parasail-java: Java JNI Interface for the Parasail C Library

Author: Jeff Daily (jeff.daily@pnnl.gov)

Table of Contents

• Installation
• Code Example
• Citing parasail
• License: Battelle BSD-style

This package contains Java JNI bindings for parasail. Parasail is a SIMD C (C99) library containing implementations of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global pairwise sequence alignment algorithms.

Installation

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Once you have installed parasail, you can then compile the Java JNI bindings. The build uses cmake. The easiest way for cmake to locate the parasail installation is to use the CMAKE_PREFIX_PATH variable. See the following example for details.

cd parasail-java
mkdir build
cd build
cmake .. -DCMAKE_PREFIX_PATH=/your/path/to/parasail/install/prefix
make

That should produce the parasail.jar as well as the JNIparasail library, named according to your platform. For example, libJNIparasail.jnilib on OSX, JNIparasail.dll on Windows, and libJNIparasail.so on Linux.

Code Example

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import parasail.Aligner;
import parasail.Matrix;
import parasail.Result;

Result result = Aligner.sw_scan_16("asdf", "asdf", 11, 1, Matrix.blosum62);
System.out.println("score = " + result.getScore());
result.delete();

Please refer to the parasail C library README.md for the naming conventions of the various functions provided. These Java bindings drop the "parasail_" prefix since the functions are naturally namespaced within the parasail.Aligner class.

Result objects should be manually deleted when no longer used in order to free allocated memory by the parasail C library. As with the parasail C library, gap open and gap extension penalties are specified as positive numbers.

There is a slightly more complicated code example that is compiled as part of the parasail.jar. See Example.java. You can run the compiled example from within the build directory by running java -cp ./parasail.jar parasail.Example <filename.fasta>.

Citing parasail

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If needed, please cite the following paper.

Daily, Jeff. (2016). Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments. BMC Bioinformatics, 17(1), 1-11. doi:10.1186/s12859-016-0930-z

http://dx.doi.org/10.1186/s12859-016-0930-z

License: Battelle BSD-style

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Copyright (c) 2015, Battelle Memorial Institute

1. Battelle Memorial Institute (hereinafter Battelle) hereby grants permission to any person or entity lawfully obtaining a copy of this software and associated documentation files (hereinafter “the Software”) to redistribute and use the Software in source and binary forms, with or without modification. Such person or entity may use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and may permit others to do so, subject to the following conditions:

   • Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimers.

   • 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.

   • Other than as used herein, neither the name Battelle Memorial Institute or Battelle may be used in any form whatsoever without the express written consent of Battelle.

   • Redistributions of the software in any form, and publications based on work performed using the software should include the following citation as a reference:

   Daily, Jeff. (2016). Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments. BMC Bioinformatics, 17(1), 1-11. doi:10.1186/s12859-016-0930-z

2. 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 BATTELLE 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.