keyword stringclasses 7
values | repo_name stringlengths 8 98 | file_path stringlengths 4 244 | file_extension stringclasses 29
values | file_size int64 0 84.1M | line_count int64 0 1.6M | content stringlengths 1 84.1M ⌀ | language stringclasses 14
values |
|---|---|---|---|---|---|---|---|
3D | OpenMS/OpenMS | src/pyOpenMS/pyTOPP/OpenSwathRTNormalizer.py | .py | 3,228 | 95 | import sys
import pyopenms
"""
python pyTOPP/OpenSwathRTNormalizer.py --in ../source/TEST/TOPP/OpenSwathRTNormalizer_1_input.mzML \
--tr ../source/TEST/TOPP/OpenSwathRTNormalizer_1_input.TraML --out OpenSwathRTNormalizer.tmp.out \
&& diff OpenSwathRTNormalizer.tmp.out ../source/TEST/TOPP/OpenSwathRTNo... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/pyTOPP/MapAlignerPoseClustering.py | .py | 8,985 | 256 | import argparse
import pyopenms as pms
from common import addDataProcessing, writeParamsIfRequested, updateDefaults
def align(in_files, out_files, out_trafos, reference_index,
reference_file, params):
in_types = set(pms.FileHandler.getType(in_) for in_ in in_files)
if in_types <= set((pms.Type.MZM... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/pyTOPP/CTDsupport.py | .py | 3,133 | 90 | import CTDopts
import sys
import os
from CTDopts.CTDopts import CTDModel, parse_cl_directives
import pyopenms as pms
import tempfile
# code related to CTD support
def addParamToCTDopts(defaults, model):
keys = defaults.keys()
for key in keys:
ctd_tags = defaults.getTags(key)
value = defaults.g... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/pyTOPP/OpenSwathChromatogramExtractor.py | .py | 3,631 | 84 | import os,sys
import pyopenms
"""
python pyTOPP/OpenSwathChromatogramExtractor.py --in ../source/TEST/TOPP/OpenSwathChromatogramExtractor_input.mzML\
--tr ../source/TEST/TOPP/OpenSwathChromatogramExtractor_input.TraML --out OpenSwathChromatogramExtractor.tmp.out \
&& diff OpenSwathChromatogramExtract... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/converters/__init__.py | .py | 789 | 18 | from .special_autowrap_conversionproviders import *
from autowrap.ConversionProvider import special_converters
def register_converters():
special_converters.append(OpenMSStringConverter())
special_converters.append(StdVectorStringConverter())
special_converters.append(StdSetStringConverter())
special_... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/converters/special_autowrap_conversionproviders.py | .py | 25,091 | 668 | from __future__ import print_function
from autowrap.Code import Code
from autowrap.ConversionProvider import (TypeConverterBase,
mangle,
StdMapConverter)
class OpenMSDPosition1(TypeConverterBase):
"""Converter for DPosition1 (1-dimen... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/extra_includes/python_ms_data_consumer.hpp | .hpp | 4,796 | 114 | #ifndef __PYTHON_MS_DATA_CONSUMER_HPP__
#define __PYTHON_MS_DATA_CONSUMER_HPP__
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/INTERFACES/IMSDataConsumer.h>
#include <OpenMS/METADATA/ExperimentalSettings.h>
// see ../pxds/PythonMSDataConsumer.pxd for Cython def
class PythonMSDataConsumer :
virtual public OpenMS... | Unknown |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/__init__.py | .py | 0 | 0 | null | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/conftest.py | .py | 2,785 | 81 | """
Pytest configuration file for pyOpenMS tests.
This file provides fixtures and configuration for test data paths,
replacing the old env.py import pattern.
"""
import os
# Import pytest only if available (needed for fixtures)
try:
import pytest
_HAS_PYTEST = True
except ImportError:
_HAS_PYTEST = False... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/integration_tests/test_MRMRTNormalizer.py | .py | 3,218 | 87 | import unittest
import os
import pytest
import pyopenms
from collections import defaultdict
eps = 2
def simple_find_best_feature(output, pairs, targeted):
f_map = defaultdict(list)
for f in output:
key = f.getMetaValue("PeptideRef".encode())
f_map[key].append(f)
get_score = lambda f: f.g... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/memoryleaktests/__init__.py | .py | 0 | 0 | null | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/memoryleaktests/testAll.py | .py | 7,809 | 265 | from __future__ import print_function
import sys
import unittest
import os
import copy
import time
import contextlib
import pyopenms
from pyopenms._sysinfo import free_mem
import numpy as np
def show_mem(label):
p = free_mem()
p /= 1024.0 * 1024
print((label+" ").ljust(50, "."), ": %8.2f MB" % p)
... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_FLASHDeconv.py | .py | 40,084 | 1,185 | """
Test suite for FLASHDeconv Python bindings.
Tests cover:
- FLASHHelperClasses (LogMzPeak, PrecalculatedAveragine, MassFeature, IsobaricQuantities)
- PeakGroup
- DeconvolvedSpectrum
- SpectralDeconvolution
- FLASHDeconvAlgorithm
- FLASHDeconvSpectrumFile
- FLASHDeconvFeatureFile
"""
import unittest
import os
impor... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_StaticMethods.py | .py | 31,908 | 801 | """
Tests for static methods converted to @staticmethod decorator pattern.
This test file covers the wrapper changes from issue #8559.
"""
import unittest
import os
import tempfile
import pyopenms
def make_peak1d(mz, intensity):
"""Helper to create Peak1D with mz and intensity."""
p = pyopenms.Peak1D()
p... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_Utf8StringInput.py | .py | 9,768 | 246 | """
Tests for libcpp_utf8_string parameter handling.
These tests verify that functions using libcpp_utf8_string accept both
Python str and bytes inputs (PR #8602).
"""
import unittest
import pyopenms
class TestMRMRTNormalizerStringInput(unittest.TestCase):
"""Test MRMRTNormalizer accepts str and bytes for outlie... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_MzXMLConsumer.py | .py | 1,171 | 39 | import pyopenms
import os.path
from .collections_ import Counter
def test0():
fh = pyopenms.MzXMLFile()
here = os.path.dirname(os.path.abspath(__file__))
path = os.path.join(here, "test2.mzXML").encode()
class Consumer(object):
def __init__(self):
self.speclevels = []
... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_MSNumpressCoder.py | .py | 6,766 | 204 | import unittest
import os
import pyopenms
class TestMSNumpressCoder(unittest.TestCase):
def setUp(self):
self.testData = [
100.0,
200.0,
300.00005,
400.00010,
]
def test_encodeNP_SLOF(self):
"""
String out;
MSNumpr... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_MzMLConsumer.py | .py | 1,169 | 39 | import pyopenms
import os.path
from .collections_ import Counter
def test0():
fh = pyopenms.MzMLFile()
here = os.path.dirname(os.path.abspath(__file__))
path = os.path.join(here, "test2.mzML").encode()
class Consumer(object):
def __init__(self):
self.speclevels = []
s... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/testLocale.py | .py | 1,478 | 48 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Test that pyOpenMS doesn't affect Python's locale settings.
This test ensures that importing pyOpenMS doesn't change the Python
locale, which would affect other Python libraries.
"""
import unittest
import locale
class TestLocale(unittest.TestCase):
"""Test that... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_FileIO.py | .py | 3,943 | 126 | import unittest
import os
import pyopenms
class TestPepXML(unittest.TestCase):
def setUp(self):
dirname = os.path.dirname(os.path.abspath(__file__))
self.filename = os.path.join(dirname, "test.pep.xml").encode()
def test_readfile(self):
pepxml_file = pyopenms.PepXMLFile()
pe... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_DIAScoring.py | .py | 2,512 | 74 | import unittest
import os
import pyopenms
class TestDIAScoring(unittest.TestCase):
def setUp(self):
pass
def test_spectrum(self):
intensity = [
100,
100,
100,
100,
100,
... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/testCVTermList.py | .py | 2,274 | 88 | import pyopenms
def testCVTermList():
term = pyopenms.CVTerm()
term.setAccession("ACC")
assert term.getAccession() == "ACC"
term.setName("NAME")
assert term.getName() == "NAME"
term.setCVIdentifierRef("CVREF")
assert term.getCVIdentifierRef() == "CVREF"
term.setValue(123)
asser... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_Math.py | .py | 2,741 | 84 | import unittest
import pyopenms
class TestMath(unittest.TestCase):
def test_getPPM(self):
"""Test Math.getPPM function"""
# Test basic PPM calculation
# If observed m/z is 1000.001 and reference is 1000.0,
# PPM = (1000.001 - 1000.0) / 1000.0 * 1e6 = 1.0
mz_obs = 1000.001
... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/testSpectrumNativeIDParser.py | .py | 5,485 | 87 | import pyopenms
def testSpectrumNativeIDParser():
"""Test the SpectrumNativeIDParser class for parsing spectrum native IDs."""
# Test isNativeID - recognized native ID prefixes
assert pyopenms.SpectrumNativeIDParser.isNativeID("scan=123")
assert pyopenms.SpectrumNativeIDParser.isNativeID("scanId=456")... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_OpenSwathDataStructures.py | .py | 5,211 | 166 | import unittest
import os
import pyopenms
class TestOpenSwathDataStructures(unittest.TestCase):
def setUp(self):
pass
def test_spectrum(self):
# Interfaces.Spectrum uses camelCase (no addon file)
spectrum = pyopenms.Interfaces.Spectrum()
mz_exp = [1,2,3]
int_exp = [4,... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_SpectraFilter.py | .py | 6,421 | 171 | import unittest
import os
import pyopenms
class TestSpectraFilter(unittest.TestCase):
def setUp(self):
dirname = os.path.dirname(os.path.abspath(__file__))
self.filename = os.path.join(dirname, "test2.mzML").encode()
self.exp = pyopenms.MSExperiment()
pyopenms.MzMLFile().load(self... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_ProteaseDigestion.py | .py | 1,981 | 64 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
## ----------------------------------------------------------------------------
## $Maintainer: $
## $Authors: Hendrik Weisser, Hannes Roest, Stephan Aiche,
## Jeremi Maciejewski $
## ----------------------------------------------------------------------------
i... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_AcquisitionInfo.py | .py | 2,033 | 69 | import unittest
import os
import pyopenms
class TestAcquisitionInfo(unittest.TestCase):
def setUp(self):
dirname = os.path.dirname(os.path.abspath(__file__))
self.filename_mzml = os.path.join(dirname, "test.mzML").encode()
def test_acquisitioninfomemberaccess(self):
exp = pyopenms.MSExperiment()
pyopenms.M... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test000.py | .py | 205,282 | 6,958 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
## ----------------------------------------------------------------------------
## $Maintainer: $
## $Authors: Hannes Roest, Timo Sachsenberg, axelwalter,
## Samuel Wein, Uwe Schmitt, Joshua Charkow,
## Nikos Patikas, Chris Bielow, Julianus Pfeuffer,
#... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_Smoothing.py | .py | 2,387 | 75 | import unittest
import os
import pyopenms
class TestGaussFilter(unittest.TestCase):
def setUp(self):
dirname = os.path.dirname(os.path.abspath(__file__))
self.filename = os.path.join(dirname, "test2.mzML").encode()
self.exp = pyopenms.MSExperiment()
pyopenms.MzMLFile().load(self.f... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_ChromatogramExtractor.py | .py | 2,311 | 55 | import unittest
import os
import pyopenms
class TestChromatogramExtractor(unittest.TestCase):
def setUp(self):
dirname = os.path.dirname(os.path.abspath(__file__))
self.filename = os.path.join(dirname, "test.TraML").encode()
self.filename_mzml = os.path.join(dirname, "test2.mzML").encode(... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_ISpectrumAccess.py | .py | 3,852 | 120 | import unittest
import os
import pyopenms
class TestSpectrumAccessOpenMS(unittest.TestCase):
def setUp(self):
dirname = os.path.dirname(os.path.abspath(__file__))
self.filename = os.path.join(dirname, "test2.mzML").encode()
def test_readfile_content(self):
exp = pyopenms.MSExperiment... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_DRange.py | .py | 4,204 | 144 | """
Tests for DRange1 Python wrapper
"""
import unittest
import pyopenms
class TestDRange1(unittest.TestCase):
"""Test DRange1 class"""
def test_default_constructor(self):
"""Test default constructor creates empty range"""
r = pyopenms.DRange1()
self.assertTrue(r.isEmpty())
def ... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/testSpecialCases.py | .py | 1,718 | 63 | import pyopenms
import numpy
def _test_container(c, i, append_method="push_back"):
# did raise segfault because of missing index check in __getitem__
# should be resolved by implementing a proper iterator:
s = c()
assert list(s) == []
try:
s[0]
except IndexError:
pass
else:
... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/__init__.py | .py | 0 | 0 | null | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_dataframe_columns.py | .py | 31,472 | 886 | """
Tests for DataFrame column selection feature in MSSpectrum and MSChromatogram.
Tests cover:
- get_df_columns() discovery method
- Column selection via get_df(columns=[...])
- Default behavior (backward compatibility)
- Non-default columns (ion_mobility_unit, chromatogram_type, comment)
- Meta value handling with c... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_Mobilogram.py | .py | 3,877 | 116 | import unittest
import pyopenms
class TestMobilogram(unittest.TestCase):
def testMobilogram(self):
mobilogram = pyopenms.Mobilogram()
p = pyopenms.MobilityPeak1D()
p.setMobility(25.0)
p.setIntensity(1e5)
mobilogram.push_back(p)
p_back, = list(mobilogram)
a... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_StandardTypes.py | .py | 154 | 5 | def test_if_available():
import pyopenms
assert pyopenms.PeakMap == pyopenms.MSExperiment
assert pyopenms.PeakSpectrum == pyopenms.MSSpectrum
| Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_BilinearInterpolation.py | .py | 10,744 | 289 | import unittest
import math
import random
import pyopenms
class TestBilinearInterpolation(unittest.TestCase):
def test_BilinearInterpolation(self):
mat = pyopenms.MatrixDouble(2, 3, 0.0)
mat.setValue(0, 0, 17)
mat.setValue(0, 1, 18.9)
mat.setValue(0, 2, 20.333)
mat.setVal... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/collections_.py | .py | 6,408 | 197 | from __future__ import print_function
from operator import itemgetter
from heapq import nlargest
from itertools import repeat
try:
from itertools import ifilter
except ImportError:
# Python 3
ifilter = filter
class Counter(dict):
'''Dict subclass for counting hashable objects. Sometimes called a bag
... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_MSSpectrum.py | .py | 7,542 | 208 | import unittest
import numpy as np
import pyopenms
class TestMSSpectrum(unittest.TestCase):
def testMSSpectrum(self):
spec = pyopenms.MSSpectrum()
p = pyopenms.Peak1D()
p.setMZ(500.0)
p.setIntensity(1e5)
spec.push_back(p)
p_back, = list(spec)
assert isinst... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_ChromatogramExtractorAlgorithm.py | .py | 2,442 | 70 | import unittest
import os
import pyopenms
class TestChromatogramExtractorAlgorithm(unittest.TestCase):
def setUp(self):
dirname = os.path.dirname(os.path.abspath(__file__))
self.filename = os.path.join(dirname, "test2.mzML").encode()
def test_readfile_content(self):
exp = pyopenms.MS... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_Isobaric_Quantitation.py | .py | 3,103 | 89 | import unittest
import os
import pyopenms
def general_setup(self):
self.eightplex = pyopenms.ItraqEightPlexQuantitationMethod()
self.fourplex = pyopenms.ItraqFourPlexQuantitationMethod()
self.tmt = pyopenms.TMTSixPlexQuantitationMethod()
class TestIsobaricQuantitationMethod(unittest.TestCase):
def s... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_Convexhull.py | .py | 813 | 34 | import pyopenms
def test_convex_hull_0():
ch = pyopenms.ConvexHull2D()
def test_convex_hull_1():
ch = pyopenms.ConvexHull2D()
points = [ [1.0, 1.0], [2.0, 1.0], [1.0, 2.0], [2.0, 2.0]]
for p in points:
ch.addPoint(p)
assert ch.encloses([1.5, 1.5])
assert not ch.encloses([.5, 1.5])
... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_tutorial.py | .py | 15,212 | 498 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function
import copy
import os
from pyopenms import String as s
from pyopenms import *
try:
long
except NameError:
long = int
from functools import wraps
def report(f):
@wraps(f)
def wrapper(*a, **kw):
print("run b... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_TargetedQuantitation.py | .py | 15,523 | 457 | """
Test suite and examples for Targeted Quantitation algorithms.
This module demonstrates the usage of the SmartPeaks-derived algorithms
for MRM/SRM and SWATH/DIA quantitation workflows.
Classes covered:
- MRMFeatureSelectorScore, MRMFeatureSelectorQMIP
- SelectorParameters
- MRMBatchFeatureSelector
- MRMFeatureFilt... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_SpectrumAccessOpenMS.py | .py | 829 | 27 | import unittest
import os
import pyopenms
class TestSpectrumAccessOpenMS(unittest.TestCase):
def setUp(self):
dirname = os.path.dirname(os.path.abspath(__file__))
self.filename = os.path.join(dirname, "test2.mzML").encode()
def test_readfile_content(self):
exp = pyopenms.MSExperiment... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_MRMFeatureFinderScoring.py | .py | 1,850 | 49 | import unittest
import os
import pytest
import pyopenms
eps = 2
class TestMRMFeatureFinderScoring(unittest.TestCase):
@pytest.fixture(autouse=True)
def setup_test_data(self, openms_test_data_dir):
"""Setup test with test data directory from pytest fixture."""
self.dirname = os.path.dirname(o... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/testLightTargetedExperiment.py | .py | 2,743 | 105 |
import pyopenms
import unittest
class TestLightTargetedExperiment(unittest.TestCase):
def setUp(self):
lt = pyopenms.LightTransition()
lt.fragment_charge = 2
lt.transition_name = b"X"
lt.peptide_ref = b"Y"
lt.library_intensity = 12.0
lt.product_mz = 22.0
... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_Hash.py | .py | 13,349 | 494 | """
Test hash functions for various OpenMS data types.
Tests that:
1. Equal objects have equal hashes
2. Objects can be used as dictionary keys
3. Objects can be used in sets
"""
import unittest
from pyopenms import (
Peak1D, Peak2D, ChromatogramPeak, MobilityPeak1D,
AASequence, EmpiricalFormula, PeptideHit, P... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_DataProcessing.py | .py | 3,256 | 88 | import unittest
import pyopenms
class TestDataProcessing(unittest.TestCase):
def test_processingActionToString(self):
"""Test converting ProcessingAction enum to string."""
# Test known processing actions
self.assertEqual(
pyopenms.DataProcessing.processingActionToString(
... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_backward_compatibility.py | .py | 14,063 | 332 | import unittest
import os
import tempfile
import warnings
import pyopenms
class TestBackwardCompatibilityIdXMLFile(unittest.TestCase):
"""Test backward compatibility for IdXMLFile with Python lists"""
def setUp(self):
dirname = os.path.dirname(os.path.abspath(__file__))
self.filename = os.path... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_InstrumentSettings.py | .py | 2,694 | 84 | import unittest
import pyopenms
class TestInstrumentSettings(unittest.TestCase):
def test_scanModeToString(self):
"""Test converting ScanMode enum to string."""
SM = pyopenms.InstrumentSettings.ScanMode
# Test known scan modes
self.assertEqual(
pyopenms.InstrumentSett... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_TraML.py | .py | 2,018 | 52 | import unittest
import os
import pyopenms
class TestTraMLFile(unittest.TestCase):
def setUp(self):
dirname = os.path.dirname(os.path.abspath(__file__))
self.filename = os.path.join(dirname, "test.TraML").encode()
def test_readfile(self):
targeted = pyopenms.TargetedExperiment();
... | Python |
3D | OpenMS/OpenMS | src/pyOpenMS/tests/unittests/test_BaselineFiltering.py | .py | 1,182 | 35 | import unittest
import os
import pyopenms
class TestMorphologicalFilter(unittest.TestCase):
def setUp(self):
dirname = os.path.dirname(os.path.abspath(__file__))
self.filename = os.path.join(dirname, "test2.mzML").encode()
self.exp = pyopenms.MSExperiment()
pyopenms.MzMLFile().loa... | Python |
3D | OpenMS/OpenMS | src/openswathalgo/include/OpenMS/OPENSWATHALGO/Macros.h | .h | 952 | 25 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// -------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ITransition.h | .h | 1,954 | 62 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// -------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/MockObjects.h | .h | 2,815 | 123 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// -------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/TransitionHelper.h | .h | 1,062 | 40 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Witold Wolski $
// --------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h | .h | 8,158 | 293 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Darren Kessner, Hannes Roest, Witold Wolski$
// -------------------... | Unknown |
3D | OpenMS/OpenMS | src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h | .h | 13,311 | 499 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// -------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h | .h | 5,387 | 134 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest, Witold Wolski $
// ----------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataFrameWriter.h | .h | 1,607 | 66 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Witold Wolski $
// --------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/SpectrumHelpers.h | .h | 519 | 21 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest, Witold Wolski $
// ----------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/Transitions.h | .h | 1,053 | 48 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// -------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h | .h | 1,876 | 73 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// -------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openswathalgo/include/OpenMS/OPENSWATHALGO/ALGO/Scoring.h | .h | 5,448 | 137 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest$
// $Authors: Hannes Roest$
// ---------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openswathalgo/include/OpenMS/OPENSWATHALGO/ALGO/StatsHelpers.h | .h | 4,938 | 206 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Witold Wolski $
// -------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openswathalgo/source/OPENSWATHALGO/DATAACCESS/SwathMap.cpp | .cpp | 444 | 15 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// -------------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/openswathalgo/source/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.cpp | .cpp | 3,032 | 103 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest, Witold Wolski $
// ----------------------------------... | C++ |
3D | OpenMS/OpenMS | src/openswathalgo/source/OPENSWATHALGO/DATAACCESS/Transitions.cpp | .cpp | 430 | 15 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// -------------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/openswathalgo/source/OPENSWATHALGO/DATAACCESS/TransitionHelper.cpp | .cpp | 2,126 | 64 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Witold Wolski $
// --------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/openswathalgo/source/OPENSWATHALGO/DATAACCESS/DataFrameWriter.cpp | .cpp | 1,958 | 83 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Witold Wolski $
// --------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/openswathalgo/source/OPENSWATHALGO/DATAACCESS/SpectrumHelpers.cpp | .cpp | 567 | 20 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest, Witold Wolski $
// $Authors: Hannes Roest, Witold Wolski $
// -------------------... | C++ |
3D | OpenMS/OpenMS | src/openswathalgo/source/OPENSWATHALGO/DATAACCESS/MockObjects.cpp | .cpp | 2,819 | 136 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// -------------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/openswathalgo/source/OPENSWATHALGO/ALGO/Scoring.cpp | .cpp | 10,443 | 313 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// -------------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/openswathalgo/source/OPENSWATHALGO/ALGO/StatsHelpers.cpp | .cpp | 3,983 | 102 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Witold Wolski $
// -------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/SpectrumRangeManager.h | .h | 5,245 | 156 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Administrator $
// --------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/Peak2D.h | .h | 9,040 | 345 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg$
// $Authors: Marc Sturm $
// ------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/RangeUtils.h | .h | 19,010 | 670 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg$
// $Authors: Marc Sturm, Chris Bielow $
// ----------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/MobilityPeak1D.h | .h | 6,041 | 216 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// -------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/ChromatogramTools.h | .h | 9,194 | 221 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// ------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/MobilityPeak2D.h | .h | 9,465 | 337 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// -------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/Peak1D.h | .h | 6,157 | 249 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg$
// $Authors: Marc Sturm $
// ------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/MSChromatogram.h | .h | 13,035 | 423 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// ------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/ConsensusFeature.h | .h | 9,196 | 314 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// ----------------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/BaseFeature.h | .h | 7,664 | 228 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser, Chris Bielow $
// -----------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/PeakIndex.h | .h | 4,030 | 132 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg$
// $Authors: Marc Sturm $
// ------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/FeatureHandle.h | .h | 5,893 | 193 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// ----------------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/Mobilogram.h | .h | 18,448 | 593 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// -------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/SpectrumHelper.h | .h | 8,116 | 213 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg$
// $Authors: Timo Sachsenberg $
// ------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/ConversionHelper.h | .h | 2,975 | 81 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// ----------------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/Feature.h | .h | 6,162 | 187 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// ----------------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/StandardTypes.h | .h | 967 | 49 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// ----------------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/MSExperiment.h | .h | 55,060 | 1,349 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm, Tom Waschischeck $
// -----------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/DPeak.h | .h | 980 | 47 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// ----------------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/OnDiscMSExperiment.h | .h | 8,235 | 275 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// -------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/RangeManager.h | .h | 28,849 | 917 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// -------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/MRMTransitionGroup.h | .h | 16,003 | 476 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// -------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/openms/include/OpenMS/KERNEL/ChromatogramPeak.h | .h | 6,359 | 250 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// ------------------------------------------... | Unknown |
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