LICENSE

   Copyright 2012 Jimmy Eng

   This project is licensed under the Apache License, Version 2.0, except
   where otherwise noted.

   ---
   
                                 Apache License
                           Version 2.0, January 2004
                        http://www.apache.org/licenses/

   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION

   1. Definitions.

      "License" shall mean the terms and conditions for use, reproduction,
      and distribution as defined by Sections 1 through 9 of this document.

      "Licensor" shall mean the copyright owner or entity authorized by
      the copyright owner that is granting the License.

      "Legal Entity" shall mean the union of the acting entity and all
      other entities that control, are controlled by, or are under common
      control with that entity. For the purposes of this definition,
      "control" means (i) the power, direct or indirect, to cause the
      direction or management of such entity, whether by contract or
      otherwise, or (ii) ownership of fifty percent (50%) or more of the
      outstanding shares, or (iii) beneficial ownership of such entity.

      "You" (or "Your") shall mean an individual or Legal Entity
      exercising permissions granted by this License.

      "Source" form shall mean the preferred form for making modifications,
      including but not limited to software source code, documentation
      source, and configuration files.

      "Object" form shall mean any form resulting from mechanical
      transformation or translation of a Source form, including but
      not limited to compiled object code, generated documentation,
      and conversions to other media types.

      "Work" shall mean the work of authorship, whether in Source or
      Object form, made available under the License, as indicated by a
      copyright notice that is included in or attached to the work
      (an example is provided in the Appendix below).

      "Derivative Works" shall mean any work, whether in Source or Object
      form, that is based on (or derived from) the Work and for which the
      editorial revisions, annotations, elaborations, or other modifications
      represent, as a whole, an original work of authorship. For the purposes
      of this License, Derivative Works shall not include works that remain
      separable from, or merely link (or bind by name) to the interfaces of,
      the Work and Derivative Works thereof.

      "Contribution" shall mean any work of authorship, including
      the original version of the Work and any modifications or additions
      to that Work or Derivative Works thereof, that is intentionally
      submitted to Licensor for inclusion in the Work by the copyright owner
      or by an individual or Legal Entity authorized to submit on behalf of
      the copyright owner. For the purposes of this definition, "submitted"
      means any form of electronic, verbal, or written communication sent
      to the Licensor or its representatives, including but not limited to
      communication on electronic mailing lists, source code control systems,
      and issue tracking systems that are managed by, or on behalf of, the
      Licensor for the purpose of discussing and improving the Work, but
      excluding communication that is conspicuously marked or otherwise
      designated in writing by the copyright owner as "Not a Contribution."

      "Contributor" shall mean Licensor and any individual or Legal Entity
      on behalf of whom a Contribution has been received by Licensor and
      subsequently incorporated within the Work.

   2. Grant of Copyright License. Subject to the terms and conditions of
      this License, each Contributor hereby grants to You a perpetual,
      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
      copyright license to reproduce, prepare Derivative Works of,
      publicly display, publicly perform, sublicense, and distribute the
      Work and such Derivative Works in Source or Object form.

   3. Grant of Patent License. Subject to the terms and conditions of
      this License, each Contributor hereby grants to You a perpetual,
      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
      (except as stated in this section) patent license to make, have made,
      use, offer to sell, sell, import, and otherwise transfer the Work,
      where such license applies only to those patent claims licensable
      by such Contributor that are necessarily infringed by their
      Contribution(s) alone or by combination of their Contribution(s)
      with the Work to which such Contribution(s) was submitted. If You
      institute patent litigation against any entity (including a
      cross-claim or counterclaim in a lawsuit) alleging that the Work
      or a Contribution incorporated within the Work constitutes direct
      or contributory patent infringement, then any patent licenses
      granted to You under this License for that Work shall terminate
      as of the date such litigation is filed.

   4. Redistribution. You may reproduce and distribute copies of the
      Work or Derivative Works thereof in any medium, with or without
      modifications, and in Source or Object form, provided that You
      meet the following conditions:

      (a) You must give any other recipients of the Work or
          Derivative Works a copy of this License; and

      (b) You must cause any modified files to carry prominent notices
          stating that You changed the files; and

      (c) You must retain, in the Source form of any Derivative Works
          that You distribute, all copyright, patent, trademark, and
          attribution notices from the Source form of the Work,
          excluding those notices that do not pertain to any part of
          the Derivative Works; and

      (d) If the Work includes a "NOTICE" text file as part of its
          distribution, then any Derivative Works that You distribute must
          include a readable copy of the attribution notices contained
          within such NOTICE file, excluding those notices that do not
          pertain to any part of the Derivative Works, in at least one
          of the following places: within a NOTICE text file distributed
          as part of the Derivative Works; within the Source form or
          documentation, if provided along with the Derivative Works; or,
          within a display generated by the Derivative Works, if and
          wherever such third-party notices normally appear. The contents
          of the NOTICE file are for informational purposes only and
          do not modify the License. You may add Your own attribution
          notices within Derivative Works that You distribute, alongside
          or as an addendum to the NOTICE text from the Work, provided
          that such additional attribution notices cannot be construed
          as modifying the License.

      You may add Your own copyright statement to Your modifications and
      may provide additional or different license terms and conditions
      for use, reproduction, or distribution of Your modifications, or
      for any such Derivative Works as a whole, provided Your use,
      reproduction, and distribution of the Work otherwise complies with
      the conditions stated in this License.

   5. Submission of Contributions. Unless You explicitly state otherwise,
      any Contribution intentionally submitted for inclusion in the Work
      by You to the Licensor shall be under the terms and conditions of
      this License, without any additional terms or conditions.
      Notwithstanding the above, nothing herein shall supersede or modify
      the terms of any separate license agreement you may have executed
      with Licensor regarding such Contributions.

   6. Trademarks. This License does not grant permission to use the trade
      names, trademarks, service marks, or product names of the Licensor,
      except as required for reasonable and customary use in describing the
      origin of the Work and reproducing the content of the NOTICE file.

   7. Disclaimer of Warranty. Unless required by applicable law or
      agreed to in writing, Licensor provides the Work (and each
      Contributor provides its Contributions) on an "AS IS" BASIS,
      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
      implied, including, without limitation, any warranties or conditions
      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
      PARTICULAR PURPOSE. You are solely responsible for determining the
      appropriateness of using or redistributing the Work and assume any
      risks associated with Your exercise of permissions under this License.

   8. Limitation of Liability. In no event and under no legal theory,
      whether in tort (including negligence), contract, or otherwise,
      unless required by applicable law (such as deliberate and grossly
      negligent acts) or agreed to in writing, shall any Contributor be
      liable to You for damages, including any direct, indirect, special,
      incidental, or consequential damages of any character arising as a
      result of this License or out of the use or inability to use the
      Work (including but not limited to damages for loss of goodwill,
      work stoppage, computer failure or malfunction, or any and all
      other commercial damages or losses), even if such Contributor
      has been advised of the possibility of such damages.

   9. Accepting Warranty or Additional Liability. While redistributing
      the Work or Derivative Works thereof, You may choose to offer,
      and charge a fee for, acceptance of support, warranty, indemnity,
      or other liability obligations and/or rights consistent with this
      License. However, in accepting such obligations, You may act only
      on Your own behalf and on Your sole responsibility, not on behalf
      of any other Contributor, and only if You agree to indemnify,
      defend, and hold each Contributor harmless for any liability
      incurred by, or claims asserted against, such Contributor by reason
      of your accepting any such warranty or additional liability.

   END OF TERMS AND CONDITIONS

   ---

   This project includes third-party components:

   - Component:        MSToolkit
   - Original Author:  Michael Hoopmann
   - Original Source:  https://github.com/mhoopmann/mstoolkit/
   - Original License: Apache 2.0

   - Component:        twiddle.c
   - Original Author:  Matthew Belmonte
   - Original Source:  https://www.netlib.org/toms-2014-06-10/382
   - Original License: permission to use; maintain copyright notice

   - Component:        AScorePro
   - Original Author:  Gygi lab and code authors
   - Original Source:  https://github.com/gygilab/MPToolkit/
   - Original License: MIT License (included below)
   - NOTE:  AScorepro was translated to C++ by Vagisha Sharma. The original
            MIT License still applies to the logic, structure, and design
            of this code.
			
   - Component:        BS::thread_pool (BS_thread_pool.hpp)
   - Original Author:  Barak Shoshany
   - Original Source:  https://github.com/bshoshany/thread-pool
   - Original License: MIT License (included below)
   
   - Component:        RawFileReader
   - Original Author:  Thermo Finnigan LLC
   - Original Source:  https://github.com/thermofisherlsms/RawFileReader
   - Original License: license terms below
			

   ---
   
   ### MIT License (for MPToolkit and BS::thread_pool)
   
   Copyright (c) 2022 Gygi Lab and the code authors.
   
   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.
   

   ### 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 © 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.