Percolator
Copyright 2006-present Lukas Käll and Percolator contributors
https://github.com/percolator/percolator

This product includes software developed by Percolator contributors.
Licensed under the Apache License, Version 2.0 (see LICENSE-Apache-2.0.txt).

Modifications from upstream:
  - Stripped XML/pin, tab-file, CLI, and protein-inference code
  - Wrapped all vendored declarations in OpenMS::Internal::Percolator::
  - Replaced Logger.h with a shim that routes through OpenMS's OPENMS_LOG_*
  - Removed CMake-generated config.h / Version.h in favor of in-tree stubs
  - Added constructor extension on DataSet to accept externally-supplied
    cross-validation grouping keys (for domain-agnostic use)

Embedded TRON solver (ssl.h, ssl.cpp, tron.h, tron.cpp):
  ssl.{cpp,h} are an OpenMS-local replacement of the legacy SVMlin-based
  L2-SVM-MFN solver. They wrap the TRON optimizer with Percolator's
  L2-loss SVM cost function (per-class costs C_i = c_i / (2*lambda)).
  Sourced from John Halloran's percolator-tron development branch
  (https://bitbucket.org/jthalloran/percolator_upgrade), retired the
  SVMlin path entirely.

  tron.{cpp,h} are a near-verbatim copy of liblinear v2.11's TRON
  optimizer (https://github.com/cjlin1/liblinear, downloaded April 2017
  per Halloran & Rocke 2018), distributed by the LIBLINEAR project under
  the BSD 3-Clause License.

    Copyright (c) 2007-2015 The LIBLINEAR Project. All rights reserved.

    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 name of copyright holders 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 REGENTS 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.

  Algorithmic references:
    Lin, Weng, Keerthi (2008), "Trust Region Newton Method for
      Large-Scale Logistic Regression", JMLR 9:627-650.
    Halloran & Rocke (2018), "A Matter of Time: Faster Percolator
      Analysis via Efficient SVM Learning for Large-Scale Proteomics",
      J. Proteome Res. 17(5):1978-1982.

  Embedded Timer files (Timer.h, Timer.cpp): Apache-2.0 (Percolator).
