fbergmann / libsbgn2

C++ Library for reading / writing SBGN-ML documents

LibSBGN 2

This project represents a library for reading / writing SBGN-ML documents in C++. This library has been generated partially using deviser. It currently targets Milestone 3 of SGBN-ML. Additionally it exposes the Render Extension classes of the SBML Render package, which facilitates the use of colors for SBGN-ML. Other languages are supported via SWIG, tested are Python, C# and Java.

Dependencies

This library requires libSBML to be present, as its XML parsing layer and rendering support will be used. We recommend the use of the expat parser.

Building

This library uses CMake to build the library, so from an initial checkout all you would need todo is to run:

mkdir build  
cd build
cmake -DLIBSBML_LIBRARY=< path to libsbml lib> -DLIBSBML_INCLUDE_DIR=< path to includes > ... -DEXTRA_LIBS= < comma separated list of xml libraries>
make  
make install

Should libSBML be installed in a default location it will be found automatically. Note that you do need to list the xml libraries that libSBML was linked against. In most cases libSBML is compiled against expat and have compression enabled, so your EXTRA_LIBS would be:

EXTRA_LIBS=expat

note the semicolon denoting the listing of several libraries. Of course you could also enter the full path to each individual file, just to give an example, on windows I use:

EXTRA_LIBS=D:/dependencies/lib/expat.lib

for linking against expat and indicating, that libSBML was compiled without compression.

License

This project is open source and freely available under the Simplified BSD license. Should that license not meet your needs, please contact me.

Copyright (c) 2013-2019, Frank T. Bergmann
All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.