libgunshotmatch 1.0.0__tar.gz

libgunshotmatch-1.0.0/LICENSE

@@ -0,0 +1,19 @@
+Copyright (c) 2023 Dominic Davis-Foster
+
+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.

libgunshotmatch-1.0.0/PKG-INFO

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+Metadata-Version: 2.2
+Name: libgunshotmatch
+Version: 1.0.0
+Summary: Base library for GunShotMatch.
+Author-email: Dominic Davis-Foster <dominic@davis-foster.co.uk>
+License: MIT
+Home-page: https://github.com/GunShotMatch/libgunshotmatch
+Project-URL: Issue Tracker, https://github.com/GunShotMatch/libgunshotmatch/issues
+Project-URL: Source Code, https://github.com/GunShotMatch/libgunshotmatch
+Project-URL: Documentation, https://libgunshotmatch.readthedocs.io/en/latest
+Platform: Windows
+Platform: macOS
+Platform: Linux
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Typing :: Typed
+Requires-Python: >=3.8
+Requires-Dist: attrs>=23.1.0
+Requires-Dist: chemistry-tools>=v1.0.0b2
+Requires-Dist: dom-toml[config]>=2.2.0
+Requires-Dist: domdf-python-tools>=3.6.1
+Requires-Dist: enum-tools>=0.10.0
+Requires-Dist: mathematical>=0.5.1
+Requires-Dist: numpy>=1.22
+Requires-Dist: pandas>=2.0.3
+Requires-Dist: pymassspec>=2.3.0
+Requires-Dist: pyms-nist-search>=0.6.1
+Requires-Dist: scipy>=1.9.0
+Requires-Dist: sdjson>=0.4.0
+Requires-Dist: tomli>=1.2.3; python_version < "3.11"
+Requires-Dist: tomli-w>=1.0.0
+Requires-Dist: typing-extensions>=4.12.2
+Description-Content-Type: text/x-rst
+
+
+================
+libgunshotmatch
+================
+
+.. start short_desc
+
+**Base library for GunShotMatch.**
+
+.. end short_desc
+
+
+.. start shields
+
+.. list-table::
+	:stub-columns: 1
+	:widths: 10 90
+
+	* - Docs
+	  - |docs| |docs_check|
+	* - Tests
+	  - |actions_linux| |actions_windows| |actions_macos| |coveralls|
+	* - PyPI
+	  - |pypi-version| |supported-versions| |supported-implementations| |wheel|
+	* - Activity
+	  - |commits-latest| |commits-since| |maintained| |pypi-downloads|
+	* - QA
+	  - |codefactor| |actions_flake8| |actions_mypy|
+	* - Other
+	  - |license| |language| |requires|
+
+.. |docs| image:: https://img.shields.io/readthedocs/libgunshotmatch/latest?logo=read-the-docs
+	:target: https://libgunshotmatch.readthedocs.io/en/latest
+	:alt: Documentation Build Status
+
+.. |docs_check| image:: https://github.com/GunShotMatch/libgunshotmatch/workflows/Docs%20Check/badge.svg
+	:target: https://github.com/GunShotMatch/libgunshotmatch/actions?query=workflow%3A%22Docs+Check%22
+	:alt: Docs Check Status
+
+.. |actions_linux| image:: https://github.com/GunShotMatch/libgunshotmatch/workflows/Linux/badge.svg
+	:target: https://github.com/GunShotMatch/libgunshotmatch/actions?query=workflow%3A%22Linux%22
+	:alt: Linux Test Status
+
+.. |actions_windows| image:: https://github.com/GunShotMatch/libgunshotmatch/workflows/Windows/badge.svg
+	:target: https://github.com/GunShotMatch/libgunshotmatch/actions?query=workflow%3A%22Windows%22
+	:alt: Windows Test Status
+
+.. |actions_macos| image:: https://github.com/GunShotMatch/libgunshotmatch/workflows/macOS/badge.svg
+	:target: https://github.com/GunShotMatch/libgunshotmatch/actions?query=workflow%3A%22macOS%22
+	:alt: macOS Test Status
+
+.. |actions_flake8| image:: https://github.com/GunShotMatch/libgunshotmatch/workflows/Flake8/badge.svg
+	:target: https://github.com/GunShotMatch/libgunshotmatch/actions?query=workflow%3A%22Flake8%22
+	:alt: Flake8 Status
+
+.. |actions_mypy| image:: https://github.com/GunShotMatch/libgunshotmatch/workflows/mypy/badge.svg
+	:target: https://github.com/GunShotMatch/libgunshotmatch/actions?query=workflow%3A%22mypy%22
+	:alt: mypy status
+
+.. |requires| image:: https://dependency-dash.repo-helper.uk/github/GunShotMatch/libgunshotmatch/badge.svg
+	:target: https://dependency-dash.repo-helper.uk/github/GunShotMatch/libgunshotmatch/
+	:alt: Requirements Status
+
+.. |coveralls| image:: https://img.shields.io/coveralls/github/GunShotMatch/libgunshotmatch/master?logo=coveralls
+	:target: https://coveralls.io/github/GunShotMatch/libgunshotmatch?branch=master
+	:alt: Coverage
+
+.. |codefactor| image:: https://img.shields.io/codefactor/grade/github/GunShotMatch/libgunshotmatch?logo=codefactor
+	:target: https://www.codefactor.io/repository/github/GunShotMatch/libgunshotmatch
+	:alt: CodeFactor Grade
+
+.. |pypi-version| image:: https://img.shields.io/pypi/v/libgunshotmatch
+	:target: https://pypi.org/project/libgunshotmatch/
+	:alt: PyPI - Package Version
+
+.. |supported-versions| image:: https://img.shields.io/pypi/pyversions/libgunshotmatch?logo=python&logoColor=white
+	:target: https://pypi.org/project/libgunshotmatch/
+	:alt: PyPI - Supported Python Versions
+
+.. |supported-implementations| image:: https://img.shields.io/pypi/implementation/libgunshotmatch
+	:target: https://pypi.org/project/libgunshotmatch/
+	:alt: PyPI - Supported Implementations
+
+.. |wheel| image:: https://img.shields.io/pypi/wheel/libgunshotmatch
+	:target: https://pypi.org/project/libgunshotmatch/
+	:alt: PyPI - Wheel
+
+.. |license| image:: https://img.shields.io/github/license/GunShotMatch/libgunshotmatch
+	:target: https://github.com/GunShotMatch/libgunshotmatch/blob/master/LICENSE
+	:alt: License
+
+.. |language| image:: https://img.shields.io/github/languages/top/GunShotMatch/libgunshotmatch
+	:alt: GitHub top language
+
+.. |commits-since| image:: https://img.shields.io/github/commits-since/GunShotMatch/libgunshotmatch/v1.0.0
+	:target: https://github.com/GunShotMatch/libgunshotmatch/pulse
+	:alt: GitHub commits since tagged version
+
+.. |commits-latest| image:: https://img.shields.io/github/last-commit/GunShotMatch/libgunshotmatch
+	:target: https://github.com/GunShotMatch/libgunshotmatch/commit/master
+	:alt: GitHub last commit
+
+.. |maintained| image:: https://img.shields.io/maintenance/yes/2026
+	:alt: Maintenance
+
+.. |pypi-downloads| image:: https://img.shields.io/pypi/dm/libgunshotmatch
+	:target: https://pypistats.org/packages/libgunshotmatch
+	:alt: PyPI - Downloads
+
+.. end shields
+
+Installation
+--------------
+
+.. start installation
+
+``libgunshotmatch`` can be installed from PyPI.
+
+To install with ``pip``:
+
+.. code-block:: bash
+
+	$ python -m pip install libgunshotmatch
+
+.. end installation

libgunshotmatch-1.0.0/README.rst

@@ -0,0 +1,124 @@
+================
+libgunshotmatch
+================
+
+.. start short_desc
+
+**Base library for GunShotMatch.**
+
+.. end short_desc
+
+
+.. start shields
+
+.. list-table::
+	:stub-columns: 1
+	:widths: 10 90
+
+	* - Docs
+	  - |docs| |docs_check|
+	* - Tests
+	  - |actions_linux| |actions_windows| |actions_macos| |coveralls|
+	* - PyPI
+	  - |pypi-version| |supported-versions| |supported-implementations| |wheel|
+	* - Activity
+	  - |commits-latest| |commits-since| |maintained| |pypi-downloads|
+	* - QA
+	  - |codefactor| |actions_flake8| |actions_mypy|
+	* - Other
+	  - |license| |language| |requires|
+
+.. |docs| image:: https://img.shields.io/readthedocs/libgunshotmatch/latest?logo=read-the-docs
+	:target: https://libgunshotmatch.readthedocs.io/en/latest
+	:alt: Documentation Build Status
+
+.. |docs_check| image:: https://github.com/GunShotMatch/libgunshotmatch/workflows/Docs%20Check/badge.svg
+	:target: https://github.com/GunShotMatch/libgunshotmatch/actions?query=workflow%3A%22Docs+Check%22
+	:alt: Docs Check Status
+
+.. |actions_linux| image:: https://github.com/GunShotMatch/libgunshotmatch/workflows/Linux/badge.svg
+	:target: https://github.com/GunShotMatch/libgunshotmatch/actions?query=workflow%3A%22Linux%22
+	:alt: Linux Test Status
+
+.. |actions_windows| image:: https://github.com/GunShotMatch/libgunshotmatch/workflows/Windows/badge.svg
+	:target: https://github.com/GunShotMatch/libgunshotmatch/actions?query=workflow%3A%22Windows%22
+	:alt: Windows Test Status
+
+.. |actions_macos| image:: https://github.com/GunShotMatch/libgunshotmatch/workflows/macOS/badge.svg
+	:target: https://github.com/GunShotMatch/libgunshotmatch/actions?query=workflow%3A%22macOS%22
+	:alt: macOS Test Status
+
+.. |actions_flake8| image:: https://github.com/GunShotMatch/libgunshotmatch/workflows/Flake8/badge.svg
+	:target: https://github.com/GunShotMatch/libgunshotmatch/actions?query=workflow%3A%22Flake8%22
+	:alt: Flake8 Status
+
+.. |actions_mypy| image:: https://github.com/GunShotMatch/libgunshotmatch/workflows/mypy/badge.svg
+	:target: https://github.com/GunShotMatch/libgunshotmatch/actions?query=workflow%3A%22mypy%22
+	:alt: mypy status
+
+.. |requires| image:: https://dependency-dash.repo-helper.uk/github/GunShotMatch/libgunshotmatch/badge.svg
+	:target: https://dependency-dash.repo-helper.uk/github/GunShotMatch/libgunshotmatch/
+	:alt: Requirements Status
+
+.. |coveralls| image:: https://img.shields.io/coveralls/github/GunShotMatch/libgunshotmatch/master?logo=coveralls
+	:target: https://coveralls.io/github/GunShotMatch/libgunshotmatch?branch=master
+	:alt: Coverage
+
+.. |codefactor| image:: https://img.shields.io/codefactor/grade/github/GunShotMatch/libgunshotmatch?logo=codefactor
+	:target: https://www.codefactor.io/repository/github/GunShotMatch/libgunshotmatch
+	:alt: CodeFactor Grade
+
+.. |pypi-version| image:: https://img.shields.io/pypi/v/libgunshotmatch
+	:target: https://pypi.org/project/libgunshotmatch/
+	:alt: PyPI - Package Version
+
+.. |supported-versions| image:: https://img.shields.io/pypi/pyversions/libgunshotmatch?logo=python&logoColor=white
+	:target: https://pypi.org/project/libgunshotmatch/
+	:alt: PyPI - Supported Python Versions
+
+.. |supported-implementations| image:: https://img.shields.io/pypi/implementation/libgunshotmatch
+	:target: https://pypi.org/project/libgunshotmatch/
+	:alt: PyPI - Supported Implementations
+
+.. |wheel| image:: https://img.shields.io/pypi/wheel/libgunshotmatch
+	:target: https://pypi.org/project/libgunshotmatch/
+	:alt: PyPI - Wheel
+
+.. |license| image:: https://img.shields.io/github/license/GunShotMatch/libgunshotmatch
+	:target: https://github.com/GunShotMatch/libgunshotmatch/blob/master/LICENSE
+	:alt: License
+
+.. |language| image:: https://img.shields.io/github/languages/top/GunShotMatch/libgunshotmatch
+	:alt: GitHub top language
+
+.. |commits-since| image:: https://img.shields.io/github/commits-since/GunShotMatch/libgunshotmatch/v1.0.0
+	:target: https://github.com/GunShotMatch/libgunshotmatch/pulse
+	:alt: GitHub commits since tagged version
+
+.. |commits-latest| image:: https://img.shields.io/github/last-commit/GunShotMatch/libgunshotmatch
+	:target: https://github.com/GunShotMatch/libgunshotmatch/commit/master
+	:alt: GitHub last commit
+
+.. |maintained| image:: https://img.shields.io/maintenance/yes/2026
+	:alt: Maintenance
+
+.. |pypi-downloads| image:: https://img.shields.io/pypi/dm/libgunshotmatch
+	:target: https://pypistats.org/packages/libgunshotmatch
+	:alt: PyPI - Downloads
+
+.. end shields
+
+Installation
+--------------
+
+.. start installation
+
+``libgunshotmatch`` can be installed from PyPI.
+
+To install with ``pip``:
+
+.. code-block:: bash
+
+	$ python -m pip install libgunshotmatch
+
+.. end installation

libgunshotmatch-1.0.0/libgunshotmatch/__init__.py

@@ -0,0 +1,33 @@
+#!/usr/bin/env python3
+#
+#  __init__.py
+"""
+Base library for GunShotMatch.
+"""
+#
+#  Copyright © 2020-2023 Dominic Davis-Foster <dominic@davis-foster.co.uk>
+#
+#  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.
+#
+
+__author__: str = "Dominic Davis-Foster"
+__copyright__: str = "2020-2023 Dominic Davis-Foster"
+__license__: str = "MIT License"
+__version__: str = "1.0.0"
+__email__: str = "dominic@davis-foster.co.uk"

libgunshotmatch-1.0.0/libgunshotmatch/comparison/__init__.py

@@ -0,0 +1,116 @@
+#!/usr/bin/env python3
+#
+#  __init__.py
+"""
+Comparison between projects and unknowns.
+
+The two submodules, :mod:`~.comparison.projects` and :mod:`~.comparison.unknowns`,
+provide identical APIs with different internals to handle reference projects (containing two or more repeats)
+and unknown samples (from a single datafile).
+
+.. versionadded:: 0.8.0
+"""
+#
+#  Copyright © 2024 Dominic Davis-Foster <dominic@davis-foster.co.uk>
+#
+#  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.
+#
+
+# stdlib
+from typing import List, Sequence, Tuple, Union
+
+# 3rd party
+from pyms.DPA.Alignment import Alignment
+from pyms.DPA.PairwiseAlignment import PairwiseAlignment, align_with_tree
+
+# this package
+from libgunshotmatch.project import Project
+
+# this package
+from . import projects, unknowns
+from ._utils import _PaddedPeakList
+
+__all__ = ("align_projects", "get_padded_peak_lists")
+
+# Aliases to prevent clashes with argument names
+_projects_mod = projects
+_unknowns_mod = unknowns
+
+
+def align_projects(
+		projects: Union[Sequence[Project], Project] = (),
+		unknowns: Union[Sequence[Project], Project] = (),
+		D: float = 2.5,
+		gap: float = 0.3,
+		) -> Alignment:
+	"""
+	Align multiple projects and/or unknowns.
+
+	:param projects:
+	:param unknowns:
+	:param D: Retention time tolerance for pairwise alignments (in seconds).
+	:param gap: Gap penalty for pairwise alignments.
+
+	:rtype:
+
+	.. versionchanged:: 0.9.0
+
+		* Added ``D`` and ``gap`` arguments.
+		* ``projects`` and ``unknowns`` can now be a single :class:`~.Project`.
+	"""
+
+	if isinstance(projects, Project):
+		projects = [projects]
+
+	if isinstance(unknowns, Project):
+		unknowns = [unknowns]
+
+	project_alignments = map(_projects_mod.filter_alignment_to_consolidate, projects)
+	unknown_alignments = map(_unknowns_mod.filter_alignment_to_consolidate, unknowns)
+
+	pwa = PairwiseAlignment([*project_alignments, *unknown_alignments], D=float(D), gap=float(gap))
+	return align_with_tree(pwa)
+
+
+def get_padded_peak_lists(
+		alignment: Alignment,
+		projects: Union[Sequence[Project], Project] = (),
+		unknowns: Union[Sequence[Project], Project] = (),
+		) -> Tuple[List[_PaddedPeakList], List[_PaddedPeakList]]:
+	"""
+	Pad the consolidated peak lists in each project/unknown, from the given between-project alignment.
+
+	:param alignment:
+	:param projects:
+	:param unknowns:
+
+	.. versionchanged:: 0.9.0  ``projects`` and ``unknowns`` can now be a single :class:`~.Project`.
+	"""
+
+	if isinstance(projects, Project):
+		projects = [projects]
+
+	if isinstance(unknowns, Project):
+		unknowns = [unknowns]
+
+	data = alignment.get_peak_alignment(require_all_expr=False, minutes=False)
+
+	projects_padded_cp = [_projects_mod.get_padded_peak_list(p, data) for p in projects]
+	unknowns_padded_cp = [_unknowns_mod.get_padded_peak_list(p, data) for p in unknowns]
+	return projects_padded_cp, unknowns_padded_cp

libgunshotmatch-1.0.0/libgunshotmatch/comparison/_utils.py

@@ -0,0 +1,60 @@
+#!/usr/bin/env python3
+#
+#  _utils.py
+"""
+Utility functions.
+"""
+#
+#  Copyright © 2024 Dominic Davis-Foster <dominic@davis-foster.co.uk>
+#
+#  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.
+#
+
+# stdlib
+from typing import List, MutableSequence, Optional
+
+# 3rd party
+import numpy
+
+# this package
+from libgunshotmatch import project
+from libgunshotmatch.consolidate import ConsolidatedPeak
+
+_PaddedPeakList = MutableSequence[Optional[ConsolidatedPeak]]
+
+
+def _get_padded_peak_list(project: project.Project, rts: List[float]) -> _PaddedPeakList:
+
+	assert project.consolidated_peaks is not None
+
+	padded_cp_list: _PaddedPeakList = []
+
+	for cp in project.consolidated_peaks:
+		if rts:
+			top_rt = rts.pop(0)
+			while numpy.isnan(top_rt):
+				padded_cp_list.append(None)
+				if rts:
+					top_rt = rts.pop(0)
+				else:  # pragma: no cover
+					# We've run out of retention times
+					break
+		padded_cp_list.append(cp)
+
+	return padded_cp_list

libgunshotmatch-1.0.0/libgunshotmatch/comparison/projects.py

@@ -0,0 +1,93 @@
+#!/usr/bin/env python3
+#
+#  project.py
+"""
+Comparison between projects.
+"""
+#
+#  Copyright © 2024 Dominic Davis-Foster <dominic@davis-foster.co.uk>
+#
+#  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.
+#
+
+# 3rd party
+import numpy
+import pandas  # type: ignore[import-untyped]
+from pyms.DPA.Alignment import Alignment
+
+# this package
+from libgunshotmatch.project import Project
+from libgunshotmatch.utils import create_alignment
+
+# this package
+from ._utils import _get_padded_peak_list, _PaddedPeakList
+
+__all__ = ("filter_alignment_to_consolidate", "get_padded_peak_list")
+
+
+def filter_alignment_to_consolidate(project: Project) -> Alignment:
+	"""
+	Filter peaks from a project's ``alignment`` to only those which survived the ``consolidate`` process.
+
+	:param project:
+	"""
+
+	assert project.consolidated_peaks is not None
+
+	# Sort expr_code and peakpos into order from datafile_data
+	desired_order = list(project.datafile_data)[::-1]
+	sort_map = [project.alignment.expr_code.index(code) for code in desired_order]
+	expr_code = [project.alignment.expr_code[idx] for idx in sort_map]
+	peakpos = [project.alignment.peakpos[idx] for idx in sort_map]
+	assert desired_order == expr_code
+
+	consolidated_peak_retention_times = []
+	for cp in project.consolidated_peaks:
+		consolidated_peak_retention_times.append([None if numpy.isnan(rt) else rt for rt in cp.rt_list])
+
+	aligned_peaks_surviving_consolidate = []
+	for aligned_peaks in zip(*peakpos):
+		aprt = [None if p is None else p.rt for p in reversed(aligned_peaks)]
+		if aprt in consolidated_peak_retention_times:
+			aligned_peaks_surviving_consolidate.append(aligned_peaks)
+
+	alignment_surviving_consolidate = list(zip(*aligned_peaks_surviving_consolidate))
+
+	# Sanity check
+	for c_expr_peaks, expr_peaks in zip(alignment_surviving_consolidate, peakpos):
+		for peak in c_expr_peaks:
+			assert peak in expr_peaks
+
+	# Create new Alignment object
+	return create_alignment(alignment_surviving_consolidate, expr_code)
+
+
+def get_padded_peak_list(project: Project, alignment_rts: pandas.DataFrame) -> _PaddedPeakList:
+	"""
+	Returns a list of consolidated peaks for the project, based on the between-project alignment.
+
+	:param project:
+	:param alignment_rts: Pandas DataFrame giving retention times for the peak alignment.
+		The output of :meth:`~pyms.DPA.Alignment.Alignment.get_peak_alignment`.
+
+	"""
+
+	rts = [numpy.mean(row[1:]) for row in alignment_rts[list(project.datafile_data)].itertuples()]
+
+	return _get_padded_peak_list(project, rts)