├── bit_vector_generator.cpp
│ ├── bit_vector_test.config
│ ├── bit_vector_test.cpp
│ ├── bits_test.cpp
│ ├── coder_test.cpp
│ ├── compile_test.cpp.cmake
│ ├── coverage
│ │ ├── .gitignore
│ │ ├── README.md
│ │ ├── clean.sh
│ │ └── run.sh
│ ├── csa_byte_test.config
│ ├── csa_byte_test.cpp
│ ├── csa_int_test.config
│ ├── csa_int_test.cpp
│ ├── cst_byte_test.config
│ ├── cst_byte_test.cpp
│ ├── cst_helper.hpp
│ ├── cst_int_test.config
│ ├── cst_int_test.cpp
│ ├── dac_vector_test.cpp
│ ├── download.cmake
│ ├── download.config
│ ├── int_vector_buffer_test.cpp
│ ├── int_vector_generator.cpp
│ ├── int_vector_mapper_test.cpp
│ ├── int_vector_test.cpp
│ ├── inv_perm_support_test.cpp
│ ├── k2_treap_test.config
│ ├── k2_treap_test.cpp
│ ├── k2_tree_test.cpp
│ ├── lcp_construct_test.config
│ ├── lcp_construct_test.cpp
│ ├── nn_dict_dynamic_test.cpp
│ ├── rank_support_test.config
│ ├── rank_support_test.cpp
│ ├── replace_int_vector_value.cpp
│ ├── rmq_test.config
│ ├── rmq_test.cpp
│ ├── sa_construct_test.config
│ ├── sa_construct_test.cpp
│ ├── sd_vector_test.cpp
│ ├── search_bidirectional_test.config
│ ├── search_bidirectional_test.cpp
│ ├── select_support_test.config
│ ├── select_support_test.cpp
│ ├── sorted_int_stack_test.cpp
│ ├── sorted_stack_support_test.cpp
│ ├── test_cases
│ │ ├── .gitignore
│ │ ├── 100a.txt
│ │ ├── README.md
│ │ ├── abc_abc_abc.txt
│ │ ├── abc_abc_abc2.txt
│ │ ├── all_symbols.txt
│ │ ├── empty.txt
│ │ ├── example01.txt
│ │ ├── keeper.int
│ │ └── one_byte.txt
│ ├── tmp
│ │ └── .gitignore
│ ├── wt_byte_test.config
│ ├── wt_byte_test.cpp
│ ├── wt_int_test.config
│ └── wt_int_test.cpp
│ ├── tutorial
│ ├── .gitignore
│ ├── Makefile
│ ├── cst-search.cpp
│ ├── cst-traversal.cpp
│ ├── csx-printf.cpp
│ ├── document_listing
│ │ ├── Makefile
│ │ ├── doc_list_index.cpp
│ │ └── generate_collection.py
│ ├── expl-01.cpp
│ ├── expl-02.cpp
│ ├── expl-03.cpp
│ ├── expl-04.cpp
│ ├── expl-05.cpp
│ ├── expl-06.cpp
│ ├── expl-07.cpp
│ ├── expl-08.cpp
│ ├── expl-09.cpp
│ ├── expl-10.cpp
│ ├── expl-11.cpp
│ ├── expl-12.cpp
│ ├── expl-13.cpp
│ ├── expl-14.cpp
│ ├── expl-15.cpp
│ ├── expl-16.cpp
│ ├── expl-17.cpp
│ ├── expl-18.cpp
│ ├── expl-19.cpp
│ ├── expl-20.cpp
│ ├── expl-21.cpp
│ ├── expl-22.cpp
│ ├── expl-23.cpp
│ ├── expl-24.cpp
│ ├── expl-25.cpp
│ ├── expl-26.cpp
│ ├── int-vector-buffer.cpp
│ ├── rmq-example.cpp
│ └── use-a-wavelet-tree.cpp
│ └── uninstall.sh
├── apps
├── CMakeLists.txt
├── counterMain.cpp
├── dumpMain.cpp
├── estimateMemoryMain.cpp
├── main.cpp
└── playground.cpp
├── build_wrapper.sh
├── cmake
└── CPM.cmake
├── conf.py
├── docs
├── Gemfile
├── LICENSE
├── Makefile
├── README.md
├── _config.yml
├── _layouts
│ └── default.html
├── _sass
│ ├── jekyll-theme-cayman.scss
│ ├── normalize.scss
│ ├── rouge-github.scss
│ └── variables.scss
├── another-page.md
├── assets
│ └── css
│ │ └── style.scss
├── docs
│ ├── CODE_OF_CONDUCT.md
│ ├── CONTRIBUTING.md
│ └── SUPPORT.md
├── index.md
├── jekyll-theme-cayman.gemspec
├── main
│ ├── .github
│ │ ├── CODEOWNERS
│ │ ├── config.yml
│ │ ├── no-response.yml
│ │ ├── settings.yml
│ │ └── stale.yml
│ ├── .gitignore
│ ├── .rubocop.yml
│ └── .travis.yml
├── make.bat
├── python
│ ├── README.md
│ ├── coloredKDataFrame.markdown
│ ├── indexing.markdown
│ ├── kDataFrame.markdown
│ ├── kDataFrameIterator.markdown
│ ├── kmerCounting.markdown
│ ├── kmerDecoder.markdown
│ └── setFunctions.markdown
├── requirements.txt
├── script
│ ├── bootstrap
│ ├── cibuild
│ ├── release
│ ├── server
│ └── validate-html
├── source
│ ├── CITATION.md
│ ├── FAQ.md
│ ├── LICENCE.md
│ ├── _static
│ │ └── images
│ │ │ └── kDataFrame.png
│ ├── conf.py
│ ├── cpp_api.rst
│ ├── get_started.md
│ ├── index.rst
│ ├── py_api.rst
│ ├── recipes.rst
│ └── recipes
│ │ ├── recipe_1.ipynb
│ │ ├── recipe_2.ipynb
│ │ ├── recipe_3.ipynb
│ │ ├── recipe_4.ipynb
│ │ ├── recipe_5.ipynb
│ │ └── recipe_6.ipynb
└── thumbnail.png
├── include
└── kProcessor
│ ├── Utils
│ └── utils.hpp
│ ├── algorithms.hpp
│ ├── batchQuery.hpp
│ ├── colorTable.hpp
│ ├── colored_kDataFrame.hpp
│ └── kDataFrame.hpp
├── kProcessor.doxygen
├── kProcessor
├── __init__.py
├── colored_kDataFrame.py
├── kDataFrame.py
├── kDataFrameIterator.py
├── kDataFrameMAP.py
├── kDataFrameMQF.py
├── kDataFramePHMAP.py
├── kmerRow.py
├── seqs_to_kmers.py
└── set_functions.py
├── setup.py
├── src
├── Utils
│ └── utils.cpp
├── algorithms.cpp
├── batchQuery.cpp
├── colorTable.cpp
└── kDataFrames
│ ├── colored_kDataFrame.cpp
│ ├── kDataFrame.cpp
│ ├── kDataFrameBMQF.cpp
│ ├── kDataFrameMAP.cpp
│ ├── kDataFrameMQF.cpp
│ └── kDataFramePHMAP.cpp
├── swig_interfaces
├── HashUtils
│ └── hashutil.i
├── Utils
│ └── kmer.i
├── algorithms
│ └── algorithms.i
├── batchQuery.i
├── colorTable.i
├── colored_kDataFrame.i
├── kDataFrame
│ ├── kDataFrame.i
│ ├── kDataFrameBMQF.i
│ ├── kDataFrameIterator.i
│ ├── kDataFrameMAP.i
│ ├── kDataFrameMQF.i
│ ├── kDataFramePHMAP.i
│ └── kmerRow.i
├── kProcessor.i
└── modules
│ ├── custom_typemaps.i
│ ├── std_map.i
│ ├── std_unordered_map.i
│ └── sys_args.i
├── tests
├── CMakeLists.txt
├── kProcessorLibTests
│ ├── CMakeLists.txt
│ ├── main.cpp
│ ├── testkDataFrame.cpp
│ └── testkDataframe.h
├── python
│ ├── params
│ │ ├── __init__.py
│ │ └── params.py
│ ├── test_indexing.py
│ ├── test_kDataFrameBMQF.py
│ ├── test_kDataFrameMAP.py
│ ├── test_kDataFrameMQF.py
│ ├── test_kDataFrameMultiColumn.py
│ ├── test_kDataFramePHMAP.py
│ ├── test_kmerCounting.py
│ ├── test_kmerDecoder.py
│ ├── test_saveAndLoad.py
│ └── test_setFunctions.py
└── testData
│ ├── .stxxl
│ ├── small.fa
│ ├── test.fastq
│ ├── test.noN.dsk.txt
│ ├── test.noN.fastq
│ ├── test.noN.fastq.ntCardRes
│ ├── test1.fa
│ ├── test1.fa.names
│ ├── test2.noN.fastq
│ ├── test2.noN.fastq.ntCardRes
│ └── test3.noN.fastq
└── version.py
/.github/workflows/ubuntu.yml:
--------------------------------------------------------------------------------
1 | name: Ubuntu
2 |
3 | on:
4 | push:
5 | branches:
6 | - master
7 | pull_request:
8 | branches:
9 | - master
10 |
11 | env:
12 | CTEST_OUTPUT_ON_FAILURE: 1
13 | CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
14 | CPM_SOURCE_CACHE: ${{ github.workspace }}/cpm_modules
15 |
16 | jobs:
17 | build:
18 | runs-on: ubuntu-18.04
19 |
20 | steps:
21 | - uses: actions/checkout@v2
22 | with:
23 | submodules: recursive
24 |
25 | - name: install boost
26 | run: sudo apt-get install libboost-all-dev
27 |
28 | - uses: actions/setup-python@v2
29 | with:
30 | python-version: '3.6'
31 |
32 | - name: install_cmake
33 | run: pip install cmake
34 |
35 | # - name: configure
36 | # run: cmake -Stest -Bbuild -DENABLE_TEST_COVERAGE=1 -DCMAKE_BUILD_TYPE=Debug
37 |
38 | - name: configure
39 | run: cmake -Bbuild
40 |
41 | - name: build
42 | run: cmake --build build -j4
43 |
44 | # - name: test
45 | # run: |
46 | # cd build
47 | # ctest --build-config Debug
48 | - name: collect code coverage
49 | run: bash <(curl -s https://codecov.io/bash) || echo "Codecov did not collect coverage reports"
--------------------------------------------------------------------------------
/.gitignore:
--------------------------------------------------------------------------------
1 | # Prerequisites
2 | *.d
3 |
4 | # Compiled Object files
5 | *.slo
6 | *.lo
7 | *.o
8 | *.obj
9 |
10 | # Precompiled Headers
11 | *.gch
12 | *.pch
13 |
14 | # Compiled Dynamic libraries
15 | *.so
16 | *.dylib
17 | *.dll
18 |
19 | # Fortran module files
20 | *.mod
21 | *.smod
22 |
23 | # Compiled Static libraries
24 | *.lai
25 | *.la
26 | *.a
27 | *.lib
28 |
29 | # Executables
30 | *.exe
31 | *.out
32 | *.app
33 |
34 | build/*
35 | Kprocessor
36 | docs/doxygen/*
37 |
38 | cmake-build-debug/tests/gtest/src/gtest2/googletest/scripts/test/Makefile
39 |
--------------------------------------------------------------------------------
/.gitmodules:
--------------------------------------------------------------------------------
1 | [submodule "ThirdParty/kmerDecoder"]
2 | path = ThirdParty/kmerDecoder
3 | url = https://github.com/dib-lab/kmerDecoder.git
4 | [submodule "ThirdParty/cereal"]
5 | path = ThirdParty/cereal
6 | url = https://github.com/USCiLab/cereal.git
7 | [submodule "ThirdParty/MQF"]
8 | path = ThirdParty/MQF
9 | url = https://github.com/dib-lab/MQF
10 |
--------------------------------------------------------------------------------
/.readthedocs.yml:
--------------------------------------------------------------------------------
1 | # .readthedocs.yml
2 | # Read the Docs configuration file
3 | # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
4 |
5 | # Required
6 | version: 2
7 |
8 | # Build documentation in the docs/ directory with Sphinx
9 | sphinx:
10 | configuration: docs/source/conf.py
11 |
12 | # Build documentation with MkDocs
13 | #mkdocs:
14 | # configuration: mkdocs.yml
15 |
16 | # Optionally build your docs in additional formats such as PDF and ePub
17 | formats: all
18 |
19 | # Optionally set the version of Python and requirements required to build your docs
20 | python:
21 | version: 3.7
22 | install:
23 | - requirements: docs/requirements.txt
--------------------------------------------------------------------------------
/Doxyfile:
--------------------------------------------------------------------------------
1 | # Configuration for Doxygen for use with CMake
2 | # Only options that deviate from the default are included
3 | # To create a new Doxyfile containing all available options, call `doxygen -g`
4 |
5 | # Get Project name and version from CMake
6 | PROJECT_NAME = @DOXYGEN_PROJECT_NAME@
7 | PROJECT_NUMBER = @DOXYGEN_PROJECT_VERSION@
8 |
9 | # Add sources
10 | INPUT = @DOXYGEN_PROJECT_ROOT@/README.md @DOXYGEN_PROJECT_ROOT@/include # @DOXYGEN_PROJECT_ROOT@/documentation/pages
11 | EXTRACT_ALL = YES
12 | RECURSIVE = YES
13 | OUTPUT_DIRECTORY = @DOXYGEN_OUTPUT_DIRECTORY@
14 |
15 | # Use the README as a main page
16 | USE_MDFILE_AS_MAINPAGE = @DOXYGEN_PROJECT_ROOT@/README.md
17 |
18 | # set relative include paths
19 | FULL_PATH_NAMES = YES
20 | STRIP_FROM_PATH = @DOXYGEN_PROJECT_ROOT@/include @DOXYGEN_PROJECT_ROOT@
21 |
22 | # We use m.css to generate the html documentation, so we only need XML output
23 | GENERATE_XML = YES
24 | GENERATE_HTML = NO
25 | GENERATE_LATEX = NO
26 | XML_PROGRAMLISTING = NO
27 | CREATE_SUBDIRS = NO
28 |
29 | # Include all directories, files and namespaces in the documentation
30 | # Disable to include only explicitly documented objects
31 | M_SHOW_UNDOCUMENTED = YES
32 |
--------------------------------------------------------------------------------
/MANIFEST.in:
--------------------------------------------------------------------------------
1 | # Include the README
2 | include *.md
3 |
4 | # Include the license file
5 | include LICENSE
6 |
7 | # Include the headers files
8 | recursive-include include *
9 | recursive-include ThirdParty/MQF/include *
10 | recursive-include ThirdParty/MQF/include *
11 | recursive-include ThirdParty/json *
12 | recursive-include ThirdParty/sdsl-lite/include *
13 | recursive-include ThirdParty/kmerDecoder/include *
14 | recursive-include ThirdParty/kmerDecoder/lib/parallel-hashmap *
15 | recursive-include ThirdParty/kmerDecoder/lib/kseq/include *
16 |
17 | recursive-include KP_BUILD lib*a
18 | recursive-include ThirdParty lib*a
19 |
20 | # Include static libs
21 | include KP_BUILD/libkProcessor.a
22 | include KP_BUILD/ThirdParty/kmerDecoder/libkmerDecoder.a
23 | include KP_BUILD/ThirdParty/MQF/src/libMQF.a
24 | include KP_BUILD/ThirdParty/sdsl-lite/lib/libsdsl.a
25 |
26 | #include version
27 | include version.py
28 |
29 | # Include SWIG interfaces
30 | recursive-include swig_interfaces *
31 |
--------------------------------------------------------------------------------
/ThirdParty/TBB/include/index.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 | Overview
5 | Include files for Intel® Threading Building Blocks (Intel® TBB).
6 |
7 | Directories
8 |
9 | - tbb
10 |
- Include files for Intel TBB classes and functions.
11 |
- serial/tbb
12 |
- Include files for a sequential implementation of the parallel_for algorithm.
13 |
14 |
15 |
16 | Up to parent directory
17 |
18 | Copyright © 2005-2018 Intel Corporation. All Rights Reserved.
19 |
20 | Intel is a registered trademark or trademark of Intel Corporation
21 | or its subsidiaries in the United States and other countries.
22 |
23 | * Other names and brands may be claimed as the property of others.
24 |
25 |
26 |
--------------------------------------------------------------------------------
/ThirdParty/TBB/include/serial/tbb/tbb_annotate.h:
--------------------------------------------------------------------------------
1 | /*
2 | Copyright (c) 2005-2018 Intel Corporation
3 |
4 | Licensed under the Apache License, Version 2.0 (the "License");
5 | you may not use this file except in compliance with the License.
6 | You may obtain a copy of the License at
7 |
8 | http://www.apache.org/licenses/LICENSE-2.0
9 |
10 | Unless required by applicable law or agreed to in writing, software
11 | distributed under the License is distributed on an "AS IS" BASIS,
12 | WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
13 | See the License for the specific language governing permissions and
14 | limitations under the License.
15 |
16 |
17 |
18 |
19 | */
20 |
21 | #ifndef __TBB_annotate_H
22 | #define __TBB_annotate_H
23 |
24 | // Macros used by the Intel(R) Parallel Advisor.
25 | #ifdef __TBB_NORMAL_EXECUTION
26 | #define ANNOTATE_SITE_BEGIN( site )
27 | #define ANNOTATE_SITE_END( site )
28 | #define ANNOTATE_TASK_BEGIN( task )
29 | #define ANNOTATE_TASK_END( task )
30 | #define ANNOTATE_LOCK_ACQUIRE( lock )
31 | #define ANNOTATE_LOCK_RELEASE( lock )
32 | #else
33 | #include
34 | #endif
35 |
36 | #endif /* __TBB_annotate_H */
37 |
--------------------------------------------------------------------------------
/ThirdParty/TBB/include/tbb/index.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 | Overview
5 | Include files for Intel® Threading Building Blocks classes and functions.
6 |
7 |
Click here to see all files in the directory.
8 |
9 | Directories
10 |
11 | - compat
12 |
- Include files for source level compatibility with other frameworks.
13 |
- internal
14 |
- Include files with implementation details; not for direct use.
15 |
- machine
16 |
- Include files for low-level architecture specific functionality; not for direct use.
17 |
18 |
19 |
20 | Up to parent directory
21 |
22 | Copyright © 2005-2018 Intel Corporation. All Rights Reserved.
23 |
24 | Intel is a registered trademark or trademark of Intel Corporation
25 | or its subsidiaries in the United States and other countries.
26 |
27 | * Other names and brands may be claimed as the property of others.
28 |
29 |
30 |
--------------------------------------------------------------------------------
/ThirdParty/TBB/include/tbb/tbb_disable_exceptions.h:
--------------------------------------------------------------------------------
1 | /*
2 | Copyright (c) 2005-2018 Intel Corporation
3 |
4 | Licensed under the Apache License, Version 2.0 (the "License");
5 | you may not use this file except in compliance with the License.
6 | You may obtain a copy of the License at
7 |
8 | http://www.apache.org/licenses/LICENSE-2.0
9 |
10 | Unless required by applicable law or agreed to in writing, software
11 | distributed under the License is distributed on an "AS IS" BASIS,
12 | WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
13 | See the License for the specific language governing permissions and
14 | limitations under the License.
15 |
16 |
17 |
18 |
19 | */
20 |
21 | //! To disable use of exceptions, include this header before any other header file from the library.
22 |
23 | //! The macro that prevents use of exceptions in the library files
24 | #undef TBB_USE_EXCEPTIONS
25 | #define TBB_USE_EXCEPTIONS 0
26 |
27 | //! Prevent compilers from issuing exception related warnings.
28 | /** Note that the warnings are suppressed for all the code after this header is included. */
29 | #if _MSC_VER
30 | #if __INTEL_COMPILER
31 | #pragma warning (disable: 583)
32 | #else
33 | #pragma warning (disable: 4530 4577)
34 | #endif
35 | #endif
36 |
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/ThirdParty/TBB/lib/intel64/gcc4.7/libtbb.so:
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1 | INPUT (libtbb.so.2)
2 |
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/ThirdParty/TBB/lib/intel64/gcc4.7/libtbb_debug.so:
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2 |
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/ThirdParty/TBB/lib/intel64/gcc4.7/libtbb_preview.so:
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2 |
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2 |
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/ThirdParty/TBB/lib/intel64/gcc4.7/libtbb_preview_debug.so.2:
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https://raw.githubusercontent.com/dib-lab/kProcessor/7fe67ec22cd2ba77f8669ee8dee82f971d29cb30/ThirdParty/TBB/lib/intel64/gcc4.7/libtbb_preview_debug.so.2
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/ThirdParty/TBB/lib/intel64/gcc4.7/libtbbmalloc.so:
--------------------------------------------------------------------------------
1 | INPUT (libtbbmalloc.so.2)
2 |
--------------------------------------------------------------------------------
/ThirdParty/TBB/lib/intel64/gcc4.7/libtbbmalloc.so.2:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/dib-lab/kProcessor/7fe67ec22cd2ba77f8669ee8dee82f971d29cb30/ThirdParty/TBB/lib/intel64/gcc4.7/libtbbmalloc.so.2
--------------------------------------------------------------------------------
/ThirdParty/TBB/lib/intel64/gcc4.7/libtbbmalloc_debug.so:
--------------------------------------------------------------------------------
1 | INPUT (libtbbmalloc_debug.so.2)
2 |
--------------------------------------------------------------------------------
/ThirdParty/TBB/lib/intel64/gcc4.7/libtbbmalloc_debug.so.2:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/dib-lab/kProcessor/7fe67ec22cd2ba77f8669ee8dee82f971d29cb30/ThirdParty/TBB/lib/intel64/gcc4.7/libtbbmalloc_debug.so.2
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/ThirdParty/TBB/lib/intel64/gcc4.7/libtbbmalloc_proxy.so:
--------------------------------------------------------------------------------
1 | INPUT (libtbbmalloc_proxy.so.2)
2 |
--------------------------------------------------------------------------------
/ThirdParty/TBB/lib/intel64/gcc4.7/libtbbmalloc_proxy.so.2:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/dib-lab/kProcessor/7fe67ec22cd2ba77f8669ee8dee82f971d29cb30/ThirdParty/TBB/lib/intel64/gcc4.7/libtbbmalloc_proxy.so.2
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/ThirdParty/TBB/lib/intel64/gcc4.7/libtbbmalloc_proxy_debug.so:
--------------------------------------------------------------------------------
1 | INPUT (libtbbmalloc_proxy_debug.so.2)
2 |
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/ThirdParty/TBB/lib/intel64/gcc4.7/libtbbmalloc_proxy_debug.so.2:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/dib-lab/kProcessor/7fe67ec22cd2ba77f8669ee8dee82f971d29cb30/ThirdParty/TBB/lib/intel64/gcc4.7/libtbbmalloc_proxy_debug.so.2
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/ThirdParty/ntCard/.gitignore:
--------------------------------------------------------------------------------
1 | .deps/*
2 | Common/.*
3 | Makefile
4 | Makefile.in
5 | aclocal.m4
6 | autom4te.cache/
7 | compile
8 | config.h
9 | config.h.in
10 | config.log
11 | config.status
12 | configure
13 | depcomp
14 | install-sh
15 | missing
16 | stamp-h1
17 | share/*
18 | src/*
19 | tmp/*
20 |
--------------------------------------------------------------------------------
/ThirdParty/ntCard/CITATION.bib:
--------------------------------------------------------------------------------
1 | @article{doi:10.1093/bioinformatics/btw832,
2 | author = {Mohamadi, Hamid and Khan, Hamza and Birol, Inanc},
3 | title = {ntCard: a streaming algorithm for cardinality estimation in genomics data},
4 | journal = {Bioinformatics},
5 | volume = {33},
6 | number = {9},
7 | pages = {1324},
8 | year = {2017},
9 | doi = {10.1093/bioinformatics/btw832},
10 | URL = { + http://dx.doi.org/10.1093/bioinformatics/btw832},
11 | eprint = {/oup/backfile/content_public/journal/bioinformatics/33/9/10.1093_bioinformatics_btw832/2/btw832.pdf}
12 | }
13 |
--------------------------------------------------------------------------------
/ThirdParty/ntCard/ChangeLog:
--------------------------------------------------------------------------------
1 | 2017-01-11 Hamid Mohamadi
2 |
3 | * Release version 1.0.0
4 |
--------------------------------------------------------------------------------
/ThirdParty/ntCard/Common/Fcontrol.cpp:
--------------------------------------------------------------------------------
1 | #include "Fcontrol.h"
2 | #include
3 |
4 | /* Set the FD_CLOEXEC flag of the specified file descriptor. */
5 | int setCloexec(int fd)
6 | {
7 | int flags = fcntl(fd, F_GETFD, 0);
8 | if (flags == -1)
9 | return -1;
10 | flags |= FD_CLOEXEC;
11 | return fcntl(fd, F_SETFD, flags);
12 | }
13 |
--------------------------------------------------------------------------------
/ThirdParty/ntCard/Common/Fcontrol.h:
--------------------------------------------------------------------------------
1 | #ifndef FCONTROL_H
2 | #define FCONTROL_H 1
3 |
4 | int setCloexec(int fd);
5 |
6 | #endif
7 |
--------------------------------------------------------------------------------
/ThirdParty/ntCard/Common/SignalHandler.h:
--------------------------------------------------------------------------------
1 | #ifndef SIGNALHANDLER_H
2 | #define SIGNALHANDLER_H 1
3 |
4 | void signalInit();
5 |
6 | #endif
7 |
--------------------------------------------------------------------------------
/ThirdParty/ntCard/Common/Uncompress.h:
--------------------------------------------------------------------------------
1 | #ifndef UNCOMPRESS_H
2 | #define UNCOMPRESS_H 1
3 |
4 | bool uncompress_init();
5 |
6 | namespace {
7 | const bool uncompressInitialized = uncompress_init();
8 | bool getUncompressInitialized() __attribute__((unused));
9 | bool getUncompressInitialized() {
10 | return uncompressInitialized;
11 | }
12 | }
13 |
14 | #endif
15 |
--------------------------------------------------------------------------------
/ThirdParty/ntCard/LICENSE:
--------------------------------------------------------------------------------
1 | MIT License
2 |
3 | Copyright (c) 2018 Hamid Mohamadi
4 |
5 | Permission is hereby granted, free of charge, to any person obtaining a copy
6 | of this software and associated documentation files (the "Software"), to deal
7 | in the Software without restriction, including without limitation the rights
8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 |
12 | The above copyright notice and this permission notice shall be included in all
13 | copies or substantial portions of the Software.
14 |
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21 | SOFTWARE.
22 |
--------------------------------------------------------------------------------
/ThirdParty/ntCard/Makefile.am:
--------------------------------------------------------------------------------
1 | noinst_LIBRARIES = libntcard.a
2 |
3 | libntcard_a_CPPFLAGS = -I$(top_srcdir)/Common
4 |
5 | libntcard_a_SOURCES = \
6 | Common/Uncompress.cpp \
7 | Common/Uncompress.h \
8 | Common/SignalHandler.cpp \
9 | Common/SignalHandler.h \
10 | Common/StringUtil.h \
11 | Common/Fcontrol.cpp \
12 | Common/Fcontrol.h \
13 | Common/nthash.hpp \
14 | Common/ntHashIterator.hpp \
15 | libntcard.cpp
16 |
17 |
18 | dist_doc_DATA = \
19 | ChangeLog \
20 | CITATION.bib \
21 | LICENSE \
22 | README.md
23 |
24 | EXTRA_DIST=autogen.sh
25 |
--------------------------------------------------------------------------------
/ThirdParty/ntCard/autogen.sh:
--------------------------------------------------------------------------------
1 | #!/bin/sh
2 | set -ex
3 | aclocal
4 | autoconf
5 | autoheader
6 | automake -a
7 |
--------------------------------------------------------------------------------
/ThirdParty/ntCard/include/ntcard.hpp:
--------------------------------------------------------------------------------
1 | #ifndef ntCard_HPP
2 | #define ntCard_HPP
3 | int main_ntCard(string inputFile,unsigned myK, uint32_t cov, int nThreads,string prefix);
4 | #endif
5 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/.gitignore:
--------------------------------------------------------------------------------
1 | Make.helper
2 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/.gitmodules:
--------------------------------------------------------------------------------
1 | [submodule "external/googletest"]
2 | path = external/googletest
3 | url = https://github.com/google/googletest.git
4 | [submodule "external/libdivsufsort"]
5 | path = external/libdivsufsort
6 | url = https://github.com/simongog/libdivsufsort.git
7 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/CMakeModules/CheckSSE4_2.cmake:
--------------------------------------------------------------------------------
1 | # Check if the CPU provides fast operations
2 | # for popcount, leftmost and rightmost bit
3 |
4 | set(BUILTIN_POPCNT 0)
5 | if(DEFINED ENV{BUILD_PORTABLE})
6 | #message(STATUS "sse4.2 disabled")
7 | # Check if we are on a Linux system
8 | elseif(CMAKE_SYSTEM_NAME STREQUAL "Linux")
9 | # Use /proc/cpuinfo to get the information
10 | file(STRINGS "/proc/cpuinfo" _cpuinfo)
11 | if(_cpuinfo MATCHES "(sse4_2)|(sse4a)")
12 | set(BUILTIN_POPCNT 1)
13 | endif()
14 | elseif(CMAKE_SYSTEM_NAME STREQUAL "Windows")
15 | # handle windows
16 | # get_filename_component(_vendor_id "[HKEY_LOCAL_MACHINE\\Hardware\\Description\\System\\CentralProcessor\\0;VendorIdentifier]" NAME CACHE)
17 | # get_filename_component(_cpu_id "[HKEY_LOCAL_MACHINE\\Hardware\\Description\\System\\CentralProcessor\\0;Identifier]" NAME CACHE)
18 | elseif(CMAKE_SYSTEM_NAME STREQUAL "Darwin")
19 | # handle MacOs
20 | execute_process(COMMAND sysctl -n machdep.cpu.features
21 | OUTPUT_VARIABLE _cpuinfo OUTPUT_STRIP_TRAILING_WHITESPACE)
22 | if(_cpuinfo MATCHES "SSE4.2")
23 | set(BUILTIN_POPCNT 1)
24 | endif()
25 | endif()
26 |
27 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/CMakeModules/FindCxaDemangle.cmake:
--------------------------------------------------------------------------------
1 | # Module that checks whether the compiler supports the
2 | # abi::__cxa_demangle function required to
3 | # make the type names returned by typeid() human-readable
4 | #
5 | # Sets the following variable:
6 | # HAVE_CXA_DEMANGLE
7 | #
8 | # perform tests
9 | include(CheckCXXSourceCompiles)
10 |
11 | CHECK_CXX_SOURCE_COMPILES("#include
12 | int main(void){
13 | int foobar = 0;
14 | const char *foo = typeid(foobar).name();
15 | int status;
16 | char *demangled = abi::__cxa_demangle( foo, 0, 0, &status );
17 | }" HAVE_CXA_DEMANGLE)
18 |
19 | include (FindPackageHandleStandardArgs)
20 | # prevent useless message from being displayed
21 | set (FIND_PACKAGE_MESSAGE_DETAILS_CxaDemangle "[1][v()]"
22 | CACHE INTERNAL "Details about finding CxaDemangle")
23 | find_package_handle_standard_args (CxaDemangle DEFAULT_MSG HAVE_CXA_DEMANGLE)
24 |
25 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/CMakeModules/check_mode_ti.cpp:
--------------------------------------------------------------------------------
1 | typedef unsigned int uint128_t __attribute__((mode(TI)));
2 |
3 | int main() {
4 | return 0;
5 | }
6 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/COPYING:
--------------------------------------------------------------------------------
1 | The sdsl copyright is as follows:
2 |
3 | Copyright (C) 2007-2014 Simon Gog All Right Reserved.
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
8 | (at your option) any later version.
9 |
10 | This program 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 this program. If not, see http://www.gnu.org/licenses/ .
17 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/Make.helper.cmake:
--------------------------------------------------------------------------------
1 | LIB_DIR = @CMAKE_INSTALL_PREFIX@/lib
2 | INC_DIR = @CMAKE_INSTALL_PREFIX@/include
3 | MY_CXX_FLAGS=@CMAKE_CXX_FLAGS@ $(CODE_COVER)
4 | MY_CXX_OPT_FLAGS=@CMAKE_CXX_OPT_FLAGS@
5 | MY_CXX=@CMAKE_CXX_COMPILER@
6 | MY_CC=@CMAKE_C_COMPILER@
7 |
8 | # Returns $1-th .-separated part of string $2.
9 | dim = $(word $1, $(subst ., ,$2))
10 |
11 | # Returns value stored in column $3 for item with ID $2 in
12 | # config file $1
13 | config_select=$(shell cat $1 | grep -v "^\#" | grep "$2;" | cut -f $3 -d';' )
14 |
15 | # Returns value stored in column $3 for a line matching $2
16 | # in config file $1
17 | config_filter=$(shell cat $1 | grep -v "^\#" | fgrep "$2" | cut -f $3 -d';' )
18 |
19 | # Get all IDs from a config file $1
20 | config_ids=$(shell cat $1 | grep -v "^\#" | cut -f 1 -d';')
21 |
22 | # Get column $2 from a config file $1
23 | config_column=$(shell cat $1 | grep -v "^\#" | cut -f $2 -d';')
24 |
25 | # Get size of file $1 in bytes
26 | file_size=$(shell wc -c < $1 | tr -d ' ')
27 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/VERSION:
--------------------------------------------------------------------------------
1 | 2.1.0
2 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/Make.download:
--------------------------------------------------------------------------------
1 | ../data/%:
2 | $(eval URL:=$(firstword $(call config_filter,test_case.config,$@,4)))
3 | @$(if $(URL),,\
4 | $(error "No download link nor generation program specified for test case $@") )
5 | @echo "Download input from $(URL) using curl"
6 | $(eval DEST_DIR:=$(shell dirname $@))
7 | cd $(DEST_DIR); curl -O $(URL)
8 | $(eval FILE:=$(DEST_DIR)/$(notdir $(URL)))
9 | @$(if $(filter %.gz,$(FILE)),\
10 | echo "Extract file $(FILE) using gunzip";\
11 | gunzip $(FILE))
12 |
13 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/data/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !get_corpus.sh
3 | !.gitignore
4 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/document_retrieval/bin/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/document_retrieval/dic.config:
--------------------------------------------------------------------------------
1 | # Configuration file for dictionary files
2 | # for integer based inputs
3 | #
4 | # (1) Identifier for test integer test file
5 | # (has to exist in test_case_int.config)
6 | # (2) Path to dictionary
7 | # (3) LaTeX name
8 | # (4) Download link (if the test is available online)
9 | ENWIKISMLINT;dic/enwiki-20130805-pages-articles1.dic;enwiki-dic;http://people.eng.unimelb.edu.au/sgog/data/enwiki-20130805-pages-articles1.dic.gz
10 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/document_retrieval/dic/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/document_retrieval/index.config:
--------------------------------------------------------------------------------
1 | # This file specified sdsl index structures that are used in the benchmark.
2 | #
3 | # Each index is specified by a triple: INDEX_ID;SDSL_TYPE;INDEX_LATEX_NAME
4 | # * INDEX_ID : An identifier for the index. Only letters and underscores
5 | # are allowed in INDEX_ID.
6 | # * TYPE : Corresponding type.
7 | # * LATEX_NAME: LaTeX name for output in the benchmark report.
8 | GREEDY;doc_list_index_greedy<>;GREEDY
9 | #GREEDYX;doc_list_index_greedy,1000000,1000000,sa_order_sa_sampling<>,isa_sampling<>,byte_alphabet>>;GREEDYX
10 | #GREEDYY;doc_list_index_greedy>,1000000,1000000,sa_order_sa_sampling<>,isa_sampling<>,byte_alphabet>>;GREEDYY
11 | #GREEDY-RRR;doc_list_index_greedy>,1000000,1000000>,wt_int>>;GREEDY-RRR
12 | #QPROBING;doc_list_index_qprobing<>;QPROBING
13 | SADA;doc_list_index_sada, 32, 1000000, text_order_sa_sampling>>>;SADA
14 | SORT;doc_list_index_sort<>;SORT
15 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/document_retrieval/index_int.config:
--------------------------------------------------------------------------------
1 | # This file specified sdsl index structures that are used in the benchmark.
2 | #
3 | # Each index is specified by a triple: INDEX_ID;SDSL_TYPE;INDEX_LATEX_NAME
4 | # * INDEX_ID : An identifier for the index. Only letters and underscores
5 | # are allowed in INDEX_ID.
6 | # * TYPE : Corresponding type.
7 | # * LATEX_NAME: LaTeX name for output in the benchmark report.
8 | GREEDYINT;doc_list_index_greedy>,1000000,1000000>>;GREEDY-I
9 | #GREEDYINTX;doc_list_index_greedy,1000000,1000000>>;GREEDY-IX
10 | #GREEDYINTY;doc_list_index_greedy>,1000000,1000000>>;GREEDY-IY
11 | SADAINT;doc_list_index_sada, 32, 1000000, text_order_sa_sampling>>>;SADA-I
12 | SORTINT;doc_list_index_sort, 32, 1000000, text_order_sa_sampling>>>;SORT-I
13 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/document_retrieval/indexes/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/document_retrieval/info/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/document_retrieval/pattern/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/document_retrieval/pattern_length.config:
--------------------------------------------------------------------------------
1 | # pattern length
2 | 3;
3 | 4;
4 | 5;
5 | 6;
6 | 7;
7 | 8;
8 | 9;
9 | 10;
10 | 11;
11 | 12;
12 | 13;
13 | 14;
14 | 15;
15 | 16;
16 | 17;
17 | 18;
18 | 19;
19 | 20;
20 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/document_retrieval/pattern_length_int.config:
--------------------------------------------------------------------------------
1 | # pattern length
2 | 2;
3 | 3;
4 | 4;
5 | 5;
6 | 6;
7 | 7;
8 | 8;
9 | 9;
10 | 10;
11 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/document_retrieval/results/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/document_retrieval/src/build_idx.cpp:
--------------------------------------------------------------------------------
1 | #include "doc_list_index.hpp"
2 | #include
3 | #include
4 | #include
5 |
6 | using namespace std;
7 | using namespace sdsl;
8 |
9 | using idx_type = IDX_TYPE;
10 |
11 | int main(int argc, char* argv[])
12 | {
13 | if (argc < 4) {
14 | cout << "Usage: " << argv[0] << " collection_file tmp_dir index_file" << endl;
15 | cout << " Generates an index and stores result in index_file" << endl;
16 | cout << " Temporary files are stored in tmp_dir." << endl;
17 | return 1;
18 | }
19 | string collection_file = argv[1];
20 | string id = util::basename(collection_file);
21 | string tmp_dir = argv[2];
22 | string idx_file = argv[3];
23 |
24 | using timer = std::chrono::high_resolution_clock;
25 | auto start = timer::now();
26 |
27 | idx_type idx;
28 | cache_config cconfig(false, tmp_dir, id);
29 | construct(idx, collection_file, cconfig, idx_type::WIDTH==8 ? 1 : 0);
30 | auto stop = timer::now();
31 | auto elapsed = stop-start;
32 | std::cout << "construction time = " << std::chrono::duration_cast(elapsed).count() << std::endl;
33 | store_to_file(idx, idx_file);
34 | }
35 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/document_retrieval/src/doc_list_index.hpp:
--------------------------------------------------------------------------------
1 | #ifndef DOC_LIST_INDEX
2 | #define DOC_LIST_INDEX
3 |
4 | #include
5 | #include
6 |
7 | struct doc_list_tag {};
8 |
9 | template
10 | void
11 | construct(t_index& idx, const std::string& file, sdsl::cache_config& config, uint8_t num_bytes, doc_list_tag)
12 | {
13 | t_index tmp_idx(file, config, num_bytes);
14 | idx.swap(tmp_idx);
15 | }
16 |
17 | #include "doc_list_index_sada.hpp"
18 | #include "doc_list_index_greedy.hpp"
19 | #include "doc_list_index_qprobing.hpp"
20 | #include "doc_list_index_sort.hpp"
21 |
22 | #endif
23 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/document_retrieval/src/size_of_idx.cpp:
--------------------------------------------------------------------------------
1 | #include "doc_list_index.hpp"
2 | #include
3 | #include
4 |
5 | using namespace std;
6 | using namespace sdsl;
7 |
8 | using idx_type = IDX_TYPE;
9 |
10 | int main(int argc, char* argv[])
11 | {
12 | if (argc < 2) {
13 | cout << "Usage: " << argv[0] << " index_file [html_file]" << endl;
14 | return 1;
15 | }
16 | string index_file = string(argv[1]);
17 | idx_type idx;
18 |
19 | if (!load_from_file(idx, index_file)) {
20 | std::cerr << "Could not load index file" << std::endl;
21 | return 1;
22 | }
23 | if (argc > 2) {
24 | ofstream out(argv[2]);
25 | write_structure(idx, out);
26 | } else {
27 | cout<<"# index_file = "< i2w;
31 | string word;
32 | while (dic_in >> word) {
33 | uint64_t nr, occ;
34 | dic_in >> nr >> occ;
35 | i2w[nr] = word;
36 | }
37 | while (pat_in.getline(buffer, buf_size)) {
38 | stringstream ss;
39 | ss << string(buffer);
40 | uint64_t w;
41 | while (ss >> w) {
42 | cout << i2w[w] << " ";
43 | }
44 | cout << "\n";
45 | }
46 | }
47 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/document_retrieval/test_case.config:
--------------------------------------------------------------------------------
1 | # Configuration for test files
2 | # (1) Identifier for test file
3 | # (2) Path to the test file
4 | # (3) LaTeX name
5 | # (4) Download link (if the test is available online)
6 | ENWIKISML;../data/enwiki-20130805-pages-articles1.txt;enwiki-sml;http://people.eng.unimelb.edu.au/sgog/data/enwiki-20130805-pages-articles1.txt.gz
7 | PROTEINS;../data/proteins.txt;proteins;http://people.eng.unimelb.edu.au/sgog/data/proteins.txt.gz
8 | #WSJ;../data/wsj.char.100MB;WSJ
9 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/document_retrieval/test_case_int.config:
--------------------------------------------------------------------------------
1 | # Configuration for integer test files
2 | # (1) Identifier for test file
3 | # (2) Path to the test file
4 | # (3) LaTeX name
5 | # (4) Download link (if the test is available online)
6 | ENWIKISMLINT;../data/enwiki-20130805-pages-articles1.int.sdsl;enwiki-sml-int;http://people.eng.unimelb.edu.au/sgog/data/enwiki-20130805-pages-articles1.int.sdsl.gz
7 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/document_retrieval/visualize/.gitignore:
--------------------------------------------------------------------------------
1 | doc_re_time.aux
2 | doc_re_time.log
3 | doc_re_time.pdf
4 | fig-runtime.tex
5 | fig-runtime_int.tex
6 | tbl-indexes.tex
7 | tbl-indexes_int.tex
8 | tbl-sizes_int.tex
9 | tbl-sizes.tex
10 | LaTeX.log
11 | R.log
12 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/document_retrieval/visualize/Makefile:
--------------------------------------------------------------------------------
1 | include ../../../Make.helper
2 | CONFIG_FILES=../index.config ../test_case.config ../pattern_length.config \
3 | ../index_int.config ../test_case_int.config ../pattern_length_int.config
4 |
5 | all: doc_re_time.pdf
6 |
7 | doc_re_time.pdf: doc_re_time.tex \
8 | fig-runtime.tex fig-runtime_int.tex \
9 | tbl-sizes.tex tbl-sizes_int.tex \
10 | tbl-indexes.tex tbl-indexes_int.tex \
11 | tbl-collections.tex tbl-collections_int.tex
12 | @echo "Use pdflatex to generate doc_re_time.pdf"
13 | @pdflatex doc_re_time.tex >> LaTeX.log 2>&1
14 |
15 | #tbl-locate.tex fig-locate.tex: ../../basic_functions.R locate.R $(CONFIG_FILES) ../results/all.txt
16 | # @echo "Use R to generate tbl-locate.tex and fig-locate.tex"
17 | fig-runtime.tex fig-runtime_int.tex tbl-indexes.tex tbl-indexes_int.tex tbl-sizes.tex tbl-sizes_int.tex tbl-collections.tex tbl-collections_int.tex: ../../basic_functions.R runtime.R \
18 | $(CONFIG_FILES) ../results/all.txt \
19 | ../info/sizes.txt ../info/sizes_int.txt
20 | @R --vanilla < runtime.R > R.log 2>&1
21 |
22 | clean:
23 | rm -f doc_re_time.pdf doc_re_time.aux \
24 | fig-runtime.tex tbl-indexes.tex \
25 | fig-runtime_int.tex tbl-indexes_int.tex \
26 | tbl-sizes.tex tbl-sizes_int.tex \
27 | tbl-collections.tex tbl-collections_int.tex \
28 | doc_re_time.log R.log LaTeX.log
29 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/document_retrieval/visualize/index-filter.config:
--------------------------------------------------------------------------------
1 | # Use this file to specify which indexes are listed in the report doc_re_time.pdf
2 | # and how they look like in the report.
3 | #
4 | # List all the index ids which should be included in the report. Note that
5 | # the listed index ids must also be present in the file `../index.config`.
6 | # Each INDEX_ID should be listed on a separate line followed by the style:
7 | # [pch];[lty];[col] (point type, line type, and color).
8 | GREEDY;1;solid;black
9 | QPROBING;2;solid;blue
10 | #GREEDYX;2;solid;blue
11 | #GREEDYY;2;solid;green
12 | SADA;3;solid;red
13 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/document_retrieval/visualize/index-filter_int.config:
--------------------------------------------------------------------------------
1 | # Use this file to specify which indexes are listed in the report doc_re_time.pdf
2 | # and how they look like in the report.
3 | #
4 | # List all the index ids which should be included in the report. Note that
5 | # the listed index ids must also be present in the file `../index_int.config`.
6 | # Each INDEX_ID should be listed on a separate line followed by the style:
7 | # [pch];[lty];[col] (point type, line type, and color).
8 | GREEDYINT;1;solid;black
9 | QPROBINGINT;2;solid;blue
10 | #GREEDYINTX;2;solid;blue
11 | #GREEDYINTY;2;solid;green
12 | SADAINT;3;solid;red
13 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_count/bin/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !HP
3 | !NOSSE
4 | !NOOPT
5 | !.gitignore
6 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_count/compile_options.config:
--------------------------------------------------------------------------------
1 | # Compile configurations
2 | # Column description (columns are separated by semicolon):
3 | # (1) Identifier for compile configuration (consisting of letters)
4 | # (2) Compile options
5 | NOOPT;-std=c++11 -DPOPCOUNT_TL -O3 -g -funroll-loops -fomit-frame-pointer -ffast-math
6 | NOSSE;-std=c++11 -O3 -g -funroll-loops -fomit-frame-pointer -ffast-math
7 | SSE;-std=c++11 -msse4.2 -O3 -g -funroll-loops -fomit-frame-pointer -ffast-math
8 | HP;-std=c++11 -DUSE_HP -msse4.2 -O3 -g -funroll-loops -fomit-frame-pointer -ffast-math
9 | O1;-std=c++11 -O1
10 | O0;-std=c++11 -O0
11 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_count/index.config:
--------------------------------------------------------------------------------
1 | # This file specified sdsl index structures that are used in the benchmark.
2 | #
3 | # Each index is specified by a triple: INDEX_ID;SDSL_TYPE;INDEX_LATEX_NAME
4 | # * INDEX_ID : An identifier for the index. Only letters and underscores
5 | # are allowed in INDEX_ID.
6 | # * SDSL_TYPE : Corresponding sdsl type.
7 | # * LATEX_NAME: LaTeX name for output in the benchmark report.
8 | FM_HUFF;csa_wt,select_support_scan<>,select_support_scan<0> >,1<<20,1<<20>;FM-HF-BV
9 | FM_HUFF_RRR15;csa_wt >,1<<20,1<<20>;FM-HF-R$^{3}$-15
10 | FM_HUFF_RRR63;csa_wt >,1<<20,1<<20>;FM-HF-R$^{3}$-63
11 | #FM_HUFF_RRR127;csa_wt >,1<<20,1<<20>;FM-HF-R$^{3}$-127
12 | #FM_HUFF_RRR255;csa_wt >,1<<20,1<<20>;FM-HF-R$^{3}$-255
13 | #CSA_SADA;csa_sada,1<<20,1<<20>;CSA
14 | FM_RLMN;csa_wt,1<<20,1<<20>;FM-RLMN
15 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_count/indexes/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !HP
3 | !NOSSE
4 | !NOOPT
5 | !.gitignore
6 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_count/info/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !HP
3 | !NOSSE
4 | !NOOPT
5 | !.gitignore
6 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_count/pattern/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !HP
3 | !NOSSE
4 | !NOOPT
5 | !.gitignore
6 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_count/results/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_count/src/build_index_sdsl.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 | #include
4 |
5 | using namespace sdsl;
6 | using namespace std;
7 |
8 | int main(int argc, char** argv)
9 | {
10 | if (argc < 4) {
11 | cout << "Usage ./" << argv[0] << " input_file tmp_dir output_file" << endl;
12 | return 0;
13 | }
14 | CSA_TYPE csa;
15 | if (argc < 3) {
16 | construct(csa, argv[1], 1);
17 | } else {
18 | // config: do not delete files, tmp_dir=argv[2], id=basename(argv[1])
19 | cache_config cconfig(false, argv[2], util::basename(argv[1]));
20 | construct(csa, argv[1], cconfig, 1);
21 | }
22 | store_to_file(csa, argv[3]);
23 | }
24 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_count/src/info.cpp:
--------------------------------------------------------------------------------
1 | /*
2 | * This program outputs the structure of an index.
3 | */
4 | #include
5 | #include
6 |
7 | #include
8 |
9 | using namespace sdsl;
10 | using namespace std;
11 |
12 | int main(int argc, char* argv[])
13 | {
14 | if (argc < 2) {
15 | cout << "./" << argv[0] << " index_file " << endl;
16 | return 1;
17 | }
18 | CSA_TYPE csa;
19 | load_from_file(csa, argv[1]);
20 | write_structure(csa, cout);
21 | }
22 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_count/test_case.config:
--------------------------------------------------------------------------------
1 | # Configuration for test files
2 | # (1) Identifier for test file (consisting of letters, no `.`)
3 | # (2) Path to the test file
4 | # (3) LaTeX name
5 | # (4) Download link (if the test is available online)
6 | ENGLISH;../data/english.200MB;english.200MB;http://pizzachili.di.unipi.it/texts/nlang/english.200MB.gz
7 | DBLPXML;../data/dblp.xml.200MB;dblp.xml.200MB;http://pizzachili.di.unipi.it/texts/xml/dblp.xml.200MB.gz
8 | DNA;../data/dna.200MB;dna.200MB;http://pizzachili.di.unipi.it/texts/dna/dna.200MB.gz
9 | PROTEINS;../data/proteins.200MB;proteins.200MB;http://pizzachili.di.unipi.it/texts/protein/proteins.200MB.gz
10 | SOURCES;../data/sources.200MB;sources.200MB;http://pizzachili.di.unipi.it/texts/code/sources.200MB.gz
11 | #INFLUENZA;../data/influenza;influenza;http://pizzachili.dcc.uchile.cl/repcorpus/real/influenza.gz
12 | #EINSTEIN-de;../data/einstein.de.txt;einstein-de;http://pizzachili.dcc.uchile.cl/repcorpus/real/einstein.de.txt.gz
13 | #EINSTEIN-en;../data/einstein.en.txt;einstein-en;http://pizzachili.dcc.uchile.cl/repcorpus/real/einstein.en.txt.gz
14 | #PARA;../data/para;para;http://pizzachili.dcc.uchile.cl/repcorpus/real/para.gz
15 | #WORLDLEADER;../data/world_leaders;world-leaders;http://pizzachili.dcc.uchile.cl/repcorpus/real/world_leaders.gz
16 | #E-COLI;../data/Escherichia_Coli;E.coli;http://pizzachili.dcc.uchile.cl/repcorpus/real/Escherichia_Coli.gz
17 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_count/visualize/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 | !Makefile
4 | !count-footer.tex
5 | !count-header.tex
6 | !count.R
7 | !index-filter.config
8 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_count/visualize/Makefile:
--------------------------------------------------------------------------------
1 | include ../../../Make.helper
2 | COMPILE_IDS:=$(call config_ids,../compile_options.config)
3 | TABLES = $(foreach COMPILE_ID,$(COMPILE_IDS),tbl-count-$(COMPILE_ID).tex)
4 |
5 | CONFIG_FILES=index-filter.config ../index.config ../test_case.config
6 |
7 | all: count.pdf
8 |
9 | count.pdf: count.tex
10 | @echo "Use pdflatex to generate count.pdf"
11 | @pdflatex count.tex >> LaTeX.Log 2>&1
12 |
13 | count.tex: ../results/all.txt ../../basic_functions.R count.R $(CONFIG_FILES)
14 | @echo "Use R to generate count.tex"
15 | @R --vanilla < count.R > R.log 2>&1
16 |
17 | clean:
18 | rm -f $(TABLES) count.pdf count.aux count.tex \
19 | count.log R.log LaTeX.log
20 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_count/visualize/count-footer.tex:
--------------------------------------------------------------------------------
1 | \end{document}
2 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_count/visualize/count-header.tex:
--------------------------------------------------------------------------------
1 | \documentclass[9pt,a4paper]{scrartcl}
2 | \usepackage{booktabs}
3 | \usepackage{array}
4 | \usepackage{ragged2e}
5 |
6 | \begin{document}
7 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_count/visualize/index-filter.config:
--------------------------------------------------------------------------------
1 | # Use this file to specify which indexes are listed in the report count.pdf.
2 | #
3 | # List all the index ids which should be included in the report. Note that
4 | # the listed index ids must also be present in the file `../index.config`.
5 | # Each IDX_ID is listed on a separate line. The listing order is used
6 | # in the report.
7 | FM_HUFF
8 | FM_HUFF_RRR15
9 | FM_RLMN
10 | FM_HUFF_RRR63
11 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_extract/bin/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_extract/index.config:
--------------------------------------------------------------------------------
1 | # Specify the extract indexes here. Use S_SA and S_ISA as generic sample parameters.
2 | # S_SA and S_ISA will be replaced by the values in sample.config
3 | #
4 | # Each index is specified by a triple: INDEX_ID;SDSL_TYPE;INDEX_LATE_NAME
5 | # * INDEX_ID : An identifier for the index. Only letters and underscores
6 | # are allowed in the name.
7 | # * SDSL_TYPE : Corresponding sdsl type.
8 | # * LATEX_NAME: LaTeX name for output in the benchmark report.
9 | FM_HUFF;csa_wt,select_support_scan<>,select_support_scan<> >,S_SA,S_ISA,text_order_sa_sampling > >;FM-HF-V5
10 | FM_HUFF_RRR15;csa_wt >,S_SA,S_ISA,text_order_sa_sampling > >;FM-HF-R$^3$15
11 | CSA_SADA;csa_sada,S_SA,S_ISA,text_order_sa_sampling > >;CSA-SADA
12 | FM_HUFF_RRR63;csa_wt >,S_SA,S_ISA,text_order_sa_sampling > >;FM-HF-R$^3$63
13 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_extract/indexes/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_extract/info/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_extract/intervals/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_extract/results/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_extract/sample.config:
--------------------------------------------------------------------------------
1 | # Specify the sample rate for suffix array (SA) and inverse suffix array (ISA).
2 | # You can use the constants SA_MAX and ISA_MAX for the maximal sparse sampling
3 | # for SA and ISA.
4 | # Each sampling pair is specified by a triple: SAMPLING_ID;SA_SAMPLE_RATE;ISA_SAMPLE_RATE
5 | # SAMPLING_ID should consist only of symbols in A-Z,a-z,0-9
6 | 4x4;4;4
7 | 8x8;8;8
8 | 16x16;16;16
9 | 32x32;32;32
10 | 64x64;64;64
11 | 128x128;128;128
12 | 256x256;256;256
13 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_extract/src/build_index_sdsl.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 | #include
4 |
5 | using namespace sdsl;
6 | using namespace std;
7 |
8 | int main(int argc, char** argv)
9 | {
10 | if (argc < 4) {
11 | cout << "Usage ./" << argv[0] << " input_file tmp_dir output_file" << endl;
12 | return 0;
13 | }
14 | CSA_TYPE csa;
15 | if (argc < 3) {
16 | construct(csa, argv[1], 1);
17 | } else {
18 | // config: do not delete files, tmp_dir=argv[2], id=basename(argv[1])
19 | cache_config cconfig(false, argv[2], util::basename(argv[1]));
20 | construct(csa, argv[1], cconfig, 1);
21 | }
22 | store_to_file(csa, argv[3]);
23 | }
24 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_extract/src/info.cpp:
--------------------------------------------------------------------------------
1 | /*
2 | * This program outputs the structure of an index.
3 | */
4 | #include
5 | #include
6 |
7 | using namespace sdsl;
8 | using namespace std;
9 |
10 | int main(int argc, char* argv[])
11 | {
12 | if (argc < 2) {
13 | cout << "./" << argv[0] << " index_file " << endl;
14 | return 1;
15 | }
16 | CSA_TYPE csa;
17 | load_from_file(csa, argv[1]);
18 | write_structure(csa, cout);
19 | }
20 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_extract/test_case.config:
--------------------------------------------------------------------------------
1 | # Configuration for test files
2 | # (1) Identifier for test file (consisting of letters, no `.`)
3 | # (2) Path to the test file
4 | # (3) LaTeX name
5 | # (4) Download link (if the test is available online)
6 | ENGLISH;../data/english.200MB;english.200MB;http://pizzachili.di.unipi.it/texts/nlang/english.200MB.gz
7 | DBLPXML;../data/dblp.xml.200MB;dblp.xml.200MB;http://pizzachili.di.unipi.it/texts/xml/dblp.xml.200MB.gz
8 | DNA;../data/dna.200MB;dna.200MB;http://pizzachili.di.unipi.it/texts/dna/dna.200MB.gz
9 | PROTEINS;../data/proteins.200MB;proteins.200MB;http://pizzachili.di.unipi.it/texts/protein/proteins.200MB.gz
10 | SOURCES;../data/sources.200MB;sources.200MB;http://pizzachili.di.unipi.it/texts/code/sources.200MB.gz
11 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_extract/visualize/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 | !Makefile
4 | !extract.R
5 | !extract.tex
6 | !index-filter.config
7 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_extract/visualize/Makefile:
--------------------------------------------------------------------------------
1 | include ../../../Make.helper
2 | CONFIG_FILES=index-filter.config ../index.config ../test_case.config ../sample.config
3 |
4 | all: extract.pdf
5 |
6 | extract.pdf: extract.tex tbl-extract.tex fig-extract.tex
7 | @echo "Use pdflatex to generate extract.pdf"
8 | @pdflatex extract.tex >> LaTeX.Log 2>&1
9 |
10 | tbl-extract.tex fig-extract.tex: ../../basic_functions.R extract.R $(CONFIG_FILES) ../results/all.txt
11 | @echo "Use R to generate fig-extract.tex and tbl-extract.tex"
12 | @R --vanilla < extract.R > R.log 2>&1
13 |
14 | clean:
15 | rm -f extract.pdf extract.aux extract.log R.log LaTeX.log \
16 | tbl-extract.tex fig-extract.tex
17 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_extract/visualize/extract.tex:
--------------------------------------------------------------------------------
1 | \documentclass[9pt,a4paper]{scrartcl}
2 | \usepackage{array}
3 | \usepackage{booktabs}
4 | \usepackage{ragged2e}
5 | \usepackage{tikz}
6 |
7 | \begin{document}
8 | \pagestyle{empty}
9 |
10 | \begin{figure}
11 | \input{fig-extract.tex}
12 | \caption{Time-space trade-offs for operation extract.}
13 | \end{figure}
14 |
15 | \begin{table}
16 | \centering
17 | \input{tbl-extract.tex}
18 | \caption{Class definition of the indexes used in the experiment.
19 | The sampling rates \texttt{S\_SA} and \texttt{S\_ISA} for
20 | suffix and inverse suffix values was varied.}
21 | \end{table}
22 |
23 | \end{document}
24 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_extract/visualize/index-filter.config:
--------------------------------------------------------------------------------
1 | # Use this file to specify which indexes are listed in the report extract.pdf
2 | # and how they look like in the report.
3 | #
4 | # List all the index ids which should be included in the report. Note that
5 | # the listed index ids must also be present in the file `../index.config`.
6 | # Each INDEX_ID should be listed on a separate line followed by the style:
7 | # [pch];[lty];[col] (point type, line type, and color).
8 | FM_HUFF; 1;solid;black
9 | FM_HUFF_RRR15; 2;solid;blue
10 | CSA_SADA; 3;solid;red
11 | FM_HUFF_RRR63; 4;solid;blue
12 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_locate/bin/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_locate/index.config:
--------------------------------------------------------------------------------
1 | # Specify the locate indexes here. Use S_SA and S_ISA as generic sample parameters.
2 | # S_SA and S_ISA will be replaced by the values in sample.config
3 | #
4 | # Each index is specified by a triple: INDEX_ID;SDSL_TYPE;INDEX_LATE_NAME
5 | # * INDEX_ID : An identifier for the index. Only letters and underscores
6 | # are allowed in the name.
7 | # * SDSL_TYPE : Corresponding sdsl type.
8 | # * LATEX_NAME: LaTeX name for output in the benchmark report.
9 | FM_HUFF;csa_wt,select_support_scan<>,select_support_scan<> >,S_SA,S_ISA,text_order_sa_sampling > >;FM-HF-V5
10 | FM_HUFF_RRR15;csa_wt >,S_SA,S_ISA,text_order_sa_sampling > >;FM-HF-R$^3$15
11 | CSA_SADA;csa_sada,S_SA,S_ISA,text_order_sa_sampling > >;CSA-SADA
12 | FM_HUFF_RRR63;csa_wt >,S_SA,S_ISA,text_order_sa_sampling > >;FM-HF-R$^3$63
13 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_locate/indexes/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !HP
3 | !NOSSE
4 | !NOOPT
5 | !.gitignore
6 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_locate/info/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !HP
3 | !NOSSE
4 | !NOOPT
5 | !.gitignore
6 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_locate/pattern/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_locate/results/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_locate/sample.config:
--------------------------------------------------------------------------------
1 | # Specify the sample rate for suffix array (SA) and inverse suffix array (ISA).
2 | # You can use the constants SA_MAX and ISA_MAX for the maximal sparse sampling
3 | # for SA and ISA.
4 | # Each sampling pair is specified by a triple: SAMPLING_ID;SA_SAMPLE_RATE;ISA_SAMPLE_RATE
5 | # SAMPLING_ID should consist only of symbols in A-Z,a-z,0-9
6 | 4x4;4;4
7 | 8x8;8;8
8 | 16x16;16;16
9 | 32x32;32;32
10 | 64x64;64;64
11 | 128x128;128;128
12 | 256x256;256;256
13 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_locate/src/build_index_sdsl.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 | #include
4 |
5 | using namespace sdsl;
6 | using namespace std;
7 |
8 | int main(int argc, char** argv)
9 | {
10 | if (argc < 4) {
11 | cout << "Usage ./" << argv[0] << " input_file tmp_dir output_file" << endl;
12 | return 0;
13 | }
14 | CSA_TYPE csa;
15 | if (argc < 3) {
16 | construct(csa, argv[1], 1);
17 | } else {
18 | // config: do not delete files, tmp_dir=argv[2], id=basename(argv[1])
19 | cache_config cconfig(false, argv[2], util::basename(argv[1]));
20 | construct(csa, argv[1], cconfig, 1);
21 | }
22 | store_to_file(csa, argv[3]);
23 | }
24 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_locate/src/info.cpp:
--------------------------------------------------------------------------------
1 | /*
2 | * This program outputs the structure of an index.
3 | */
4 | #include
5 | #include
6 |
7 | #include
8 |
9 | using namespace sdsl;
10 | using namespace std;
11 |
12 | int main(int argc, char* argv[])
13 | {
14 | if (argc < 2) {
15 | cout << "./" << argv[0] << " index_file " << endl;
16 | return 1;
17 | }
18 | CSA_TYPE csa;
19 | load_from_file(csa, argv[1]);
20 | write_structure(csa, cout);
21 | }
22 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_locate/test_case.config:
--------------------------------------------------------------------------------
1 | # Configuration for test files
2 | # (1) Identifier for test file (consisting of letters, no `.`)
3 | # (2) Path to the test file
4 | # (3) LaTeX name
5 | # (4) Download link (if the test is available online)
6 | ENGLISH;../data/english.200MB;english.200MB;http://pizzachili.di.unipi.it/texts/nlang/english.200MB.gz
7 | DBLPXML;../data/dblp.xml.200MB;dblp.xml.200MB;http://pizzachili.di.unipi.it/texts/xml/dblp.xml.200MB.gz
8 | DNA;../data/dna.200MB;dna.200MB;http://pizzachili.di.unipi.it/texts/dna/dna.200MB.gz
9 | PROTEINS;../data/proteins.200MB;proteins.200MB;http://pizzachili.di.unipi.it/texts/protein/proteins.200MB.gz
10 | SOURCES;../data/sources.200MB;sources.200MB;http://pizzachili.di.unipi.it/texts/code/sources.200MB.gz
11 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_locate/visualize/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 | !Makefile
4 | !index-filter.config
5 | !locate.R
6 | !locate.tex
7 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_locate/visualize/Makefile:
--------------------------------------------------------------------------------
1 | include ../../../Make.helper
2 | CONFIG_FILES=index-filter.config ../index.config ../test_case.config ../sample.config
3 |
4 | all: locate.pdf
5 |
6 | locate.pdf: locate.tex tbl-locate.tex fig-locate.tex
7 | @echo "Use pdflatex to generate locate.pdf"
8 | @pdflatex locate.tex >> LaTeX.Log 2>&1
9 |
10 | tbl-locate.tex fig-locate.tex: ../../basic_functions.R locate.R $(CONFIG_FILES) ../results/all.txt
11 | @echo "Use R to generate tbl-locate.tex and fig-locate.tex"
12 | @R --vanilla < locate.R > R.log 2>&1
13 |
14 | clean:
15 | rm -f locate.pdf locate.aux fig-locate.tex tbl-locate.tex \
16 | locate.log R.log LaTeX.log
17 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_locate/visualize/index-filter.config:
--------------------------------------------------------------------------------
1 | # Use this file to specify which indexes are listed in the report locate.pdf
2 | # and how they look like in the report.
3 | #
4 | # List all the index ids which should be included in the report. Note that
5 | # the listed index ids must also be present in the file `../index.config`.
6 | # Each INDEX_ID should be listed on a separate line followed by the style:
7 | # [pch];[lty];[col] (point type, line type, and color).
8 | FM_HUFF; 1;solid;black
9 | FM_HUFF_RRR15; 2;solid;blue
10 | CSA_SADA; 3;solid;red
11 | FM_HUFF_RRR63; 4;solid;blue
12 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/indexing_locate/visualize/locate.tex:
--------------------------------------------------------------------------------
1 | \documentclass[9pt,a4paper]{scrartcl}
2 | \usepackage{array}
3 | \usepackage{booktabs}
4 | \usepackage{ragged2e}
5 | \usepackage{tikz}
6 |
7 | \begin{document}
8 | \pagestyle{empty}
9 |
10 | \begin{figure}
11 | \input{fig-locate.tex}
12 | \caption{Time-space trade-offs for operation locate.}
13 | \end{figure}
14 |
15 | \begin{table}
16 | \centering
17 | \input{tbl-locate.tex}
18 | \caption{Class definition of the indexes used in the experiment.
19 | The sampling rates \texttt{S\_SA} and \texttt{S\_ISA} for
20 | suffix and inverse suffix values was varied.}
21 | \end{table}
22 |
23 | \end{document}
24 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/k2_trees/bin/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/k2_trees/compile_options.config:
--------------------------------------------------------------------------------
1 | # Compile options
2 | -O3 -funroll-loops -fomit-frame-pointer -ffast-math -DNDEBUG
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/k2_trees/results/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/k2_trees/test_case.config:
--------------------------------------------------------------------------------
1 | # Configuration for test files
2 | # (1) Identifier for test file (consisting of letters, no `.`)
3 | # (2) Path to the test file
4 | # (3) LaTeX name
5 | # (4) Download link (if the test is available online)
6 | EXAMPLE;../data/example_arcs;examples;http://webdatacommons.org/hyperlinkgraph/data/example_arcs
7 | HOSTGRAPH;../data/hostgraph.arc;hostgraph;http://users.dcc.uchile.cl/~fmontoto/static/hostgraph.arc.gz
8 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/k2_trees/visualize/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 | !Makefile
4 | !k2-footer.tex
5 | !k2-header.tex
6 | !k2.R
7 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/k2_trees/visualize/Makefile:
--------------------------------------------------------------------------------
1 | include ../../../Make.helper
2 |
3 | CONFIG_FILES= ../test_case.config
4 |
5 | all: k2.pdf
6 |
7 | k2.pdf: k2.tex
8 | @echo "Use pdflatex to generate k2.pdf"
9 | @pdflatex k2.tex >> LaTeX.Log 2>&1
10 |
11 | k2.tex: ../results/all.txt ../../basic_functions.R k2.R $(CONFIG_FILES)
12 | @echo "Use R to generate k2.tex"
13 | @R --vanilla < k2.R > R.log 2>&1
14 |
15 | clean:
16 | rm -f k2.pdf k2.aux k2.tex fig* \
17 | k2.log R.log LaTeX.log
18 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/k2_trees/visualize/k2-footer.tex:
--------------------------------------------------------------------------------
1 | \end{document}
2 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/k2_trees/visualize/k2-header.tex:
--------------------------------------------------------------------------------
1 | \documentclass[9pt,a4paper,DIV10]{scrartcl}
2 | \usepackage{tikz}
3 | \usepackage{booktabs}
4 | \usepackage{array}
5 | \usepackage{ragged2e}
6 | \usepackage{float}
7 |
8 | \begin{document}
9 |
10 | \pagestyle{empty}
11 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/lcp/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 | !lcp.config
4 | !README.md
5 | !bin/
6 | !src/
7 | !visualize/
8 | !compile_options.config
9 | !Makefile
10 | !results/
11 | !test_case.config
12 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/lcp/bin/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/lcp/compile_options.config:
--------------------------------------------------------------------------------
1 | # Compile options
2 | -O3 -funroll-loops -fomit-frame-pointer -ffast-math -DNDEBUG
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/lcp/lcp.config:
--------------------------------------------------------------------------------
1 | # This file specifies wavelettrees that are used in the benchmark.
2 | #
3 | # Each LCP algorithm is specified by a 4-tupel: LCP_ID;LCP_ALGORITHM;LCP_LATEX_NAME;BWT_NEEDED
4 | # * LCP_ID : An identifier for the index. Only letters and underscores are allowed in ID.
5 | # * LCP_ALGORITHM : Corresponding lcp alogrithm.
6 | # * LCP_LATEX_NAME: LaTeX name for output in the benchmark report.
7 | # * BWT_NEEDED : T(rue) if lcp algorithm needs bwt as input, otherwise F(alse).
8 | kasai;construct_lcp_kasai<8>;lcp-kasai;F
9 | phi_algorithm;construct_lcp_PHI<8>;lcp-$\Phi$;F
10 | semi_extern_phi;construct_lcp_semi_extern_PHI;lcp-semi-extern-$\Phi$;F
11 | go;construct_lcp_go;lcp-go;T
12 | goPhi;construct_lcp_goPHI;lcp-go-$\Phi$;T
13 | bwtb;construct_lcp_bwt_based;lcp-bwt-based;T
14 | bwtb2;construct_lcp_bwt_based2;lcp-bwt-based2;T
15 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/lcp/results/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/lcp/src/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 | !create_lcp.cpp
4 | !create_sa_bwt.cpp
5 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/lcp/src/create_lcp.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 | #include
4 | #include
5 | #include
6 | #include
7 |
8 | using namespace sdsl;
9 | using namespace std;
10 | using namespace std::chrono;
11 |
12 | #define S(x) #x
13 | #define SX(x) S(x)
14 |
15 | int main()
16 | {
17 | memory_monitor::start();
18 | string dir = ".";
19 | string id = "tmp";
20 | cache_config config(false, dir, id);
21 |
22 | register_cache_file(conf::KEY_TEXT, config);
23 | register_cache_file(conf::KEY_SA, config);
24 | register_cache_file(conf::KEY_BWT, config);
25 |
26 | auto start = high_resolution_clock::now();
27 | LCP_TYPE(config);
28 | auto stop = high_resolution_clock::now();
29 | memory_monitor::stop();
30 | cout << "# " SX(LCPID) "_TIME = " << duration_cast(stop-start).count()/(double)1000 << endl;
31 | cout << "# " SX(LCPID) "_MMPEAK = "<< memory_monitor::peak() << endl;
32 |
33 | return 0;
34 | }
35 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/lcp/test_case.config:
--------------------------------------------------------------------------------
1 | # Configuration for test files
2 | # (1) Identifier for test file (consisting of letters, no `.`)
3 | # (2) Path to the test file
4 | # (3) LaTeX name
5 | # (4) Download link (if the test is available online)
6 | ENGLISH;../data/english.200MB;english.200MB;http://pizzachili.di.unipi.it/texts/nlang/english.200MB.gz
7 | DBLPXML;../data/dblp.xml.200MB;dblp.xml.200MB;http://pizzachili.di.unipi.it/texts/xml/dblp.xml.200MB.gz
8 | DNA;../data/dna.200MB;dna.200MB;http://pizzachili.di.unipi.it/texts/dna/dna.200MB.gz
9 | PROTEINS;../data/proteins.200MB;proteins.200MB;http://pizzachili.di.unipi.it/texts/protein/proteins.200MB.gz
10 | SOURCES;../data/sources.200MB;sources.200MB;http://pizzachili.di.unipi.it/texts/code/sources.200MB.gz
11 | INFLUENZA;../data/influenza;influenza;http://pizzachili.dcc.uchile.cl/repcorpus/real/influenza.gz
12 | EINSTEIN-de;../data/einstein.de.txt;einstein-de;http://pizzachili.dcc.uchile.cl/repcorpus/real/einstein.de.txt.gz
13 | EINSTEIN-en;../data/einstein.en.txt;einstein-en;http://pizzachili.dcc.uchile.cl/repcorpus/real/einstein.en.txt.gz
14 | PARA;../data/para;para;http://pizzachili.dcc.uchile.cl/repcorpus/real/para.gz
15 | WORLDLEADER;../data/world_leaders;world-leaders;http://pizzachili.dcc.uchile.cl/repcorpus/real/world_leaders.gz
16 | E-COLI;../data/Escherichia_Coli;E.coli;http://pizzachili.dcc.uchile.cl/repcorpus/real/Escherichia_Coli.gz
17 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/lcp/visualize/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 | !Makefile
4 | !lcp-header.tex
5 | !lcp-footer.tex
6 | !lcp.R
7 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/lcp/visualize/Makefile:
--------------------------------------------------------------------------------
1 | include ../../../Make.helper
2 |
3 | CONFIG_FILES= ../test_case.config
4 |
5 | all: lcp.pdf
6 |
7 | lcp.pdf: lcp.tex
8 | @echo "Use pdflatex to generate lcp.pdf"
9 | @pdflatex lcp.tex >> LaTeX.Log 2>&1
10 |
11 | lcp.tex: ../results/all.txt ../../basic_functions.R lcp.R $(CONFIG_FILES)
12 | @echo "Use R to generate lcp.tex"
13 | @R --vanilla < lcp.R > R.log 2>&1
14 |
15 | clean:
16 | rm -f lcp.pdf lcp.aux lcp.tex fig* \
17 | lcp.log R.log LaTeX.log
18 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/lcp/visualize/lcp-footer.tex:
--------------------------------------------------------------------------------
1 | \end{document}
2 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/lcp/visualize/lcp-header.tex:
--------------------------------------------------------------------------------
1 | \documentclass[9pt,a4paper,DIV10]{scrartcl}
2 | \usepackage{booktabs}
3 | \usepackage{array}
4 | \usepackage{ragged2e}
5 |
6 | \begin{document}
7 |
8 | \pagestyle{empty}
9 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/rrr_vector/bin/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/rrr_vector/block_size.config:
--------------------------------------------------------------------------------
1 | # Specify block sizes in [0..255] for which rrr_vector should be tested.
2 | # Each block size on one line. Default initialization is generated by
3 | #
4 | 5
5 | 7
6 | 8
7 | 9
8 | 11
9 | 14
10 | 15
11 | 16
12 | 26
13 | 31
14 | 32
15 | 46
16 | 56
17 | 63
18 | 64
19 | 84
20 | 104
21 | 124
22 | 127
23 | 128
24 | 168
25 | 208
26 | 248
27 | 255
28 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/rrr_vector/compile_options.config:
--------------------------------------------------------------------------------
1 | # Compile configurations
2 | # Column description (columns are separated by semicolon):
3 | # (1) Identifier for compile configuration (consisting of letters)
4 | # (2) Compile options
5 | O3;-msse4.2 -O3 -funroll-loops -fomit-frame-pointer -ffast-math -DNDEBUG
6 | #NOOPT;-DRRR_NO_OPT -msse4.2 -O3 -funroll-loops -fomit-frame-pointer -ffast-math -DNDEBUG
7 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/rrr_vector/results/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/rrr_vector/test_case.config:
--------------------------------------------------------------------------------
1 | # Configuration for test files
2 | # (1) Identifier for test file (consisting of letters, no `.`)
3 | # (2) Path to the test file
4 | # (3) LaTeX name
5 | # (4) Download link (if not generated automatically, like rnd_X.Y)
6 | RND50-16M;../data/rnd_50.16MB;rnd-50.16M;
7 | WT-DNA-16MB;../data/WT-DNA-16MB;wt-dna.16M;http://people.eng.unimelb.edu.au/sgog/data/WT-DNA-16MB.gz
8 | WT-WEB-16MB;../data/WT-WEB-16MB;wt-web.16M;http://people.eng.unimelb.edu.au/sgog/data/WT-WEB-16MB.gz
9 | WT-DNA-1GB;../data/WT-DNA-1GB;wt-dna.1G;http://people.eng.unimelb.edu.au/sgog/data/WT-DNA-1GB.gz
10 | WT-WEB-1GB;../data/WT-WEB-1GB;wt-web.1G;http://people.eng.unimelb.edu.au/sgog/data/WT-WEB-1GB.gz
11 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/rrr_vector/visualize/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 | !Makefile
4 | !rrr-footer.tex
5 | !rrr-header.tex
6 | !rrr.R
7 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/rrr_vector/visualize/Makefile:
--------------------------------------------------------------------------------
1 | include ../../../Make.helper
2 |
3 | CONFIG_FILES= ../test_case.config
4 |
5 | all: rrr.pdf
6 |
7 | rrr.pdf: rrr.tex
8 | @echo "Use pdflatex to generate rrr.pdf"
9 | @pdflatex rrr.tex >> LaTeX.Log 2>&1
10 |
11 | rrr.tex: ../results/all.txt ../../basic_functions.R rrr.R $(CONFIG_FILES)
12 | @echo "Use R to generate rrr.tex"
13 | @R --vanilla < rrr.R > R.log 2>&1
14 |
15 | clean:
16 | rm -f rrr.pdf rrr.aux rrr.tex fig-rrr* \
17 | rrr.log R.log LaTeX.log
18 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/rrr_vector/visualize/rrr-footer.tex:
--------------------------------------------------------------------------------
1 | \end{document}
2 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/rrr_vector/visualize/rrr-header.tex:
--------------------------------------------------------------------------------
1 | \documentclass[9pt,a4paper]{scrartcl}
2 | \usepackage{tikz}
3 |
4 | \begin{document}
5 |
6 | \pagestyle{empty}
7 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/self_delimiting_codes/bin/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/self_delimiting_codes/compile_options.config:
--------------------------------------------------------------------------------
1 | # Compile options
2 | -O3 -funroll-loops -fomit-frame-pointer -ffast-math -DNDEBUG
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/self_delimiting_codes/results/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/self_delimiting_codes/vectors.config:
--------------------------------------------------------------------------------
1 | # This file specifies integer vectors that are used in the benchmark.
2 | # (1) Identifier for test file (consisting of letters, no `.`)
3 | # (2) Integer Vector sdsl-type (no whitespaces)
4 | # (3) LaTeX name of testet Vector (no whitespaces)
5 | # VLC Vectors
6 | VLC_EG;vlc_vector;VLC-Elias-Gamma
7 | VLC_ED;vlc_vector;VLC-Elias-Delta
8 | VLC_FIB;vlc_vector;VLC-Fibonacci
9 | VLC_C2;vlc_vector>;VLC-Comma-Base3
10 | #VLC_C3;vlc_vector>;VLC-Comma-Base7
11 | #VLC_C8;vlc_vector>;VLC-Comma-Base254
12 | # ENC Vectors
13 | ENC_EG;enc_vector;ENC-Elias-Gamma
14 | ENC_ED;enc_vector;ENC-Elias-Delta
15 | ENC_FIB;enc_vector;ENC-Fibonacci
16 | ENC_C2;enc_vector>;ENC-Comma-Base3
17 | #ENC_C3;enc_vector>;ENC-Comma-Base7
18 | #ENC_C8;enc_vector>;ENC-Comma-Base254
19 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/self_delimiting_codes/visualize/Makefile:
--------------------------------------------------------------------------------
1 | # Makefile will also automatically generate a tex file with system information
2 |
3 | #utility
4 | empty:=
5 | space:= $(empty) $(empty)
6 |
7 | auto: self_delimiting_codes.pdf
8 |
9 | self_delimiting_codes.pdf: ../results/result.csv ../results/tc.csv ../results/vat.csv
10 | $(eval CPUINFO := $(strip $(patsubst \\%, $(space),\
11 | $(shell cat /proc/cpuinfo | grep "model name.*" | uniq | cut -d':' -f 2))))
12 | $(eval MEMINFO := $(strip \
13 | $(firstword $(shell free -k | grep "Mem.*" | uniq | cut -d':' -f 2))))
14 | $(eval MEMINFO := $(addsuffix " KB", $(MEMINFO)))
15 | $(eval DISTINFO := $(strip $(patsubst \\%, $(space),\
16 | $(shell cat /etc/issue))))
17 | @echo "Creating system information file"
18 | @echo "\\\\begin{tabular}{ll}" > sysinfo.tex
19 | @echo "\\\\toprule" >> sysinfo.tex
20 | @echo "CPU & \\\\verb\\\\$(CPUINFO)\\\\ \\\\\\\\" >> sysinfo.tex
21 | @echo "Total Memory & \\\\verb\\\\$(MEMINFO)\\\\ \\\\\\\\" >> sysinfo.tex
22 | @echo "Distribution & \\\\verb\\\\$(DISTINFO)\\\\ \\\\\\\\" >> sysinfo.tex
23 | @echo "\\\\bottomrule" >> sysinfo.tex
24 | @echo "\\\\end{tabular}" >> sysinfo.tex
25 | @echo "Use pdflatex to generate self_delimiting_codes.pdf"
26 | @pdflatex self_delimiting_codes.tex >> LaTeX.log 2>&1
27 |
28 | cleanall:
29 | rm -f self_delimiting_codes.pdf self_delimiting_codes.aux \
30 | self_delimiting_codes.log LaTeX.log sysinfo.tex
31 |
32 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/suffix_trees/bin/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/suffix_trees/compile_options.config:
--------------------------------------------------------------------------------
1 | # Compile configurations
2 | # Column description (columns are separated by semicolon):
3 | # (1) Identifier for compile configuration (consisting of letters)
4 | # (2) Compile options
5 | O3;-O3 -ffast-math -funroll-loops
6 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/suffix_trees/index.config:
--------------------------------------------------------------------------------
1 | # This file specified fully compressed suffix tree implementations that are
2 | # used in the benchmark.
3 | #
4 | # Each index is specified by a triple: INDEX_ID;SDSL_TYPE;INDEX_LATEX_NAME
5 | # * INDEX_ID : An identifier for the index. Only letters and underscores
6 | # are allowed in INDEX_ID.
7 | # * SDSL_TYPE : Corresponding sdsl type of index under test.
8 | # * LATEX_NAME : LaTeX name for output in the benchmark report.
9 | SCT3;cst_sct3 >, 32, 32, text_order_sa_sampling<>, text_order_isa_sampling_support<> > >;\texttt{cst\_sct3}
10 | SADA;cst_sada >, 32, 32, text_order_sa_sampling<>, text_order_isa_sampling_support<> > >;\texttt{cst\_sada}
11 | FULLY;cst_fully >, 32, 32, text_order_sa_sampling<>, text_order_isa_sampling_support<> > >;\texttt{cst\_fully}
12 |
13 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/suffix_trees/index_int.config:
--------------------------------------------------------------------------------
1 | # This file specified fully compressed suffix tree implementations that are
2 | # used in the benchmark.
3 | #
4 | # Each index is specified by a triple: INDEX_ID;SDSL_TYPE;INDEX_LATEX_NAME
5 | # * INDEX_ID : An identifier for the index. Only letters and underscores
6 | # are allowed in INDEX_ID.
7 | # * SDSL_TYPE : Corresponding sdsl type of index under test.
8 | # * LATEX_NAME : LaTeX name for output in the benchmark report.
9 | SCT3;cst_sct3 >, 32, 32, text_order_sa_sampling<>, text_order_isa_sampling_support<> > >;\texttt{cst\_sct3}
10 | SADA;cst_sada >, 32, 32, text_order_sa_sampling<>, text_order_isa_sampling_support<> > >;\texttt{cst\_sada}
11 | FULLY;cst_fully >, 32, 32, text_order_sa_sampling<>, text_order_isa_sampling_support<> > >;\texttt{cst\_fully}
12 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/suffix_trees/indexes/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/suffix_trees/results/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/suffix_trees/stats/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/suffix_trees/test_case_int.config:
--------------------------------------------------------------------------------
1 | # Configuration for test files
2 | # (1) Identifier for test file (consisting of letters, no `.`)
3 | # (2) Path to the test file
4 | # (3) LaTeX name
5 | # (4) Download link (if not generated automatically, like rnd_X.Y)
6 | #ENWIKISMLINT;../data/text_int_SURF.sdsl;Wiki;http://algo2.iti.kit.edu/gog/projects/ALENEX15/collections/ENWIKISMLINT/text_int_SURF.sdsl
7 | #ENWIKISMLINT;../data/text_int_SURF.sdsl;Wiki;http://christianocker.com/texts/wiki/text_int_SURF.sdsl.gz
8 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/suffix_trees/visualize/.gitignore:
--------------------------------------------------------------------------------
1 | *.log
2 | *.aux
3 | *.tex
4 | *.pdf
5 | !suffix_trees.tex
6 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/suffix_trees/visualize/Makefile:
--------------------------------------------------------------------------------
1 | include ../../../Make.helper
2 |
3 | CONFIG_FILES=../test_case.config
4 |
5 | all: suffix_trees.pdf
6 |
7 | suffix_trees.pdf: suffix_trees.tex
8 | @echo "Use pdflatex to generate suffix_trees.pdf"
9 | @pdflatex suffix_trees.tex >> LaTeX.log 2>&1
10 |
11 | suffix_trees.tex: ../results/all.txt ../../basic_functions.R suffix_trees.R $(CONFIG_FILES)
12 | @echo "Use R to generate tex files."
13 | @R --vanilla < suffix_trees.R > R.log 2>&1
14 |
15 | graph_data: ../results/all.txt ../../basic_functions.R graph_data.R $(CONFIG_FILES)
16 | @echo "Use R to generate raw graph data."
17 | @R --vanilla < graph_data.R > R.log 2>&1
18 |
19 | clean:
20 | rm -f suffix_trees.pdf suffix_trees.aux suffix_trees.log fig-space.tex fig-time.tex R.log LaTeX.log
21 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/suffix_trees/visualize/output/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/suffix_trees/visualize/suffix_trees.tex:
--------------------------------------------------------------------------------
1 | \documentclass[9pt,a4paper]{scrartcl}
2 | \begin{document}
3 | \pagestyle{empty}
4 |
5 | \begin{table}
6 | \centering
7 | \input{fig-space.tex}
8 | \caption{Space Requirements of CSTs.}
9 | \end{table}
10 |
11 | \begin{table}
12 | \centering
13 | \input{fig-time.tex}
14 | \caption{Query times of CSTs, in microseconds.}
15 | \end{table}
16 |
17 | \end{document}
18 |
19 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/tmp/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
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/ThirdParty/sdsl-lite/benchmark/wavelet_trees/bin/.gitignore:
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1 | *
2 | !.gitignore
3 |
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/ThirdParty/sdsl-lite/benchmark/wavelet_trees/compile_options.config:
--------------------------------------------------------------------------------
1 | # Compile options
2 | -O3 -funroll-loops -fomit-frame-pointer -ffast-math -DNDEBUG
3 |
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/ThirdParty/sdsl-lite/benchmark/wavelet_trees/results/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
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/ThirdParty/sdsl-lite/benchmark/wavelet_trees/visualize/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 | !Makefile
4 | !wt-footer.tex
5 | !wt-header.tex
6 | !wt.R
7 |
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/ThirdParty/sdsl-lite/benchmark/wavelet_trees/visualize/Makefile:
--------------------------------------------------------------------------------
1 | include ../../../Make.helper
2 |
3 | CONFIG_FILES= ../test_case.config
4 |
5 | all: wt.pdf
6 |
7 | wt.pdf: wt.tex
8 | @echo "Use pdflatex to generate wt.pdf"
9 | @pdflatex wt.tex >> LaTeX.Log 2>&1
10 |
11 | wt.tex: ../results/all.txt ../../basic_functions.R wt.R $(CONFIG_FILES)
12 | @echo "Use R to generate wt.tex"
13 | @R --vanilla < wt.R > R.log 2>&1
14 |
15 | clean:
16 | rm -f wt.pdf wt.aux wt.tex fig* \
17 | wt.log R.log LaTeX.log
18 |
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/ThirdParty/sdsl-lite/benchmark/wavelet_trees/visualize/wt-footer.tex:
--------------------------------------------------------------------------------
1 | \end{document}
2 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/benchmark/wavelet_trees/visualize/wt-header.tex:
--------------------------------------------------------------------------------
1 | \documentclass[9pt,a4paper,DIV10]{scrartcl}
2 | \usepackage{tikz}
3 | \usepackage{booktabs}
4 | \usepackage{array}
5 | \usepackage{ragged2e}
6 | \usepackage{float}
7 |
8 | \begin{document}
9 |
10 | \pagestyle{empty}
11 |
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/ThirdParty/sdsl-lite/build/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 | !build.sh
4 | !clean.sh
5 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/build/build.sh:
--------------------------------------------------------------------------------
1 | #!/bin/bash
2 | CUR_DIR=`pwd`
3 | OLD_DIR="$( cd "$( dirname "$0" )" && pwd )" # gets the directory where the script is located in
4 | cd "${OLD_DIR}"
5 |
6 | cmake .. -DCMAKE_INSTALL_PREFIX=${HOME} && make install
7 |
8 | cd ${CUR_DIR}
9 |
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/ThirdParty/sdsl-lite/build/clean.sh:
--------------------------------------------------------------------------------
1 | #!/bin/bash
2 | # activate globbing
3 | shopt -s extglob
4 | # removes all but the listed files in the directory
5 | # and subdirectories
6 | rm -rf !(build.sh|clean.sh|.gitignore|..|.)
7 |
8 |
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/ThirdParty/sdsl-lite/examples/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !*.cpp
3 | !Makefile
4 | !.gitignore
5 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/examples/Makefile:
--------------------------------------------------------------------------------
1 | include ../Make.helper
2 | CXX_FLAGS=$(MY_CXX_FLAGS) $(MY_CXX_OPT_FLAGS) -I$(INC_DIR) -L$(LIB_DIR)
3 | CCLIB=-lsdsl -ldivsufsort -ldivsufsort64
4 | SOURCES=$(wildcard *.cpp)
5 | EXECS=$(SOURCES:.cpp=.x)
6 |
7 | all: $(EXECS)
8 |
9 | build-test: $(EXECS)
10 |
11 | %.x:%.cpp
12 | $(MY_CXX) $(CXX_FLAGS) -o $@ $< $(CCLIB)
13 |
14 | clean:
15 | rm -f $(EXECS)
16 | rm -rf *.dSYM
17 |
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/ThirdParty/sdsl-lite/examples/bit-vector.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 |
4 | using namespace std;
5 | using namespace sdsl;
6 |
7 | int main()
8 | {
9 |
10 | bit_vector b(10000000, 0);
11 | b[8] = 1;
12 | rank_support_v<> rb(&b);
13 |
14 | cout< rrrb(b);
21 | rrr_vector<127>::rank_1_type rank_rrrb(&rrrb);
22 | cout<::select_1_type select_rrrb(&rrrb);
30 | cout<<"position of first one in b: "< v(100, 5, 7);
36 |
37 | cout<<"v[5]="<
2 | #include
3 | #include
4 |
5 | using namespace std;
6 | using namespace sdsl;
7 |
8 | typedef cst_sct3<> cst_t;
9 |
10 | int main(int argc, char* argv[])
11 | {
12 | if (argc < 2) {
13 | cout << "usage: "< iterator;
21 | iterator begin = iterator(&cst, cst.root());
22 | iterator end = iterator(&cst, cst.root(), true, true);
23 |
24 | for (iterator it = begin; it != end; ++it) {
25 | std::cout << cst.depth(*it) << "-[" << cst.lb(*it) << "," << cst.rb(*it) << "]" << std::endl;
26 | }
27 |
28 | }
29 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/examples/cst-node-child-iterator.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 | #include
4 |
5 | using namespace std;
6 | using namespace sdsl;
7 |
8 | typedef cst_sct3<> cst_t;
9 | typedef cst_sada<> csts_t;
10 |
11 | int main(int argc, char* argv[])
12 | {
13 | if (argc < 2) {
14 | cout << "usage: "<(stop-start).count() << endl;
20 | cout << "sum="<" << endl;
27 | cout << " (1) Creates a CST for a byte file. " << endl;
28 | cout << " (2) Runs a benchmark with enabled/disabled hugepages." << endl;
29 | return 1;
30 | }
31 |
32 | if (argc==3) {
33 | // memory_manager::use_hugepages(500ULL*1024ULL*1024ULL);
34 | // use all available hugepages if nothing is specified
35 | memory_manager::use_hugepages();
36 | }
37 |
38 | cst_sct3<> cst;
39 | auto start = timer::now();
40 | construct(cst, argv[1], 1);
41 | auto stop = timer::now();
42 | cout << "construction time in seconds: " << duration_cast(stop-start).count() << endl;
43 | do_something(cst); // before it is mapped
44 | }
45 |
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/ThirdParty/sdsl-lite/examples/int-vector-buffer-iterator.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 | #include
4 |
5 | using namespace sdsl;
6 | using namespace std;
7 |
8 | int main()
9 | {
10 | string file = "int_vector_buffer_iterator.sdsl";
11 | {
12 | int_vector<> iv = {1,2,3,4,5,9,8,7,6};
13 | store_to_file(iv, file);
14 | }
15 | int_vector_buffer<> ivb(file);
16 | cout << std::accumulate(ivb.begin(), ivb.end(), 0) << endl;
17 | cout << std::count_if(ivb.begin(), ivb.end(), [](uint64_t x) {
18 | return 0 == x%2;
19 | }) << endl;
20 | }
21 |
22 |
23 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/examples/int-vector-entry.cpp:
--------------------------------------------------------------------------------
1 | //! Program for debugging. Load vector v of type int_vector<> from
2 | // file argv[1]. Then the program outputs for each integer i,
3 | // which is read from stdin, the value v[i].
4 | #include
5 | #include
6 | #include
7 |
8 | using namespace std;
9 | using namespace sdsl;
10 |
11 | int main(int argc, char* argv[])
12 | {
13 | if (argc < 2) {
14 | cout << "Usage: " << argv[0] << " file [lb] [rb]" << endl;
15 | cout << " Reads a serialized int_vector<> from disk." < v;
20 | load_from_file(v, argv[1]);
21 | cout<<"loaded int_vector<> containing "<3) {
24 | size_t a=stoull(argv[2]);;
25 | size_t b=stoull(argv[3]);
26 | if (b >= v.size())
27 | b = v.size()-1;
28 | if (a > b)
29 | a = b;
30 | for (size_t i=a; i<=b; ++i) {
31 | cout<<"v["<>i) {
37 | cout<<"v["<
2 | #include
3 |
4 | using namespace sdsl;
5 | using namespace std;
6 |
7 | int main()
8 | {
9 | wt_int<> wt;
10 | //0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2
11 | construct_im(wt, int_vector<> {1,2,2,4,5,3,2,4,5,3,2,4,7,4,2,52,7,4,2,1,5,74,3});
12 |
13 | cout << "wt = " << wt << endl;
14 | cout << "wt[0,3] intersect with wt[7,10]" << endl;
15 | auto res = intersect(wt, {{0,3},{7,10}});
16 | cout << "element : sum of occurrences in ranges" << endl;
17 | for (auto x : res) {
18 | cout << x.first << " : " << x.second <
2 | #include
3 |
4 | using namespace sdsl;
5 | using namespace std;
6 |
7 | template
8 | void output_node(const typename t_cst::node_type& v, const t_cst& cst)
9 | {
10 | cout << cst.depth(v) << "-[" << cst.lb(v) << ","
11 | << cst.rb(v) << "]" << endl;
12 | }
13 |
14 | template
15 | void run()
16 | {
17 | t_cst cst;
18 | construct_im(cst, "ananas", 1);
19 | for (auto v : cst) {
20 | output_node(v, cst);
21 | }
22 | cout<<"--"<>();
38 | run>();
39 | }
40 |
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/ThirdParty/sdsl-lite/examples/standalone_lcp.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 | #include
4 |
5 | using namespace std;
6 | using namespace sdsl;
7 |
8 | int main(int argc, char* argv[])
9 | {
10 | if (argc < 2) {
11 | cout << "Usage: " << argv[0] << " file" << endl;
12 | return 1;
13 | }
14 | string file = argv[1];
15 |
16 | cache_config cc(false); // do not delete temp files after csa construction
17 | csa_wt<> csa;
18 | construct(csa, file, 1);
19 |
20 | cc.delete_files = true; // delete temp files after lcp construction
21 | lcp_wt<> lcp;
22 | construct(lcp, file, 1);
23 |
24 | if (csa.size() < 1000) {
25 | cout << csa << endl;
26 | cout << "-------" << endl;
27 | cout << lcp << endl;
28 | }
29 | }
30 |
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/ThirdParty/sdsl-lite/examples/storage-visualization.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 | #include
4 | #include
5 |
6 | using timer = std::chrono::high_resolution_clock;
7 | using namespace std::chrono;
8 | using namespace sdsl;
9 |
10 | int main(int argc, char** argv)
11 | {
12 | if (argc < 2) {
13 | std::cout << "Usage: " << argv[0] << " file" << std::endl;
14 | std::cout << " Creates a CST for a byte file and visualizes the space used by the data structure." << std::endl;
15 | return 1;
16 | }
17 | cst_sct3<> cst;
18 | auto start = timer::now();
19 | std::cout << "constructing cst..." << std::endl;
20 | construct(cst, argv[1], 1);
21 | std::cout << "construction cst time in seconds: " << duration_cast(timer::now()-start).count() << std::endl;
22 |
23 | std::ofstream ofs("cst-space-usage.html");
24 | std::cout << "writing storage visualization to cst-space-usage.html" << std::endl;
25 | sdsl::write_structure(cst,ofs);
26 | }
27 |
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/ThirdParty/sdsl-lite/examples/store_to_file.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 | #include
4 |
5 | using namespace sdsl;
6 | using namespace std;
7 |
8 | int main()
9 | {
10 | cout << (has_serialize::value) << endl;
11 | cout << (has_serialize::value) << endl;
12 |
13 | {
14 | ofstream out("data.sdsl");
15 | bit_vector b = {1,0,0,0,1,1,0};
16 | serialize(b, out);
17 | }
18 | {
19 | ifstream in("data.sdsl");
20 | bit_vector b;
21 | load(b, in);
22 | cout << b << endl;
23 | }
24 | {
25 | uint64_t x = 42;
26 | store_to_file(x, "data.sdsl");
27 | }
28 | {
29 | uint64_t x = 0;
30 | load_from_file(x, "data.sdsl");
31 | cout << x << endl;
32 | }
33 | {
34 | std::vector x(10, 5);
35 | store_to_file(x, "data.sdsl");
36 | }
37 | {
38 | std::vector x;
39 | load_from_file(x, "data.sdsl");
40 | cout << x.size() << endl;
41 | for (size_t i=0; i
2 | #include
3 |
4 | using namespace std;
5 | using namespace sdsl;
6 |
7 | typedef cst_sct3<> cst_t;
8 | typedef cst_t::char_type char_type;
9 |
10 | int main(int argc, char* argv[])
11 | {
12 | if (argc < 2) {
13 | cout << "Usage: "<< argv[0] << " file" << endl;
14 | cout << "(1) Generates the CST of file." << endl;
15 | cout << "(2) Calculates the avg LCP value and the runs in the BWT." << endl;
16 | return 1;
17 | }
18 | cst_t cst;
19 | construct(cst, argv[1], 1);
20 |
21 | long double runs = 1;
22 | long double avg_lcp = 0;
23 | if (cst.csa.size()) {
24 | char_type prev_bwt = cst.csa.bwt[0];
25 | for (uint64_t i=1; i
2 | #include
3 | #include
4 |
5 | using namespace sdsl;
6 | using namespace std;
7 |
8 | int main()
9 | {
10 | csa_wt<> csa;
11 | construct_im(csa, "This is how it works", 1);
12 | // write only one object to std::cout
13 | write_structure(csa, cout);
14 | wt_int<> wt;
15 | construct_im(wt, int_vector<>(1000,3));
16 | // write multiple objects into one file
17 | {
18 | ofstream out("write_structure.html");
19 | write_structure(out, csa, wt);
20 | }
21 | // write one object into a file
22 | write_structure(csa, "csa_structure.html");
23 | }
24 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/examples/wt_ap.cpp:
--------------------------------------------------------------------------------
1 | #include
2 |
3 | using namespace sdsl;
4 | using namespace std;
5 |
6 | int main(int argc, char* argv[])
7 | {
8 | if (argc < 2) {
9 | return 1;
10 | }
11 | wt_ap<> wt;
12 | memory_monitor::start();
13 | construct(wt, argv[1], 1);
14 | memory_monitor::stop();
15 | {
16 | std::ofstream csaofs("wt-construction.html");
17 | cout << "writing memory usage visualization to csa-construction.html\n";
18 | memory_monitor::write_memory_log(csaofs);
19 | }
20 | {
21 | std::ofstream out("wt-space.html");
22 | write_structure(wt,out);
23 | }
24 | }
25 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/external/CMakeLists.txt:
--------------------------------------------------------------------------------
1 | ## Add libdivsufsort
2 | set(divsufsort_cmake_file ${CMAKE_CURRENT_LIST_DIR}/libdivsufsort/CMakeLists.txt)
3 | if(NOT EXISTS ${divsufsort_cmake_file})
4 | EXECUTE_PROCESS(COMMAND git submodule update --init external/libdivsufsort
5 | WORKING_DIRECTORY ${CMAKE_CURRENT_LIST_DIR}/..
6 | OUTPUT_QUIET
7 | )
8 | endif(NOT EXISTS ${divsufsort_cmake_file})
9 |
10 | set(BUILD_SHARED_LIBS OFF CACHE BOOL "Do not build a shared library for libdivsufsort")
11 | set(BUILD_EXAMPLES OFF CACHE BOOL "Do not build libdivsufsort example")
12 | set(BUILD_DIVSUFSORT64 ON CACHE BOOL "Build libdivsufsort in 64-bits mode")
13 |
14 | add_subdirectory(libdivsufsort)
15 |
16 | ## Add gtest
17 | set(gtest_dir ${CMAKE_CURRENT_LIST_DIR}/googletest)
18 | set(gtest_file ${gtest_dir}/CMakeLists.txt)
19 | if(NOT EXISTS ${gtest_file})
20 | EXECUTE_PROCESS(COMMAND git submodule update --init external/googletest
21 | WORKING_DIRECTORY ${CMAKE_CURRENT_LIST_DIR}/..
22 | OUTPUT_QUIET
23 | )
24 | endif(NOT EXISTS ${gtest_file})
25 |
26 | # add_subdirectory(googletest/googletest)
27 |
28 |
29 |
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/ThirdParty/sdsl-lite/external/libdivsufsort/.gitignore:
--------------------------------------------------------------------------------
1 | # Object files
2 | *.o
3 | *.ko
4 | *.obj
5 | *.elf
6 |
7 | # Precompiled Headers
8 | *.gch
9 | *.pch
10 |
11 | # Libraries
12 | *.lib
13 | *.a
14 | *.la
15 | *.lo
16 |
17 | # Shared objects (inc. Windows DLLs)
18 | *.dll
19 | *.so
20 | *.so.*
21 | *.dylib
22 |
23 | # Executables
24 | *.exe
25 | *.out
26 | *.app
27 | *.i*86
28 | *.x86_64
29 | *.hex
30 |
31 | # CMake files/directories
32 | build/
33 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/external/libdivsufsort/CHANGELOG.md:
--------------------------------------------------------------------------------
1 | # libdivsufsort Change Log
2 |
3 | See full changelog at: https://github.com/y-256/libdivsufsort/commits
4 |
5 | ## [2.0.1] - 2010-11-11
6 | ### Fixed
7 | * Wrong variable used in `divbwt` function
8 | * Enclose some string variables with double quotation marks in include/CMakeLists.txt
9 | * Fix typo in include/CMakeLists.txt
10 |
11 | ## 2.0.0 - 2008-08-23
12 | ### Changed
13 | * Switch the build system to [CMake](http://www.cmake.org/)
14 | * Improve the performance of the suffix-sorting algorithm
15 |
16 | ### Added
17 | * OpenMP support
18 | * 64-bit version of divsufsort
19 |
20 | [Unreleased]: https://github.com/y-256/libdivsufsort/compare/2.0.1...HEAD
21 | [2.0.1]: https://github.com/y-256/libdivsufsort/compare/2.0.0...2.0.1
22 |
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/ThirdParty/sdsl-lite/external/libdivsufsort/CMakeModules/CheckFunctionKeywords.cmake:
--------------------------------------------------------------------------------
1 | include(CheckCSourceCompiles)
2 |
3 | macro(check_function_keywords _wordlist)
4 | set(${_result} "")
5 | foreach(flag ${_wordlist})
6 | string(REGEX REPLACE "[-+/ ()]" "_" flagname "${flag}")
7 | string(TOUPPER "${flagname}" flagname)
8 | set(have_flag "HAVE_${flagname}")
9 | check_c_source_compiles("${flag} void func(); void func() { } int main() { func(); return 0; }" ${have_flag})
10 | if(${have_flag} AND NOT ${_result})
11 | set(${_result} "${flag}")
12 | # break()
13 | endif(${have_flag} AND NOT ${_result})
14 | endforeach(flag)
15 | endmacro(check_function_keywords)
16 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/external/libdivsufsort/LICENSE:
--------------------------------------------------------------------------------
1 | The MIT License (MIT)
2 |
3 | Copyright (c) 2003 Yuta Mori All rights reserved.
4 |
5 | Permission is hereby granted, free of charge, to any person obtaining a copy
6 | of this software and associated documentation files (the "Software"), to deal
7 | in the Software without restriction, including without limitation the rights
8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 |
12 | The above copyright notice and this permission notice shall be included in all
13 | copies or substantial portions of the Software.
14 |
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21 | SOFTWARE.
22 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/external/libdivsufsort/VERSION.cmake:
--------------------------------------------------------------------------------
1 | set(PROJECT_VERSION_MAJOR "2")
2 | set(PROJECT_VERSION_MINOR "0")
3 | set(PROJECT_VERSION_PATCH "2")
4 | set(PROJECT_VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}")
5 | set(PROJECT_VERSION_FULL "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH}")
6 |
7 | set(LIBRARY_VERSION "3.0.1")
8 | set(LIBRARY_SOVERSION "3")
9 |
10 | ## Git revision number ##
11 | if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/.git")
12 | execute_process(COMMAND git describe --tags HEAD
13 | WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
14 | OUTPUT_VARIABLE GIT_DESCRIBE_TAGS ERROR_QUIET)
15 | if(GIT_DESCRIBE_TAGS)
16 | string(REGEX REPLACE "^v(.*)" "\\1" GIT_REVISION "${GIT_DESCRIBE_TAGS}")
17 | string(STRIP "${GIT_REVISION}" GIT_REVISION)
18 | if(GIT_REVISION)
19 | set(PROJECT_VERSION_FULL "${GIT_REVISION}")
20 | endif(GIT_REVISION)
21 | endif(GIT_DESCRIBE_TAGS)
22 | endif(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/.git")
23 |
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/ThirdParty/sdsl-lite/external/libdivsufsort/examples/CMakeLists.txt:
--------------------------------------------------------------------------------
1 | ## Add definitions ##
2 | add_definitions(-D_LARGEFILE_SOURCE -D_LARGE_FILES -D_FILE_OFFSET_BITS=64)
3 |
4 | ## Targets ##
5 | include_directories("${CMAKE_CURRENT_SOURCE_DIR}/../include"
6 | "${CMAKE_CURRENT_BINARY_DIR}/../include")
7 | link_directories("${CMAKE_CURRENT_BINARY_DIR}/../lib")
8 | foreach(src suftest mksary sasearch bwt unbwt)
9 | add_executable(${src} ${src}.c)
10 | target_link_libraries(${src} divsufsort)
11 | endforeach(src)
12 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/external/libdivsufsort/lib/CMakeLists.txt:
--------------------------------------------------------------------------------
1 | include_directories("${CMAKE_CURRENT_SOURCE_DIR}/../include"
2 | "${CMAKE_CURRENT_BINARY_DIR}/../include")
3 |
4 | set(divsufsort_SRCS divsufsort.c sssort.c trsort.c utils.c)
5 |
6 | ## libdivsufsort ##
7 | add_library(divsufsort ${divsufsort_SRCS})
8 | install(TARGETS divsufsort
9 | RUNTIME DESTINATION ${CMAKE_INSTALL_RUNTIMEDIR}
10 | LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
11 | ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
12 | set_target_properties(divsufsort PROPERTIES
13 | VERSION "${LIBRARY_VERSION}"
14 | SOVERSION "${LIBRARY_SOVERSION}"
15 | DEFINE_SYMBOL DIVSUFSORT_BUILD_DLL
16 | RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/../examples")
17 |
18 | ## libdivsufsort64 ##
19 | if(BUILD_DIVSUFSORT64)
20 | add_library(divsufsort64 ${divsufsort_SRCS})
21 | install(TARGETS divsufsort64
22 | RUNTIME DESTINATION ${CMAKE_INSTALL_RUNTIMEDIR}
23 | LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
24 | ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
25 | set_target_properties(divsufsort64 PROPERTIES
26 | VERSION "${LIBRARY_VERSION}"
27 | SOVERSION "${LIBRARY_SOVERSION}"
28 | DEFINE_SYMBOL DIVSUFSORT_BUILD_DLL
29 | COMPILE_FLAGS "-DBUILD_DIVSUFSORT64"
30 | RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/../examples")
31 | endif(BUILD_DIVSUFSORT64)
32 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/external/libdivsufsort/pkgconfig/CMakeLists.txt:
--------------------------------------------------------------------------------
1 | ## generate libdivsufsort.pc ##
2 | set(W64BIT "")
3 | configure_file("${CMAKE_CURRENT_SOURCE_DIR}/libdivsufsort.pc.cmake" "${CMAKE_CURRENT_BINARY_DIR}/libdivsufsort.pc" @ONLY)
4 | install(FILES "${CMAKE_CURRENT_BINARY_DIR}/libdivsufsort.pc" DESTINATION ${CMAKE_INSTALL_PKGCONFIGDIR})
5 | if(BUILD_DIVSUFSORT64)
6 | set(W64BIT "64")
7 | configure_file("${CMAKE_CURRENT_SOURCE_DIR}/libdivsufsort.pc.cmake" "${CMAKE_CURRENT_BINARY_DIR}/libdivsufsort64.pc" @ONLY)
8 | install(FILES "${CMAKE_CURRENT_BINARY_DIR}/libdivsufsort64.pc" DESTINATION ${CMAKE_INSTALL_PKGCONFIGDIR})
9 | endif(BUILD_DIVSUFSORT64)
10 |
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/ThirdParty/sdsl-lite/external/libdivsufsort/pkgconfig/libdivsufsort.pc.cmake:
--------------------------------------------------------------------------------
1 | prefix=@CMAKE_INSTALL_PREFIX@
2 | exec_prefix=${prefix}
3 | libdir=@CMAKE_INSTALL_LIBDIR@
4 | includedir=@CMAKE_INSTALL_INCLUDEDIR@
5 |
6 | Name: @PROJECT_NAME@@W64BIT@
7 | Description: @PROJECT_DESCRIPTION@
8 | Version: @PROJECT_VERSION_FULL@
9 | URL: @PROJECT_URL@
10 | Libs: -L${libdir} -ldivsufsort@W64BIT@
11 | Cflags: -I${includedir}
12 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/extras/README.md:
--------------------------------------------------------------------------------
1 | # Additional resources
2 |
3 |
4 | ## Cheatsheet
5 |
6 | A short reference for the use of the library can be generated by executing
7 | `make` in the [cheatsheet](./cheatsheet) directory.
8 |
9 |
10 | ## Debugging
11 |
12 | Sometimes even the best coder produces bugs. For this case we provide a
13 | useful resource for the [GNU Debugger][gdb].
14 | Copy the content of `sdsl.gdb` into your .gdbinit file an you can display the
15 | elements of `sdsl::vector<>` (and `sdsl::bitvector`) with the command `pv` in
16 | gdb.
17 |
18 | ## Code style
19 |
20 | The install script will copy the [pre-commit](./pre-commit) file into the
21 | `.git/hooks` directory of your library clone. It will run [astyle][as]
22 | before code gets committed. Please make sure that you have it installed
23 | [astyle][as], if you plan to push your changes to the project.
24 |
25 | [gdb]: http://www.gnu.org/software/gdb/ "GDB: The GNU Project Debugger"
26 | [as]: http://astyle.sourceforge.net/ "Astyle"
27 |
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/ThirdParty/sdsl-lite/extras/cheatsheet/.gitignore:
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1 | *
2 | !.gitignore
3 | !Makefile
4 | !sdsl-cheatsheet.tex
5 | !hyperendnotes.sty
6 | !viz.pdf
7 |
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/ThirdParty/sdsl-lite/extras/cheatsheet/Makefile:
--------------------------------------------------------------------------------
1 |
2 | sdsl-cheatsheet.pdf: sdsl-cheatsheet.tex
3 | pdflatex sdsl-cheatsheet.tex
4 |
5 | clean:
6 | rm -f sdsl-cheatsheet.pdf \
7 | sdsl-cheatsheet.aux
8 |
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/ThirdParty/sdsl-lite/extras/cheatsheet/viz.pdf:
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https://raw.githubusercontent.com/dib-lab/kProcessor/7fe67ec22cd2ba77f8669ee8dee82f971d29cb30/ThirdParty/sdsl-lite/extras/cheatsheet/viz.pdf
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/ThirdParty/sdsl-lite/extras/resources/space-vis.png:
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https://raw.githubusercontent.com/dib-lab/kProcessor/7fe67ec22cd2ba77f8669ee8dee82f971d29cb30/ThirdParty/sdsl-lite/extras/resources/space-vis.png
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/ThirdParty/sdsl-lite/extras/sdsl.natvis:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 | {{ size={ m_size/m_width } width={ (int)m_width } }}
5 |
6 | - m_size/m_width
7 | - (int)m_width
8 |
9 | m_size/m_width
10 | (uint64_t*)m_data
11 |
12 |
13 | m_size/m_width
14 | (uint32_t*)m_data
15 |
16 |
17 | m_size/m_width
18 | (uint8_t*)m_data
19 |
20 |
21 |
22 |
23 | {{ size={ m_size/8 } } }}
24 |
25 | - m_size/8
26 |
27 | m_size/8
28 | (uint8_t*)m_data
29 |
30 |
31 |
32 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/extras/sdsl_definitions.sty:
--------------------------------------------------------------------------------
1 | \newcommand{\Order}[1]{\mathcal{O}(#1)} % big O-Notation
2 | \newcommand{\order}[1]{\mathcal{o}(#1)} % small o-Notation
3 |
4 | \newcommand{\lcpaccess}[0]{\ensuremath{t_{LCP}}}
5 | \newcommand{\saaccess}[0]{\ensuremath{t_{SA}}}
6 | \newcommand{\isaaccess}[0]{\ensuremath{t_{SA^{-1}}}}
7 | \newcommand{\rrenclose}[0]{\ensuremath{t_{\mathit{rr-enclose}}}}
8 |
9 | \newcommand{\CSA}[0]{\ensuremath{\mathcal{CSA}}}
10 | \newcommand{\CST}[0]{\ensuremath{\mathcal{CST}}}
11 |
12 | \newcommand{\SUF}[0]{\ensuremath{\mathcal{SA}}}
13 | \newcommand{\ISA}[0]{\ensuremath{\mathcal{SA}^{-1}}}
14 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/include/CMakeLists.txt:
--------------------------------------------------------------------------------
1 | add_subdirectory(sdsl)
2 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/include/sdsl/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !experimental/
3 | !CMakeLists.txt
4 | !.gitignore
5 | !*.hpp
6 | !*.cmake
7 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/include/sdsl/CMakeLists.txt:
--------------------------------------------------------------------------------
1 | include(CheckIncludeFile)
2 | include(CheckIncludeFileCXX)
3 | include(CheckTypeSize)
4 |
5 | ## Check for header files ##
6 | check_include_file_CXX(cstdio HAVE_STDIO)
7 |
8 | ## copy hpp files to the binary tree ##
9 |
10 | file(GLOB hppFiles RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} "${CMAKE_CURRENT_SOURCE_DIR}/*.hpp") # select all .hpp-files
11 |
12 | foreach(hppFile ${hppFiles}) # copy each file
13 | configure_file( "${CMAKE_CURRENT_SOURCE_DIR}/${hppFile}" "${CMAKE_CURRENT_BINARY_DIR}/${hppFile}" COPYONLY )
14 | install(FILES "${CMAKE_CURRENT_BINARY_DIR}/${hppFile}" DESTINATION include/sdsl)
15 | # MESSAGE(${hppFile})
16 | endforeach(hppFile)
17 |
18 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/include/sdsl/bit_vectors.hpp:
--------------------------------------------------------------------------------
1 | /*! \file bit_vectors.hpp
2 | \brief bit_vectors.hpp contains classes for uncompressed and compressed bit vector representations.
3 | \author Simon Gog
4 | */
5 | #ifndef INCLUDED_SDSL_BITVECTORS
6 | #define INCLUDED_SDSL_BITVECTORS
7 |
8 | #include "int_vector.hpp"
9 | #include "bit_vector_il.hpp"
10 | #include "rrr_vector.hpp"
11 | #include "sd_vector.hpp"
12 | #include "hyb_vector.hpp"
13 |
14 | #endif
15 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/include/sdsl/construct_config.hpp:
--------------------------------------------------------------------------------
1 | #ifndef INCLUDED_SDSL_CONSTRUCT_CONFIG
2 | #define INCLUDED_SDSL_CONSTRUCT_CONFIG
3 |
4 | #include "config.hpp"
5 |
6 | namespace sdsl
7 | {
8 |
9 | class construct_config
10 | {
11 | public:
12 | static byte_sa_algo_type byte_algo_sa;
13 |
14 | construct_config() = delete;
15 | };
16 |
17 | }
18 |
19 | #endif
20 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/include/sdsl/construct_isa.hpp:
--------------------------------------------------------------------------------
1 | /* sdsl - succinct data structures library
2 | Copyright (C) 2010 Simon Gog
3 |
4 | This program is free software: you can redistribute it and/or modify
5 | it under the terms of the GNU General Public License as published by
6 | the Free Software Foundation, either version 3 of the License, or
7 | (at your option) any later version.
8 |
9 | This program is distributed in the hope that it will be useful,
10 | but WITHOUT ANY WARRANTY; without even the implied warranty of
11 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
12 | GNU General Public License for more details.
13 |
14 | You should have received a copy of the GNU General Public License
15 | along with this program. If not, see http://www.gnu.org/licenses/ .
16 | */
17 | /*! \file construct_isa.hpp
18 | \brief construct_isa.hpp contains a space and time efficient construction method for the inverse suffix array
19 | \author Simon Gog
20 | */
21 | #ifndef INCLUDED_SDSL_CONSTRUCT_ISA
22 | #define INCLUDED_SDSL_CONSTRUCT_ISA
23 |
24 | #include "int_vector.hpp"
25 | #include "util.hpp"
26 |
27 | #include
28 | #include
29 | #include
30 |
31 | namespace sdsl
32 | {
33 |
34 | void construct_isa(cache_config& config);
35 |
36 | }// end namespace
37 |
38 | #endif
39 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/include/sdsl/fast_cache.hpp:
--------------------------------------------------------------------------------
1 |
2 | #ifndef INCLUDED_SDSL_FAST_CACHE
3 | #define INCLUDED_SDSL_FAST_CACHE
4 |
5 | #include "int_vector.hpp"
6 |
7 | namespace sdsl
8 | {
9 |
10 | #define CACHE_SIZE 0x3FFULL
11 |
12 | struct fast_cache {
13 | typedef int_vector<>::size_type size_type;
14 | size_type m_table[2*(CACHE_SIZE+1)];
15 | // Constructor
16 | fast_cache() {
17 | for (size_type i=0; i < (CACHE_SIZE+1); ++i) {
18 | m_table[i<<1] = (size_type)-1;
19 | }
20 | }
21 | // Returns true if the request i is cached and
22 | // x is set to the answer of request i
23 | bool exists(size_type i, size_type& x) {
24 | if (m_table[(i&CACHE_SIZE)<<1 ] == i) {
25 | x = m_table[((i&CACHE_SIZE)<<1) + 1 ];
26 | return true;
27 | } else
28 | return false;
29 | }
30 | // Writes the answer for request i to the cache
31 | void write(size_type i, size_type x) {
32 | m_table[(i&CACHE_SIZE)<<1 ] = i;
33 | m_table[((i&CACHE_SIZE)<<1) + 1 ] = x;
34 | }
35 | };
36 |
37 | } // end namespace sdsl
38 |
39 | #endif
40 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/include/sdsl/raster_img.hpp:
--------------------------------------------------------------------------------
1 | #ifndef SDSL_INC_RASTER_IMG
2 | #define SDSL_INC_RASTER_IMG
3 |
4 | #include
5 |
6 | namespace sdsl
7 | {
8 |
9 | struct raster_img {
10 | typedef uint64_t size_type;
11 |
12 | uint64_t max_x; // max x value
13 | uint64_t max_y; // max y value
14 | uint64_t max_z; // max z value in the compacted range
15 | uint32_t offset;
16 | bit_vector value_map;
17 | int_vector<> data;
18 |
19 | //! Serializes the data structure into the given ostream
20 | uint64_t serialize(std::ostream& out, structure_tree_node* v=nullptr, std::string name="")const;
21 |
22 | //! Loads the data structure from the given istream.
23 | void load(std::istream& in);
24 | };
25 |
26 | }
27 |
28 | #endif
29 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/include/sdsl/uintx_t.hpp:
--------------------------------------------------------------------------------
1 | #ifndef INCLUDED_SDSL_UINTX_T
2 | #define INCLUDED_SDSL_UINTX_T
3 |
4 | #include
5 |
6 | using std::int8_t;
7 | using std::int16_t;
8 | using std::int32_t;
9 | using std::int64_t;
10 |
11 | using std::uint8_t;
12 | using std::uint16_t;
13 | using std::uint32_t;
14 | using std::uint64_t;
15 |
16 | #endif
17 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/include/sdsl/vectors.hpp:
--------------------------------------------------------------------------------
1 | /** \defgroup int_vector int_vector */
2 | #ifndef SDSL_INCLUDED_VECTORS
3 | #define SDSL_INCLUDED_VECTORS
4 |
5 | #include "int_vector.hpp"
6 | #include "enc_vector.hpp"
7 | #include "vlc_vector.hpp"
8 | #include "dac_vector.hpp"
9 |
10 | #endif
11 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/install.bat:
--------------------------------------------------------------------------------
1 | @echo off
2 | cls
3 | set CUR_DIR=%cd%
4 | echo CUR_DIR=%CUR_DIR%
5 |
6 | set SDSL_INSTALL_PREFIX=%USERPROFILE%
7 | if not "%1"=="" (
8 | pushd .
9 | cd %~dp0
10 | set SDSL_INSTALL_PREFIX=%~f1
11 | popd
12 | )
13 | echo Library will be installed in %SDSL_INSTALL_PREFIX%
14 |
15 | rem Change to the directory in which this script is located in
16 | cd %~dp0
17 |
18 | rem TODO git hook
19 |
20 | cd build
21 | if errorlevel 1 (
22 | exit /b %errorlevel%
23 | )
24 |
25 |
26 | rem TODO clean-up build directory
27 |
28 | cmake -DCMAKE_INSTALL_PREFIX="${SDSL_INSTALL_PREFIX}" -G"Visual Studio 14 2015" ..
29 | if errorlevel 1 (
30 | echo ERROR: CMake build failed
31 | exit /b %errorlevel%
32 | )
33 |
34 | "%VS140COMNTOOLS%..\IDE\devenv.com" /build release /project sdsl sdsl.sln
35 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/lib/.gitignore:
--------------------------------------------------------------------------------
1 | structure_tree.cpp
2 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/lib/CMakeLists.txt:
--------------------------------------------------------------------------------
1 | include_directories(#"${CMAKE_CURRENT_SOURCE_DIR}/../include"
2 | "${CMAKE_CURRENT_BINARY_DIR}/../include"
3 | "${CMAKE_CURRENT_BINARY_DIR}/../external/libdivsufsort/include"
4 | )
5 |
6 |
7 | file(GLOB libFiles RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} "${CMAKE_CURRENT_SOURCE_DIR}/*.cpp") # select all .cpp-files
8 | if(MSVC)
9 | file(GLOB headerFiles RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} "${CMAKE_CURRENT_SOURCE_DIR}/../include/sdsl/*.hpp") # select all .hpp-files
10 | endif()
11 |
12 | set( sdsl_SRCS ${libFiles} ${headerFiles})
13 |
14 | add_library( sdsl ${sdsl_SRCS} )
15 |
16 | install(TARGETS sdsl
17 | RUNTIME DESTINATION bin
18 | LIBRARY DESTINATION lib
19 | ARCHIVE DESTINATION lib)
20 |
21 | math(EXPR SOVERSION "${LIBRARY_VERSION_MAJOR}+1")
22 |
23 | set_target_properties(sdsl PROPERTIES
24 | VERSION "${LIBRARY_VERSION_FULL}"
25 | SOVERSION "${SOVERSION}"
26 | # DEFINE_SYMBOL SDSL_BUILD_DLL
27 | # RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/../examples"
28 | )
29 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/lib/config.cpp:
--------------------------------------------------------------------------------
1 | #include "sdsl/config.hpp"
2 | #include "sdsl/util.hpp"
3 |
4 | namespace sdsl
5 | {
6 | cache_config::cache_config(bool f_delete_files, std::string f_dir, std::string f_id, tMSS f_file_map) : delete_files(f_delete_files), dir(f_dir), id(f_id), file_map(f_file_map)
7 | {
8 | if ("" == id) {
9 | id = util::to_string(util::pid())+"_"+util::to_string(util::id());
10 | }
11 | }
12 |
13 | template<>
14 | const char* key_text_trait<0>::KEY_TEXT = conf::KEY_TEXT_INT;
15 | template<>
16 | const char* key_text_trait<8>::KEY_TEXT = conf::KEY_TEXT;
17 |
18 | template<>
19 | const char* key_bwt_trait<0>::KEY_BWT = conf::KEY_BWT_INT;
20 | template<>
21 | const char* key_bwt_trait<8>::KEY_BWT = conf::KEY_BWT;
22 |
23 | }// end namespace sdsl
24 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/lib/construct_config.cpp:
--------------------------------------------------------------------------------
1 | #include "sdsl/construct_config.hpp"
2 |
3 | namespace sdsl
4 | {
5 |
6 | byte_sa_algo_type construct_config::byte_algo_sa = LIBDIVSUFSORT;
7 |
8 | }
9 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/lib/construct_isa.cpp:
--------------------------------------------------------------------------------
1 | /* sdsl - succinct data structures library
2 | Copyright (C) 2010 Simon Gog
3 | */
4 | #include "sdsl/construct_isa.hpp"
5 | #include
6 |
7 | namespace sdsl
8 | {
9 |
10 | void construct_isa(cache_config& config)
11 | {
12 | typedef int_vector<>::size_type size_type;
13 | if (!cache_file_exists(conf::KEY_ISA, config)) { // if isa is not already on disk => calculate it
14 | int_vector_buffer<> sa_buf(cache_file_name(conf::KEY_SA, config));
15 | if (!sa_buf.is_open()) {
16 | throw std::ios_base::failure("cst_construct: Cannot load SA from file system!");
17 | }
18 | int_vector<> isa(sa_buf.size());
19 | for (size_type i=0; i < isa.size(); ++i) {
20 | isa[ sa_buf[i] ] = i;
21 | }
22 | store_to_cache(isa, conf::KEY_ISA, config);
23 | }
24 | }
25 |
26 | }// end namespace
27 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/lib/construct_sa.cpp:
--------------------------------------------------------------------------------
1 | #include "sdsl/construct_sa.hpp"
2 |
3 | namespace sdsl
4 | {
5 |
6 | void construct_sa_se(cache_config& config)
7 | {
8 | int_vector<8> text;
9 | load_from_file(text, cache_file_name(conf::KEY_TEXT, config));
10 |
11 | if (text.size() <= 2) {
12 | // If text is c$ or $ write suffix array [1, 0] or [0]
13 | int_vector_buffer<> sa(cache_file_name(conf::KEY_SA, config), std::ios::out, 8, 2);
14 | if (text.size() == 2) {
15 | sa.push_back(1);
16 | }
17 | sa.push_back(0);
18 | } else {
19 | _construct_sa_se>(text, cache_file_name(conf::KEY_SA, config), 256, 0);
20 | }
21 | register_cache_file(conf::KEY_SA, config);
22 | }
23 |
24 | }
25 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/lib/lcp_support_tree.cpp:
--------------------------------------------------------------------------------
1 | #include "sdsl/lcp_support_tree.hpp"
2 |
3 | namespace sdsl
4 | {
5 |
6 | void construct_first_child_lcp(int_vector_buffer<>& lcp_buf, int_vector<>& fc_lcp)
7 | {
8 | typedef int_vector_size_type size_type;
9 | size_type n = lcp_buf.size();
10 | if (n == 0) { // if n == 0 we are done
11 | fc_lcp = int_vector<>(0);
12 | }
13 | {
14 | int_vector<> tmp(n, 0, bits::hi(n)+1);
15 | fc_lcp.swap(tmp);
16 | }
17 |
18 | size_type fc_cnt=0; // first child counter
19 | sorted_multi_stack_support vec_stack(n);
20 | size_type y;
21 | for (size_type i=0, x; i < n; ++i) {
22 | x = lcp_buf[i];
23 | while (!vec_stack.empty() and x < vec_stack.top()) {
24 | y = vec_stack.top();
25 | if (vec_stack.pop()) {
26 | fc_lcp[fc_cnt++] = y;
27 | }
28 | }
29 | vec_stack.push(x);
30 | }
31 |
32 | while (!vec_stack.empty()) {
33 | y = vec_stack.top();
34 | if (vec_stack.pop()) {
35 | fc_lcp[fc_cnt++] = y;
36 | }
37 | }
38 | if (fc_cnt < fc_lcp.size()) {
39 | fc_lcp.resize(fc_cnt);
40 | }
41 | }
42 |
43 | }
44 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/lib/louds_tree.cpp:
--------------------------------------------------------------------------------
1 | #include "sdsl/louds_tree.hpp"
2 |
3 | namespace sdsl
4 | {
5 | std::ostream& operator<<(std::ostream& os, const louds_node& v)
6 | {
7 | os<<"("<> 64), (uint64_t)x};
10 | for (int j=0; j < 2; ++j) {
11 | for (int i=0; i < 16; ++i) {
12 | os << std::hex << ((X[j]>>60)&0xFULL) << std::dec;
13 | X[j] <<= 4;
14 | }
15 | }
16 | return os;
17 | }
18 |
19 | } // end namespace
20 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/lib/uint256_t.cpp:
--------------------------------------------------------------------------------
1 | #include "sdsl/uint256_t.hpp"
2 |
3 | //! Namespace for the succinct data structure library
4 | namespace sdsl
5 | {
6 | std::ostream& operator<<(std::ostream& os, const uint256_t& x)
7 | {
8 | uint64_t X[4] = {(uint64_t)(x.m_high >> 64), (uint64_t)x.m_high, x.m_mid, x.m_lo};
9 | for (int j=0; j < 4; ++j) {
10 | for (int i=0; i < 16; ++i) {
11 | os << std::hex << ((X[j]>>60)&0xFULL) << std::dec;
12 | X[j] <<= 4;
13 | }
14 | }
15 | return os;
16 | }
17 | } // end namespace
18 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/lib/wt_helper.cpp:
--------------------------------------------------------------------------------
1 | #include "sdsl/wt_helper.hpp"
2 |
3 | namespace sdsl
4 | {
5 |
6 | bool empty(const range_type& r)
7 | {
8 | return std::get<0>(r) == (std::get<1>(r) + 1);
9 | }
10 |
11 | int_vector<>::size_type size(const range_type& r)
12 | {
13 | return std::get<1>(r) - std::get<0>(r) + 1;
14 | }
15 |
16 |
17 | pc_node::pc_node(uint64_t freq, uint64_t sym, uint64_t parent,
18 | uint64_t child_left, uint64_t child_right):
19 | freq(freq), sym(sym), parent(parent)
20 | {
21 | child[0] = child_left;
22 | child[1] = child_right;
23 | }
24 |
25 | pc_node& pc_node::operator=(const pc_node& v)
26 | {
27 | freq = v.freq;
28 | sym = v.sym;
29 | parent = v.parent;
30 | child[0] = v.child[0];
31 | child[1] = v.child[1];
32 | return *this;
33 | }
34 |
35 | }
36 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/sdsl-lite.pc.cmake:
--------------------------------------------------------------------------------
1 | prefix=@CMAKE_INSTALL_PREFIX@
2 | exec_prefix=${prefix}
3 | libdir=${prefix}/lib
4 | includedir=${prefix}/include
5 |
6 | Name: @PROJECT_NAME@
7 | Description: @PROJECT_DESCRIPTION@
8 | Version: @PROJECT_VERSION_FULL@
9 | URL: @PROJECT_URL@
10 | Libs: -L${libdir} -lsdsl -ldivsufsort -ldivsufsort64
11 | Cflags: -I${includedir}
12 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/.gitignore:
--------------------------------------------------------------------------------
1 | *.x
2 | *.x.dSYM
3 | *.gcno
4 | *.gcda
5 | *.swp
6 | *.swo
7 | compile_test.cpp
8 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/bit_vector_test.config:
--------------------------------------------------------------------------------
1 | # Inputs which should be used in BitVectorTest,
2 | # RankSupportTest, SelectSupportTest, and
3 | # SelectSupport0Test
4 | # Each line contains a path to a bit_vector.
5 | int-vec.0.1.0
6 | int-vec.1.1.0
7 | int-vec.1000000.1.0
8 | int-vec.1000000.1.1
9 | int-vec.7.1.1
10 | int-vec.8.1.0
11 | int-vec.9.1.1
12 | int-vec.10.1.0
13 | int-vec.11.1.1
14 | int-vec.12.1.0
15 | int-vec.13.1.1
16 | int-vec.14.1.0
17 | int-vec.15.1.1
18 | int-vec.8.1.r.17
19 | int-vec.16.1.r.42
20 | int-vec.32.1.r.111
21 | int-vec.64.1.r.222
22 | int-vec.128.1.r.73
23 | int-vec.256.1.r.4887
24 | int-vec.512.1.r.432
25 | int-vec.1024.1.r.898
26 | int-vec.2048.1.r.5432
27 | int-vec.4096.1.r.793
28 | int-vec.8192.1.r.1043
29 | int-vec.1000000.1.r.815
30 | bit-vec.CRAFTED-32
31 | bit-vec.CRAFTED-SPARSE-0
32 | bit-vec.CRAFTED-SPARSE-1
33 | bit-vec.CRAFTED-BLOCK-0
34 | bit-vec.CRAFTED-BLOCK-1
35 | bit-vec.CRAFTED-MAT-SELECT
36 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/compile_test.cpp.cmake:
--------------------------------------------------------------------------------
1 | #include "gtest/gtest.h"
2 | @SDSL_INCLUDE_ALL@
3 |
4 | namespace
5 | {
6 | // The fixture for testing the compilation of all header files.
7 | class CompileTest : public ::testing::Test { };
8 |
9 | //! Test constructors
10 | TEST_F(CompileTest, Compile) { }
11 |
12 | } // namespace
13 |
14 | int main(int argc, char** argv)
15 | {
16 | ::testing::InitGoogleTest(&argc, argv);
17 | return RUN_ALL_TESTS();
18 | }
19 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/coverage/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !README.md
3 | !clean.sh
4 | !run.sh
5 | !.gitignore
6 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/coverage/README.md:
--------------------------------------------------------------------------------
1 | # Code coverage of tests
2 |
3 | This directory contains a script which generates statistics
4 | about the code coverage of the tests.
5 |
6 | A call of `./run.sh` will compile all tests with code coverage
7 | parameters and execute all tests to gather the information.
8 |
9 |
10 | ## Prerequisites
11 |
12 | * The GCC utility [gcov][GCOV] has to be installed and
13 | `g++` has to be used as compiler.
14 | * The HTML output is generated by the [lcov][LCOV] tool.
15 |
16 |
17 | [GCOV]: http://gcc.gnu.org/onlinedocs/gcc/Gcov.html "gcov"
18 | [LCOV]: http://ltp.sourceforge.net/coverage/lcov.php "lcov"
19 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/coverage/clean.sh:
--------------------------------------------------------------------------------
1 | #!/bin/bash
2 | # activate globbing
3 | shopt -s extglob
4 | # removes all but the listed files in the directory
5 | # and subdirectories
6 | rm -rf !(run.sh|clean.sh|.gitignore|README.md)
7 |
8 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/coverage/run.sh:
--------------------------------------------------------------------------------
1 | #!/bin/bash
2 |
3 | CUR_DIR=`pwd`
4 | cd "${CUR_DIR}"
5 | OLD_DIR="$( cd "$( dirname "$0" )" && pwd )" # gets the directory where the script is located in
6 | cd "${OLD_DIR}"
7 | OLD_DIR=`pwd`
8 |
9 | lcov --directory .. --zerocounters
10 |
11 | cd ..
12 | make clean
13 | make CODE_COVER="-g -fprofile-arcs -ftest-coverage -lgcov" $1
14 | MAKERET=$?
15 | cd ${OLD_DIR}
16 |
17 | if [ ${MAKERET} != 0 ]; then
18 | echo "ERROR: tests failed."
19 | exit 1
20 | fi
21 |
22 | INC_STR=`grep 'INC_DIR = ' ../../Make.helper`
23 | INC_DIR=${INC_STR#INC_DIR = }
24 |
25 | lcov -d .. -d ${INC_DIR}/sdsl --no-recursion --no-external --capture --output-file sdsl-lite.info
26 | genhtml -o output --legend sdsl-lite.info
27 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/csa_byte_test.config:
--------------------------------------------------------------------------------
1 | empty.txt
2 | example01.txt
3 | 100a.txt
4 | faust.txt
5 | zarathustra.txt
6 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/csa_int_test.config:
--------------------------------------------------------------------------------
1 | # Each line contains [TEST_CASE_NAME];[NUM_BYTE]
2 | empty.txt;1
3 | example01.txt;1
4 | 100a.txt;1
5 | faust.txt;1
6 | zarathustra.txt;1
7 | keeper.int;8
8 | moby.int;8
9 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/cst_byte_test.config:
--------------------------------------------------------------------------------
1 | empty.txt
2 | example01.txt
3 | 100a.txt
4 | faust.txt
5 | #zarathustra.txt
6 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/cst_int_test.config:
--------------------------------------------------------------------------------
1 | # Texts which should be used in the CstIntTest.
2 | # Each line contains [TEST_CASE_FILE];[NUM_BYTE]
3 | empty.txt;1
4 | example01.txt;1
5 | 100a.txt;1
6 | faust.txt;1
7 | #zarathustra.txt;1
8 | keeper.int;8
9 | moby.int;8
10 | int-vec-sa.100000.18.r;0
11 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/download.cmake:
--------------------------------------------------------------------------------
1 | GET_FILENAME_COMPONENT(file_name ${download_url} NAME)
2 | SET(test_case_tar_gz ${test_case_dir}/${file_name})
3 | MESSAGE("test_case_tar_gz=${test_case_tar_gz}")
4 | FILE(DOWNLOAD ${download_url} ${test_case_tar_gz} STATUS status SHOW_PROGRESS)
5 | LIST(GET status 0 status_code)
6 | IF(NOT ${status_code} EQUAL 0)
7 | MESSAGE(FATAL_ERROR "Downloading test file failed.\n ${status}\n")
8 | ENDIF(NOT ${status_code} EQUAL 0)
9 | EXECUTE_PROCESS(COMMAND ${CMAKE_COMMAND} -E tar xzf ${test_case_tar_gz}
10 | WORKING_DIRECTORY ${test_case_dir})
11 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/download.config:
--------------------------------------------------------------------------------
1 | # [TC_PATH];[TC_DOWNLOAD_URL]
2 | faust.txt;http://algo2.iti.kit.edu/gog/sdsl/faust.txt.tar.gz
3 | zarathustra.txt;http://algo2.iti.kit.edu/gog/sdsl/zarathustra.txt.tar.gz
4 | moby.int;http://algo2.iti.kit.edu/gog/sdsl/moby.int.tar.gz
5 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/k2_treap_test.config:
--------------------------------------------------------------------------------
1 | # Inputs which should be used
2 | # each row contains 3 times parameters for the int_vector generator
3 | 0.1.0.0;0.1.0.0;0.1.0.0
4 | 100.16.r.42;100.16.r.23;100.8.r.81
5 | 10000.16.r.42;10000.16.r.23;10000.8.r.81
6 | 100000.39.r.42;100000.47.r.23;100000.35.r.81
7 | 1000000.52.r.42;1000000.57.r.23;1000000.45.r.81
8 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/lcp_construct_test.config:
--------------------------------------------------------------------------------
1 | empty.txt
2 | example01.txt
3 | 100a.txt
4 | faust.txt
5 | zarathustra.txt
6 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/rank_support_test.config:
--------------------------------------------------------------------------------
1 | # Each line contains a bit_vector test
2 | int-vec.0.1.0
3 | int-vec.1.1.0
4 | int-vec.1000000.1.0
5 | int-vec.1000000.1.1
6 | int-vec.7.1.1
7 | int-vec.8.1.0
8 | int-vec.9.1.1
9 | int-vec.10.1.0
10 | int-vec.11.1.1
11 | int-vec.12.1.0
12 | int-vec.13.1.1
13 | int-vec.14.1.0
14 | int-vec.15.1.1
15 | int-vec.8.1.r.17
16 | int-vec.16.1.r.42
17 | int-vec.32.1.r.111
18 | int-vec.64.1.r.222
19 | int-vec.128.1.r.73
20 | int-vec.256.1.r.4887
21 | int-vec.512.1.r.432
22 | int-vec.1024.1.r.898
23 | int-vec.2048.1.r.5432
24 | int-vec.4096.1.r.793
25 | int-vec.8192.1.r.1043
26 | int-vec.1000000.1.r.815
27 | bit-vec.CRAFTED-32
28 | bit-vec.CRAFTED-SPARSE-0
29 | bit-vec.CRAFTED-SPARSE-1
30 | bit-vec.CRAFTED-BLOCK-0
31 | bit-vec.CRAFTED-BLOCK-1
32 | bit-vec.CRAFTED-MAT-SELECT
33 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/replace_int_vector_value.cpp:
--------------------------------------------------------------------------------
1 | #include "sdsl/int_vector.hpp"
2 | #include
3 | #include
4 |
5 | using namespace std;
6 | using namespace sdsl;
7 |
8 | int main(int argc, char* argv[])
9 | {
10 | if (argc < 4) {
11 | cout << "Usage: " << argv[0] << " FILE X Y" << endl;
12 | cout << " Loads an int_vector<>(SIZE, DEFAULT_VALUE, WIDTH)" << endl;
13 | cout << " and replaces all values X with Y and stores the " << endl;
14 | cout << " result in the same file." << endl;
15 | return 1;
16 | }
17 | uint64_t x = atoi(argv[2]);
18 | uint64_t y = atoi(argv[3]);
19 | int_vector_buffer<> v(argv[1]);
20 | if (v.good()) {
21 | for (size_t i=0; i file " << argv[1] << endl;
29 | return 1;
30 | }
31 | }
32 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/rmq_test.config:
--------------------------------------------------------------------------------
1 | int-vec.0.1.0
2 | int-vec.1.64.42
3 | int-vec.1000000.64.i
4 | int-vec.1000000.32.i.42
5 | int-vec.1000000.64.i.17
6 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/sa_construct_test.config:
--------------------------------------------------------------------------------
1 | empty.txt
2 | one_byte.txt
3 | example01.txt
4 | 100a.txt
5 | faust.txt
6 | zarathustra.txt
7 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/search_bidirectional_test.config:
--------------------------------------------------------------------------------
1 | # Texts which should be used in the SerachBidirectionalTest.
2 | # Format: [TC_PATH]
3 | empty.txt
4 | example01.txt
5 | 100a.txt
6 | faust.txt
7 | zarathustra.txt
8 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/select_support_test.config:
--------------------------------------------------------------------------------
1 | # Each line contains a bit_vector file.
2 | int-vec.0.1.0
3 | int-vec.1.1.0
4 | int-vec.1000000.1.0
5 | int-vec.1000000.1.1
6 | int-vec.7.1.1
7 | int-vec.8.1.0
8 | int-vec.9.1.1
9 | int-vec.10.1.0
10 | int-vec.11.1.1
11 | int-vec.12.1.0
12 | int-vec.13.1.1
13 | int-vec.14.1.0
14 | int-vec.15.1.1
15 | int-vec.8.1.r.17
16 | int-vec.16.1.r.42
17 | int-vec.32.1.r.111
18 | int-vec.64.1.r.222
19 | int-vec.128.1.r.73
20 | int-vec.256.1.r.4887
21 | int-vec.512.1.r.432
22 | int-vec.1024.1.r.898
23 | int-vec.2048.1.r.5432
24 | int-vec.4096.1.r.793
25 | int-vec.8192.1.r.1043
26 | int-vec.1000000.1.r.815
27 | bit-vec.CRAFTED-32
28 | bit-vec.CRAFTED-SPARSE-0
29 | bit-vec.CRAFTED-SPARSE-1
30 | bit-vec.CRAFTED-BLOCK-0
31 | bit-vec.CRAFTED-BLOCK-1
32 | bit-vec.CRAFTED-MAT-SELECT
33 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/test_cases/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !100a.txt
3 | !README.md
4 | !abc_abc_abc.txt
5 | !abc_abc_abc2.txt
6 | !empty.txt
7 | !example01.txt
8 | !keeper.int
9 | !one_byte.txt
10 | !all_symbols.txt
11 | !.gitignore
12 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/test_cases/100a.txt:
--------------------------------------------------------------------------------
1 | aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/test_cases/README.md:
--------------------------------------------------------------------------------
1 | # Test inputs
2 |
3 | This directory contains some small inputs and will
4 | be populated by larger inputs when running the
5 | all tests.
6 |
7 | TODO: describe what the ending of the files mean.
8 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/test_cases/abc_abc_abc.txt:
--------------------------------------------------------------------------------
1 | abc abc abc
2 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/test_cases/abc_abc_abc2.txt:
--------------------------------------------------------------------------------
1 | abc abc abc
2 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/test_cases/all_symbols.txt:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/dib-lab/kProcessor/7fe67ec22cd2ba77f8669ee8dee82f971d29cb30/ThirdParty/sdsl-lite/test/test_cases/all_symbols.txt
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/test_cases/empty.txt:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/dib-lab/kProcessor/7fe67ec22cd2ba77f8669ee8dee82f971d29cb30/ThirdParty/sdsl-lite/test/test_cases/empty.txt
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/test_cases/example01.txt:
--------------------------------------------------------------------------------
1 | mississippi
2 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/test_cases/keeper.int:
--------------------------------------------------------------------------------
1 |
2 |
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/test_cases/one_byte.txt:
--------------------------------------------------------------------------------
1 | a
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/tmp/.gitignore:
--------------------------------------------------------------------------------
1 | *
2 | !.gitignore
3 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/wt_byte_test.config:
--------------------------------------------------------------------------------
1 | # Each line contains a test file
2 | empty.txt
3 | example01.txt
4 | 100a.txt
5 | all_symbols.txt
6 | faust.txt
7 | #zarathustra.txt
8 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/test/wt_int_test.config:
--------------------------------------------------------------------------------
1 | # Each line contains a text file.
2 | int-vec.0.1.0
3 | int-vec.1023.1.0
4 | int-vec.100023.1.0
5 | int-vec.64.2.0
6 | int-vec.100000.18.r
7 | #int-vec.10000000.18.r
8 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/tutorial/.gitignore:
--------------------------------------------------------------------------------
1 | *.x
2 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/tutorial/Makefile:
--------------------------------------------------------------------------------
1 | include ../Make.helper
2 | CXX_FLAGS=$(MY_CXX_FLAGS) $(MY_CXX_OPT_FLAGS) -I$(INC_DIR) -L$(LIB_DIR)
3 | CCLIB=-lsdsl -ldivsufsort -ldivsufsort64
4 | SOURCES=$(wildcard *.cpp)
5 | EXECS=$(SOURCES:.cpp=.x)
6 |
7 | all: $(EXECS)
8 |
9 | build-test: $(EXECS)
10 |
11 | %.x:%.cpp
12 | $(MY_CXX) $(CXX_FLAGS) -o $@ $< $(CCLIB) $(LDFLAGS)
13 |
14 | clean:
15 | rm -f $(EXECS)
16 | rm -rf *.dSYM
17 |
18 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/tutorial/cst-traversal.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 | #include
4 |
5 | using namespace sdsl;
6 | using namespace std;
7 |
8 | int main(int argc, char* argv[])
9 | {
10 | if (argc < 3) {
11 | cout << "Usage: " << argv[0] << " file " << "int [max_depth]" << endl;
12 | return 1;
13 | }
14 | cst_sct3<> cst;
15 | construct(cst, argv[1], 1);
16 | uint64_t max_depth = stoull(argv[2]);
17 |
18 | // use the DFS iterator to traverse `cst`
19 | for (auto it=cst.begin(); it!=cst.end(); ++it) {
20 | if (it.visit() == 1) { // node visited the first time
21 | auto v = *it; // get the node by dereferencing the iterator
22 | if (cst.depth(v) <= max_depth) { // if depth node is <= max_depth
23 | // process node, e.g. output it in format d-[lb, rb]
24 | cout<
2 | #include
3 |
4 | using namespace std;
5 | using namespace sdsl;
6 |
7 | int main()
8 | {
9 | int_vector<> v = {3,2,1,0,2,1,3,4,1,1,1,3,2,3};
10 | v[1] = 0;
11 | util::bit_compress(v);
12 | cout << v << endl;
13 | cout << size_in_bytes(v) << endl;
14 | }
15 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/tutorial/expl-02.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 |
4 | using namespace std;
5 | using namespace sdsl;
6 |
7 | int main()
8 | {
9 | int_vector<> v(10*(1<<20));
10 | for (size_t i=0; i<10; ++i)
11 | for (size_t j=0; j < 1U<<20; ++j)
12 | v[i*(1<<20)+j] = j;
13 | cout << size_in_mega_bytes(v) << endl;
14 | util::bit_compress(v);
15 | cout << size_in_mega_bytes(v) << endl;
16 | enc_vector> ev(v);
17 | cout << size_in_mega_bytes(ev) << endl;
18 | }
19 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/tutorial/expl-03.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 | #include
4 | #include
5 | #include
6 |
7 | using namespace std;
8 | using namespace sdsl;
9 |
10 | int main()
11 | {
12 | int_vector<> v(10*(1<<20), 0);
13 | v[0] = 1ULL<<63;
14 | //util::bit_compress(v);
15 | cout << size_in_mega_bytes(v) << endl;
16 | vlc_vector vv(v);
17 | cout << size_in_mega_bytes(vv) << endl;
18 | cout << "Percentage: " << size_in_mega_bytes(vv) / size_in_mega_bytes(v) * 100 << endl;
19 | }
20 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/tutorial/expl-04.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 |
4 | using namespace std;
5 | using namespace sdsl;
6 |
7 | int main()
8 | {
9 | bit_vector b = {1,1,0,1,0,0,1};
10 | cout << b << endl;
11 | b = bit_vector(80*(1<<20), 0);
12 | for (size_t i=0; i < b.size(); i+=100)
13 | b[i] = 1;
14 | cout << size_in_mega_bytes(b) << endl;
15 | }
16 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/tutorial/expl-05.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 |
4 | using namespace std;
5 | using namespace sdsl;
6 |
7 | int main()
8 | {
9 | bit_vector b = bit_vector(80*(1<<20), 0);
10 | for (size_t i=0; i < b.size(); i+=100)
11 | b[i] = 1;
12 | cout << size_in_mega_bytes(b) << endl;
13 | rrr_vector<63> rrrb(b);
14 | cout << size_in_mega_bytes(rrrb) << endl;
15 | sd_vector<> sdb(b);
16 | cout << size_in_mega_bytes(sdb) << endl;
17 | }
18 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/tutorial/expl-06.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 |
4 | using namespace std;
5 | using namespace sdsl;
6 |
7 | int main()
8 | {
9 | bit_vector b = bit_vector(80*(1<<20), 0);
10 | for (size_t i=0; i < b.size(); i+=100)
11 | b[i] = 1;
12 | sd_vector<> sdb(b);
13 | write_structure(sdb, cout);
14 | }
15 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/tutorial/expl-07.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 |
4 | using namespace std;
5 | using namespace sdsl;
6 |
7 | int main()
8 | {
9 | bit_vector b = bit_vector(8000, 0);
10 | for (size_t i=0; i < b.size(); i+=100)
11 | b[i] = 1;
12 | rank_support_v<1> b_rank(&b);
13 | for (size_t i=0; i<=b.size(); i+= b.size()/4)
14 | cout << "(" << i << ", " << b_rank(i) << ") ";
15 | cout << endl;
16 | }
17 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/tutorial/expl-08.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 |
4 | using namespace std;
5 | using namespace sdsl;
6 |
7 | int main()
8 | {
9 | bit_vector b = bit_vector(8000, 0);
10 | for (size_t i=0; i < b.size(); i+=100)
11 | b[i] = 1;
12 | sd_vector<> sdb(b);
13 | sd_vector<>::rank_1_type sdb_rank(&sdb);
14 | for (size_t i=0; i<=sdb.size(); i+= sdb.size()/4)
15 | cout << "(" << i << ", " << sdb_rank(i) << ") ";
16 | cout << endl;
17 | rrr_vector<> rrrb(b);
18 | rrr_vector<>::rank_1_type rrrb_rank(&rrrb);
19 | for (size_t i=0; i<=rrrb.size(); i+= rrrb.size()/4)
20 | cout << "(" << i << ", " << rrrb_rank(i) << ") ";
21 | cout << endl;
22 | }
23 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/tutorial/expl-09.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 |
4 | using namespace std;
5 | using namespace sdsl;
6 |
7 | int main()
8 | {
9 | bit_vector b = {0,1,0,1};
10 | rank_support_v<1> b_r1(&b);
11 | rank_support_v<0> b_r0(&b);
12 | rank_support_v<10,2> b_r10(&b);
13 | rank_support_v<01,2> b_r01(&b);
14 | for (size_t i=0; i<=b.size(); ++i)
15 | cout << i << ": "<< b_r1(i) << " " << b_r0(i)
16 | << " " << b_r10(i) << " " << b_r01(i) << endl;
17 | }
18 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/tutorial/expl-10.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 |
4 | using namespace std;
5 | using namespace sdsl;
6 |
7 | int main()
8 | {
9 | bit_vector b = {0,1,0,1,1,1,0,0,0,1,1};
10 | size_t zeros = rank_support_v<0>(&b)(b.size());
11 | bit_vector::select_0_type b_sel(&b);
12 |
13 | for (size_t i=1; i <= zeros; ++i) {
14 | cout << b_sel(i) << " ";
15 | }
16 | cout << endl;
17 | }
18 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/tutorial/expl-11.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 |
4 | using namespace std;
5 | using namespace sdsl;
6 |
7 | int main()
8 | {
9 | bit_vector b = {0,1,0,1,1,1,0,0,0,1,1};
10 | size_t cnt10 = rank_support_v<10,2>(&b)(b.size());
11 | select_support_mcl<10,2> b_sel10(&b);
12 |
13 | for (size_t i=1; i <= cnt10; ++i)
14 | cout << b_sel10(i) << " ";
15 | cout << endl;
16 | }
17 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/tutorial/expl-12.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 | #include
4 |
5 | using namespace std;
6 | using namespace sdsl;
7 |
8 | int main()
9 | {
10 | sd_vector<> sd_b = bit_vector {1,0,1,1,1,0,1,1,0,0,1,0,0,1};
11 | size_t ones = sd_vector<>::rank_1_type(&sd_b)(sd_b.size());
12 | sd_vector<>::select_1_type sdb_sel(&sd_b);
13 |
14 | cout << sd_b << endl;
15 |
16 | for (size_t i=1; i <= ones; ++i)
17 | cout << sdb_sel(i) << " ";
18 | cout << endl;
19 | }
20 |
21 |
22 |
--------------------------------------------------------------------------------
/ThirdParty/sdsl-lite/tutorial/expl-13.cpp:
--------------------------------------------------------------------------------
1 | #include
2 | #include
3 |
4 | using namespace std;
5 | using namespace sdsl;
6 |
7 | int main()
8 | {
9 | wt_blcd<> wt;
10 | construct(wt, "expl-13.cpp", 1);
11 | for (size_t i=0; i < wt.size() and wt[i]!='\n'; ++i)
12 | cout << wt[i];
13 | cout << endl;
14 | cout << "number of lines : " << wt.rank(wt.size(), '\n') << endl;
15 | cout << "first '=' in line: " << wt.rank(wt.select(1, '='),'\n')+1 << endl;
16 | }
17 |
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/ThirdParty/sdsl-lite/tutorial/expl-14.cpp:
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1 | #include
2 | #include
3 |
4 | using namespace std;
5 | using namespace sdsl;
6 |
7 | int main()
8 | {
9 | wt_hutu> wt;
10 | construct_im(wt, "こんにちは世界", 1);
11 | for (size_t i=0; i < wt.size(); ++i)
12 | cout << wt[i];
13 | cout << endl;
14 | auto t1 = wt.lex_count(0, wt.size(), 0x80);
15 | auto t2 = wt.lex_count(0, wt.size(), 0xbf);
16 | cout << "# of bytes : " << wt.size() << endl;
17 | cout << "# of UTF-8 symbols: " << get<1>(t1) + get<2>(t2) << endl;
18 | }
19 |
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/ThirdParty/sdsl-lite/tutorial/expl-15.cpp:
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1 | #include
2 | #include
3 | #include
4 |
5 | using namespace std;
6 | using namespace sdsl;
7 |
8 | template
9 | ostream& operator<<(ostream& os, const std::pair& p)
10 | {
11 | return os << "(" << p.first << "," << p.second << ")";
12 | }
13 |
14 | int main()
15 | {
16 | wt_int> wt;
17 | construct_im(wt, "6 1000 1 4 7 3 18 6 3", 'd');
18 | auto res = wt.range_search_2d(1, 5, 4, 18);
19 | for (auto point : res.second)
20 | cout << point << " ";
21 | cout << endl;
22 | }
23 |
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/ThirdParty/sdsl-lite/tutorial/expl-16.cpp:
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1 | #include
2 | #include
3 |
4 | using namespace std;
5 | using namespace sdsl;
6 |
7 | int main()
8 | {
9 | wt_huff_int> wt;
10 | construct_im(wt, int_vector<>({1981, 1974, 1990, 1974, 2014, 1974}));
11 | cout << "wt.sigma : " << wt.sigma << endl;
12 | cout << wt << endl;
13 | size_t idx = 5;
14 | auto r_c = wt.inverse_select(idx);
15 | cout << get<0>(r_c)+1 << " occurrence(s) of "
16 | << get<1>(r_c) << " in [0.." << idx << "]" << endl;
17 | }
18 |
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/ThirdParty/sdsl-lite/tutorial/expl-17.cpp:
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1 | #include
2 | #include
3 |
4 | using namespace std;
5 | using namespace sdsl;
6 |
7 | int main()
8 | {
9 | csa_bitcompressed<> csa;
10 | construct_im(csa, "abracadabra", 1);
11 | cout << "csa.size(): " << csa.size() << endl;
12 | cout << "csa.sigma : " << csa.sigma << endl;
13 | cout << csa << endl;
14 | cout << extract(csa, 0, csa.size()-1) << endl;
15 | }
16 |
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/ThirdParty/sdsl-lite/tutorial/expl-18.cpp:
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1 | #include
2 | #include
3 | #include
4 |
5 | using namespace std;
6 | using namespace sdsl;
7 |
8 | int main()
9 | {
10 | csa_wt>,4,8> csa; // 接尾辞配列
11 | construct(csa, "expl-18.cpp", 1);
12 | cout << "count(\"配列\") : " << count(csa, "配列") << endl;
13 | auto occs = locate(csa, "\n");
14 | sort(occs.begin(), occs.end());
15 | auto max_line_length = occs[0];
16 | for (size_t i=1; i < occs.size(); ++i)
17 | max_line_length = std::max(max_line_length, occs[i]-occs[i-1]+1);
18 | cout << "max line length : " << max_line_length << endl;
19 | }
20 |
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/ThirdParty/sdsl-lite/tutorial/expl-19.cpp:
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1 | #include
2 | #include
3 | #include
4 |
5 | using namespace std;
6 | using namespace sdsl;
7 |
8 | int main()
9 | {
10 | csa_wt>> csa;
11 | construct_im(csa, "1 8 15 23 1 8 23 11 8", 'd');
12 | cout << " i SA ISA PSI LF BWT T[SA[i]..SA[i]-1]" << endl;
13 | csXprintf(cout, "%2I %2S %3s %3P %2p %3B %:3T", csa);
14 | }
15 |
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/ThirdParty/sdsl-lite/tutorial/expl-20.cpp:
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1 | #include
2 | #include
3 |
4 | using namespace sdsl;
5 | using namespace std;
6 |
7 | int main()
8 | {
9 | memory_monitor::start();
10 | csa_wt<> csa;
11 | construct(csa, "english.200MB", 1);
12 | memory_monitor::stop();
13 | memory_monitor::write_memory_log(cout);
14 | }
15 |
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/ThirdParty/sdsl-lite/tutorial/expl-21.cpp:
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1 | #include
2 | #include
3 |
4 | using namespace sdsl;
5 | using namespace std;
6 |
7 | int main()
8 | {
9 | cst_sct3<> cst;
10 | construct_im(cst, "umulmundumulmum", 1);
11 | cout << "inner nodes : " << cst.nodes() - cst.csa.size() << endl;
12 | auto v = cst.select_child(cst.child(cst.root(), 'u'),1);
13 | auto d = cst.depth(v);
14 | cout << "v : " << d << "-[" << cst.lb(v) << "," << cst.rb(v) << "]" << endl;
15 | cout << "extract(cst, v) : " << extract(cst, v) << endl;
16 | }
17 |
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/ThirdParty/sdsl-lite/tutorial/expl-22.cpp:
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1 | #include
2 | #include
3 |
4 | using namespace sdsl;
5 | using namespace std;
6 |
7 | int main()
8 | {
9 | cst_sct3>>> cst;
10 | int_vector<> data(100000, 0, 10);
11 | for (size_t i=0; i < data.size(); ++i)
12 | data[i] = 1 + rand()%1023;
13 | construct_im(cst, data);
14 | cout << "cst.csa.sigma: " << cst.csa.sigma << endl;
15 | for (size_t k=0; k<3; ++k)
16 | cout << "H" << k << "(data) : " << get<0>(Hk(cst, k)) << endl;
17 | }
18 |
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/ThirdParty/sdsl-lite/tutorial/expl-23.cpp:
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1 | #include
2 | #include
3 |
4 | using namespace sdsl;
5 | using namespace std;
6 |
7 | int main()
8 | {
9 | cst_sct3>>, lcp_support_sada<>> cst1;
10 | construct(cst1, "english.200MB", 1);
11 | cout << "cst1.lcp in MiB : " << size_in_mega_bytes(cst1.lcp) << endl;
12 | util::clear(cst1);
13 | cst_sct3>>, lcp_dac<>> cst2;
14 | construct(cst2, "english.200MB", 1);
15 | cout << "cst2.lcp in MiB : " << size_in_mega_bytes(cst2.lcp) << endl;
16 | }
17 |
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/ThirdParty/sdsl-lite/tutorial/expl-24.cpp:
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1 | #include
2 | #include
3 |
4 | using namespace std;
5 | using namespace sdsl;
6 |
7 | int main()
8 | {
9 | // 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9
10 | // ( ( ( ) ( ) ) ( ) ( ( ( ) ( ) ) ( ) ) )
11 | bit_vector b = {1,1,1,0,1,0,0,1,0,1,1,1,0,1,0,0,1,0,0,0};
12 | bp_support_sada<> bps(&b); // <- pointer to b
13 | cout << bps.find_close(0) << ", "
14 | << bps.find_open(3) << ", "
15 | << bps.enclose(4) << ", "
16 | << bps.double_enclose(13, 16) << endl;
17 | }
18 |
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/ThirdParty/sdsl-lite/tutorial/expl-25.cpp:
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1 |
2 | #include
3 | #include
4 |
5 | using namespace std;
6 | using namespace sdsl;
7 |
8 | int main()
9 | {
10 | // 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9
11 | // ( ( ( ) ( ) ) ( ) ( ( ( ) ( ) ) ( ) ) )
12 | bit_vector b = {1,1,1,0,1,0,0,1,0,1,1,1,0,1,0,0,1,0,0,0};
13 | bp_support_sada<> bps(&b); // <- pointer to b
14 | for (size_t i=0; i < b.size(); ++i)
15 | cout << bps.excess(i)<< " ";
16 | cout << endl;
17 | cout << bps.rank(0) << ", " // inclusive rank for BPS!!!
18 | << bps.select(4) << endl;
19 | }
20 |
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/ThirdParty/sdsl-lite/tutorial/expl-26.cpp:
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1 | #include
2 | #include
3 |
4 | using namespace std;
5 | using namespace sdsl;
6 |
7 | int main()
8 | {
9 | // 0 1 2 3 4 5 6 7 8 9 0
10 | int_vector<> v = {5,3,8,9,1,2,5,3,9,0,7};
11 | rmq_succinct_sct<> rmq(&v); // <- pointer to b
12 | util::clear(v);
13 | cout << "v.size() = " << v.size() << endl;
14 | cout << rmq(0, 10) << ", " << rmq(2, 7) << endl;
15 | }
16 |
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/ThirdParty/sdsl-lite/tutorial/int-vector-buffer.cpp:
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1 | #include
2 | #include
3 |
4 | using namespace sdsl;
5 | using namespace std;
6 |
7 | int main()
8 | {
9 | std::string tmp_file = "tmp_file.sdsl";
10 | {
11 | // generate int_vector and store to a file
12 | int_vector<> v = {1,3,5,7,2,3,4,9,8,7,10,1};
13 | store_to_file(v, tmp_file);
14 | }
15 | {
16 | // use int_vector_buffer to open the file
17 | int_vector_buffer<> ivb(tmp_file);
18 | // output elements and assign 42 to each of them
19 | for (auto x : ivb) {
20 | cout << x << endl;
21 | x = 42;
22 | }
23 | // int_vector_buffer is destroy at the end of the
24 | // scope and all value are written to disk
25 | }
26 | {
27 | // read vector from file and output it
28 | int_vector<> v;
29 | load_from_file(v, tmp_file);
30 | cout << v << endl;
31 | }
32 | // delete temporary file
33 | sdsl::remove(tmp_file);
34 | }
35 |
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/ThirdParty/sdsl-lite/tutorial/rmq-example.cpp:
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1 | #include
2 | #include
3 |
4 | using namespace sdsl;
5 | using namespace std;
6 |
7 |
8 | int main()
9 | {
10 | rmq_succinct_sct<> rmq;
11 | {
12 | // initilaize int_vector object A
13 | int_vector<> A = {6,7,3,2,4,2,1,5,8,2};
14 | // output a
15 | cout << "A = " << A << endl;
16 |
17 | // generate range-minimum structure by passing
18 | // pointer to ordered array
19 | rmq = rmq_succinct_sct<>(&A);
20 |
21 | // calculate index of minimal element in a[0..a.size()-1]
22 | auto min_idx = rmq(0, A.size()-1);
23 |
24 | cout << "A[" << min_idx << "]=" << A[min_idx];
25 | cout << " is the samllest element in A[0.." << A.size()-1 << "]" << endl;
26 |
27 | // calculate index of minimal element in a[2..5]
28 | min_idx = rmq(2,5);
29 |
30 | cout << "A[" << min_idx << "]=" << A[min_idx];
31 | cout << " is the smallest element in A[2..5]" << endl;
32 | }
33 | // no A does not exist any more, queries can still be answered
34 | auto min_idx = rmq(1,5);
35 | cout << "A[" << min_idx << "] is the smallest in A[1..5]" << endl;
36 | return 0;
37 | }
38 |
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/ThirdParty/sdsl-lite/tutorial/use-a-wavelet-tree.cpp:
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1 | #include
2 | #include
3 |
4 | using namespace sdsl;
5 | using namespace std;
6 |
7 | int main(int argc, char* argv[])
8 | {
9 | if (argc < 2) {
10 | cout << "Usage: " << argv[0] << " file" << endl;
11 | return 1;
12 | }
13 | wt_huff> wt;
14 | construct(wt, argv[1], 1);
15 |
16 | cout << "wt.size()="<< wt.size() << endl;
17 | cout << "wt.sigma ="<< wt.sigma << endl;
18 | if (wt.size() > 0) {
19 | // access an element
20 | cout << "wt[0]=" << wt[0] << endl;
21 | // rank an element (exclude)
22 | uint64_t r = wt.rank(wt.size(), wt[0]);
23 | cout << "wt.rank(wt.size(), wt[0])=" << r << endl;
24 | // select element ()
25 | cout << "wt.select(r, wt[0]) = " << wt.select(r, wt[0]) << endl;
26 | }
27 | }
28 |
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/ThirdParty/sdsl-lite/uninstall.sh:
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1 | #!/bin/bash
2 | # This script removes all installed sdsl files
3 | # on a LINUX or Mac OS X system
4 |
5 | CUR_DIR=`pwd`
6 | SDSL_INSTALL_PREFIX=${HOME}
7 | if [ $# -ge 1 ]; then
8 | SDSL_INSTALL_PREFIX=${1}
9 | fi
10 |
11 | echo "Library files will be removed from"
12 | echo "'${SDSL_INSTALL_PREFIX}/lib' and"
13 | echo "'${SDSL_INSTALL_PREFIX}/include'"
14 |
15 |
16 | cd "${CUR_DIR}"
17 | OLD_DIR="$( cd "$( dirname "$0" )" && pwd )" # gets the directory where the script is located in
18 | cd "${OLD_DIR}"
19 | OLD_DIR=`pwd`
20 |
21 | cd build # change into the build directory
22 | if [ $? != 0 ]; then
23 | exit 1
24 | fi
25 |
26 | if [ -f Makefile ]; then
27 | make uninstall-sdsl
28 | fi
29 |
30 | if [ $? != 0 ]; then
31 | exit 1
32 | fi
33 |
34 | ./clean.sh # clean-up build directory
35 | if [ $? != 0 ]; then
36 | exit 1
37 | fi
38 |
39 | echo "Installed sdsl files were removed."
40 |
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/apps/CMakeLists.txt:
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1 | file(GLOB SRCS *.cpp)
2 |
3 | ADD_EXECUTABLE(kProcessorApp ${SRCS})
4 |
5 | TARGET_LINK_LIBRARIES(kProcessorApp kProcessor MQF)
6 |
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/apps/dumpMain.cpp:
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1 | #include
2 | #include
3 | #include "CLI11.hpp"
4 | #include
5 | #include
6 | #include