Merge pull request #45 from hgb-bin-proteomics/develop

add ms amanda license info

amanda/ChemicalUtils.cs

@@ -1,4 +1,57 @@
-namespace MSAMANDA_CHEMICALUTILS
+/*
+CODE FROM THE MS AMANDA SEARCH ENGINE
+https://ms.imp.ac.at/?goto=msamanda
+
+WHEN USED PLEASE CITE
+https://doi.org/10.1021/pr500202e
+https://doi.org/10.1002/rcm.9088
+
+MS AMANDA LICENSE AGREEMENT
+
+1.	This is the "MS Amanda" Freeware Software License Agreement, applying to the MS Amanda software with the copyright owners University of Applied Sciences Upper Austria GmbH (FH OÖ), Franz-Fritsch-Straße 11, 4600 Wels, and Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, 1030 Vienna, Austria. The software "MS Amanda" is provided as freeware. Authors of the software are Viktoria Dorfer, Marina Strobl, Sergey Maltsev, Peter Pichler, Stephan Winkler, and Karl Mechtler. All authors must be indicated on "MS Amanda". 
+2.	Using the software MS Amanda you automatically agree to the terms and conditions contained within this Freeware Software License which is effective while using the software MS Amanda in the freeware version.
+3.	The University of Applied Sciences Upper Austria GmbH (FH OÖ) and the Research Institute of Molecular Pathology (IMP) grant the Licensee a non-exclusive and non-transferable license to reproduce and use the software for personal purposes.
+4.	Licensees may not rent, lease, lend, sell, reverse engineer, decompile, or disassemble "MS Amanda".
+5.	Any proprietary rights, titles, ownership and intellectual property rights of "MS Amanda" remain with the University of Applied Sciences Upper Austria GmbH (FH OÖ) and the Research Institute of Molecular Pathology (IMP). The product is protected by copyright and intellectual property laws.
+6.	The copyright holder reserves the right to reclassify this software as a non-freeware product at any time. This will not automatically affect the license agreement of previously distributed copies of the software. The University of Applied Sciences Upper Austria GmbH (FH OÖ) and the Research Institute of Molecular Pathology (IMP) may also terminate this agreement without any specified reason or if the licensee breaches any of its terms.
+7.	Upon termination of this agreement the licensee is obliged to destroy all personal copies of "MS Amanda" obtained under this license.
+8.	Licensees are not entitled to receive any documentation, technical support or updates to "MS Amanda".
+9.	This agreement does not affect terms of other agreements regarding "MS Amanda".
+10.	THE SOFTWARE "MS Amanda" IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+11.	Austrian Law is applicable to this license agreement. The relevant court for all disputes arising out of or in connection with this agreement is the competent court in Linz, Austria.
+
+
+MS Amanda uses and incorporates third-party libraries or other resources 
+that may be distributed under licenses different than the MS Amanda software.
+
+MessagePack 
+    https://msgpack.org
+    Copyright (c) 2017 Yoshifumi Kawai and contributors
+	MIT License
+
+MIT License
+=========================================
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of 
+this software and associated documentation files (the "Software"), to deal in 
+the Software without restriction, including without limitation the rights to 
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies 
+of the Software, and to permit persons to whom the Software is furnished to do 
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all 
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 
+SOFTWARE.
+ */
+
+namespace MSAMANDA_CHEMICALUTILS
 {
     public class ChemicalElement
     {

amanda/FASTAParser.cs

@@ -1,4 +1,57 @@
-using System.Collections.Concurrent;
+/*
+CODE FROM THE MS AMANDA SEARCH ENGINE
+https://ms.imp.ac.at/?goto=msamanda
+
+WHEN USED PLEASE CITE
+https://doi.org/10.1021/pr500202e
+https://doi.org/10.1002/rcm.9088
+
+MS AMANDA LICENSE AGREEMENT
+
+1.	This is the "MS Amanda" Freeware Software License Agreement, applying to the MS Amanda software with the copyright owners University of Applied Sciences Upper Austria GmbH (FH OÖ), Franz-Fritsch-Straße 11, 4600 Wels, and Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, 1030 Vienna, Austria. The software "MS Amanda" is provided as freeware. Authors of the software are Viktoria Dorfer, Marina Strobl, Sergey Maltsev, Peter Pichler, Stephan Winkler, and Karl Mechtler. All authors must be indicated on "MS Amanda". 
+2.	Using the software MS Amanda you automatically agree to the terms and conditions contained within this Freeware Software License which is effective while using the software MS Amanda in the freeware version.
+3.	The University of Applied Sciences Upper Austria GmbH (FH OÖ) and the Research Institute of Molecular Pathology (IMP) grant the Licensee a non-exclusive and non-transferable license to reproduce and use the software for personal purposes.
+4.	Licensees may not rent, lease, lend, sell, reverse engineer, decompile, or disassemble "MS Amanda".
+5.	Any proprietary rights, titles, ownership and intellectual property rights of "MS Amanda" remain with the University of Applied Sciences Upper Austria GmbH (FH OÖ) and the Research Institute of Molecular Pathology (IMP). The product is protected by copyright and intellectual property laws.
+6.	The copyright holder reserves the right to reclassify this software as a non-freeware product at any time. This will not automatically affect the license agreement of previously distributed copies of the software. The University of Applied Sciences Upper Austria GmbH (FH OÖ) and the Research Institute of Molecular Pathology (IMP) may also terminate this agreement without any specified reason or if the licensee breaches any of its terms.
+7.	Upon termination of this agreement the licensee is obliged to destroy all personal copies of "MS Amanda" obtained under this license.
+8.	Licensees are not entitled to receive any documentation, technical support or updates to "MS Amanda".
+9.	This agreement does not affect terms of other agreements regarding "MS Amanda".
+10.	THE SOFTWARE "MS Amanda" IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+11.	Austrian Law is applicable to this license agreement. The relevant court for all disputes arising out of or in connection with this agreement is the competent court in Linz, Austria.
+
+
+MS Amanda uses and incorporates third-party libraries or other resources 
+that may be distributed under licenses different than the MS Amanda software.
+
+MessagePack 
+    https://msgpack.org
+    Copyright (c) 2017 Yoshifumi Kawai and contributors
+	MIT License
+
+MIT License
+=========================================
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of 
+this software and associated documentation files (the "Software"), to deal in 
+the Software without restriction, including without limitation the rights to 
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies 
+of the Software, and to permit persons to whom the Software is furnished to do 
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all 
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 
+SOFTWARE.
+ */
+
+using System.Collections.Concurrent;
 using System.Text.RegularExpressions;
 using System.Text;
 using MessagePack;

amanda/IonCalculator.cs

@@ -1,4 +1,57 @@
-using System.Text;
+/*
+CODE FROM THE MS AMANDA SEARCH ENGINE
+https://ms.imp.ac.at/?goto=msamanda
+
+WHEN USED PLEASE CITE
+https://doi.org/10.1021/pr500202e
+https://doi.org/10.1002/rcm.9088
+
+MS AMANDA LICENSE AGREEMENT
+
+1.	This is the "MS Amanda" Freeware Software License Agreement, applying to the MS Amanda software with the copyright owners University of Applied Sciences Upper Austria GmbH (FH OÖ), Franz-Fritsch-Straße 11, 4600 Wels, and Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, 1030 Vienna, Austria. The software "MS Amanda" is provided as freeware. Authors of the software are Viktoria Dorfer, Marina Strobl, Sergey Maltsev, Peter Pichler, Stephan Winkler, and Karl Mechtler. All authors must be indicated on "MS Amanda". 
+2.	Using the software MS Amanda you automatically agree to the terms and conditions contained within this Freeware Software License which is effective while using the software MS Amanda in the freeware version.
+3.	The University of Applied Sciences Upper Austria GmbH (FH OÖ) and the Research Institute of Molecular Pathology (IMP) grant the Licensee a non-exclusive and non-transferable license to reproduce and use the software for personal purposes.
+4.	Licensees may not rent, lease, lend, sell, reverse engineer, decompile, or disassemble "MS Amanda".
+5.	Any proprietary rights, titles, ownership and intellectual property rights of "MS Amanda" remain with the University of Applied Sciences Upper Austria GmbH (FH OÖ) and the Research Institute of Molecular Pathology (IMP). The product is protected by copyright and intellectual property laws.
+6.	The copyright holder reserves the right to reclassify this software as a non-freeware product at any time. This will not automatically affect the license agreement of previously distributed copies of the software. The University of Applied Sciences Upper Austria GmbH (FH OÖ) and the Research Institute of Molecular Pathology (IMP) may also terminate this agreement without any specified reason or if the licensee breaches any of its terms.
+7.	Upon termination of this agreement the licensee is obliged to destroy all personal copies of "MS Amanda" obtained under this license.
+8.	Licensees are not entitled to receive any documentation, technical support or updates to "MS Amanda".
+9.	This agreement does not affect terms of other agreements regarding "MS Amanda".
+10.	THE SOFTWARE "MS Amanda" IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+11.	Austrian Law is applicable to this license agreement. The relevant court for all disputes arising out of or in connection with this agreement is the competent court in Linz, Austria.
+
+
+MS Amanda uses and incorporates third-party libraries or other resources 
+that may be distributed under licenses different than the MS Amanda software.
+
+MessagePack 
+    https://msgpack.org
+    Copyright (c) 2017 Yoshifumi Kawai and contributors
+	MIT License
+
+MIT License
+=========================================
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of 
+this software and associated documentation files (the "Software"), to deal in 
+the Software without restriction, including without limitation the rights to 
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies 
+of the Software, and to permit persons to whom the Software is furnished to do 
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all 
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 
+SOFTWARE.
+ */
+
+using System.Text;
 using MSAMANDA_CHEMICALUTILS;
 
 namespace MSAMANDA_IONCALCULATION

amanda/MGFParser.cs

@@ -1,4 +1,57 @@
-using System.Globalization;
+/*
+CODE FROM THE MS AMANDA SEARCH ENGINE
+https://ms.imp.ac.at/?goto=msamanda
+
+WHEN USED PLEASE CITE
+https://doi.org/10.1021/pr500202e
+https://doi.org/10.1002/rcm.9088
+
+MS AMANDA LICENSE AGREEMENT
+
+1.	This is the "MS Amanda" Freeware Software License Agreement, applying to the MS Amanda software with the copyright owners University of Applied Sciences Upper Austria GmbH (FH OÖ), Franz-Fritsch-Straße 11, 4600 Wels, and Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, 1030 Vienna, Austria. The software "MS Amanda" is provided as freeware. Authors of the software are Viktoria Dorfer, Marina Strobl, Sergey Maltsev, Peter Pichler, Stephan Winkler, and Karl Mechtler. All authors must be indicated on "MS Amanda". 
+2.	Using the software MS Amanda you automatically agree to the terms and conditions contained within this Freeware Software License which is effective while using the software MS Amanda in the freeware version.
+3.	The University of Applied Sciences Upper Austria GmbH (FH OÖ) and the Research Institute of Molecular Pathology (IMP) grant the Licensee a non-exclusive and non-transferable license to reproduce and use the software for personal purposes.
+4.	Licensees may not rent, lease, lend, sell, reverse engineer, decompile, or disassemble "MS Amanda".
+5.	Any proprietary rights, titles, ownership and intellectual property rights of "MS Amanda" remain with the University of Applied Sciences Upper Austria GmbH (FH OÖ) and the Research Institute of Molecular Pathology (IMP). The product is protected by copyright and intellectual property laws.
+6.	The copyright holder reserves the right to reclassify this software as a non-freeware product at any time. This will not automatically affect the license agreement of previously distributed copies of the software. The University of Applied Sciences Upper Austria GmbH (FH OÖ) and the Research Institute of Molecular Pathology (IMP) may also terminate this agreement without any specified reason or if the licensee breaches any of its terms.
+7.	Upon termination of this agreement the licensee is obliged to destroy all personal copies of "MS Amanda" obtained under this license.
+8.	Licensees are not entitled to receive any documentation, technical support or updates to "MS Amanda".
+9.	This agreement does not affect terms of other agreements regarding "MS Amanda".
+10.	THE SOFTWARE "MS Amanda" IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+11.	Austrian Law is applicable to this license agreement. The relevant court for all disputes arising out of or in connection with this agreement is the competent court in Linz, Austria.
+
+
+MS Amanda uses and incorporates third-party libraries or other resources 
+that may be distributed under licenses different than the MS Amanda software.
+
+MessagePack 
+    https://msgpack.org
+    Copyright (c) 2017 Yoshifumi Kawai and contributors
+	MIT License
+
+MIT License
+=========================================
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of 
+this software and associated documentation files (the "Software"), to deal in 
+the Software without restriction, including without limitation the rights to 
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies 
+of the Software, and to permit persons to whom the Software is furnished to do 
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all 
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 
+SOFTWARE.
+ */
+
+using System.Globalization;
 using System.Text.RegularExpressions;
 
 namespace MSAMANDA_MGFPARSER