FragmentationAnalyzer

FragmentationAnalyzer has been developed by Harald Barsnes (University of Bergen, Norway) under the guidance of Prof. Dr. Lennart Martens.

Project home page: http://compomics.github.io/projects/fragmentation-analyzer.html

FragmentationAnalyzer is based on the ms-lims project.

In addition code from the following projects is used:

Mascot dat file parsing is done using the MascotDatfile library
OMSSA parsing is done using omssa-parser
The platform independent graphical user interface is based on code from JGoodies
Advanced GUI components from SwingLabs SwingX
Plotting is done using JFreeChart
Spectrum visualization is done using the compomics-utilities library
Correlation is calculated using Commons-Math
Exporting plots to SVG is done using Batik

Licenses:

FragmentationAnalyzer: Apache License 2.0.

This license applies to all files in the FragmentationAnalyzer code archive. Except the FragmentationAnalyzer icons, and the third-party icons which may have separate licenses.

Please note that some of the JAR files used by the FragmentationAnalyzer may not have the same license as the FragmentationAnalyzer itself. If you want to use any of these in a different context, make sure to obtain the original license for the JAR file in question.

The platform independent graphical user interface design is based on JGoodies and has a separate license.

For licenses regarding Java see www.sun.com.

Questions?

Any further questions can be forwarded to harald.barsnes@uib.no.

Supported Platforms:

The tool has been tested on Windows XP, Windows Vista, Linux and Mac. But should also work on older Windows versions and on other platforms, as long as Java 1.5 (or newer) is installed.

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The BSD License for the JGoodies Looks

Copyright (c) 2001-2007 JGoodies Karsten Lentzsch. All rights reserved.

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

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

o 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.

o Neither the name of JGoodies Karsten Lentzsch nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

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.

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