From 92381785fb046778cb66cb6a7cb1317a0fda1f17 Mon Sep 17 00:00:00 2001 From: Dominik Kempa Date: Mon, 17 May 2021 20:01:19 -0700 Subject: [PATCH] Reorganize the directory structure --- AUTHORS | 2 + LICENCE | 20 ++++++ README.md | 65 ++++++++++++++++++++ release/wt-fbb-0.1.0/VERSION => VERSION | 0 {release/wt-fbb-0.1.0 => include}/wt_fbb.hpp | 14 ++++- release/wt-fbb-0.1.0/AUTHORS | 2 - release/wt-fbb-0.1.0/LICENCE | 24 -------- release/wt-fbb-0.1.0/README | 51 --------------- 8 files changed, 98 insertions(+), 80 deletions(-) create mode 100644 AUTHORS create mode 100644 LICENCE create mode 100644 README.md rename release/wt-fbb-0.1.0/VERSION => VERSION (100%) rename {release/wt-fbb-0.1.0 => include}/wt_fbb.hpp (99%) delete mode 100644 release/wt-fbb-0.1.0/AUTHORS delete mode 100644 release/wt-fbb-0.1.0/LICENCE delete mode 100644 release/wt-fbb-0.1.0/README diff --git a/AUTHORS b/AUTHORS new file mode 100644 index 0000000..af53cfd --- /dev/null +++ b/AUTHORS @@ -0,0 +1,2 @@ +Juha Karkkainen +Dominik Kempa (contact person) diff --git a/LICENCE b/LICENCE new file mode 100644 index 0000000..38e548b --- /dev/null +++ b/LICENCE @@ -0,0 +1,20 @@ +Copyright 2015-2021 Dominik Kempa, Juha Karkkainen + +Permission is hereby granted, free of charge, to any person obtaining +a copy of this software and associated documentation files (the +"Software"), to deal in the Software without restriction, including +without limitation the rights to use, copy, modify, merge, publish, +distribute, sublicense, and/or sell copies of the Software, and to +permit persons to whom the Software is furnished to do so, subject to +the following conditions: + +The above copyright notice and this permission notice shall be +included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF +MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE +LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION +OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION +WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. diff --git a/README.md b/README.md new file mode 100644 index 0000000..dd7c41e --- /dev/null +++ b/README.md @@ -0,0 +1,65 @@ +Faster-Minuter index +==================== + + +Description +----------- + +This repository contains the implementation of a wavelet tree data +structure using the fixed block boosting (FBB) technique. The result +of plugging this wavelet tree into an FM-index is called the Faster +Minuter index. + +For the description of the new wavelet tree, the Faster Minuter +index, and reports of experimental evaluation, refer to the following +paper. + + @article{fasterminuter, + author = {Simon Gog and Juha K{\"{a}}rkk{\"{a}}inen and + Dominik Kempa and Matthias Petri and Simon J. Puglisi}, + title = {Fixed Block Compression Boosting in FM-Indexes: + Theory and Practice}, + journal = {Algorithmica}, + volume = {81}, + number = {4}, + pages = {1370--1391}, + year = {2019}, + doi = {10.1007/s00453-018-0475-9}, + } + +The latest version of the wavelet tree based on FBB is available from +https://github.com/dominikkempa/faster-minuter. + + + +Usage +----- + +The wavelet tree is implemented as a C++ class wt_fbb. The class is +compatible with the sdsl library (https://github.com/simongog/sdsl-lite). +The current version has been tested on Linux/PC. + +The class comes with default parameters chosen for good overall +performance and in nearly all practical scenarios should be used as +is. The key customization of the class is in plugging in different +bitvector implementations. The default is the hybrid bitvector, but +faster (and larger) alternatives are available in the sdsl library. +Refer to the paper above for details and experimental comparisons. + + + +Terms of use +------------ + +wt_fbb is released under the MIT/X11 license. See the file LICENCE for +more details. If you use this code, please cite the paper mentioned +above. + + + +Authors +------- + +wt_fbb was implemented by: +- [Dominik Kempa](https://scholar.google.com/citations?user=r0Kn9IUAAAAJ) +- [Juha Karkkainen](https://scholar.google.com/citations?user=oZepo1cAAAAJ) diff --git a/release/wt-fbb-0.1.0/VERSION b/VERSION similarity index 100% rename from release/wt-fbb-0.1.0/VERSION rename to VERSION diff --git a/release/wt-fbb-0.1.0/wt_fbb.hpp b/include/wt_fbb.hpp similarity index 99% rename from release/wt-fbb-0.1.0/wt_fbb.hpp rename to include/wt_fbb.hpp index a20b266..9b61f84 100644 --- a/release/wt-fbb-0.1.0/wt_fbb.hpp +++ b/include/wt_fbb.hpp @@ -2,7 +2,10 @@ * @file wt_fbb.cpp * @section LICENCE * - * Copyright (C) 2015-2019 + * This file is part of the "Faster Minuter" index v0.1.0 + * See: https://github.com/dominikkempa/faster-minuter + * + * Copyright (C) 2015-2021 * Juha Karkkainen * Dominik Kempa * @@ -56,11 +59,16 @@ * * @ingroup wt * - * \par Reference: + * \par References: * [1] Simon Gog, Juha Karkkainen, Dominik Kempa, - Matthias Petri, Simon J. Puglisi: + * Matthias Petri, Simon J. Puglisi: * Faster, Minuter. * DCC 2016: 53-62 + * [2] Simon Gog, Juha Kärkkäinen, Dominik Kempa, + * Matthias Petri, Simon J. Puglisi: + * Fixed Block Compression Boosting in FM-Indexes: Theory + * and Practice. + * Algorithmica 81(4): 1370-1391 (2019) */ template, class t_rank = typename t_bitvector::rank_1_type, diff --git a/release/wt-fbb-0.1.0/AUTHORS b/release/wt-fbb-0.1.0/AUTHORS deleted file mode 100644 index ea0c897..0000000 --- a/release/wt-fbb-0.1.0/AUTHORS +++ /dev/null @@ -1,2 +0,0 @@ -Juha Karkkainen -Dominik Kempa diff --git a/release/wt-fbb-0.1.0/LICENCE b/release/wt-fbb-0.1.0/LICENCE deleted file mode 100644 index f5e4e5f..0000000 --- a/release/wt-fbb-0.1.0/LICENCE +++ /dev/null @@ -1,24 +0,0 @@ -Copyright (C) 2015-2019 -Juha Karkkainen -Dominik Kempa - -Permission is hereby granted, free of charge, to any person -obtaining a copy of this software and associated documentation -files (the "Software"), to deal in the Software without -restriction, including without limitation the rights to use, -copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the -Software is furnished to do so, subject to the following -conditions: - -The above copyright notice and this permission notice shall be -included in all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, -EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES -OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND -NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT -HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, -WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING -FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR -OTHER DEALINGS IN THE SOFTWARE. diff --git a/release/wt-fbb-0.1.0/README b/release/wt-fbb-0.1.0/README deleted file mode 100644 index 85a026b..0000000 --- a/release/wt-fbb-0.1.0/README +++ /dev/null @@ -1,51 +0,0 @@ -wt_fbb - Wavelet tree based on a fixed block boosting technique -=============================================================== - - -Description ------------ - -This package contains implementation of the wavelet tree data -structure using the fixed block boosting (FBB) technique. The -data structure is described in the paper - - Simon Gog, Juha Kärkkäinen, Dominik Kempa, Matthias Petri, Simon - J. Puglisi: Faster, Minuter. - In Proc. 2016 Data Compression Conference (DCC), 2016. - -The latest version of wt_fbb is available from -https://github.com/dkempa/faster-minuter. - - - -Usage ------ - -wt_fbb is implemented as a plugin into the sdsl library -(https://github.com/simongog/sdsl-lite). The current version has been -tested on Linux/PC. - -The class comes with default parameters chosen for good overall -performance and in nearly all practical scenarios should be used as -is. The key customization of the class is in plugging in different -bitvector implementations. The default is the hybrid bitvector, but -faster (and larger) alternatives are available in the sdsl library. -Refer to the paper above for details and experimental comparisons. - - - - -Terms of use ------------- - -wt_fbb is released under the MIT/X11 license. See the file LICENCE for -more details. - -If you use this code, please cite the paper mentioned above and -publish the URL from which you downloaded the code. - - - - -Written by Dominik Kempa. -Coventry, July 2019.