Merge pull request #357 from xxsds/int_vector_mapper

Int vector mapper

Author: simongog

README.md

@@ -1,294 +1 @@
-SDSL - Succinct Data Structure Library
-=========
-
-[![Build Status](https://travis-ci.org/simongog/sdsl-lite.svg?branch=master)](https://travis-ci.org/simongog/sdsl-lite)
-
-What is it?
------------
-
-The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11
-library implementing succinct data structures. In total, the library contains
-the highlights of 40 [research publications][SDSLLIT]. Succinct data structures
-can represent an object (such as a bitvector or a tree) in space close to the
-information-theoretic lower bound of the object while supporting operations
-of the original object efficiently. The theoretical time complexity of an
-operation performed on the classical data structure and the equivalent
-succinct data structure are (most of the time) identical.
-
-Why SDSL?
---------
-
-Succinct data structures have very attractive theoretical properties. However,
-in practice implementing succinct data structures is non-trivial as they are
-often composed of complex operations on bitvectors. The SDSL Library provides
-high quality, open source implementations of many succinct data structures
-proposed in literature.
-
-Specifically, the aim of the library is to provide basic and complex succinct
-data structure which are
-
-  * Easy and intuitive to use (like the [STL][STL], which provides classical data structures),
-  * Faithful to the original theoretical results,
-  * Capable of handling large inputs (yes, we support 64-bit),
-  * Provide efficient construction of all implemented succinct data structures,
-  while at the same time enable good run-time performance.
-
-<a href="http://simongog.github.io/assets/data/space-vis.html" >
-<img align="right" src="extras/resources/space-vis.png?raw=true" />
-</a>
-
-In addition we provide additional functionality which can help you use succinct
-data structure to their full potential.
-
-  * Each data structure can easily be serialized and loaded to/from disk.
-  * We provide functionality which helps you analyze the storage requirements of any
-  SDSL based data structure (see right)
-  * We support features such as hugepages and tracking the memory usage of each
-  SDSL data structure.
-  * Complex structures can be configured by template parameters and therefore
-    easily be composed. There exists one simple method which constructs
-    all complex structures.
-  * We maintain an extensive collection of examples which help you use the different
-    features provided by the library.
-  * All data structures are tested for correctness using a unit-testing framework.
-  * We provide a large collection of supporting documentation consisting of examples,
-    [cheat sheet][SDSLCS], [tutorial slides and walk-through][TUT].
-
-The library contains many succinct data structures from the following categories:
-
- * Bitvectors supporting Rank and Select
- * Integer Vectors
- * Wavelet Trees
- * Compressed Suffix Arrays (CSA)
- * Balanced Parentheses Representations
- * Longest Common Prefix (LCP) Arrays
- * Compressed Suffix Trees (CST)
- * Range Minimum/Maximum Query (RMQ) Structures
-
-For a complete overview including theoretical bounds see the
-[cheat sheet][SDSLCS] or the
-[wiki](https://github.com/simongog/sdsl-lite/wiki/List-of-Implemented-Data-Structures).
-
-Documentation
--------------
-
-We provide an extensive set of documentation describing all data structures
-and features provided by the library. Specifically we provide
-
-* A [cheat sheet][SDSLCS] which succinctly
-describes the usage of the library.
-* An doxygen generated [API reference][DOXYGENDOCS] which lists all types and functions
-of the library.
-* A set of [example](examples/) programs demonstrating how different features
-of the library are used.
-* A tutorial [presentation][TUT] with the [example code](tutorial/) using in the
-sides demonstrating all features of the library in a step-by-step walk-through.
-* [Unit Tests](test/) which contain small code snippets used to test each
-library feature.
-
-Requirements
-------------
-
-The SDSL library requires:
-
-* A modern, C++11 ready compiler such as `g++` version 4.9 or higher or `clang` version 3.2 or higher.
-* The [cmake][cmake] build system.
-* A 64-bit operating system. Either Mac OS X or Linux are currently supported.
-* For increased performance the processor of the system should support fast bit operations available in `SSE4.2`
-
-Installation
-------------
-
-To download and install the library use the following commands.
-
-```sh
-git clone https://github.com/simongog/sdsl-lite.git
-cd sdsl-lite
-./install.sh
-```
-
-This installs the sdsl library into the `include` and `lib` directories in your
-home directory. A different location prefix can be specified as a parameter of
-the `install.sh` script:
-
-```sh
-./install /usr/local/
-```
-
-To remove the library from your system use the provided uninstall script:
-
-```sh
-./uninstall.sh
-```
-
-Getting Started
-------------
-
-To get you started with the library you can start by compiling the following
-sample program which constructs a compressed suffix array (a FM-Index) over the
-text `mississippi!`, counts the number of occurrences of pattern `si` and
-stores the data structure, and a space usage visualization to the
-files `fm_index-file.sdsl` and `fm_index-file.sdsl.html`:
-
-```cpp
-#include <sdsl/suffix_arrays.hpp>
-#include <fstream>
-
-using namespace sdsl;
-
-int main() {
-    csa_wt<> fm_index;
-    construct_im(fm_index, "mississippi!", 1);
-    std::cout << "'si' occurs " << count(fm_index,"si") << " times.\n";
-    store_to_file(fm_index,"fm_index-file.sdsl");
-    std::ofstream out("fm_index-file.sdsl.html");
-    write_structure<HTML_FORMAT>(fm_index,out);
-}
-```
-
-To compile the program using `g++` run:
-
-```sh
-g++ -std=c++11 -O3 -DNDEBUG -I ~/include -L ~/lib program.cpp -o program -lsdsl -ldivsufsort -ldivsufsort64
-```
-
-Next we suggest you look at the comprehensive [tutorial][TUT] which describes
-all major features of the library or look at some of the provided [examples](examples).
-
-Test
-----
-
-Implementing succinct data structures can be tricky. To ensure that all data
-structures behave as expected, we created a large collection of unit tests
-which can be used to check the correctness of the library on your computer.
-The [test](./test) directory contains test code. We use [googletest][GTEST]
-framework and [make][MAKE] to run the tests. See the README file in the
-directory for details.
-
-To simply run all unit tests after installing the library type
-
-```sh
-cd sdsl-lite/build
-make test-sdsl
-```
-
-Note: Running the tests requires several sample files to be downloaded from the web
-and can take up to 2 hours on slow machines.
-
-
-Benchmarks
-----------
-
-To ensure the library runs efficiently on your system we suggest you run our
-[benchmark suite](benchmark). The benchmark suite recreates a
-popular [experimental study](http://arxiv.org/abs/0712.3360) which you can
-directly compare to the results of your benchmark run.
-
-Bug Reporting
-------------
-
-While we use an extensive set of unit tests and test coverage tools you might
-still find bugs in the library. We encourage you to report any problems with
-the library via the [github issue tracking system](https://github.com/simongog/sdsl-lite/issues)
-of the project.
-
-The Latest Version
-------------------
-
-The latest version can be found on the SDSL github project page https://github.com/simongog/sdsl-lite .
-
-If you are running experiments in an academic settings we suggest you use the
-most recent [released](https://github.com/simongog/sdsl-lite/releases) version
-of the library. This allows others to reproduce your experiments exactly.
-
-Licensing
----------
-
-The SDSL library is free software provided under the GNU General Public License
-(GPLv3). For more information see the [COPYING file][CF] in the library
-directory.
-
-We distribute this library freely to foster the use and development of advanced
-data structure. If you use the library in an academic setting please cite the
-following paper:
-
-    @inproceedings{gbmp2014sea,
-      title     = {From Theory to Practice: Plug and Play with Succinct Data Structures},
-      author    = {Gog, Simon and Beller, Timo and Moffat, Alistair and Petri, Matthias},
-      booktitle = {13th International Symposium on Experimental Algorithms, (SEA 2014)},
-      year      = {2014},
-      pages     = {326-337},
-      ee        = {http://dx.doi.org/10.1007/978-3-319-07959-2_28}
-    }
-
-A preliminary version if available [here on arxiv][SEAPAPER].
-
-## External Resources used in SDSL
-
-We have included the code of two excellent suffix array
-construction algorithms.
-
-* Yuta Mori's incredible fast suffix [libdivsufsort][DIVSUF]
-  algorithm for byte-alphabets.
-* An adapted version of [Jesper Larsson's][JESL] [implementation][QSUFIMPL] of
-  suffix array sorting on integer-alphabets (description of [Larsson and Sadakane][LS]).
-
-Additionally, we use the [googletest][GTEST] framework to provide unit tests.
-Our visualizations are implemented using the [d3js][d3js]-library.
-
-Authors
---------
-
-The main contributors to the library are:
-
-* [Johannes Bader] (https://github.com/olydis)
-* [Timo Beller](https://github.com/tb38)
-* [Simon Gog](https://github.com/simongog) (Creator)
-* [Matthias Petri](https://github.com/mpetri)
-
-This project is also supported by code contributions
-from other researchers. E.g. Juha Kärkkäinen,
-[Dominik Kempa](https://github.com/dkempa),
-and Simon Puglisi contributed a compressed bitvector
-implementation ([hyb_vector][HB]).
-This project further profited from excellent input of our students
-Markus Brenner, Alexander Diehm, Christian Ocker, and Maike Zwerger. Stefan
-Arnold helped us with tricky template questions. We are also grateful to
-[Diego Caro](https://github.com/diegocaro),
-[Travis Gagie](https://github.com/TravisGagie),
-Kalle Karhu,
-[Bruce Kuo](https://github.com/bruce3557),
-Jan Kurrus,
-[Shanika Kuruppu](https://github.com/skuruppu),
-Jouni Siren,
-and [Julio Vizcaino](https://github.com/garviz)
-for bug reports.
-
-Contribute
-----------
-
-Are you working on a new or improved implementation of a succinct data structure?
-We encourage you to contribute your implementation to the SDSL library to make
-your work accessible to the community within the existing library framework.
-Feel free to contact any of the authors or create an issue on the
-[issue tracking system](https://github.com/simongog/sdsl-lite/issues).
-
-
-[STL]: http://www.sgi.com/tech/stl/ "Standard Template Library"
-[pz]: http://pizzachili.di.unipi.it/ "Pizza&amp;Chli"
-[d3js]: http://d3js.org "D3JS library"
-[cmake]: http://www.cmake.org/ "CMake tool"
-[MAKE]: http://www.gnu.org/software/make/ "GNU Make"
-[gcc]: http://gcc.gnu.org/ "GNU Compiler Collection"
-[DIVSUF]: https://github.com/y-256/libdivsufsort/ "libdivsufsort"
-[LS]: http://www.sciencedirect.com/science/article/pii/S0304397507005257 "Larson &amp; Sadakane Algorithm"
-[GTEST]: https://code.google.com/p/googletest/ "Google C++ Testing Framework"
-[SDSLCS]: http://simongog.github.io/assets/data/sdsl-cheatsheet.pdf "SDSL Cheat Sheet"
-[SDSLLIT]: https://github.com/simongog/sdsl-lite/wiki/Literature "Succinct Data Structure Literature"
-[TUT]: http://simongog.github.io/assets/data/sdsl-slides/tutorial "Tutorial"
-[QSUFIMPL]: http://www.larsson.dogma.net/qsufsort.c "Original Qsufsort Implementation"
-[JESL]: http://www.itu.dk/people/jesl/ "Homepage of Jesper Larsson"
-[CF]: https://github.com/simongog/sdsl-lite/blob/master/COPYING "Licence"
-[SEAPAPER]: http://arxiv.org/pdf/1311.1249v1.pdf "SDSL paper"
-[HB]: https://github.com/simongog/sdsl-lite/blob/hybrid_bitvector/include/sdsl/hybrid_vector.hpp "Hybrid bitevctor"
-[DOXYGENDOCS]: http://algo2.iti.kit.edu/gog/docs/html/index.html "API Reference"
+Development repository for SDSL Version 3

include/sdsl/config.hpp

@@ -5,6 +5,12 @@
 #include <map>
 #include <string>
 
+#ifndef MSVC_COMPILER
+#define SDSL_UNUSED __attribute__ ((unused))
+#else
+#define SDSL_UNUSED
+#endif
+
 namespace sdsl
 {
 namespace conf  // namespace for library constant
@@ -35,6 +41,7 @@ enum byte_sa_algo_type {LIBDIVSUFSORT, SE_SAIS};
 //! Helper class for construction process
 struct cache_config {
     bool 		delete_files;   // Flag which indicates if all files which were created
+    bool        delete_data;    // Flag which indicates if the original data can be deleted
     // during construction should be deleted.
     std::string dir;    		// Directory for temporary files.
     std::string id;     		// Identifier is part of temporary file names. If