THIRD_PARTY_NOTICES.txt

THIRD-PARTY SOFTWARE NOTICES AND INFORMATION
=============================================
inSeqAPI and Scarif incorporate components from third-party projects.
The following notices are provided to satisfy attribution and license
requirements. Full license texts are referenced by URL where applicable.

========================================================================
SUMMARY TABLE
========================================================================

Package                              Version   License       Notes
--------------------------------------------------------------------
CSMSL                                (bundled) Apache-2.0    Bundled DLL
RawFileReader (MSFileReader)         (bundled) Proprietary   Bundled DLLs; see full license below
Accord                               3.8.0     LGPL-2.1      See note *
Accord.MachineLearning               3.8.0     LGPL-2.1      See note *
Accord.Math                          3.8.0     LGPL-2.1      See note *
Accord.Statistics                    3.8.0     LGPL-2.1      See note *
Google.Apis                          1.46.0    Apache-2.0
Google.Apis.Auth                     1.46.0    Apache-2.0
Google.Apis.Core                     1.46.0    Apache-2.0
Google.Protobuf                      3.24.4    BSD-3-Clause
Grpc                                 2.44.0    Apache-2.0
Grpc.Core                            2.44.0    Apache-2.0
Grpc.Core.Api                        2.44.0    Apache-2.0
HarfBuzzSharp                        7.3.0.3   MIT
HarfBuzzSharp.NativeAssets.*         7.3.0.3   MIT
LightGBM                             2.3.1     MIT
LumenWorksCsvReader                  4.0.0     MIT
Microsoft.Data.Sqlite                8.0.1     MIT
Microsoft.Data.Sqlite.Core           8.0.1     MIT
Microsoft.Extensions.Logging.*       3.0.3     MIT
Microsoft.ML                         1.6.0     MIT
Microsoft.ML.CpuMath                 1.6.0     MIT
Microsoft.ML.DataView                1.6.0     MIT
Microsoft.ML.FastTree                1.6.0     MIT
Microsoft.ML.LightGbm                1.6.0     MIT
Microsoft.ML.OnnxRuntime             1.8.1     MIT
Microsoft.ML.OnnxRuntime.Managed     1.8.1     MIT
Microsoft.ML.OnnxTransformer         1.6.0     MIT
Microsoft.ML.TensorFlow              1.6.0     MIT
Newtonsoft.Json                      13.0.1    MIT
NumSharp.Lite                        0.1.8     Apache-2.0
OpenTK                               3.1.0     MIT
OpenTK.GLControl                     3.1.0     MIT
Protobuf.Text                        0.4.0     Apache-2.0
ScottPlot                            5.0.47    MIT
ScottPlot.WinForms                   5.0.47    MIT
SkiaSharp                            2.88.9    MIT
SkiaSharp.HarfBuzz                   2.88.9    MIT
SkiaSharp.NativeAssets.*             2.88.9    MIT
SkiaSharp.Views.*                    2.88.9    MIT
SQLitePCLRaw.bundle_e_sqlite3        2.1.6     Apache-2.0
SQLitePCLRaw.core                    2.1.6     Apache-2.0
SQLitePCLRaw.lib.e_sqlite3           2.1.6     Apache-2.0
SQLitePCLRaw.provider.dynamic_cdecl  2.1.6     Apache-2.0
System.*  (NuGet / .NET Foundation)  various   MIT
TensorFlow.NET                       0.20.1    Apache-2.0

* Accord packages are licensed under LGPL-2.1. They are used here as
  dynamically linked assemblies via standard NuGet references, which
  satisfies the LGPL dynamic-linking requirement. The LGPL-2.1 license
  text is available at: https://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt

========================================================================
CSMSL (C# Mass Spectrometry Library)
========================================================================
Copyright (c) Derek Bailey
License: Apache-2.0
Source:  https://github.com/dbaileychess/CSMSL

========================================================================
RAWFILEREADER (Thermo Fisher Scientific)
========================================================================
Package: RawFileReader (MSFileReader)
Copyright (c) 2016 Thermo Fisher Scientific, Inc.
License: Proprietary (Thermo Finnigan LLC)
All rights reserved.

SOFTWARE LICENSE AGREEMENT ("License") FOR RawFileReader

These License terms are an agreement between you and Thermo Finnigan LLC
("Licensor"). They apply to Licensor's MSFileReader software program
("Software"), which includes documentation and any media on which you
received it. These terms also apply to any updates or supplements for this
Software, unless other terms accompany those items, in which case those
terms apply. If you use this Software, you accept this License. If you do
not accept this License, you are prohibited from using this software. If
you comply with these License terms, you have the rights set forth below.

1. Rights Granted:

1.1. You may install and use this Software on any of your computing
devices.

1.2. You may distribute this Software to others, but only in combination
with other software components and/or programs that you provide and
subject to the distribution requirements and restrictions below.

2. Use Restrictions:

2.1. You may not decompile, disassemble, reverse engineer, use reflection
or modify this Software.

3. Distribution Requirements:

If you distribute this Software to others, you agree to:

3.1. Indemnify, defend and hold harmless the Licensor from any claims,
including attorneys' fees, related to the distribution or use of this
Software;

3.2. Display the following text in your software's "About" box:
"RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher
Scientific, Inc. All rights reserved.";

3.3. Require your end users to agree to a license agreement that prohibits
them from redistributing this Software to others.

4. Distribution Restrictions:

4.1. You may not use the Licensor's trademarks in a way that suggests your
software components and/or programs are provided by or are endorsed by the
Licensor; and

4.2. You may not commercially exploit this Software or products that
incorporate this Software without the prior written consent of Licensor.
Commercial exploitation includes, but is not limited to, charging a
purchase price, license fee, maintenance fee, or subscription fee; or
licensing, transferring or redistributing the Software in exchange for
consideration of any kind.

4.3. Your rights to this Software do not include any license, right, power
or authority to subject this Software in whole or in part to any of the
terms of an Excluded License. "Excluded License" means any license that
requires as a condition of use, modification and/or distribution of
software subject to the Excluded License, that such software or other
software combined and/or distributed with such software be (a) disclosed
or distributed in source code form; or (b) licensed for the purpose of
making derivative works. Without limiting the foregoing obligation, you are
specifically prohibited from distributing this Software with any software
that is subject to the General Public License (GPL) or similar license in a
manner that would create a combined work.

5. Additional Terms Applicable to Software:

5.1. This Software is licensed, not sold. This License only gives you some
rights to use this Software; the Licensor reserves all other rights. Unless
applicable law gives you more rights despite this limitation, you may use
this Software only as expressly permitted in this License.

5.2. Licensor has no obligation to fix, update, supplement or support this
Software.

5.3. This Software is not designed, manufactured or intended for any use
requiring fail-safe performance in which the failure of this Software could
lead to death, serious personal injury or severe physical and environmental
damage ("High Risk Activities"), such as the operation of aircraft, medical
or nuclear facilities. You agree not to use, or license the use of, this
Software in connection with any High Risk Activities.

5.4. Your rights under this License terminate automatically if you breach
this License in any way. Termination of this License will not affect any of
your obligations or liabilities arising prior to termination. The following
sections of this License shall survive termination: 2.1, 3.1, 3.2, 3.3,
4.1, 4.2, 4.3, 5.1, 5.2, 5.3, 5.5, 5.6, 5.7, 5.8, and 5.9.

5.5. This Software is subject to United States export laws and regulations.
You agree to comply with all domestic and international export laws and
regulations that apply to this Software. These laws include restrictions on
destinations, end users and end use.

5.6. This License shall be construed and controlled by the laws of the
State of California, U.S.A., without regard to conflicts of law. You
consent to the jurisdiction of the state and federal courts situated in the
State of California in any action arising under this License. The
application of the U.N. Convention on Contracts for the International Sale
of Goods to this License is hereby expressly excluded. If any provision of
this License shall be deemed unenforceable or contrary to law, the rest of
this License shall remain in full effect and interpreted in an enforceable
manner that most nearly captures the intent of the original language.

5.7. THIS SOFTWARE IS LICENSED "AS IS". YOU BEAR ALL RISKS OF USING IT.
LICENSOR GIVES NO AND DISCLAIMS ALL EXPRESS AND IMPLIED WARRANTIES,
REPRESENTATIONS OR GUARANTEES. YOU MAY HAVE ADDITIONAL CONSUMER RIGHTS
UNDER YOUR LOCAL LAWS WHICH THIS LICENSE CANNOT CHANGE. TO THE EXTENT
PERMITTED UNDER YOUR LOCAL LAWS, LICENSOR EXCLUDES THE IMPLIED WARRANTIES
OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT.

5.8. LICENSOR'S TOTAL LIABILITY TO YOU FOR DIRECT DAMAGES ARISING UNDER
THIS LICENSE IS LIMITED TO U.S. $1.00. YOU CANNOT RECOVER ANY OTHER
DAMAGES, INCLUDING CONSEQUENTIAL, LOST PROFITS, SPECIAL, INDIRECT OR
INCIDENTAL DAMAGES, EVEN IF LICENSOR IS EXPRESSLY MADE AWARE OF THE
POSSIBILITY THEREOF OR IS NEGLIGENT. THIS LIMITATION APPLIES TO ANYTHING
RELATED TO THIS SOFTWARE, SERVICES, CONTENT (INCLUDING CODE) ON THIRD
PARTY INTERNET SITES, OR THIRD PARTY PROGRAMS, AND CLAIMS FOR BREACH OF
CONTRACT, BREACH OF WARRANTY, GUARANTEE OR CONDITION, STRICT LIABILITY,
NEGLIGENCE, OR OTHER TORT TO THE EXTENT PERMITTED BY APPLICABLE LAW.

5.9. Use, duplication or disclosure of this Software by the U.S. Government
is subject to the restricted rights applicable to commercial computer
software (under FAR 52.227019 and DFARS 252.227-7013 or parallel
regulations). The manufacturer for this purpose is Thermo Finnigan LLC,
355 River Oaks Parkway, San Jose, California 95134, U.S.A.

========================================================================
ACCORD.NET FRAMEWORK
========================================================================
Packages: Accord, Accord.MachineLearning, Accord.Math, Accord.Statistics
Version:  3.8.0
Copyright (c) 2011-2017 Cesar Souza
License:  GNU Lesser General Public License v2.1 (LGPL-2.1)
Source:   https://github.com/accord-net/framework
Full license text: https://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt

Note: These libraries are used as dynamically-linked assemblies. End users
may replace the Accord DLLs with modified versions compiled from the
source code available at the URL above.

========================================================================
GOOGLE APIS CLIENT LIBRARY FOR .NET
========================================================================
Packages: Google.Apis, Google.Apis.Auth, Google.Apis.Core
Version:  1.46.0
Copyright (c) Google LLC
License:  Apache-2.0
Source:   https://github.com/googleapis/google-api-dotnet-client

========================================================================
GOOGLE PROTOCOL BUFFERS
========================================================================
Package: Google.Protobuf
Version: 3.24.4
Copyright (c) 2015, Google Inc.
License: BSD-3-Clause
Source:  https://github.com/protocolbuffers/protobuf

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.
3. Neither the name of Google Inc. 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.

========================================================================
GRPC
========================================================================
Packages: Grpc, Grpc.Core, Grpc.Core.Api
Version:  2.44.0
Copyright (c) gRPC Authors
License:  Apache-2.0
Source:   https://github.com/grpc/grpc

========================================================================
HARFBUZZSHARP
========================================================================
Packages: HarfBuzzSharp, HarfBuzzSharp.NativeAssets.*
Version:  7.3.0.3
Copyright (c) The HarfBuzz Project, Microsoft Corporation
License:  MIT
Source:   https://github.com/mono/SkiaSharp

========================================================================
LIGHTGBM
========================================================================
Package: LightGBM
Version: 2.3.1
Copyright (c) Microsoft Corporation
License: MIT
Source:  https://github.com/microsoft/LightGBM

========================================================================
LUMENWORKS CSV READER
========================================================================
Package: LumenWorksCsvReader
Version: 4.0.0
Copyright (c) 2005 Sebastien Lorion
License: MIT
Source:  https://github.com/phatcher/CsvReader

========================================================================
MICROSOFT.DATA.SQLITE
========================================================================
Packages: Microsoft.Data.Sqlite, Microsoft.Data.Sqlite.Core
Version:  8.0.1
Copyright (c) Microsoft Corporation
License:  MIT
Source:   https://github.com/dotnet/efcore

========================================================================
MICROSOFT.EXTENSIONS.LOGGING
========================================================================
Package: Microsoft.Extensions.Logging.Abstractions
Version: 3.0.3
Copyright (c) Microsoft Corporation
License: MIT
Source:  https://github.com/dotnet/extensions

========================================================================
ML.NET
========================================================================
Packages: Microsoft.ML, Microsoft.ML.CpuMath, Microsoft.ML.DataView,
          Microsoft.ML.FastTree, Microsoft.ML.LightGbm,
          Microsoft.ML.OnnxRuntime, Microsoft.ML.OnnxRuntime.Managed,
          Microsoft.ML.OnnxTransformer, Microsoft.ML.TensorFlow
Version:  1.6.0 / 1.8.1
Copyright (c) .NET Foundation and Contributors
License:  MIT
Source:   https://github.com/dotnet/machinelearning

========================================================================
NEWTONSOFT.JSON
========================================================================
Package: Newtonsoft.Json
Version: 13.0.1
Copyright (c) 2007 James Newton-King
License: MIT
Source:  https://github.com/JamesNK/Newtonsoft.Json

========================================================================
NUMSHARP.LITE
========================================================================
Package: NumSharp.Lite
Version: 0.1.8
Copyright (c) 2018 The SciSharp Stack
License: Apache-2.0
Source:  https://github.com/SciSharp/NumSharp

========================================================================
OPENTK
========================================================================
Packages: OpenTK, OpenTK.GLControl
Version:  3.1.0
Copyright (c) 2006-2020 the OpenTK contributors
License:  MIT
Source:   https://github.com/opentk/opentk

========================================================================
PROTOBUF.TEXT
========================================================================
Package: Protobuf.Text
Version: 0.4.0
License: Apache-2.0
Source:  https://github.com/googleapis/protobuf-text-format

========================================================================
SCOTTPLOT
========================================================================
Packages: ScottPlot, ScottPlot.WinForms
Version:  5.0.47
Copyright (c) Scott W Harden
License:  MIT
Source:   https://github.com/ScottPlot/ScottPlot

========================================================================
SKIASHARP
========================================================================
Packages: SkiaSharp, SkiaSharp.HarfBuzz, SkiaSharp.NativeAssets.*,
          SkiaSharp.Views.Desktop.Common, SkiaSharp.Views.WindowsForms
Version:  2.88.9
Copyright (c) Microsoft Corporation
License:  MIT
Source:   https://github.com/mono/SkiaSharp

========================================================================
SQLITEPCLRAW
========================================================================
Packages: SQLitePCLRaw.bundle_e_sqlite3, SQLitePCLRaw.core,
          SQLitePCLRaw.lib.e_sqlite3, SQLitePCLRaw.provider.dynamic_cdecl
Version:  2.1.6
Copyright (c) 2014-2021 Zumero, LLC (Eric Sink)
License:  Apache-2.0
Source:   https://github.com/ericsink/SQLitePCL.raw

========================================================================
SYSTEM.* / .NET FOUNDATION PACKAGES
========================================================================
Packages: System.Buffers, System.CodeDom, System.Collections.*,
          System.Diagnostics.*, System.IO.*, System.Linq.*,
          System.Memory, System.Net.*, System.Numerics.Vectors,
          System.Reflection.*, System.Runtime.*,
          System.Security.*, System.Text.*, System.Threading.*,
          System.ValueTuple, System.Xml.*, NETStandard.Library,
          Microsoft.NETCore.Platforms, Microsoft.Win32.Primitives
Copyright (c) .NET Foundation and Contributors
License:  MIT
Source:   https://github.com/dotnet/runtime

========================================================================
TENSORFLOW.NET
========================================================================
Package: TensorFlow.NET
Version: 0.20.1
Copyright (c) 2019 The SciSharp Stack
License: Apache-2.0
Source:  https://github.com/SciSharp/TensorFlow.NET

========================================================================
APACHE LICENSE 2.0 (reference copy)
========================================================================
Full text: https://www.apache.org/licenses/LICENSE-2.0

Applies to: CSMSL, Google.Apis.*, Grpc.*, NumSharp.Lite, Protobuf.Text,
            SQLitePCLRaw.*, TensorFlow.NET

========================================================================
MIT LICENSE (reference copy)
========================================================================
Full text: https://opensource.org/licenses/MIT

Applies to: HarfBuzzSharp, LightGBM, LumenWorksCsvReader,
            Microsoft.Data.Sqlite, Microsoft.Extensions.Logging.*,
            Microsoft.ML.*, Newtonsoft.Json, OpenTK, ScottPlot,
            SkiaSharp, System.* / .NET Foundation packages