Changed implementation of WeightedRips to store simplex values (max distance between simplices' vertices) as an invisible layer on top of each simplex object, so that the data() field of WeightedRips has been freed for use by the users again.
% Dionysus README
% Dmitriy Morozov
## Dependencies
* [CGAL]-3.4 --- for alpha-shapes and kinetic data structures
* [DSR-PDB] --- for reading in PDB files (if use_dsrpdb is turned on in cmake)
* [CMake] --- for controlling the build process
* [boost] --- great set of C++ libraries
* [Doxygen] --- for building documentation
* [rlog] --- for logging only (is not needed by default)
* [SYNAPS] --- for solving polynomials (for kinetic kernel), which in turn requires GMP
[CGAL]: http://www.cgal.org
[DSR-PDB]: http://www.salilab.org/~drussel/pdb/
[CMake]: http://www.cmake.org
[boost]: http://www.boost.org
[Doxygen]: http://www.stack.nl/~dimitri/doxygen/
[rlog]: http://www.arg0.net/rlog
[SYNAPS]: http://www-sop.inria.fr/galaad/synaps/
## Building
To build examples, create a directory build (to keep everything in one place),
go to that directory and run cmake and make:
mkdir build
cd build
cmake .. (or "ccmake .." if you want a curses interface)
make
In the cmake line you can provide `-Ddebug:bool=on` to turn on debugging,
`-Dcounters:bool=on` to turn on counters, `-Doptimize:bool=on` to turn on
optimization, `-Duse_dsrpdb:bool=on` to turn on reading PDB files. Depending on
the combination of debugging and optimization, a particular `CMAKE_CXX_FLAGS*`
is chosen. All of this can be set using a text user interface by running
`ccmake` instead of `cmake`.
When compiling on a 64 bit platform (with Boost 1.34) add
`-DBOOST_NO_INTRINSIC_INT64_T` to `CMAKE_CXX_FLAGS`.
## Author
Dmitriy Morozov <dmitriy@mrzv.org>