CHANGELOG

Glossary:
OpenMS - Name of the project and our C++ library
TOPP - "The OpenMS PiPeline", a collection of chainable tools for flexible HPLC/MS workflows. Formerly known as "The OpenMS Proteomics Pipeline"
TOPPAS - "The OpenMS PiPeline Assistant", a graphical tool to interactively build and run HPLC/MS workflows
TOPPView - Versatile viewer for HPLC/MS data
INI file - parameter configuration file, holding custom parameter settings for TOPP tools
INIFileEditor - graphical parameter editor for INI files
Parameters - list of algorithm or TOPP tool parameters that changed in this release
PR - Pull Request (on GitHub), i.e. integration of a new feature or bugfix
#<number>, e.g. #4957 - a reference to an issue or pull request on GitHub, visit e.g. https://github.com/OpenMS/OpenMS/pull/XXXX (replace XXXX with number of interest) for details



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----                                OpenMS 3.6.0     (under development)              ----
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General:
  - macOS Intel builds discontinued; macOS deployment target raised to macOS 14
  - Ubuntu CI runners updated to 24.04
  - macOS code signing and notarization integrated directly into CI (#8486, #8494, #8527)
  - Parquet support enabled across all platforms; Arrow/Parquet is now a required dependency and the WITH_PARQUET CMake option has been removed (#8370, #8422, #8991)
  - Modernized TransformationDescription to use std::unique_ptr for memory safety
  - Fix undefined behavior in ProteinIdentification get*DataArrayByName by throwing ElementNotFound when the name is missing
  - Removed leftover traces of removed doc_internal target (#2256)
  - BREAKING: QDateTime/QDate/QSysInfo/QLocale replaced with std::chrono and platform APIs in DateTime, Date, BuildInfo, DimMapper, and TOPPBase; QDate constructor removed from Date class (#8937)
  - BREAKING: QDir/QFile/QFileInfo replaced with std::filesystem in the core library; copyDirRecursively/removeDir signatures changed from QString& to String&; ToolHandler returns StringList instead of QStringList; new PathUtils.h added with UTF-8-safe to_path() helper (#8938)
  - BREAKING: QProcess/QObject replaced with boost::process in ExternalProcess, PythonInfo, JavaInfo, and RWrapper; ExternalProcess no longer inherits from QObject; ExternalProcess::run(), TOPPBase::runExternalProcess_(), RWrapper::findR()/runScript(), and ExternalProcessMBox::run() now use String/vector<String> instead of QString/QStringList (#8939)
  - BREAKING: Qt string interop removed from core String and DataValue API; String(const QString&), String::toQString(), DataValue(const QString&), DataValue::toQString(), and StringListUtils::fromQStringList() removed; Qt5Port.h deleted (#8940)
  - BREAKING: Qt6::Core removed from libOpenMS PUBLIC CMake link dependencies; downstream CMake projects must now link Qt6::Core directly if needed (#8965)
  - Fix: UpdateCheck no longer crashes TOPP tools when $HOME is not writable (e.g., in container environments where $HOME=/); the update check is skipped gracefully (#9075, fixes #9074)
  - Fix: TheoreticalSpectrumGenerator: corrected m/z calculation for b/a neutral-loss fragment ions; the neutral-loss loop previously omitted the first residue mass, causing all b/a neutral-loss fragments to report masses that were too low by the first residue's internal mass (#9078, #9084)
  - Fix: LinearResampler: right_index was clamped to the number of raw data points instead of the number of resampled points; when resampled points far outnumber raw points (e.g. fine spacing over a wide m/z range), this caused extreme intensity spikes; bug introduced in 2008 and masked by LinearResamplerAlign which has an independent correct implementation (#9127)
  - Transparent .zip decompression for XML-based formats (mzML, idXML, etc.) and Bruker .d directories: files with a .zip extension are now decompressed on-the-fly during parsing; .d.zip archives are extracted to a temporary directory and loaded via BrukerTimsFile; no conversion step required (#9139)
  - Compressed XML writing: all XML-based formats (idXML, consensusXML, featureXML, mzML, etc.) can now be written as .gz or .bz2 compressed files by using the corresponding extension (e.g. "output.idXML.gz"); uses zlib and libbz2 C APIs directly for cross-platform support (#7560, #9259)
  - Fix: BrukerTimsFile: DDA-PASEF and DIA-PASEF spectra are now marked as CENTROID (PeakType::PEAK) so downstream tools that check spectrum type (e.g. FeatureFinderMultiplex, OpenSwathWorkflow) accept them without extra conversion (#9154)
  - Bruker TimsTOF MS1 frame aggregation for DIA-PASEF and DDA-PASEF: new BrukerTimsFile::Config fields (ms1_n_neighbors, ms1_min_support, ms1_max_rt_distance_sec, ms1_centroid_max_peaks) sum peaks from 2N+1 adjacent MS1 frames into a sparse (mz_bin, scan_id) grid per center frame, composable with the existing within-frame IM centroiding (ms1_centroid_mz_ppm and ms1_centroid_im_pct). Exposed through FileConverter as -bruker:ms1_n_neighbors, -bruker:ms1_min_support, -bruker:ms1_max_rt_distance_sec, -bruker:ms1_centroid_max_peaks. Disabled by default. Also renames the internal DIAFrameAggregator class to FrameAggregator (scope-agnostic now that MS1 uses it), guards its (mz_bin, scan_id) grid lookups against uint32 wrap at scan_id=0, and switches the skip_denoise predicate in the MS2 aggregation loop from index-span to actual contributing-frame count (closes #9151 TODO).
  - BrukerTimsFile: DDA MS2 native IDs changed from "scan=<precursor_id>" to "frame=<frame_id> scan=<scan_begin> precursor=<precursor_id>". The frame/scan pair follows the PSI-MS MS:1002818 ("Bruker TDF nativeID format") convention (scan is the TIMS isolation-window scan_begin); the trailing "precursor=<P>" token is required for uniqueness under OpenMS's per-Precursors.Id aggregation (different precursors can share the same (frame, scan_begin) via PASEF co-isolation with different IsolationMz, and multi-cycle precursors can collide on their first entry) — this mirrors the convention pwiz uses in its "combined" mode ("merged=N frame=F scanStart=A scanEnd=B"), where extra tokens are added while the SourceFile CV accession remains MS:1002818. The Bruker Precursors.Id is ALSO duplicated as a typed MetaValue "bruker_precursor_id" for direct programmatic access. SpectrumNativeIDParser now recognizes MS:1002818 and the "frame=" prefix so downstream scan-number extraction (SpectrumLookup, USI, PepXMLFile, PercolatorInfile, IDMapper) works for Bruker .d output. New BrukerTimsFile::Config field load_ms1 (CLI: -bruker:load_ms1, default true): disable to skip MS1 loading entirely for MS2-only workflows (peptide database search) — cuts memory and time substantially. CometAdapter automatically sets load_ms1=false when searching MS2. BrukerTimsFile::transform() progress now matches actually-emitted spectra in DIA mode (per-WindowGroup sum, not frames × all_windows) and respects load_ms1 across all modes.
  - CometAdapter: workaround for a latent bug in Comet's bundled mzParser (MSToolkit/saxmzmlhandler.cpp) that segfaults when mzML files contain mixed "frame=..." and "scan=..." native IDs with overlapping numeric values — which is exactly the Bruker .d DDA/DIA case. CometAdapter rewrites Bruker .d native IDs to monotonic "index=N" before handing the temp mzML to Comet, and translates PSM spectrum references back to the original Bruker IDs after Comet finishes. Upstream fix for cindex::compare's strict-weak-ordering violation should be filed against UWPR/Comet.
  - New Constants::UserParam::MEAN_INVERSE_REDUCED_ION_MOBILITY_ARRAY constant ("mean inverse reduced ion mobility array", CV MS:1003006) for Bruker timsTOF data; IMDataConverter::getIMUnit now recognises all three IM array name prefixes (Ion Mobility, inverse reduced ion mobility, mean inverse reduced ion mobility array) ensuring correct unit detection across timsTOF, MSConvert, and Bruker raw data (#9181)
  - MascotGenericFile: SEQ= sequence-query field is now parsed on load (stored as "SEQ" meta value; multiple SEQ= lines per query accumulate into a StringList) and emitted on store, enabling lossless MGF round-trips with peptide-sequence annotations (#9186)
  - MSPGenericFile: CCS field is now parsed into a typed numeric meta value (Constants::UserParam::MSM_CCS, in Angstrom^2 as written by MS-DIAL/MoNA), so MetaboliteSpectralMatching can use library CCS for ion-mobility filtering; non-numeric values are kept verbatim as strings. The line reader was also switched from a fixed 64 KiB char buffer to std::string/std::getline to avoid silent truncation of long fields (#8816)
  - Fix: MSExperiment::reset() now clears chromatograms as well as spectra; previously chromatograms were left intact, causing duplicate chromatogram entries when an experiment was reset and reloaded; FileFilter's RT-block filtering loop was updated accordingly (#9211)
  - Fix: BrukerTimsFile: off-by-one in MS1 centroid cap; the ms1_centroid_max_peaks limit used `>` instead of `>=`, causing capped MS1 spectra to emit exactly max_peaks + 1 peaks rather than max_peaks; the ion-mobility array length is now kept aligned with the peak count (#9233)
  - Native .idparquet identification format: a new directory-based Parquet bundle (psms.parquet, proteins.parquet, protein_groups.parquet, search_params.parquet) for lossless round-trip storage of PeptideIdentification/ProteinIdentification data; supported by FileHandler, IDMerger, IDFileConverter, PercolatorAdapter, CometAdapter, MSGFPlusAdapter, and SageAdapter (#9225, #9232)
  - IDRipper: split merged .idparquet into per-run .idparquet outputs; -in accepts a merged .idparquet directory and emits one .idparquet output directory per IdentificationRun, mirroring the existing .idXML behavior; output format follows input format (#9237)
  - Perf: BrukerTimsFile FrameAggregator: switched grid_, denoised, and smoothed internal maps from std::unordered_map to boost::unordered_flat_map; 2.1x–3.2x faster finalize/finalizeCentroided per call, ~18% end-to-end wall-time reduction on DIA-PASEF .d files (#9243)
  - Native .featureparquet and .consensusparquet formats: FileHandler now loads and stores FeatureMap as .featureparquet directory bundles and ConsensusMap as .consensusparquet directory bundles via Parquet, parallel to .idparquet; FileTypes::FEATUREPARQUET and FileTypes::CONSENSUSPARQUET registered with isDirectoryType() = true (#9242)
  - Fix: FeatureMapArrowIO: FeatureMap-level MetaValues are now preserved across .featureparquet store/load via a new fmap_metavalues key in file-level Parquet metadata; previously only document_id / loaded_file_path / loaded_file_type / data_processing round-tripped, so FeatureMap::setPrimaryMSRunPath (which stores its argument as a spectra_data meta-value on the map itself per FeatureMap.cpp:415) was silently dropped, propagating filename='UNKNOWN' to downstream FLUKD / TextExporter / MzTabExporter steps; mirrors the existing cmap_metavalues handling in ConsensusMapArrowIO (extends #9242)
  - Fix: ProteinIdentificationArrowIO: parquet load now synthesizes fresh ProteinIdentification run identifiers (`<search_engine>_<date>_<UniqueIdGenerator>`) mirroring IdXMLFile.cpp:530, wired into the 3 parquet load entry points (PSMArrowIO::importFromParquet, FeatureMapArrowIO::importFromParquet, ConsensusMapArrowIO::importFromParquet); each entry point re-stamps every owned PeptideIdentification collection via a new applyRunIdentifierRename helper. Complementary store-side defense via a new checkUniqueIdentifiers helper rejects duplicate identifiers before any Arrow builder is allocated (Exception::InvalidValue, message text mirroring XMLHandler::checkUniqueIdentifiers_); wired into the 3 parquet store entry points. Closes the post-IDRipper-then-IDMerger collision scenario that previously collapsed two ripped .idparquet files sharing a stored run_identifier into a single in-memory IdentificationRun. Stored identifiers on disk are now informational; existing .featureparquet / .consensusparquet / .idparquet files load unchanged (extends #9232)
  - Fix: MapAlignmentAlgorithmIdentification::align() no longer leaks reference_ state between consecutive calls that use an internal reference (reference_index >= 0); previously checkParameters_ inspected the stale reference_ left over from the prior call, inflating the effective run count and, when min_run_occur was higher than the actual number of input maps, silently degrading subsequent alignments to identity transforms. MapAlignerTreeGuided's tree-walking align_algorithm_ reuse hit this latent bug; the fix clears reference_ at the top of align() when reference_index >= 0, before checkParameters_ runs.
  - Fix: MapAlignerTreeGuided exported transformations whose data points were synthesized from (original_RT, already_transformed_RT) pairs of the merged map, so a spline fit through those pairs essentially recovered the spline's own outputs and reported near-zero residuals; computeTrafosByOriginalRT() now re-aligns each original input map against the final tree-guided consensus via MapAlignmentAlgorithmIdentification, so exported transformations map original input RT to the final consensus RT scale and the alignment statistics reported by downstream consumers like ProteomicsLFQ become meaningful (transformed feature RTs may shift slightly compared to the previous per-feature approximation).
  - ProteomicsLFQ: re-enabled tree_guided as a valid value for -alignment_order. It had been disabled because the previous MapAlignerTreeGuided trafo was tautological, leaving max_alignment_diff (used to calibrate the linker's RT tolerance) at ~0 and effectively useless; with the trafo fix above, post-alignment residual statistics are now informative and the tree-guided code path is usable end-to-end. Default remains star.
  - pyOpenMS: BrukerTimsFile bindings (nanobind) exposing load() / readDIAMetadata() with the nested Config struct (incl. ExportMode, TimsCalibrationStrategy, PressureCompensation enums) and DIAStreamingMetadata; gated by the WITH_OPENTIMS CMake flag and feature-detectable via hasattr(pyopenms, "BrukerTimsFile"). Streaming consumer paths (loadDIAStreaming, transform) deferred. The Bruker SDK (timsdata.dll / libtimsdata.so) is not bundled in the wheel; supply it via OPENMS_BRUKER_SDK_PATH or Config.bruker_sdk_path at runtime. (#9379)
  - BrukerTimsFile: IM-axis hill centroiding via new PASEFHillCentroider class; detects peaks along the ion-mobility axis using hill detection with valley splitting, configurable m/z linking tolerance (pasef_hill_mz_linking_ppm), minimum hill length, and maximum scan gap; applied to MS1 and DIA/DDA MS2; exposed in BrukerTimsFile::Config (centroid_algorithm = HILL) and via FileConverter (-bruker:centroid_algorithm hill) and PeakPickerIM (-algorithm hill); modeled on Biosaur2 hill detection (#9380)
  - New IMAGING module for imaging mass spectrometry: IonImage (dense W×H×D intensity grid with per-pixel validity mask and m/z extraction window), MSImagingGeometry (pixel list with (x,y,z)→spectrum-index lookup and pixel-size metadata), and MSImagingExperiment (integrates MSExperiment with MSImagingGeometry for pixel-based spectrum access and sum-based ion-image extraction); pyOpenMS bindings included (#9381)
  - New BrukerTimsImagingFile class for loading Bruker .d MALDI imaging data: reads pixel-layout metadata from MaldiApplicationInfo (x/y offsets and pixel size), maps each spot to an (x, y) coordinate in MSImagingGeometry, and populates an MSImagingExperiment; supports CENTROID and PROFILE export modes; gated by WITH_OPENTIMS (#9383)
  - BrukerTimsFile: new Config fields frame_id_min/frame_id_max for raw frame-ID range filtering and rt_min_sec/rt_max_sec for retention-time range filtering; the RT range is resolved to a frame-ID sub-range at load time via SQL; honored by load(), transform(), loadDIAStreaming(), and readDIAMetadata(); memory and I/O now scale with the requested range rather than the full file size (#9387)
  - Fix: SwathMapMassCorrection: removed null-pointer dereference and memory leak in correctMZ/correctIM when fetchSpectrumSwath returns an empty spectrum; empty-spectrum iterations are now skipped cleanly via continue or a null-pointer guard (#9386)
  - Fix: SimpleSearchEngineAlgorithm: removed default(none) from the OpenMP parallel-for pragma that unconditionally listed annotated_hits_lock in its shared() clause; on macOS/Xcode where _OPENMP is not defined, this caused "use of undeclared identifier" compile errors and prevented building on those platforms (#9388)
  - New ThermoRawFile class for native reading of Thermo .raw files into MSExperiment via the openms-thermo-bridge (.NET managed DLL bridge); fetched automatically via CMake FetchContent; controlled by WITH_THERMO_RAW CMake option (ON by default, except on Linux/aarch64); registered in FileHandler and FileTypes (#9389)
  - Optimized MzIdentML parser performance by caching CV lookups and added mzIdentML 1.3 schema support (#8764)

Dependencies:
  - PyOpenMS: Autowrap/Cython replaced with nanobind; nanobind 2.10.0+ fetched automatically (#8699)
  - Eigen minimum version updated from 3.3.4 to 3.4.0 (#8366)
  - Qt6::Network replaced with libcurl for all HTTP operations in the core library (#8841)
  - minizip-ng replaced with libzip for ZIP64 archive support (#8808)
  - Qt6 usage reduced in core library (incremental steps toward making Qt optional):
    - QDateTime/QDate/QSysInfo/QLocale replaced with std::chrono and platform APIs in Date, DateTime, BuildInfo (#8937)
    - QDir/QFile/QFileInfo replaced with std::filesystem in File, PathUtils, ExperimentalDesignFile, and others; ToolHandler now returns StringList instead of QStringList (#8938)
    - QProcess/QObject replaced with boost::process in ExternalProcess, PythonInfo, JavaInfo, RWrapper; public APIs now use String/vector<String> instead of QString/QStringList (#8939)
    - QJsonDocument/QJsonObject replaced with nlohmann/json in OMSFileLoad (#8936)
    - Qt string interop removed from String, DataValue, StringUtils, StringListUtils; Qt5Port.h deleted (#8940)
    - Qt6::Core removed from libOpenMS PUBLIC CMake link dependencies; downstream CMake targets must link Qt6::Core directly if they use Qt (#8965)
    - Qt6::Core removed from all non-GUI TOPP tools; Qt is now only required when building with WITH_GUI=ON; ExecutePipeline, INIUpdater, and ImageCreator moved from src/topp/ to the GUI library (#9041)
  - boost-process added as a header-only dependency for cross-platform subprocess management (#8939)
  - ENABLE_TDL CMake option (required for CWL/Common Workflow Language file support) now defaults to OFF; set -DENABLE_TDL=ON to re-enable (#9067)
  - Boost minimum version requirement raised from 1.78 to 1.81 (#9095)
  - opentims: CMake now searches for a system-installed opentims_cpp via FindOpentims.cmake before falling back to a FetchContent git clone; packagers and users with opentims already installed can set opentims_DIR or opentims_ROOT to skip the download (#9147, #9148)
  - contrib: the contrib directory is now a git submodule; developers and packagers building from a git clone must run `git submodule update --init` (or clone with `--recurse-submodules`) to obtain the vendored third-party libraries (#9155)
  - Fix: CMake now accepts Arrow/Parquet 24.x and later; the find_package version argument was dropped and a VERSION_LESS guard enforces the >= 23 minimum, so any future Arrow major release is accepted without an explicit CMake update; pyOpenMS excludes pyarrow 24.0.0 (cp310-only wheels on PyPI) to ensure pyarrow installs correctly on Python 3.11/3.12/3.13 (#9196)
  - Fix: pyOpenMS standalone build (cibuildwheel path) now accepts Arrow 24.x; the standalone CMakeLists.txt called find_package(Arrow 23 CONFIG REQUIRED) which uses SameMajorVersion compatibility and therefore rejects Arrow 24.0.0; the version pin is dropped and a manual VERSION_LESS guard enforces the >= 23 minimum, mirroring the fix in cmake_findExternalLibs.cmake (#9221)
  - wnetalign/wnet/pylmcf: three header-only C++ libraries fetched via CMake FetchContent for Wasserstein network alignment; pylmcf v0.9.5, wnet v0.9.9, wnetalign v0.9.6; controlled by WITH_WNETALIGN CMake option (ON by default) (#8992)
  - HiGHS LP solver added as a third linear-programming backend alternative to COIN-OR and GLPK; selectable via the LP_SOLVER CMake variable (AUTO/COIN/GLPK/HIGHS); AUTO tries COIN-OR, then GLPK, then fetches HiGHS via FetchContent if neither is found (#9246)

PyOpenMS:
  - BREAKING: Binding backend replaced from Autowrap/Cython to hand-maintained nanobind C++ bindings (#8699)
    - Python-level API is backward compatible (same class names, method signatures, return types)
    - 544 classes wrapped across 10 domain-based modules for parallel compilation
    - Custom type casters for OpenMS::String, DataValue, DPosition, etc.
    - Addon system preserved: pure Python methods injected via @addon("ClassName") decorator
    - PEP 561 type stub generation (.pyi) for IDE autocompletion
    - Smaller binaries, faster builds, and improved error messages
  - Pythonic convenience methods added:
    - __len__() for ConsensusMap, FeatureMap (#8510)
    - __str__() and __repr__() for NASequence, FeatureMap, ConsensusMap, ConvexHull2D, DPosition, DRange, FloatDataArray, IntegerDataArray, StringDataArray, Residue (#8503, #8501)
    - __hash__() for 40+ classes enabling use as dictionary keys (AASequence, EmpiricalFormula, Peak1D, PeptideHit, Precursor, etc.) (#8576)
    - append() and extend() for ConsensusMap, FeatureMap, PeptideIdentificationList (#8510)
  - DataFrame support:
    - get_df() methods for MSSpectrum, MSChromatogram, Mobilogram, MSExperiment, ConsensusMap, FeatureMap (#8520)
    - get_df_columns() method for column discovery (#8436)
    - MRMTransitionGroupCP: get_chromatogram_df(), get_feature_df() (#8520)
    - Arrow/Parquet export with to_df(), to_chromatogram_df(), to_feature_df() methods (#8655)
    - Zero-copy Python interop via pyarrow for MSExperiment (#8655)
    - PSM DataFrame export from PeptideIdentificationList (#8632)
    - Arrow/DataFrame/Parquet export for ConsensusMap (#8729)
  - New wrappers:
    - Math.getPPM(), Math.getPPMAbs() (#8525)
    - MSSpectrum.getType(bool) (#8589)
    - DRange1 with conversion provider (#8504)
    - Drift time accessors: get_drift_time_array(), get_drift_time_unit() (#8423)
    - SpectrumNativeIDParser with static methods for native ID parsing (#8637)
    - MSExperiment.rasterize2D() for rasterizing 2D ion mobility data (#8739)
    - FAIMSHelper: getCompensationVoltages(PeakMap) and filterPeptidesByFAIMSCV(PeptideIdentificationList, target_cv, cv_tolerance) for FAIMS compensation voltage detection and per-CV peptide ID filtering (#9275)
    - MZTrafoModel.setRANSACSeed(seed) for reproducible RANSAC-based m/z calibration (#9407)
    - EmpiricalFormula.getNumberOf(Element), EmpiricalFormula.getLightestIsotopeWeight(), Residue.getHydrophobicity(HydrophobicityScaleMethod) + new HydrophobicityScaleMethod enum, TheoreticalSpectrumGenerator.getPrefixAndSuffixIonsMZ(peptide, charge) returning a numpy float array, and SpectralMatch CCS accessors (getCCS/setFoundCCS) added (#9415, #9412)
  - String handling: Functions now accept both str and bytes via libcpp_utf8_string (#8602, #8604)
  - Backward compatibility restored for file I/O methods in IdXMLFile, PepXMLFile, MzIdentMLFile (#8553)
  - Static methods modernized using @staticmethod decorator (#8562)
  - Type hints added to docstrings for 133 functions (#8483)
  - Build system modernized with py-build-cmake and cibuildwheel for PEP 517/518/621 compliance (#8530)
  - BREAKING: Metadata enums converted to strongly typed enum classes (#8604)
  - BREAKING: Activation methods enum handling changed (#8405)
  - BREAKING: DataFrame methods renamed to Pythonic conventions: get_df() → to_df(), get_df_columns() → df_columns(), etc. Deprecated aliases provided for backward compatibility (#8655)
  - Fix: AASequence copy constructor dispatch corrected; AASequence(existing_seq) now copies instead of round-tripping via __str__; __str__ now returns the peptide sequence string via toString() (#9098)
  - Fix: copy constructor registration order fixed for 11 additional classes (ProteinHit, Software, CVTerm, PeptideEvidence, USI, Ribonucleotide, FIAMSScheduler, CachedmzML, IndexedMzMLHandler, XICParquetFile, XIMParquetFile) (#9098)
  - Fix: getAAFrequencies() loop bug in AASequence addon (#8502)
  - Fix: ~50 mutable reference output parameter bugs fixed across all bindings (#8699)
  - Fix: ~100 missing default arguments restored (#8699)
  - Fix: AASequence.__str__() now returns the peptide sequence string instead of repr format; copy constructor dispatch fixed for AASequence and 11 other classes (ProteinHit, Software, CVTerm, PeptideEvidence, USI, and others) to prevent implicit string conversion (#9098)
  - Test: Docstring format validation tests added (#8674)
  - ProForma v2 support: Full Python bindings for ProFormaParser (#8648)
    - Parse ProForma strings: Peptidoform.fromString(), PeptidoformIon.fromString()
    - Serialize back: toString() with LOSSLESS/CANONICAL modes
    - Convert to/from AASequence with configurable policies (FAIL_ON_LOSS, DROP_UNLOCALISED, BEST_EFFORT)
    - Mass calculation: getMonoWeight(), getMZ(), canCalculateMass()
    - JSON serialization: toJSON()/fromJSON() for AST persistence
    - Pythonic API: __str__, __repr__, __len__ on Peptidoform and PeptidoformIon
  - USI support: Python bindings for Universal Spectrum Identifier (#8684)
    - USI class with constructor from string, tryParse(), isValidUSI()
    - PeptideIdentification.buildUSI() for generating USIs
  - PEFF support: Full Python bindings for PSI Extended FASTA Format (#8690)
    - PEFFFile class for reading/writing PEFF files with batch and streaming APIs
    - PEFFEntry with rich annotations: modifications, variants, processed regions
    - PEFFDatabaseMetadata for header information
    - Conversion methods: toFASTAEntry(), fromFASTAEntry(), toProForma()
    - Sequence accessors: getSequence(), getModifiedSequence(), getVariantSequences(), getProcessedSequence()
  - Param to_dict quality-of-life improvements: dict-like API for parameter access (#8631)
  - Fix: FileTypes wrapping updated with missing enum values and static methods (#8720)
  - XICParquetFile: Python bindings with multi-file support and filtering for reading XIC data from Parquet files (#8737, #8738)
  - XIMParquetFile: Python bindings for reading extracted ion mobilogram data from Parquet files (#8894)
  - Zero-copy get_peaks_struct() accessor for MSChromatogram and Mobilogram (#8825, #8842)
  - Complete FileHandler wrapper: 14 new load/store methods for FeatureMap, ConsensusMap, identifications, and transformations (#8762)
  - PeptideAndProteinQuant: getPeptideResults() and getProteinResults() now exposed (#8543)
  - IDConflictResolverAlgorithm: resolveAllHitRankAggregation() for FeatureMap and ConsensusMap now exposed (#8907)
  - BREAKING: Zero-copy _mv methods renamed to _view (e.g., get_data_mv() → get_data_view()); deprecated _mv aliases provided for backward compatibility (#8857)

TOPP tools:
  Changes:
    all:
      - BREAKING: Command-line duplicate parameter behavior changed (#8670, fixes #5345)
        When a parameter is specified multiple times on the command line, the LAST occurrence now wins
        (previously, the FIRST occurrence was used). This enables the nextflow pattern of using ${ext.args}
        at the end of commands to override hardcoded defaults. A warning is issued when duplicates are detected.
        Example: tool -param default -param override  # Now uses 'override' (previously used 'default')
      - Improved error messages for command-line parameter errors (#8670)
    CometAdapter:
      - Merges compatible variable modifications for improved search performance (3x+ speedup) (#8407)
      - Added Bruker TimsTOF .d DDA-PASEF input support; .d directories are converted to mzML on-the-fly via BrukerTimsFile before search; requires WITH_TIMSRUST=ON (#9126)
      - Fix: Bruker native-ID rewrite (index=N workaround for Comet's mzParser) now also applied when the input is an mzML file previously converted from a .d directory; detects "frame=" in spectrum native IDs and rewrites them to monotonic index=N before handing to Comet (#9168)
      - Added .idparquet output support; -out now accepts .idparquet format in addition to idXML (#9232)
    ProSE:
      - BREAKING: renamed from PeptideDataBaseSearchFI to ProSE; the old executable name is no longer available (#9137)
      - BREAKING: precursor tolerance schema changed to asymmetric positive-magnitude pair (#9108, #9132)
        The scalar `precursor:mass_tolerance` and the `precursor:open_window_lower/_upper`
        params are REMOVED and replaced by `precursor:mass_tolerance_lower` and
        `precursor:mass_tolerance_upper`, both non-negative magnitudes applied internally as
        `[-lower, +upper]` around the precursor mass. Matches MSFraggerAdapter convention.
        Default widened from 10 to 20 ppm per side. The calibration pass now preserves signed
        precursor bias (median of signed errors + MAD-of-residuals) instead of clobbering
        asymmetric user bounds to symmetric; an extreme-bias guard (`|shift| >= spread`)
        discards the calibration result and warns rather than silently loosening. Open-search
        auto-detection trips when `max(lower, upper) > 1000 ppm` or `> 1 Da`. pyOpenMS users
        setting `precursor:mass_tolerance` must migrate to the new param names. Fixes a latent
        calibration-filter bug that flipped the signed-error band for asymmetric windows.
      - Expanded fragment index open search with modification discovery and FDR filtering (#8414)
      - FragmentIndex: default fragment:min_ion_index changed from 0 to 2, skipping b1/b2/y1/y2 ions by default (matches Sage behavior); improves PSM count, reduces memory and runtime; set fragment:min_ion_index=0 to include all ions (#9094)
      - FragmentIndex: faster index build using bitmask-based modification enumeration and SoA memory layout with SIMD-accelerated query loop (#9088)
      - Multi-file search: -in now accepts a file list; the fragment index is built once and reused across all inputs; new advanced -out_mod_analysis_dir parameter writes per-file and aggregate modification-analysis TSVs (#9109)
      - BREAKING: -out replaced by three dedicated output parameters: -out_idxml (per-file idXML, must match -in count), -out_qpx (directory; writes per-file <basename>.psm.parquet and <basename>.pg.parquet in QPX exchange format plus a merged quantms.psm/pg.parquet), -out_parquet (directory; writes per-file and merged OpenMS-internal Parquet files including PSM, protein, protein-group, and search-params tables); unique input basenames are required for -out_qpx and -out_parquet to avoid collisions (#9146)
      - Added peptide:enzyme_specificity parameter (full/semi/none) to enable semi-tryptic and non-specific (e.g. immunopeptidomics) searches; fixes EnzymaticDigestion underflow for very short peptides and FragmentIndex crash on empty search results (#9112)
      - New annotate:PSM options: num_matched_peaks, matched_b_ions, matched_y_ions, longest_peptide_ion_sequence, fragment_annotation; matched ion counts and fragment annotations are also exported to PSM/QPX parquet output (#9117)
      - Runtime search diagnostics: after every search a summary (matched spectra count, MS2 ID rate, unique peptides/proteins, missed cleavage distribution) and per-run tolerance estimation (median ± MAD of precursor/fragment errors with recommended tolerances) are logged (#9121)
      - Automatic mass accuracy calibration (two-pass search): optional Search:calibration:enabled parameter runs a fast first-pass search on a subset of spectra (default: top 10% by TIC) to estimate tighter precursor and fragment tolerances; tolerances are applied without rebuilding the index (#9122)
      - Protein-level FDR: new FDR:protein parameter applies picked-protein FDR (Savitski 2015) after PSM-level FDR using BasicProteinInferenceAlgorithm for score aggregation; supported in both single-file and multi-file search modes (#9123)
      - New -out_pin parameter writes Percolator input (.pin/.tsv) files for external rescoring without requiring a -percolator_executable; works independently and in parallel with -out_idxml/-out_qpx/-out_parquet (#9166)
      - Fix: ions:add_a/b/c/x/y/z_ions parameters now correctly forwarded to TheoreticalSpectrumGenerator in the scoring path; previously the fragment index and scorer were inconsistent (e.g. c/z ions were indexed but not scored), breaking ETD/EThcD searches (#9167)
      - BREAKING: PSM annotation UserParams matched_b_ions/matched_y_ions renamed to matched_prefix_ions/matched_suffix_ions to reflect that all a/b/c and x/y/z ion series are counted, not just b/y; delta_score (best minus second-best PSM score per spectrum) and matched_ion_current (sum of matched peak intensities) added to PSM annotations and Percolator features; Fix: HyperScore factorial boost now counts all prefix/suffix ions (not just b/y), improving ETD/EThcD scoring (#9175)
      - Database chunking for large FASTA inputs: new -Search:database:chunk_size parameter (default 0 = disabled) splits the protein database into chunks, each building its own FragmentIndex and scoring all spectra, then accumulating hits before a single FDR pass; designed for MHC-II immunopeptidomics and variant-heavy searches where the full index exceeds available memory (#9177)
      - Fix: precursor_mz_error_ppm Percolator feature now subtracts the matched isotope offset; SpectrumAlignment for fragment-error Percolator features now runs at the actual fragment tolerance instead of the 0.3 Da default; calibration pass switched from median ± 3×MAD to 0.5%/99.5% empirical quantiles for more robust tolerance estimation (#9177)
      - Fix: calibration in chunked search mode now uses a strided sample across the full database (instead of only the first chunk), preventing silent calibration no-ops when chunk_size is small; asymmetric calibrated precursor bounds are now correctly preserved through chunked and multi-file search paths instead of being collapsed to the symmetric max (#9185)
      - BREAKING: default precursor isotope error range changed from [-1, +1] to [0, +2]; Orbitrap/timsTOF monoisotopic peak picking fails predominantly upward, so the symmetric range wasted a query slot on rare downward mispicks; matches MetaMorpheus/MSFragger defaults; isotope_error is now also exposed as a Percolator rescoring feature (#9188)
      - SNES (Single-N/Single-C mother-peptide indexing) for non-specific enzyme searches: when peptide:enzyme_specificity=none (e.g. immunopeptidomics), ProSE can index ~2L mother peptides per protein instead of O(L²) sub-peptides, substantially reducing memory and build time; opt-in via new snes_enabled parameter (default false); variable modifications on mothers are not yet supported in v1 (#9191)
      - Fix: SNES mother peptides are now truncated at ambiguous residues (X/B/Z); proteins containing X/B/Z are split into contiguous unambiguous spans and Single-N/Single-C mothers are indexed per span, preventing mother windows that span an ambiguous position (#9224)
      - Fix: FDR:PSM is now deferred (alongside FDR:protein) when -percolator_executable is set, and applied post-rescoring on Percolator q-values. Previously FDR:PSM=0.01 filtered raw HyperScore q-values before Percolator ran and also stripped decoys, causing "No decoys found" and skipping Percolator entirely; fallback files (Percolator skipped/failed) still apply PSM FDR on HyperScore q-values via FalseDiscoveryRate (#9195)
      - Fix: -out_pin output is now a valid, percolator-CLI-consumable .pin file. Previously the header was missing the mandatory SpecId/Label/ScanNr columns and the standard mass/charge/enzyme feature columns (ExpMass, CalcMass, mass, peplen, charge{N}, enzN, enzC, enzInt, dm, absdm), which are populated on hits by PercolatorInfile::preparePin_ but were not declared in the feature list. Both ProSE -out_pin and PercolatorAdapter now build their feature set from the new PercolatorInfile::getStandardFeatureSet() helper so the two emit consistent .pin files (#9195)
      - Fix: FragmentIndex bucket_size is now fixed at 4096 instead of sqrt(N); reduces per-query scan overhead on large immunopeptidomics indices (~11% wall-time reduction on unspecific human searches) (#9203)
      - Fix: PercolatorAdapter sibling binary is now resolved via File::findSiblingTOPPExecutable before the per-file search loop; previously the bare name "PercolatorAdapter" was passed to boost::process which only searches $PATH, causing silent fallback to HyperScore results in dev builds or installs where the OpenMS bin/ directory is not on PATH (#9204)
      - Fix: -out_merged write failure no longer discards per-file outputs. Per-file -out_idxml/-out_pin/-out_qpx/-out_parquet writes now complete before the merged write is attempted, and the merged write is wrapped in try/catch (#9205, #9197 item 1a)
      - Fix: merged idXML write no longer crashes with "Invalid protein reference 'DECOY_...'" when target+decoy shared peptides are present and protein FDR is enabled. Added IDFilter::removeDanglingProteinReferences pass after decoy/protein cleanup (#9205, #9197 item 1b)
    PercolatorAdapter:
      - In-process rescoring backend: PercolatorAdapter now defaults to running Percolator in-process via the new OpenMS::Percolator class (vendored Percolator 3.08 + TRON solver) without requiring an external percolator binary; covers idXML/mzid input with PSM-level FDR; use -use_subprocess true to revert to the external binary path; OSW input, protein-level FDR, and peptide-level FDR still require the subprocess (#9218)
      - -percolator_executable is now optional (not required) when -use_subprocess false (the default); the parameter is still validated when -use_subprocess true (#9218)
      - Added .idparquet input/output support; -in and -in_decoy now accept .idparquet bundles and -out can produce .idparquet output (#9232)
      - Fix: -score:fdr and -best_per_spectrum_only post-filters are now applied when using the in-process backend (default); previously these filters were only applied on the subprocess path, causing different output depending on which backend was used (#9240)
      - Fix: Percolator in-process backend memory leaks fixed; Normalizer singleton was not freed between train()/rescore() calls (~1.7 KB per call) and Logger file handles were not released on destruction; both are now cleaned up in the Percolator destructor (#9257)
    SimpleSearchEngine:
      - Added peptide:enzyme_specificity parameter (full/semi/none) to enable semi-tryptic and non-specific searches (#9112)
      - New annotate:PSM options: num_matched_peaks, matched_b_ions, matched_y_ions, longest_peptide_ion_sequence, fragment_annotation (#9117)
    ProteomicsLFQ:
      - Removed unnecessary group reindexing, added stricter validation (#8752)
      - Arrow/DataFrame/Parquet export for ConsensusMap (#8729)
      - Added -in_feat parameter to accept pre-computed featureXML files, bypassing internal feature finding (#8796)
      - BREAKING: -out_feature_qpx (single file) replaced with -out_qpx (directory); exports quantms.feature.parquet, quantms.psm.parquet, and quantms.pg.parquet following the QPX/quantms schema (#8973, #8974)
      - Added Bruker TimsTOF .d (BRUKER_TDF) input support with Biosaur2-based seed generation; IM_PEAK data path with automatic FWHM estimation and skip of PeakPickerHiRes/PrecursorCorrection; new Seeding:algorithm parameter (#9030)
      - Added PeptideQuantification:seed_apex_rt_tolerance parameter (default 5.0 s, advanced) to FeatureFinderIdentificationAlgorithm; seed features whose detected apex RT deviates more than the tolerance from the seed apex are discarded, removing unreliable extractions (#9102)
      - Added .idparquet and .mzId input support; -ids now accepts .idparquet directories and .mzId files in addition to idXML (#9236)
    MetaProSIP:
      - Added detailed documentation of CSV output column formats (#4400)
        Flags with trailing arguments now produce clearer warnings instead of cryptic "trailing text arguments" errors.
    MSstatsConverter:
      - Added -remove_shared_peptides parameter (default true) to explicitly control whether shared peptides
        (mapping to multiple indistinguishable protein groups) are removed from MSstats output; previously
        this filtering was silent and hardcoded; a warning is now emitted reporting how many hits were dropped (#9068)
    MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerTreeGuided:
      - Added optional spectra file transformation (-in_spectra_files, -out_spectra_files) to transform mzML files along with alignment (#8536)
    FileInfo:
      - Now prints both assigned and unassigned peptide identification counts for FeatureXML and ConsensusXML files (#8395)
      - Added sequence length stats and nucleic acid support for FASTA files (#8643)
    FileConverter:
      - Added MSP file format support (#8650)
      - Added OpenSwath sqMass to XIC Parquet conversion support (#8829)
      - Added experimental Bruker TimsTOF .d directory (BRUKER_TDF) to mzML conversion via BrukerTimsFile; requires WITH_TIMSRUST=ON (#8975)
    IsobaricWorkflow:
      - Fixed mzTab export when processing multiple mzML/idXML pairs (#8519)
      - Handles MS2 spectra without corresponding MS3 in SPS-MS3 workflow (#8592)
      - Arrow/Parquet export for ConsensusMap (#8729)
      - BREAKING: -out_feature_qpx (single file) replaced with -out_qpx (directory); exports quantms.feature.parquet, quantms.psm.parquet, and quantms.pg.parquet following the QPX/quantms schema (#8973, #8974)
      - Added TMT 32-plex and 35-plex quantitation support; isotope correction matrix defaults to identity until calibrated values are provided (#9003)
      - Added .idparquet and .mzId input support; -in_id now accepts .idparquet directories and .mzId files in addition to idXML (#9241)
    SageAdapter:
      - Fixed thread handling - removed duplicate parameter registration (#8441)
      - Added .idparquet output support; -out now accepts .idparquet format in addition to idXML (#9232)
    OpenSwathWorkflow:
      - Priority peptide sampling for iRT calibration (#8373)
      - Decoy generation speed optimizations (#8569)
      - Added SRM support (#8700)
      - Added Parquet chromatogram output support (#8737)
      - Direct Bruker .d (TDF) file input: Bruker TimsTOF files can now be passed directly without prior mzML conversion; requires WITH_TIMSRUST=ON (#9019)
      - Performance: new automatic SWATH wave scheduler reduces wall time on large spectral libraries; batchSize=0 (default) now selects the wave scheduler automatically when working in memory; new advanced parameters innerBatchSize (inner scoring batch size, <=0 for auto), maxConcurrentSwaths (max concurrent SWATH maps in memory, -1 for auto), and outer_loop_threads (legacy nested-OpenMP outer threads, -1 for auto) expose tuning knobs; OSW output is written via a memory-aware buffered writer that flushes when free system RAM falls below a configurable threshold (#9190)
      - Fix: OSW RUN.ID column now stored as INTEGER instead of BLOB; the previous BLOB type caused JOIN queries between the FEATURE and RUN tables to return 0 rows (#9190)
      - Fix: duplicate TLS initialization symbol for PickerPoolShared on macOS arm64/clang; g_picker_pool_shared moved from inline thread_local in MRMTransitionGroupPicker.h to a single definition in MRMTransitionGroupPicker.cpp to avoid multiple weak-symbol emission under Mach-O, which caused linker errors on macOS arm64 (#9223)
    PeakPickerHiRes:
      - New parameter to allow peak cores with no leading flank peaks (#8649)
      - Warns when given IM_PEAK format (per-peak ion mobility) data; partial support via intensity-weighted mean IM per picked peak (#9018)
    PeakPickerIM:
      - Direct Bruker TimsTOF .d directory input: files can now be passed directly without prior mzML conversion; requires WITH_TIMSRUST=ON (#9022)
      - Built-in Sage IM centroiding via new bruker:ms1_centroid_mz_ppm and bruker:ms1_centroid_im_pct parameters; when both are set, centroiding is performed on raw gridded TOF data and the subsequent IM picking step is skipped (#9022)
      - Rejects IM_SPECTRUM format input with a clear error message (#9022)
    Resampler, FeatureFinderCentroided:
      - Now error out with INCOMPATIBLE_INPUT_DATA when given IM_PEAK format (per-peak ion mobility) data that cannot be processed (#9018)
    FileMerger:
      - Documented input/output file type combinations (#8615)
    TextExporter:
      - Added support for XIC Parquet files (#8737, #8738)
    FeatureFinderMultiplex, MultiplexResolver:
      - BREAKING: Parameter `missed_cleavages` renamed to `max_nr_labelled_aas` (#8911)
      - Now errors out with INCOMPATIBLE_INPUT_DATA when given IM_PEAK format (per-peak ion mobility) data (#9018)
    MaRaClusterAdapter:
      - Consensus spectra now annotated with original native IDs, file origins, and cluster size (#8864)
    MetaboliteAdductDecharger:
      - Added multimer detection (dimers, trimers, etc.) with new max_multimer and multimer_log_penalty parameters; features annotated with [nM+adduct]+ style strings (#8888)
    IDConflictResolver:
      - Added rank aggregation resolve method (--resolve_method rank_aggregation) for consensus replicate identifications (#8907)
    GenericWrapper:
      - BREAKING: GenericWrapper tool removed; migrate to direct TOPP tool invocations or TOPPAS workflows (#8981)
    FeatureFinderCentroided:
      - Reworked the underlying algorithm to omit a RAM-costly copy statement. RAM usage is now reduced by around 20% (#9159)
    FeatureFinderAlgorithmPicked:
      - Fix: `mass_trace:mz_tolerance` and `isotopic_pattern:mz_tolerance` parameters were swapped in updateMembers_(); pattern_tolerance_ (used for isotopic-pattern scoring) received the mass-trace value and vice versa; had no effect with default values (both 0.03) but caused incorrect behavior when users tuned the parameters independently (#9247, #9250)
    FeatureFinderMetaboIdent:
      - Added optional "Adduct" column to the TSV input format; uses AdductInfo for m/z calculation from any supported adduct notation (e.g. [M+Na]+, [M-H]-, [2M+H]+); output features are annotated with the adduct; backward-compatible (defaults to [M+H]+ / [M-H]- when omitted) (#9382)
    IDMerger:
      - Added .idparquet input support; -in now accepts .idparquet bundles in addition to idXML and oms (#9232)
      - Fix: merged output now preserves input file order; previously IdentificationRuns were sorted alphabetically by run identifier rather than emitted in the order the input files were given (#9240)
    IDRipper:
      - Added .idparquet input/output support; -in now accepts a merged .idparquet directory and emits one .idparquet output directory per IdentificationRun, mirroring the existing .idXML behavior; output format follows input format (#9237)
    MSGFPlusAdapter:
      - Added .idparquet output support; -out now accepts .idparquet format in addition to idXML (#9232)
    IDFileConverter:
      - Added .idparquet input/output support; can now convert to and from the native .idparquet identification Parquet bundle (#9232)
    PeptideIndexer:
      - Added .idparquet input/output support; -in and -out now accept .idparquet bundles in addition to idXML (#9396)
    IDScoreSwitcher:
      - Added .idparquet input/output support; -in and -out now accept .idparquet bundles in addition to idXML (#9396)
    PSMFeatureExtractor:
      - Added .idparquet input/output support; -in, -out and -out_type now accept .idparquet in addition to idXML and mzid (#9396)
    IDFilter:
      - Added .idparquet input/output support; -in, -out and the whitelist/blacklist peptide inputs now accept .idparquet bundles in addition to idXML (#9396)
    OpenSwathChromatogramExtractor:
      - Compound identifiers in output chromatograms for metabolite targets now use the CompoundName user-param (compound_name field) instead of the compound id, aligning with OpenSwathWorkflow behavior (#9271)
    MetaboliteSpectralMatcher:
      - New ccs_error_percent parameter (default 0 = disabled) filters spectral-library candidates by relative CCS error |observed − library| / library × 100 %; missing observed CCS is non-filtering (Skyline convention); mzTab output gains opt_observed_ccs, opt_library_ccs, and opt_ccs_error_percent columns; 1/K0 drift times are converted to CCS automatically (#8784, #9412)
  New tools:
    - FeatureLinkerWNet: groups corresponding features across multiple label-free maps using Wasserstein (optimal transport) distance over (m/z, RT) space; solves a minimum-cost network flow problem via the wnetalign library; supports Da and ppm m/z tolerances, L1/L2/L∞ distance metrics, and intensity normalization
    - OpenSwathInfer: Added topp tool for performing peptidoform, peptide, protein and gene inference for OpenSwath analysis. (#9280) 
    - OpenSwathExport: Added topp tool for exporting OpenSwathWorkflow results to TSV/Parquet files (#9377)

OpenMS Library:
  Added:
    - Statistical functions ported from PyProphet (#8524)
      - KernelDensityEstimation: FFT-based kernel density estimation using Silverman's algorithm
      - RankData: Rank computation with multiple tie-handling methods (average, min, max, dense, ordinal)
      - MultipleTesting: FDR control and multiple testing corrections (computeModelFDR, pEmp, qValue, pi0est, lfdr, pNorm)
    - PeakFileOptions: setPrecursorMZRange()/getPrecursorMZRange() for precursor m/z range filtering (#8526)
    - OnDiscMSExperiment: Full PeakFileOptions support with filtering (#8512)
    - ParamIterator: STL-compatible iterator type aliases (iterator_category, value_type, etc.) (#8362)
    - PeptideIndexer settings stored as metavalues in SearchParameters (#8489)
    - LightTransition methods for MRMAssay, MRMDecoy, TransitionTSVFile, TransitionPQPFile (#8544)
    - SpectrumAnnotator: addPeakAnnotationsToPeptideHit() method (#8421)
    - iRT/CiRT transition files in share/OpenMS/CHEMISTRY/ (#8372)
    - CalibrationWorkflow: refactored OpenSwathWorkflowCalibration workflow logic into a separate reusable CalibrationWorkflow class. (#8743)
    - Fragment index open search expanded with modification discovery and FDR filtering (#8414)
    - CCS (collisional cross section) support for ion mobility data (#8735)
    - Rasterize2D function for MSExperiment to rasterize 2D ion mobility data (#8739)
    - SequenceCoverage: Reusable API extracted for computing protein sequence coverage (#8728)
    - Arrow/DataFrame/Parquet export for ConsensusMap with batch and streaming APIs (#8729)
    - PSM DataFrame export from PeptideIdentificationList (#8632)
    - SpectrumNativeIDParser class for parsing spectrum native IDs (extractScanNumber, getRegExFromNativeID, isNativeID) (#8637)
    - ArrowExport helper for exporting MSExperiment to Apache Arrow/Parquet formats with configurable layouts and compression (#8655)
    - ProFormaParser: Full ProForma v2 notation parser with AST representation (#8648)
      - Recursive descent parser for peptidoforms with modifications, cross-links, and chimeric spectra
      - Supports all ProForma v2 features: CV accessions (UNIMOD, MOD, RESID, XLMOD, GNO), mass deltas, formulas, glycans, info tags
      - Bidirectional conversion: parse() and toString() with LOSSLESS/CANONICAL write modes
      - AASequence integration: toAASequence()/fromAASequence() with configurable conversion policies
      - Mass calculation: getMonoWeight(), getMZ() for peptidoforms and ions
      - JSON serialization for AST persistence and interoperability
      - Theoretical spectrum generation via tryGenerateSpectrum() for single-chain and cross-linked peptides
        Uses TheoreticalSpectrumGenerator for linear peptides, TheoreticalSpectrumGeneratorXLMS for cross-links
    - MzPAF: HUPO-PSI mzPAF (Peak Annotation Format) parser and serializer (#8686). Parse fragment ion annotations: MzPAF::parse("y4-H2O^2/3.2ppm*0.75"). pyOpenMS bindings included
    - USI: Universal Spectrum Identifier support per HUPO-PSI standard (#8684)
      - USI class for parsing and building USI strings (mzspec:collection:msrun:index_type:index[:interpretation])
      - Static methods: tryParse() (non-throwing), isValidUSI(), createFromScanNumber(), createFromNativeID()
      - Uses SpectrumNativeIDParser for robust scan number extraction from vendor formats
      - PeptideIdentification.buildUSI() for generating USIs from identification results
      - TextExporter USI output with optional dataset_id/ms_run parameters
      - pyOpenMS bindings included
    - OpenSwathWorkflow:
      - Added Parquet-based archive (.oswpq) to store spectral library information and multi-run feature scores. (#8813)
      - Added support for reading/writing Parquet extracted ion chromatogram files (.xic) and extracted ion mobilogram files (.xim). (#8737, #8871)
    - FeatureFindingMetabo: Added ion mobility support with local_im_range parameter for coeluting mass trace filtering (#8758)
    - IDMapper: Preserve upstream identification data processing metadata when annotating featureXML/consensusXML (#8852)
    - ProteinGroupArrowExport: new class for exporting protein group quantification data to Parquet per the QPX pg schema; one row per protein group per run file with per-channel intensities (#8973)
    - ArrowSchemaRegistry: centralizes all Arrow/Parquet schema definitions with strict (write) and subset (read) validation modes (#8970)
    - PSMArrowIO: new class for reading and writing OpenMS identification data as a native .idparquet directory bundle (four parquet files: psms.parquet, proteins.parquet, protein_groups.parquet, search_params.parquet); round-trip lossless from PeptideIdentification/ProteinIdentification (#9225, #9232)
    - FileTypes::IDPARQUET: new enum value for the .idparquet identification Parquet bundle directory format; FileTypes::isDirectoryType() returns true for both IDPARQUET and BRUKER_TDF (#9225)
    - QPXFile::importFromArrow(): new free-standing reader that converts a PSMSchema Arrow table directly to a PeptideIdentificationList without ConsensusFeature linkage; refactored from ConsensusMapArrowIO (#9225)
    - FileTypes::FEATUREPARQUET, FileTypes::CONSENSUSPARQUET: new enum values for the .featureparquet and .consensusparquet directory-based Parquet bundle formats; FileHandler dispatches these to FeatureMapArrowIO and ConsensusMapArrowIO respectively (#9242)
    - FeatureGroupingAlgorithmWNet: new class for grouping features across multiple maps using Wasserstein (optimal transport) network flow over (m/z, RT) space; WNetMatcher handles pairwise matching and union-find consensus building (#8992)
    - ModifiedSincSmoother: new class for profile data smoothing using Modified Sinc interpolation with configurable degree, window size, and passband correction coefficients (#8217)
    - BrukerTimsFile: experimental reader for Bruker TimsTOF .d directory format (BRUKER_TDF file type); supports DDA-PASEF, DIA-PASEF, and raw frame-level 4D access; requires CMake option WITH_TIMSRUST=ON (#8975)
    - BrukerTimsFile: tiered scan→1/K0 calibration with three fallback levels: Bruker SDK → rational function from TimsCalibration table (open-source) → linear; RationalScan2ImConverter added for the rational function model (#8999)
    - TMTThirtyTwoPlexQuantitationMethod, TMTThirtyFivePlexQuantitationMethod: new classes for TMT 32-plex and 35-plex isobaric quantitation; isotope correction matrix defaults to identity until calibrated values are provided (#9003)
    - IMPeakType enum (IM_PROFILE, IM_CENTROIDED, UNKNOWN) added to SpectrumSettings to track per-peak ion mobility processing state independently of data layout (IMFormat); IMFormat::CENTROIDED deprecated (#9007)
  Changes:
    - BREAKING: Matrix<T> no longer inherits from Eigen; uses std::vector<T> for storage (#8511)
    - BREAKING: Eigen moved from PUBLIC to PRIVATE linking - downstream users no longer need Eigen headers (#8511)
    - BREAKING: IDFilter::updateProteinReferences() renamed to removeDanglingProteinReferences() (#8500)
    - BREAKING: Exception::InvalidSize constructor requires mandatory context message parameter (#8437)
    - BREAKING: FileWatcher moved from OpenMS/SYSTEM/ to OpenMS/VISUAL/ (GUI library) (#8591)
    - BREAKING: PeptideAndProteinQuant channel identifiers changed from Int to UInt (#8516)
    - BREAKING: Plain enums migrated to enum class (Sample::SampleState, OpenMS_OS, etc.) (#8622)
    - ILPDCWrapper: Performance improvement using std::unordered_map (~3.5x speedup) (#8618)
    - DELETION: deleted Class LinearResampler and refactored functionality into LinearResamplerAlign (#9153)
    - OpenSwath: Use unordered_map for O(1) lookups, improving performance (#8651)
    - DataValue: Enhanced conversion error messages with type and value context (#8572)
    - BayesianProteinInferenceAlgorithm: Now requires single merged ProteinIdentification run (#8480)
    - EMGScoring: Default init_mom changed from false to true for consistency (#8593)
    - ElementDB: Standardize map lookup pattern (#8660)
    - IDFilter: Eliminate code duplication (#8662)
    - Iterator patterns, container checks, and memory allocation optimized in hot paths (#8656)
    - Simplified redundant boolean return statements (#8659)
    - OPENMS_LOG_WARN now writes to std::cerr instead of std::cout (#8754)
    - External Enzymes.xml is now optional — enzyme definitions are built-in by default (#8409)
    - Date class refactored from QDate inheritance to composition (#8710)
    - Thread-safe logging with OPENMS_LOG_* macro optimizations (#8620)
    - MetaInfo: Iterator support and merge optimizations (#8621)
    - BREAKING: QuantmsIO renamed to QPXFile; PSM Parquet export rewritten using QPX pattern (#8756)
    - Vectorized dotprodScoring and manhattanScoring in StatsHelpers using Eigen (#8848)
    - Vectorized cross-correlation in OpenSwath Scoring using Eigen (#8849)
    - Data provider pattern extracted for ModificationsDB, RibonucleotideDB, ProteaseDB, and RNaseDB (#8775, #8779)
    - Use unordered_map in PrecursorPurity, PeptideProteinResolution, and PeptideIndexing for faster lookups (#8806, #8763)
    - OpenSwath scoring speedups: cap XCorr maxdelay, vectorize DIAScoring, hoist loop-invariant computations, pass SwathMap by const& (#8787, #8785)
    - BREAKING: ChromatogramPeak::IntensityType changed from double to float for consistency with Peak1D (#8857)
    - BREAKING: IMFormat enum values renamed for clarity: CONCATENATED → IM_PEAK, MULTIPLE_SPECTRA → IM_SPECTRUM (#8993)
    - BREAKING: IMFormat::MIXED removed; determineIMFormat(MSExperiment) replaced with determineIMFormat(MSExperiment, int ms_level) requiring explicit MS level for unambiguous format detection (#9011)
    - AccurateMassSearchEngine: Performance improvement when use_feature_adducts is set and a specific adduct is observed; only that adduct is evaluated instead of the full list (fixes #5867) (#8635)
    - BREAKING: Transitive Qt and other includes trimmed from core KERNEL and METADATA headers (ConsensusMap.h, FeatureMap.h, ProteinIdentification.h, SpectrumSettings.h, ExperimentalSettings.h); downstream code relying on these transitive includes must now include headers directly (#8946)
    - Residue: added function that returns hydrophobicity (#9179)
    - HydrophobicityProfile: added a class used for calculating hydrophobicity profiles of peptides and hydrophobic moments in peptides (#9179)
    - SysInfo: added getFreeSystemMemory() returning currently available physical RAM in KB; on Linux this uses MemAvailable from /proc/meminfo so reclaimable page-cache is counted as available (#9190)
    - OpenSwathWorkflowScheduler: new class encapsulating the SWATH wave scheduling logic extracted from OpenSwathWorkflow; manages compound batches, per-SWATH scoring job queues, and deferred OSW output with memory-based flushing (#9190)
    - OpenSwathOSWWriter: added getRowCount() and estimateMemoryUsage() for memory-aware buffered output (#9190)
    - Percolator: new class providing an in-process semi-supervised target/decoy rescoring engine based on a vendored subset of Percolator 3.08 (with TRON solver); exposes rescore() for combined train+score, train()+score() for split workflows, and saveModel()/loadModel() for model persistence; note: concurrent calls across instances race on process-wide Percolator statics — serialize at the call site (#9218)
    - BREAKING: OpenSwath::Scoring: deprecated pointer-based (C-array) overloads of NormalizedManhattanDist, RootMeanSquareDeviation, SpectralAngle, normalize_sum, and calcxcorr_legacy_mquest_ removed; use the std::vector& overloads (#9252)
    - BREAKING: ChromatogramExtractor::prepare_coordinates(TargetedExperiment) overload removed; callers should convert via OpenSwathDataAccessHelper::convertTargetedExp and use the LightTargetedExperiment overload; the Python API in pyOpenMS is unchanged (#9271)
    - OpenSwath::LightCompound gained rt_start and rt_end fields (NaN by default) to carry per-compound RT extraction ranges; populated by OpenSwathDataAccessHelper::convertTargetedExp from TargetedExperiment::Peptide/Compound rts vectors (#9271)
    - OpenSWATH inference infrastructure ported from PyProphet (#9280)
      - OpenSwathInferenceData: compact row types (LevelContextInputRow, LevelContextResultRow, IPFPrecursorRow, IPFTransitionRow, IPFAlignmentRow, IPFResultRow) and enums (InferenceLevel, InferenceContext) used by all inference classes
      - OpenSwathInferenceConfig: configuration structs (ErrorEstimationConfig, LevelContextInferenceConfig, PeptidoformInferenceConfig) that mirror the PyProphet CLI defaults
      - LevelContextInference: file-format-agnostic context inference for peptide-, protein-, and gene-level rows using statistical methods from MultipleTesting/KernelDensityEstimation; adapted from Rosenberger et al. Nat. Methods 2017
      - OpenSwathGeneInference: gene-level context inference wrapping LevelContextInference
      - OpenSwathPeptideInference: peptide-level context inference wrapping LevelContextInference
      - OpenSwathProteinInference: protein-level context inference wrapping LevelContextInference
      - OpenSwathPeptidoformInference: peptidoform (IPF) inference implementing the Inference of PeptidoForms algorithm
      - OSWFile: new methods readIPFPrecursorData(), readIPFTransitionData(), readIPFAlignmentData(), readIPFAlignmentData(double), writeIPFResults(), readLevelContextData(), writeLevelContextResults(), readRunBasenames() for inference workflows
      - KernelDensityEstimation: bandwidth fallback for degenerate inputs (all-zero p-values) now matches PyProphet behaviour, guaranteeing a strictly positive bandwidth
    - OpenSWATH export infrastructure ported from PyProphet (#9377)
      - OpenSwathExportConfig: configuration structs (FilterConfig, ResultsConfig, MatrixConfig, ParquetConfig) for controlling score filters, output format, pivot-matrix dimensions, and Parquet compression
      - OpenSwathExportData: shared data structures (FeatureRow, ProteinRow, etc.) used across all export paths
      - OpenSwathMatrixExporter: builds peptide- and protein-level score matrices from .osw feature data with configurable top_N selection
      - OpenSwathParquetExporter: writes per-feature score tables to Parquet format via Apache Arrow
      - OpenSwathResultsExporter: exports combined results in TSV and Parquet formats; reads gene-decoy and transition-annotation columns from OSWFile
      - OSWFile: extended SQL queries to include gene decoy flags and transition annotation fields required by the new export classes

Fixes:
  - Fix inverted use_all_hits logic causing NucleicAcidSearchEngine crash with multiple hits per spectrum (#8542)
  - Fix LogConfigHandler: flush buffers on stream removal and restore streams when lowering log level (#8440)
  - Fix Heavy path decoy duplicate detection to use modified sequences (#8575)
  - Fix decoy generation with improved duplicate detection and speed optimizations (#8569)
  - Fix MetaboliteSpectralMatching GNPS library compatibility and COMPOUND_NAME support (#8163)
  - Fix uninitialized variable warning for best_rate in MetaProSIP.cpp (#8396)
  - Fix spectrum/chromatogram filters to properly handle DataArrays (#8645)
  - Fix UniqueIdGenerator seed collision in parallel pipelines by mixing process ID into seed (#8678)
  - Correct defaultArrayLength in MzMLFile_negative_offsets.mzML test file (#8672)
  - Remove unused variable block_start in FileFilter (#8399)
  - Fix SIMD type mismatch and unaligned memory access in Base64 decoding (ARM64 crash) (#8689)
  - Fix empty GENE table causing PQP file reading to return zero transitions (#8688)
  - Fix PeptideIndexer AhoCorasick segfault for short peptides (#8685)
  - Fix redundant PRAGMA foreign_keys execution in OMSFileStore
  - Fix potential memory leak in SwathFile::loadMzXML on exception by using std::unique_ptr
  - Fix: disable auto_irt and ignore tr_irt_priority_sampling when linear_irt_file is provided in OpenSwathWorkflow (#8830)
  - Fix MSstatsConverter to allow subset of experimental design files (#8846, fixes #7314)
  - Fix massdev_score denominator to count only observed transitions instead of total (#8831)
  - Fix OpenSwathWorkflow run_id mismatch between Parquet/mzML XIC files and OSW/sqMass output (#8833)
  - Fix OpenSwathWorkflow batch counting and loop bounds for empty compound sets (#8790)
  - Fix OpenSwathWorkflow run_id type mismatch between FEATURE table RUN_ID (INTEGER) and RUN table ID (BLOB) in OSW-Sqlite output (#8869)
  - Fix IDMapper duplicate spectrum reference insertion when the same spectrum is mapped multiple times (#8905)
  - Fix segfault in FeatureLinkerUnlabeledKD with charge_merging=Any when all candidate features have a non-matching charge, causing best_index to remain unset (#8944)
  - Fix TOPPView performance regression when right-clicking in large mzML files (#8997)
  - Fix: TOPPView: prevent segfault on extreme zoom in 1D view in SNAP intensity mode; when the visible m/z range contains no peaks the intensity range collapsed to [0, 0], causing divide-by-zero in dataToWidget_ and a crash in Qt's painter; now falls back to the layer's overall intensity range (#9206, #9263)
  - Fix: ChromatogramExtractor::prepare_coordinates (TargetedExperiment overload) now honours the ms1_isotopes parameter; a `&& false` guard introduced in 2018 silently disabled the isotope-coordinate block, so callers passing ms1=true with ms1_isotopes > 0 received fewer chromatograms than requested; the LightTargetedExperiment overload was unaffected (#7284, #9270)

Documentation:
  - Comprehensive documentation for Targeted Quantitation algorithms (#8588)
  - Retention time units [s] added to TOPP tool parameter descriptions (#8597)
  - FileMerger input/output file type combinations documented (#8615)
  - ProteomicsLFQ automatic median normalization behavior documented (#8438)
  - ProteomicsLFQ FAIMS support documented (#8478)
  - pyOpenMS wrapping guide for classes with deleted/private constructors (#8561)
  - Parameter direction annotations (@param[in], @param[out], @param[in,out]) across 95+ header files (#8507)
  - AGENTS.md AI coding guidance added and improved (#8537, #8560, #8563)
  - Test creation documentation updated with modern test file template (#8548)

Build System:
  - macOS notarization with timestamping integrated into CI (#8486, #8494, #8527)
  - CMAKE_PREFIX_PATH handling fixed for Parquet support (#8370)
  - Qt subpackages used instead of full Qt metapackage on macOS (#8368)
  - OpenMP validation: CMake fails if OpenMP requested but not found (#8368)
  - External libraries from Debian repos to prevent deb package conflicts (#8496)
  - pytest fixtures replace fragile import env hacks in pyOpenMS tests (#8594)
  - Security patterns added to .gitignore (#8545)
  - setuptools deprecation warnings fixed for pyOpenMS data directories (#8484)
  - Configure return value checking in CI packaging (#8515)
  - pyOpenMS build system modernized with py-build-cmake and cibuildwheel (#8530)
  - Claude GitHub Actions workflows added for CI automation (#8675, #8676)
  - IsoSpec and eol-bspline converted to proper CMake library targets (#8331)
  - Arrow 23+ compatibility: removed version pin, CURL workaround (#8679)
  - uv made optional for isolated build environments (#8706)
  - CMake 4.x compatibility: exclude MSVC runtime DLLs from runtime dependency resolution (#8880)
  - Fix pyOpenMS dev build RPATH: BUILD_WITH_INSTALL_RPATH now conditional on NO_DEPENDENCIES to prevent libOpenMS.so not found (#8892)
  - Correctly locate a locally installed nanobind in CMake (#8874)
  - Fix pyOpenMS MSVC compile-time error caused by nanobind __forceinline expansion in heavily templated code (#8933)
  - Fix Windows CI Release builds: removed erroneous /Od /Ob0 flag override that caused all Windows CI Release binaries to be unoptimized since 2021; builds now use CMake defaults (/O2 /Ob2) (#8961)
  - Arrow/Parquet made a required dependency; WITH_PARQUET CMake option removed (#8991)
  - Qt6::Core removed from libOpenMS PUBLIC CMake link dependencies; downstream CMake targets must now explicitly link Qt6::Core if needed (#8965)
  - Minimum Boost version bumped to 1.81 (#9042, #9095)
  - Qt6 find_package guarded by WITH_GUI block; Qt is no longer needed for non-GUI TOPP tool builds (#9041)
  - yaml-cpp bumped to 0.9.0 in tool_description_lib; fixes broken hash/map type parsing in YAML CTD config files (#9056)
  - OpenMP SIMD: when the OpenMP runtime is absent (e.g. on macOS without libomp), CMake now falls back to -fopenmp-simd so that `#pragma omp simd` directives still enable auto-vectorisation; the flag is applied PRIVATE to all OpenMS targets (#9267)


------------------------------------------------------------------------------------------
----                                OpenMS 3.5.0     (Released December 2025)         ----
------------------------------------------------------------------------------------------
NOTICE: 3.5.0 was the last official release for MacOS on Intel processors.
If you need support for OpenMS on that platform moving forward, please contact us.

General:
 - speed improvements:
    - loading .gz files is about 7% faster (#8069)
    - loading of mzML files with more than than m/z+intensity (e.g. ion mobility) is 20-40% faster (#8074)
    - loading of mzML files is 7-25% faster in general (SIMD ASCII conversion) (#8105)
 - linux arm64 support:
	- OpenMS releases now include a .deb for arm64 machines
    
Dependencies:
    - PyOpenMS now depends on Autowrap 0.24.0
    - PyOpenMS now supports Cython 3.1
    - CMake now accepts Eigen 5 in addition to Eigen 3.4+ (#8366)
    - Apache Arrow/Parquet integration for high-performance columnar data export (#8091, #8145)

PyOpenMS:
    - PyOpenMS now has wheels for arm64 linux machines
	- PyOpenMS wheels are now available for Python 3.14 on all supported operating systems
	- Parquet support enabled in pyopenms wheels (#8422)
	- BREAKING: DataFrame column names standardized to lowercase snake_case for PEP 8 compliance.
	  Affected methods: MSSpectrum.get_df(), MSChromatogram.get_df(), ConsensusMap.get_metadata_df(),
	  FeatureMap.get_df(). Example changes: 'RT' -> 'rt', 'MZ' -> 'mz', 'nativeID' -> 'native_id',
	  'precursorMZ' -> 'precursor_mz'. Update code that references old column names.
    - Pythonic convenience methods added:
      - __len__() for MSSpectrum, MSChromatogram, MSExperiment, AASequence (#8151, #8415, #8417)
      - __str__() and __repr__() for core classes (#8429)
      - Python accessors for drift time on MSSpectrum and OpenSwathSpectrum (#8423)
    - New Python bindings for Mobilogram and MobilityPeak1D classes (#8377)
    - DataFrame wrapper for MSSpectrum with get_df() method (#8435)
    - Enum class support in Python bindings with IntEnum (#8405)
    - Static methods to query enum names for METADATA classes (#8353)
    - Fix: PyOpenMS import no longer affects Python locale settings (#8322)
    - Improved pyOpenMS documentation for Feature, MRMFeature, FeatureMap classes (#8247)

TOPP tools:
  Changes:
    FileFilter:
      - Filter RT by blocks of MS levels (#8239)
    SageAdapter:
      - Improved parameter documentation and tolerance validation (#8259)
      - Now correctly passes threads parameter via RAYON_NUM_THREADS (#8260)
    CometAdapter:
      - All enzymes now available by adding CometIDs to database (#8280)
    DecoyDatabase:
      - Added repeated shuffle option for improved decoy generation (#8339)
    MassTraceExtractor:
      - support for Bruker Ion Mobility (experimental). Note: requires IM peak picked data.
    FeatureFinderCentroided, FeatureFinderMetabo, FeatureFinderMultiplex:
      - FAIMS support (experimental): Automatic detection and separate processing of FAIMS compensation voltage (CV) groups.
        Features from different CVs representing the same analyte are merged by default.
    FeatureFinderMetaboIdent, FeatureFinderIdentification:
      - FAIMS support (experimental): Automatic detection and separate processing of FAIMS compensation voltage (CV) groups.
        Features from different CVs representing the same analyte are merged by default.
      - Bruker TimsTOF ion mobility support (experimental): Requires concatenated IM spectra in mzML format
        (use msconvert with --combineIonMobilitySpectra option). IM values can be specified in the input TSV/idXML.
    NucleicAcidSearchEngine:
      - add support for global fixed modifications as a search parameter
    Digestor:
      - supports replacing ambiguous amino acids (X,B,J,Z) in the FASTA input with random unambiguous amino acids in the output (#8167)
    all:
      - show load/store progress for files in all TOPP tools (#8041)
    IonMobilityBinning:
      - Detect FAIMS data automatically and split output per FAIMS compensation voltage (CV)
    FLASHDeconv:
      - Major update with improved scoring, FDR estimation, and isobaric quantification support (#8257)
      - Automatic mass tolerance estimation from data
      - Per-MS-level deconvolved spectrum outputs
      - TopFD version 1.7 compatible feature and TSV export formats
      - Improved precursor mass assignment for MSn spectra
  Added Tools:
    - OpenNuXL - A peptide-RNA/DNA cross-linking search engine
    - ProSE - Experimental peptide database search engine using a fragment index (FI) and the new ProSEAlgorithm
    - FeatureFinderLFQ (experimental) - Feature detection for label-free proteomics DDA-LFQ based on the Biosaur2 algorithm with support for FAIMS and TimsTOF ion mobility
    - PeakPickerIM - Ion mobility peak picker for TimsTOF and other IM data. Supports three methods: mobilogram-based,
      clustering, and elution profile-based picking. Supports both in-memory and low-memory streaming modes. (#8177)
    - IsobaricWorkflow (experimental) - Simple, targeted, fast workflow for isobaric quantification (#7298)
  Removed Tools:
    - OpenPepXLLF - Experimental search for cross-linked peptide pairs in tandem MS spectra (showed inferior performance in benchmarks)
    - IDMassAccuracy - Calculates a distribution of the mass error from given mass spectra and IDs
    - SpecLibCreator - Creates an MSP formatted spectral library
    - SpecLibSearcher - Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library

GUI tools:
 - fix TOPPAS crash when using TOPP tools with multiple output formats (#8120)
 

OpenMS Library:
  Added:
    - PeakPickerIM (experimental): New algorithm for ion mobility peak picking with three methods (mobilogram, cluster, elution profiles). (#8177)
    - IMFormat: Added CENTROIDED and UNKNOWN format types for ion mobility data. (#8177)
    - MSSpectrum/SpectrumSettings: Added setIMFormat()/getIMFormat() API for per-spectrum ion mobility format tracking. (#8177)
    - FeatureFinderAlgorithmBiosaur2 (experimental): Feature detection algorithm for label-free proteomics DDA-LFQ based on the Biosaur2 algorithm with support for FAIMS and TimsTOF ion mobility.
    - PeptideHit: Added TargetDecoyType (TARGET, DECOY, TARGET_DECOY, UNKNOWN) and setTargetDecoyType()/getTargetDecoyType(); supports target+decoy peptide hits.
    - IDScoreSwitcherAlgorithm: Added findScoreType() method for generic score type detection. Checks if main score matches requested ScoreType (PEP, QVAL, FDR, etc.) or finds it in meta values..
    - ProteinHit: Added TargetDecoyType (TARGET, DECOY, UNKNOWN) and setTargetDecoyType()/getTargetDecoyType().
    - Both: Added isDecoy().
    - unify isotopic distributions (coarse vs. fine) for EmpiricalFormulas with charge (#8099)
    - FragmentIndex (experimental): New fragment index for fast peptide fragment lookup supporting FI-based peptide database search.
    - ProSEAlgorithm (experimental): Library algorithm leveraging FragmentIndex for peptide database search; used by the ProSE TOPP tool.
    - AhoCorasick: Improved high-performance string matching algorithm with path compression (#8269, #8304)
    - HashGrid: Exposed cellIndexAtClusterCenter method (#8318)
  Changes:
    - removed `assignRanks` and `sortByRanks` in PeptideIdentifications and sort and filter by score instead. Also removed `updateHitRanks` in IDFilter (#7991)
    - remove rank member in PeptideHit and store ranks as meta value (for backwards compatibility). (#7997)
    - std::vector<PeptideIdentification> now is encapsulated in a class PeptideIdentificationList.
    - Zlibcompression using zlib (not Qt) and Base64 decoding for zlib-compressed data using SIMD (not Qt) (#8161)
    - Exception::InvalidSize now includes mandatory context message (#8437)
    - Matrix::operator== no longer throws assert when comparing different-sized matrices (#8305)
    - Removed boost::smart_ptr dependency, using std::shared_ptr instead (#8405)
    - C++20 modernization: std::erase_if, range-based for loops, default constructors (#8229, #8230, #8233)
  New Features:
    - FAIMSHelper: dataset-wide FAIMS detection; ignore DRIFTTIME_NOT_SET sentinel; improved warning
    - IMDataConverter::splitByFAIMSCV: retain MS2 without explicit FAIMS CV by assigning to prior FAIMS CV
    - added `EnzymaticDigestion.semiSpecificDigestion_()`
    - ProteaseDigestion: add support for semi-specific digestion (#8130)
    - TransformationModelLowess: Add option to automate span selection via cross-validation (#8166)
    - OpenSwath:
      - Added automated iRT calibration using input transition list (#8146)
      - Added automated RT, m/z, and IM extraction window estimation based on iRT calibration (#8188)
      - Added lowess span grid search params and updated documentation for OpenSwathWorkflow TOPP tool (#8297)
      - Added priority inclusion list for iRT sampling from PQP when using automated iRT calibration (#8373)

Fixes:
  - Fix overlap test in crowded FAIMS data (#8418)
  - Fix window estimation when no MS1 maps available in OpenSwath (#8308)
  - Fix column header filenames for all maps in Decharger/MetaboliteAdductDecharger (#8265)
  - Fix ternary operator misuse in FileMerger append_method logic (#8263)
  - Fix Qt6 deprecation warnings (#8248)
  - Fix FileNotFound exception misuse for file access errors (#8274)
  - Fix peaks being skipped in OpenSwath wide boundary selection method (#8316)
  - Fix mzTab-M validation errors for missing identification and database metadata (#8363)
  - Fix negative offset handling in mzML readers (#8336)

Documentation:
  - Build instructions rewritten for macOS and Linux (#8042)
  - Comprehensive documentation added to DeMeanderize tool (#8264)


------------------------------------------------------------------------------------------
----                                OpenMS 3.4.1     (May 2025)                       ----
------------------------------------------------------------------------------------------

Documentation:
  - TOPPAS: tutorial update (#8025)
  
Fixes: 
 - TOPPView: fix a few error messages boxes (in IM frames, and 2D projections) (#8047)
 - RANSAC algorithm: avoid r^2 is zero; fixes crash in OpenSwathWorkflow (#8052 )

------------------------------------------------------------------------------------------
----                                OpenMS 3.4.0     (May 2025)                       ----
------------------------------------------------------------------------------------------

General:
- OpenMS now expects a compiler that supports C++20
- OpenMSInfo TOPP tool now informs about custom CXX compile flags (#7846)
- speed improvements:
  - TOPP tool FeatureFinderCentroided TOPP tool is 28-44% faster (internally GaussTraceFitter is 4-7x faster) (#7950)
  - mzML parsing is 6% faster (#7850)
  
Dependencies:
- switch to Qt 6 (>= 6.5)  (#7525)

OpenSwath:
- changes to -out_features (# 7793)
	- Deprecate .tsv feature output
	- Deprecate -out_osw, -out_tsv. -out_features is used for outputting .osw or .featureXML files and file format is autodetected.
	- Enable outputting any feature file (.osw or .featureXML) from a .tsv library 
- add warning message if irt_im_extraction_window not set and im_window is set (#7813)
- add auto add up spectra across the peak width in retention time for ion mobility extraction (#7742)
- add peak-picking for extracted ion mobilogram (#7759)
- add ion mobility scoring for identifying transitions for IPF (#7760)
- bug fix: pass `im_range` to `scoreIdentification_` instead of computing it in the function. Addresses issue #7883. (PR #7885)

Misc:
- pyOpenMS: improve developer experience (installation/compilation) (#7735)
- TOPP tools and TOPPAS/ExecutePipeline return exit code 14 when external third-party tools (such as Comet or Sage) are not found (#7758)
- ProteinInference tool: Algorithm:score_type allows switching the main score (e.g., "RAW", "PEP") for BasicProteinInference. (#7769)
- README.md: Added dedicated "Building OpenMS" section with direct links to platform-specific build instructions (#7912)
- TOPPAS: tutorial now includes Pipeline and Node updating (#8025)

Fixes:
- fix AScore algorithm when counting phosphorylation events (#7905)
- add option to PeakFileOption to ignore loading of chromatograms or spectra from mzML (#7901)
- fix Doxygen Docs contain stty warning for TOPP tool output (#7865)
- fix various issues with the Windows installer (#7995, #7996, #8001)
- TOPPView: open theoretical spectra immediately in 1D to avoid crash when opening in 3D mode (#8019)

Library:
- IDScoreSwitcherAlgorithm: Added switchToScoreType and switchBackScoreType methods for score switching and reversion. (#7769)
- made FASTA file reader more robust in presence of whitespaces (#7960)
- add 3' cyclophosphate version of RNAse 4, fix handling of cleavage gains (#7928)

Removed tools:
  - XTandemAdapter
  - MascotAdapter (note: MascotAdapterOnline still exists) (#7927)

------------------------------------------------------------------------------------------
----                                OpenMS 3.3.0                                      ----
------------------------------------------------------------------------------------------

What's new:
- Changes breaking backward compatibility: 
  - the QualityControl TOPP tool has some renamed parameters and supports output directories (#7497)
- Low-level  peak extraction helper for MSExperiments (#7628)
- pyOpenMS: use Numpy2 (#7539)
- Docker files are now part of the main OpenMS repo (#7303)
- Added new functionality to SageAdapter + compatibility with new Sage versions (#7577)

Library:
- TOPPView: 
  - offer Ion mobility view from 2D spectra view (#7423)
  - view ion mobility frames, irrespective of its MS level (formerly only MS1 was supported) (#7427)
- OpenSwath: 
  - Add output on peak shape metrics to .osw file (#7222)
  - Update IonMobilityScoring to use Mobilogram Kernel datastructure (#7587)

Misc:
- FileInfo:
    - support MzTab files (#7568)
- TOPPAS 
    - supports writing results to output directories  (for TOPP tools that have such parameters) (#7497)
    - TOPPAS tutorial enhanced (#7497)
- TOPPAS & TOPPView: new splash screen with new OpenMS logo (#7712)
- FeatureFinderMetabo
    - added report_smoothed_intensities parameter (#7594)
- Write out percolator features in search engine adapters (by default, no PSMFeatureExtractor is needed)
- Add isobaric correction defaults for tmt6plex and 11plex (#7601) 
- Decoy phosho added to unimod.xml (#7612)
- Add additional convenience functions for MSExperiment (#7630)
- Improve file list comparison (#7645)
- pyOpenMS: Add more convenient constructor for AASequence (#7650)
- Add annotate_features param in Deisotoper.cpp (#7643)
- internal enhancements (#7652)

Fixes:
- OpenMS does not compile when using GLPK (instead of COINOR) (#7626)
- fix MassCalculator error ('residue type has no name') (#7698)
- pyOpenMS
  - get_feature_df() in MRMTransitionGroupCP, output is now as expected (#7646)
- Fix scan number extraction for merged spectra (#7599)
- Cmake fix (#7625) 
  - use Boost config instead of find module (new policy of CMake)
  - escape quotes in whitespace strings
  - remove invalid PRE_BUILD option (in combination with OUTPUT)
  - update diff regex and actual results (which seem to have changed with recent Sage versions...)
- MzTab: preallocate enough memory instead of allocating in the loops (#7624)
  - add check that otherwise will result in out of memory error
  - reduce memory fragmentation on huge files
- KNIME Plugin: Fix categories (#7622)


------------------------------------------------------------------------------------------
----                                OpenMS 3.2.0       (released 09/2024)             ----
------------------------------------------------------------------------------------------

What's new:
- Changes breaking backwards compatibility: 
   - Rename of parameters for TOPP tool FeatureFinderCentroided (debug -> advanced), and PeakPickerWavelet/TOFCalibration (optimization -> optimization:type) (#7154)
   - Rename of parameters for TOPP tool IDFilter (score:pep -> score:psm; score:prot -> score:protein; score:protgroup -> score:proteingroup) with 'nan' as new default (#7541)
   - 3.2.0 KNIME package requires KNIME 5.3 or later
- Support for SubsetNeighborSearch (SNS) via DecoyDatabase (#7565)
- SageAdapter received large updates including added functionality for PTM discovery + enabling features such as chimera seach, RT prediction, filtering by q-value, etc. 

Library:
- Extend FileHandler to support load and store operations for our major datastructures (spectra, features, identifications, etc.). Replaced file type specific code with the more generic FileHandler calls to decouple the IO code from other parts of the library.
- SiriusAdapter reworked to SiriusExport: Instead of running SIRIUS directly, this reworked tool takes multiple mzML and feautureXML (optional) files exporting a single SIRIUS .ms input file as well as an input table with compound info from features for the new AssayGeneratorMetaboSirius tool. (#7234)
- Splitting AssayGeneratorMetabo into two tools: In line with the changes to SiriusExport this tool has been split into two separate workflows. AssayGeneratorMetabo generates an assay library from mzML and feautreXML files using an heuristic approach picking the highest intensity MS2 peaks (like before). AssayGeneratorMetaboSirius takes an existing SIRIUS project directory as input to generate an assay library based on fragmentation trees. (#7234)
- better documentation for all SpectraFilter... tools (#7183)
- TOPPView: offer Ion mobility view from 2D spectra view (#7423)
- TOPPView: view ion mobility frames, irrespective of its MS level (formerly only MS1 was supported) (#7427)
- OpenSwath: Add output on peak shape metrics to .osw file (#7222)

New Tools:
- IonMobilityBinning - Merges spectra with similar IM values and creates @p N output mzML's by discretizing the IM range (#7459)
- AssayGeneratorMetaboSirius -- Assay library generation from a SIRIUS project directory (Metabolomics)
- SiriusExport -- Metabolite identification using single and tandem mass spectrometry


Fixes:
- FileConverter: more robust (#7176)
- MSFragger: allow relative path to database (#7155)
- MSGFPlusAdapter: allow concurrent creation of indexed database (#7272)
- CometAdapter: work around bug in Comet 2024.01 rev. 0 to avoid empty results (#7540)
- ParamEditor: fixed error for the subsection parameter (ParamNode) to go through store function (#7180)
- TOPPView:
   - fix crash when viewing certain Chromatograms (#7220)
   - in 2D view, show correct adjacent layers in context menu, if user clicked to the right of the last MS1 scan (now shows the 4 rightmost MS1 scans, used to show the 4 leftmost scans) (#7423)
   - fix glitches in 1D view and layer names (#7549)
   - Show prefix ions (e.g. b1) when generating theoretical spectra (#7567)
- TOPPAS: open files in TOPPView (#7213)
- pyOpenMS: Log warnings in pure Python code with warnings.warn instead of print (#7418)
- more robust parsing of mzIdentML (#7153)
- SageAdapter now works with sage v0.15.0 and beyond
- OpenSwath: Fix bug in diaPASEF window determination (#7546)  

Misc:
- FileInfo: Report ion mobility ranges (if any) (#7459)
- OpenMSInfo reports the ILP solver (CoinOr or glpk) (#7156)
- add citation information for OpenMS 3.0 (Nat. Methods) (#7383)
- Add export for Common Workflow Language (CWL) (#6156)
- Add tool description lib (TDL) dependency (#6156)
- Docker containers have been optimized (#7303)

Changed/new parameters: see CHANGELOG_PARAMS for details

Note: The goal of our library is to provide useful, reusable code in a way that’s easy to understand and use.
To make OpenMS simpler, more focused and more accessible we gradually remove potentially outdated tools and algorithms.
If you, as a user, are negatively affected by this step please contact us. We listen to our users and will try to find 
an alternative solution or reverse a particular decision for removal.

Cleanup/Removal:

- removed tools:
  - SpectraFilterMarkerMower -- Applies thresholdfilter to peak spectra (#7183)
  - FeatureFinderIsotopeWavelet -- Detects two-dimensional features in LC-MS data
  - PeakPickerWavelet -- Finds mass spectrometric peaks in profile mass spectra
  - PrecursorMassCorrector -- Corrects the precursor entries of MS/MS spectra, by using MS1 information
  - TOFCalibration -- Applies time of flight calibration
  - ERPairFinder -- Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans
  - RNPxlSearch -- Annotate RNA/DNA-peptide cross-links in MS/MS spectra
  - SpectraFilterSqrtMower -- Applies thresholdfilter to peak spectra
  - FeatureFinderMRM -- Detects two-dimensional features in LC-MS data
  - MapAlignerSpectrum -- Corrects retention time distortions between maps by spectrum alignment
  - ProteinResolver -- protein inference
  - SiriusAdapter -- Tool for metabolite identification using single and tandem mass spectrometry
  - SpectraFilterBernNorm -- Applies thresholdfilter to peak spectra
  - SpectraFilterScaler -- Applies thresholdfilter to peak spectra

- removed library code:
  - HiddenMarkovModel
  - PeakPickerMaxima
  - DeNovo related, old marker code

- removed tutorials:
  - Tutorial_PeakPickerCWT
  - Tutorial_TOFCalibration

- removed tests:
  - TOFCalibration_test
  - ContinuousWaveletTransformNumIntegration_test
  - ContinuousWaveletTransform_test
  - FeatureFinderAlgorithmIsotopeWavelet_test
  - IsotopeWaveletTransform_test
  - IsotopeWavelet_test
  - OptimizePeakDeconvolution_test
  - OptimizePick_test
  - PeakPickerCWT_test
  - PeakShape_test

- Deprecated (and likely removed in the next release)
  - XTandemAdapter

------------------------------------------------------------------------------------------
----                                OpenMS 3.1     (released 10/2023)                 ----
------------------------------------------------------------------------------------------

We are excited to share an experimental update with our community, mainly targeted at platforms that depend on Conda packages.
Please note that this is a partial and unannounced release, focused on delivering novel features and major changes that we're actively testing and refining.
While these features are still in an experimental phase, we encourage adventurous users and platform integrators to explore and provide feedback.

Important Notes:
- Features are experimental and may undergo changes or be removed in future releases based on user feedback and stability.
- We welcome your feedback and suggestions to help us improve and refine these experimental features.
- For stability and production use, we recommend sticking with the latest stable release.

Please use this opportunity to test and provide feedback on these new features, as your input will play a vital role in shaping their development.

Thank you for being a part of our community and for helping us make OpenMS even better!

What's new:
- Major change: removed the distinction between TOPP tool and util and the TOPP and UTIL build targets were merged to a single TOPP target. All utils are considered tools now and categorized as "Utilities".
- Added SageAdapter. Support for standard identification tasks with sage (https://github.com/lazear/sage) (experimental).
- Require some advanced instruction sets for x64 CPUs: SSE3 (g++/clang) or AVX (MSVC); and NEON for ARM64 CPUs (#6978)
  and report them via the OpenMSInfo tool (#7022)
- Base64 encoding/decoding using the SIMDe library (#6978)
- Filter features in ProteomicsLFQ according to feature p-value (additional parameters feature_with(out)_id_min_score, MBR is automatically active if targeted_only = false)
- TOPPAS: filter TOPP tools by name for faster access when building a pipeline (#7139)

Fixes:
- Fix a crash when loading mzML data with multiple threads which contains non-MS spectra, e.g. 'electromagnetic radiation spectrum' (#7011)
- InternalCalibration: improve visualization of calibration plots (#7064)
- Restore TOPPAS tutorial (#7076)
- various low impact UBSan fixes
- make mzData more robust against wrong 'length' attributes for binary data (#7113)

Misc:
- Report reading/writing throughput (MiB/sec) when loading/storing mzML (#7035)
- Add ability to create decoy features in FeatureFinderIdentification
- Restore developer quick guide in Doxygen docu - see https://openms.de/current_doxygen/html/index.html (#7109)
- Updated the changelog helper to set LD_LIBRARY_PATH automatically and other fixes
- Added "area" column to EICextractor output

Cleanup of old/unused tools and code:
- Removed old tools and associated code in the library for InclusionExclusionListCreator, SvmTheoreticalSpectrumGenerator, PrecursorIonSelector, and MSSimulator
  Note: general SVC and SVR is still supported with the SimpleSVM class.
- Removed old RT and PT predict code and tools RTModel, RTPredict, PTModel, PTPredict, RTEvaluation and associated library code (SVMWrapper and LibSVMEncoder).
- Removed PepNovoAdapter
- Removed CompNovoAdapter and library code
- Removed simplistic evaluation tools FFEval, LabeledEval, TransformationEvaluation
- Removed EnzymaticDigestionLogModel
- Removed FidoAdapter (same functionality now in our own inference engines)

------------------------------------------------------------------------------------------
----                                OpenMS 3.0     (released 7/2023)                  ----
------------------------------------------------------------------------------------------

New Tools:

    FLASHDeconv -- Ultra-fast high-quality deconvolution enables online processing of top-down MS data (TOPP)
    FLASHDeconvWizard -- A GUI assistant for FLASHDeconv execution.

New Features:

e.g.

    TMT18plex support (#6390)
    ProteinQuantifier supports iBAQ (#6107)
    OpenSwath: Add support for diaPASEF data with overlapping m/z and IM windows, and add new outputs on ion mobility features (delta_im), IM calibration (#5911, #6234, #6268)
    OpenSwathDecoyGenerator speed improvement and remove duplicates (#6054)
    NucleicAcidSearchEngine (NASE): user defined ribonucleotides with phosphorothioate linkages (#6337), JSON based ribonucleotides and updated to latest Modomics database (#6482)
    TargetedSpectraExtractor: more features (#6106)
    TOPPView: TheoreticalSpectrumGenerationDialog now supports generation of isotope patterns for metabolites (#6023); faster loading of external drag'n'drop data (#6837)
    colored commandline/console on all platforms (#6275)
    support for 'no cleavage' for XTandemAdapter and CometAdapter (#6133).
    Percolator pin file reader (#6824)
    JSON export for OMS files(SQLite) (#6114)
    ParamEditor with more convenient StringList editing (#5135)
    load parameter values from a JSON formatted .json file. (Accessible via -ini. This will be
    helpful for Common Workflow Language users and others)
    FileFilter can remove convex hulls of features and consensusFeatures to reduce file size (#6140)
    Faster compile time (#6618)
    Improving code quality by fixing lots of linting warnings and leaks (e.g. #6839, #6831, #6829)

Documentation:

    website redesign (visit openms.org)
    OpenMS user documentation is moved to openms.readthedocs.io/en/latest.
    OpenMS API reference and advanced developer documentation remains inside OpenMS doxygen
    documentation (https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/release/)
    pyopenms: pyopenms-extra is renamed to pyopenms-docs.

Bug fixes

e.g.

    GaussFilter when using ppm as width (#6830)
    NASE a-B ion masses (#6718), ID-Mapper for TMT data (#6758)
    FeatureFinderMetaboliteIdentification speed improvements (#6619)
    IDRipper speed improvements (#6584)
    Honor MissedCleavages in SimpleSearchEngine (#6889)
    TOPPView: fixed lots of display glitches, e.g. axis labels, goto dialog and easier re-use of components, etc (#6673, #6616, #6592, #6703, #6793)
    mzTab fixes for empty IDs (#6445)
    Fix GNPS error for empty scans in Bruker files (#6898)
    PrecursorPurity: handle unknown charge (#6283)
    OpenSwath: Fix duplicated transition error when multiple genes map to a single peptide (#5653)
    Fixed race condition when logging messages.

Removed tools:

    InspectAdapter
    OMSSAAdapter
    MyriMatchAdapter
    CruxAdapter

Supported compilers (when building from source):

    g++ (7.0 or later, tested up to v13.0)
    clang (?, tested up to v16)
    Visual Studio (2019(v16.8.4) or later)

Full changelog: [OpenMS 2.8 &rarr; 3.0](https://github.com/OpenMS/OpenMS/compare/Release2.8.0...Release3.0.0)

------------------------------------------------------------------------------------------
----                                OpenMS 2.8     (released 2/2022)                  ----
------------------------------------------------------------------------------------------

- source + conda release only
- Restructuring of Imported CMake targets and pyOpenMS CMake
- Reduce exposition of third-party libraries to interface
- greatly improved pyOpenMS documentation and extra functions (in the pyopenms-extra submodule)
- Fixes IDMapper for isobaric labelling experiments (will lead to much more identifications)
- Deisotoping algorithm using KL
- PeptideIndexer supports ambiguous AA's in Peptide sequence (as reported by recent Mascot versions) (#5776)
- SeqAn external library removed from source tree (not needed anymore)
- Resolve compatibility issues between IDRipper and IDMerger (#4957)
- Basic MzTabM support for AccurateMassSearch
- Changed default parameter keep_unidentified_masses to "true" (AccurateMassSearch/AccurateMassSearchEngine)
- Added parameter allow_nterm_protein_cleavage to PeptideIndexer to support no cleavage.
- Fixes and improves TheoreticalSpectrumGenerationDialog in TOPPView (closes #5787) (#5883)

------------------------------------------------------------------------------------------
----                                OpenMS 2.7     (released 9/2021)                  ----
------------------------------------------------------------------------------------------

General:
- OpenMS now expects a compiler that supports C++17
- Config storage path on linux changed to ~/.config/
- Some documentation improvements to pyOpenMS https://pyopenms.readthedocs.io/en/latest/
- PyOpenMS checks if `OPENMS_DATA_PATH` environment variable is set, before setting to default value

Adapters/Third-party support:
- Added support for SIRIUS 4.9.0
- Added basic Triqler export
- Improved NOVOR support
- Improved MSFragger support
- Removed Inspect support
- Easier 15N-labeling support for XTandemAdapter by shipping the required AA mass modification file (#5026)

What's new:
- Add some support for integrating spectral information when conducting DDA metabolomics experiments
- SimpleSearchEngine and algorithm: Additional spectrum features for percolator added
- FeatureFinderMetaboIdent: Targeted feature extraction is now also available from pyOpenMS
- AssayGeneratorMetabo: Added SIRIUS 4.9.0 support, allowing internal decoy generation and added internal feature linking support
- QCCalculator: export in mzQC file format is now available

New Tools:
- OpenMSDatabasesInfo -- Prints the content of OpenMS' enzyme and modification databases to TSV (UTIL)
- TriqlerConverter -- Converter to input for Triqler (UTIL)

Removed Tools:
- FeatureFinderSuperHirn -- Finds mass spectrometric features in mass spectra (TOPP)
- InspectAdapter -- Annotates MS/MS spectra using Inspect (TOPP)

Further fixes:
- Support for GLPK 5.x (#5127)
- IPF (identification of peptidoforms): add a check for terminal residue modification when generating theoretical peptidoforms
- Reduced build times on Windows
- Reduced AddressSanitizer warnings

File formats:
- Exporter for MSP files
- Improved support for reading NIST MSP files

Dependencies:
- Promoted SeqAn v1 to C17. Moved Seqan from contrib to main source tree (as it is not officially maintained anymore).

Library:
- Removed Elements.xml and Residues.xml. Hard-coded elements and residues for better performance/startup times.
- Moved algorithm of FeatureFinderMetaboIdent into library
- Added support for isotopic labelling experiments (MDV) 
- Removed SuperHirn library

GUI tools:
- TOPPView: Various bug fixes
- TOPPView: Dynamic detection of tools in TOPPView upon startup
- TOPPView: Improved DIA data browsing
- TOPPAS: add a `recent files` submenu
- ParamEditor: with more convenient StringList editing
- SwathWizard: Allow opening in TOPPView


------------------------------------------------------------------------------------------
----                                OpenMS 2.6     (released 10/2020)                 ----
------------------------------------------------------------------------------------------

We now create nightly pyopenms wheels (https://pypi.org/project/pyopenms-nightly/) and conda packages (https://anaconda.org/OpenMS/)

Adapters/Third-party support:
- LuciphorAdapter now stores which modifications were used for localization (#4771) and localization scores are reported in mzTab #4772 
- Added Percolator3.0 support, fixed ConsensusID reading from wrong (Percolator-overwritten) meta data (#4829), and adapted the Regex parsing of XTandem Percolator output files #4849 
- Added options introduced in new MSGF versions #4713 
- Updated IsoSpec fine structure isotopic calculator sources to v 2.1.0 #4733 
- Updated other third-party tools

What's new:
- Introduced a Wizard for Swath data (#4647 #4706 #4758 #4769 #4773 #4837), which also reports summary statistics about Swath TargetedExperiments #4788 #4790
- UTIL StaticModification: Applies a set of modifications to all PeptideIDs in an idXML file (UTIL)
- TOPP DatabaseSuitability: Computes a suitability score for a database which was used for a peptide identification search. Also reports the quality of LC-MS spectra. #4791 #4781 #4814
- Added support for QC of labeled experiments (iTRAQ/TMT)
- Added automated QC computations for MRM (#4637)
- Adapted consensusXML and mzTab to support protein groups (#4630)
- Consensus/IDMerger: Introduced use of merge idx to ensure keeping track of primaryRuns
- Epifany: Added calculation of protein group FDR, ID filtering for protein group scores (#4802) and support for inference on not just individual samples but also consensusXML files
- FeatureFinderCentroided/FeatureFinderAlgorithmPicked: Improved runtime performance #4652 #4701 
- FeatureFinderIdentification: Improved SLIM-labeling experiment support
- FileConverter: Improved runtime performance when producing mzML output #4750
- FeatureLinkerQT: Introduced Fibonacci heaps for large runtime optimization (#4721) and fixed related preconditions/segfaults #4756 #4760 #4778 
- IDFilter: added support for consensusXMLs #4798 #4799
- MapAlignerIdentification: New option to use an "identity" transformation when data is too sparse to determine alignment model #4628
- MzTabExporter: changed to only export one main score, and to derive nativeIDs from data (#4767). Now ensures that all output rows contain the same number of columns #4801 
- MzTabExporter on LFQ consensusXMLs produces 100% PRIDE validated mzTabs now
- ProteomicsLFQ: Added spectral counting as quantification method (#4726). Introduced performance improvements for AASequence and string parsing, especially for modified sequences. Various further improvements (e.g. #4669)
- SimpleSearchEngine (multithreaded), TheoreticalSpectrumGenerator, MSSpectrum: Runtime optimization #4709
- Further introduction of more file streaming to address possible memory consumption issues #4682 #4694

Further fixes:
- We now limit double precision to 17 digits during file writes #4636 
- Ensure that CometAdapter always writes indexed mzML fixes for CometAdapter (#4653), fixed the writing of terminal modifications with specific origin in Comet (#4742), the writing of protein terminal mods in Comet and MSGF adapter #4710, and the Comet pepXML modification parsing #4755 
- Removed secondary search engine settings duplication in mzTab MTD section. #4720 
- Improved XTandem output protein parsing #4789 to fix Issue #4770
- Increased (partial) support for parsing mzid with nonstandard, non-CV-term scores, fixes #4859
- Fixes to NucleicAcidSearchEngine mzTab output #4692
- ConsensusID now passes spectrum reference meta values along #4703
- Fix to LFQ requantification #4633
- Improved MapAlignerTreeGuided memory usage (#4704) and fixed segfault when featureXML contains no IDs #4665 
- TOPPAS fixes #4780 

Various:
- OMMSAAdapter now writes out native ids and spectrum references #4852 
- FileInfo: Report more charge distribution and MS2 activation-method information for Raw files #4836 
- Added sum formula output in RNAMassCalculator #4677 
- Added automatic OpenMS tool reporting of peak memory usage #4712 
- Some extra tools documentation outputs #4822 #4823
- Extended mapping of filetypes and mimetypes for knime output formats documentation #4839
- RTEvaluation: fixed output formats #4533 
- Some further clarifications, standardization/consolidation of outputs formats/consistency
- Continued fixes/improvement of documentation
- Removed deprecated version of PeakPickerHiRes (LowMemPeakPickerHiResRandomAccess and LowMemPeakPickerHiRes). Their functionality can be accessed through options of PeakPickerHiRes
- moved the config storage location for unix installations to comply with X Display Group (freedesktop.org) guidelines.


-------------------------------------------------------------------------------------------
----                                OpenMS 2.5     (released 2/2020)                   ----
-------------------------------------------------------------------------------------------

OpenMS 2.5 ships exciting new tools and improvements. 

General:
- support for RNA mass spectrometry
- TMT16plex support for IsobaricAnalyzer (see PR #4295)
- improved MsStats/MsStatsTMT output support (see PR #4181, #4207)
- extended MaxQuant-compatible mzXML support (via FileConverter) (see PR #4432, #4423)
- QualityControl Workflow (all in the QC folder)
- OpenMS and pyOpenMS support for oligonucleotides
- OpenSWATH support for ion mobility extraction and scoring
- OpenSWATH support for metabolite assay library building through SIRIUS (and metabolite extraction and scoring)
- OpenSWATH support for PRM
- TOPPAS improvements (see PR #4100, #4121, #4266, #4497)
- fixes to PeptideIndexer for X!Tandem special cutting rules and ambiguous amino acids (see PR #4356)
- support for HDF5
- support for hyperfine isotopic distributions (through IsoSpec)
- JSON support (see PR #3786)
- speed improvements (loading/storing files, handling peptide sequences)
- support for VS2019 and GCC 9.1 (see PR #4211)
- support for outlier removal in IDPosteriorErrorProbability
- reduced memory footprint of FeatureFinderIdentification through batch processing

New Tools:
- Epifany -- Runs a Bayesian protein inference (UTIL)
- FeatureFinderMetaboIdent -- Detects features in MS1 data based on metabolite identifications (UTIL)
- GNPSExport -- Tool to export consensus features into MGF format (TOPP)
- NucleicAcidSearchEngine -- Annotate nucleic acid identifications to MS/MS spectra (UTIL)
- ProteomicsLFQ -- A standard proteomics LFQ pipeline (TOPP) (experimental)
- QualityControl -- Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get (TOPP)
- RNAMassCalculator -- Calculates masses and mass-to-charge ratios of RNA sequences (UTIL)
- MapAlignerTreeGuided -- Aligns maps through hierarchical clustering based on distances computed between shared IDs.

Deprecated and removed Tools:

Changed Tools:
- OpenPepXL and OpenPepXLLF runtime and memory efficiency improved by orders of magnitude
- IDFilter can now filter by using all MetaValues available in the ID files
- ImageCreator uses updated gradients and has gained RT and m/z filtering options (PR #4188)

Status changed:
- OpenPepXL (UTIL -> TOPP)
- OpenPepXLLF (UTIL -> TOPP)
- XFDR (UTIL -> TOPP)


-------------------------------------------------------------------------------------------
----                                OpenMS 2.4     (released 9/2021)                   ----
-------------------------------------------------------------------------------------------
OpenMS 2.4 introduces changes from 322 pull requests including new features and bug fixes.

Notable changes since version 2.3 are:

Dependencies:
- Switch to Qt 5 (>= 5.5)

Documentation:
- New developer documentation to get started developing tools with OpenMS

Library:
- Improved mass calculations for isotope distributions 
- Moved tool code from the tool to the library
- BinnedSpectrum now also supports offsets
- Improved peak type estimation
- Improved adduct grouping
- New EMG fitter for peak intensity imputation
- Targeted / untargeted spectra extraction and matching
- Spectra matching against a spectra library, using contrast angle similary function
- More precise peak integration (trapezoid, simpson)

New tools:
- AssayGeneratorMetabo -- Assay library generation from DDA data (Metabolomics) (UTIL)
- ClusterMassTraces -- Creates pseudo spectra (UTIL)
- ClusterMassTracesByPrecursor -- Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile (UTIL)
- CruxAdapter -- Identifies MS/MS spectra using Crux (TOPP)
- MSFraggerAdapter -- Peptide Identification with MSFragger (UTIL)
- MSstatsConverter -- Converter to input for MSstats (UTIL)
- MaRaClusterAdapter -- Facilitate input to MaRaCluster and reintegrate (TOPP)
- NovorAdapter -- Template for Tool creation (UTIL)
- RNADigestor -- Digests an RNA sequence database in-silico (UTIL)

Deprecated and removed tools:
- AdditiveSeries -- Computes an additive series to quantify a peptide in a set of samples (TOPP)
- IDEvaluator -- Computes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifications for a certain q-value (UTIL)
- IDEvaluatorGUI -- Computes a 'q-value vs. #PSM' plot to visualize the number identifications for a certain q-value (UTIL)
- RNPxl -- Tool for RNP cross linking experiment analysis (UTIL) (superseded by RNPxlSearch)
  
Changed Tools:
- SiriusAdapter now supports several input data
- FileFilter now supports filtering spectra by similarity
- PeptideIndexer now supports automatic detection of decoy suffix/prefix string and position
- PeakPickerHiRes now supports automatic detection and picking of profile spectra
- Support for MSFragger search engine through MSFraggerAdapter
- Support for Crux search engine through CruxAdapter
- Support for Maracluster through MaraClusterAdapter
- OpenPepXL was improved in efficiency and usability
- IDFileConverter now supports the Cross-Linking MS specific xquest.xml format

TOPPView:
- Improved visualization of identification results and ion annotations
- Support for visualization of Ion Mobility and DIA data

Major changes in functionality:
- None   

File formats:
- Importer for MSP files
  
Scripts:
- None
 
Databases:
- None

Third-party software:
- New: maracluster (0.05)
- Update: MS-GF+ to Release (2018.01.30)
- Update: Sirius 4 for Windows 64bit, Linux 64bit, and MacOS 64bit
- Update: Crux (crux-3.1.8b78546) on all 64bit platforms.


-------------------------------------------------------------------------------------------
----                                OpenMS 2.3     (released 1/18)                   ----
-------------------------------------------------------------------------------------------
OpenMS 2.3 introduces a considerable number of new features and bug fixes.

Notable changes since version 2.2 are:

TOPPView:
   - Deletion of selections of Peak Annotations is reflected in the Peptide Hit
   - Buttons for saving ID files were merged to one single button. Format is determined by file extension or selected filter
   - Clicking on a data point in 2D view, the search range for close fragment ion spectra is extended if no spectra are found initially
   
New tools:
  - CometAdapter -- Annotates MS/MS spectra using Comet (TOPP)
  - MetaboliteAdductDecharger -- Decharges and merges different feature charge variants of the same metabolite (UTIL)
  - OpenPepXL -- Tool for protein-protein cross-linking identification using labeled linkers (UTIL)
  - OpenPepXLLF -- Tool for protein-protein cross linking with label-free linkers (UTIL)
  - PSMFeatureExtractor -- Computes extra features for each input PSM (UTIL)
  - SiriusExport -- Tool for metabolite identification using single and tandem mass spectrometry (UTIL)
  - XFDR -- Calculates false discovery rate estimates on protein-protein-crosslink identifications (UTIL)

Deprecated and removed tools:
  - None

Renamed tool:
  - LowMemPeakPickerHiRes_RandomAccess was renamed to LowMemPeakPickerHiResRandomAccess

Major changes in functionality:
  - Experimental design
    - Add support for fractions
  - FeatureLinkerUnlabeledKD
    - m/z and retention time tolerances for warping and linking are now separate parameters 
  - IsobaricAnalyzer
    - Support for TMT11plex (https://www.thermofisher.com/order/catalog/product/A34808)
  - FileInfo
    - For idXML files, the tool computes the average length of contained peptides
  - TopPerc
    - Renamed in PercolatorAdapter (still experimental)
  - OpenSWATH:
    - RT normalization now allows more models
    - Add S/N ratio for each ion trace
  - Support for C++11 (requires a compiler that supports C++11)

    
Library:
  - TOPP tools report their peak memory usage when using -debug 1 (or higher)
  - idXML files can now be written faster (about 10%)
  - pyOpenMS bindings for DataArrayByName getters
  - Python build are now split in compilation units and can thus run in parallel
  - FASTA files can now be written
  - Allow String values to be passed to EnzymaticDigestion::isValidProduct

File formats:
  - consensusXML now supports both channels and MS runs. Information will also be exported in mzTab
  
Scripts:
 - None
 
Databases:
 - None

Third-party software:
  - New: Comet "2016.01 rev. 3" for Windows 32bit/64bit, Linux 64bit, and MacOS 64bit
  - New: Percolator 3.1.2 for Windows 32bit/64bit, Linux 64bit, and MacOS 64bit (still experimental)
  - New: Sirius 3.5.1 for Windows 64bit, Linux 64bit, and MacOS 64bit
  - New: SpectraST 5.0 for Windows 64bit, Linux 64bit, and MacOS 64bit
  - Update MS-GF+ to Release (v2017.07.21)  


-------------------------------------------------------------------------------------------
----                                OpenMS 2.2     (released 11/2016)                  ----
-------------------------------------------------------------------------------------------
OpenMS 2.2 introduces a considerable number of new features and bug fixes.

Notable changes since version 2.1 are:

New tools:
  - RNPxlSearch -- Annotate RNA to peptide crosslinks in MS/MS spectra (UTIL)
  - SpectraSTSearchAdapter -- Interface to the SEARCH Mode of the SpectraST executable (UTIL)
  - FeatureLinkerUnlabeledKD -- Feature linking using a KD tree (TOPP)
  - DatabaseFilter -- Filters a protein database (FASTA format) based on identified proteins (UTIL)
  - TargetedFileConverter -- Conversion of multiple targeted file formats (CSV, TraML etc)
  
Deprecated and removed tools:
  - ITRAQAnalyzer -- superseded by IsobaricAanalyzer
  - TMTAnalyzer -- superseded by IsobaricAanalyzer
  - ConvertTSVToTraML - superseded by TargetedFileConverter
  - ConvertTraMLToTSV - superseded by TargetedFileConverter
  - MapAlignmentEvaluation -- removed as deprecated
   
Major changes in functionality:
  - OpenSWATH analysis
    - Support for metabolomics workflows
    - Support for scanning SWATH (SONAR)
    - Support for SQL-based file formats
  - XTandemAdapter 
    - Simplified usage
    - Improved support for PTMs and newer X! Tandem versions ("Vengeance", "Alanine")
  - IsobaricAnalyzer
    - Support for TMT10plex
    - Support for quantification in MS3 data
  - IDMapper
    - Allows to map unidentified tandem mass spectra to features
  - FeatureFinderIdentification
    - Advanced multi-sample support using machine learning
  - FileFilter
    - Allows users to enable zlib and lossy compression (see "-lossy_compression")
    - Allows users to set desired mass accuracy
  - IDFilter
    - Added option to filter for valid digestion products
  - FalseDiscoveryRate
    - Allow filtering by q-value in the tool (no need for IDFilter with "score:pep" option)
    
Library:
  - Averagine approximation for fragment isotope distributions
  - Precursor mass correction supports correction to highest intensity peak in tolerance window
  - Functionality for resampling and adding of spectra
  - Protein-protein cross-link spectrum generator
  - Terminal modifications are now separated by "." in text output
  - SQLite support in OpenSWATH
  - TheoreticalSpectrumGenerator speed-up and removal of RichPeak code
  - Removal of template parameters from MSExperiment (reduced compile time and binary size)
  - Allow estimation of isotope distributions with predefined numbers of sulfur atoms
  - Improved handling of bracket notation for modified residues (e.g. N[2457.877]VSVK)
  - Improved handling of terminal and residue specificity of modifications
  - Improved annotation of peptide identifications with spectrum references
  - Improved handling of unknown amino acids ("X") in sequences

File formats:
  - Improved mzML support for SONAR data and mzML with drift time (experimental)
  - Improved support for cross-link data and unknown modifications in mzIdentML
  - mzXML writer able to write MaxQuant-compatible files
  - mzML files now routinely support substantial compression (up to 5x compression, see #2449, #2458)
  - Support for Percolator result files based on X! Tandem searches

Scripts:
  - New R script for visualizing RT transformations (trafoXML) 
 
Databases:
  - By default, decoy sequences are now denoted by the prefix "DECOY_"

Third-party software:
  

-------------------------------------------------------------------------------------------
----                                OpenMS 2.1     (released 11/2016)                  ----
-------------------------------------------------------------------------------------------
OpenMS 2.1 introduces a considerable number of new features and bug fixes.

Notable changes since version 2.0.1 are:

New tools:
  - ExternalCalibration -- Applies an external mass recalibration (TOPP)
  - OpenSwathFileSplitter -- Splits SWATH files into n files, each containing one window (TOPP)
  - MultiplexResolver -- Completes peptide multiplets and resolves conflicts within them (UTIL)
  - TICCalculator -- Calculates the TIC from a mass spectrometric raw file (useful for benchmarking) (UTIL)

Deprecated and removed tools:
  - PILISIdentification -- performs a peptide/protein identification with the PILIS engine (TOPP)
  - PILISModelCV -- Perform a cross validation of the PILIS model parameters (TOPP)
  - PILISModelTrainer -- Train the PILIS model with a given set of spectra and identifications (TOPP)
  - PILISSpectraGenerator -- Generate spectra given a list of peptides and a PILIS model (TOPP)

Major changes in functionality:
  - Update notification: starting with OpenMS 2.1 all TOPP tools will check for updated versions of the tools 
      online and will print an information message if a newer version is available. This version check occurs only 
      once per day and tool. Information on which tools are executed will be collected anonymously to identify which 
      tools are no longer used and to optimally distribute development resources. If the feature causes problems or
      concerns, it can be disabled through a command line switch or environment variable (see the documentation).
  - InternalCalibration:
    - supports calibration using a table of lock masses and peptide ids.
    - global or RT-chunked calibration
    - linear & quadratic models (with intensity weighting)
    - outlier removal via RANSAC
    - reoccurring calibrations can be quickly applied to other files using the novel ExternalCalibration tool
  - OpenSwathWorkflow
    - support for metabolites / small molecules
  - MapAlignerIdentification
    - support for "lowess" transformation model
  - AccurateMassSearch:
    - support for multiple databases
  - FeatureFinderMetabo
    - isotope spacing model for carbon rich molecules (e.g. lipids)
  - PeakPickerHiRes and MassTraceExtractor:
    - support for FWHM annotation

File formats:
  - Improved mzIdentML support (experimental)
  - Improved pepXML support
  - Improved support for indexed mzML files
  - Improved TraML support

Databases:
  - By default, decoy sequences are now denoted by a prefix 'DECOY_'.

Third-party software:
  - update for 64-bit X!Tandem VENGEANCE (2015.12.15) NOTE: 32-bit version kept at SLEDGEHAMMER (2013.09.01)
  - update for MS-GF+ Release v2016.10.14, released October 14, 2016
  - update for pwiz 3.0.9935


-------------------------------------------------------------------------------------------
----                                OpenMS 2.0.1   (released 4/2016)                   ----
-------------------------------------------------------------------------------------------
OpenMS 2.0.1 is a source only release of the core libraries and tools. 
With over 300 merged pull requests, it introduces a considerable number of new features, 
bug fixes and speed improvements.

Notable changes are:

File formats:
  - Improved mzIdentML support (experimental)
  - Improved mzTab support (experimental)
  - Comet pepXML file reading support (experimental) 
  - Search parameter units are retained through id files
  - Faster base64 decoding in XML files

Databases:
  - HMDB has been updated to version 3.6

TOPPView:
  - Added slight margin around data range (%2) for improved visualization
  - Added FeatureFinderMultiplex to the tools accessible from TOPPView
  - Some fixes to the scrollbar behaviour

Added tools:
  - IDScoreSwitcher -- Switches between different scores of peptide or protein hits in identification data (UTIL)
  - LuciphorAdapter -- Modification site localisation using LuciPHOr2 (TOPP)
  - MetaProSIP -- Performs proteinSIP on peptide features for elemental flux analysis (UTIL)
  - MzMLSplitter -- Splits an mzML file into multiple parts (UTIL)
  - OpenSwathAssayGenerator -- Generates assays according to different models for a specific TraML (TOPP)

Removed tools:
  - RTAnnotator -- Annotates identification files that are missing the RT field (UTIL)

Tools with major changes:
  - OpenSWATH now outputs peak apices
    - Improved iRT correction
    - Assay generator
    - UIS scoring
  - Deuterium labeling in MetaProSIP (experimental)
  - XTandemAdapter allows for external config file
  - TextExporter can optionally export PeptideIdentification and PeptideHits meta-values
  - FeatureLinkerUnlabeledQT speed improvements
  - FileMerger allows to concatenate files in RT
  - MzTabExporter supports protein IDs
  - PeakPickerWavelet speedup
  - HiResPrecursorMassCorrector supports correction of precursors to detected features
  - FeatureFinderMultiplex speed improvements

Library:
  - Support for user definable enzymes available in EnzymesDB.xml
  - PeptideIndexing is now available as internal algorithm
  - EnzymaticDigestion allows for minimum / maximum length constraints
  - HyperScore and PScore implementations
  - Fits allow extrapolation of data values
  - QT clustering is now order independent
  - Additional convinience functions to access the nearest spectrum peak in a mass tolerance window
  - User defined averagine compositions
  - A fast linear lowess implementation has been added
  - MetaInfoInterface has been added to FeatureMap to store additional meta-values
  - Calculation of Median Absolute Deviation

General:
  - OpenMS writes indexed mzML by default
  - OpenMS home directory can be configured through OPENMS_HOME_DIR environment variable
  - Updated GenericWrapper definitions for MS-GF+ and Mascot

Third party software:
  - LuciphorAdapter (experimental) PTM localization using the LuciPHOr2 algorithm (http://luciphor2.sourceforge.net/)


-------------------------------------------------------------------------------------------
----                                OpenMS 2.0     (released 4/2015)                   ----
-------------------------------------------------------------------------------------------
Release date: February 2015

OpenMS 2.0 is the first release after the switch to git and a complete overhaul of the
build system. It introduces a considerable number of new features and bug fixes.

Furthermore, we removed the dependency to GSL and replaced the functionality using
Eigen3 and Wildmagic. Thus, the OpenMS core and the full build are now under a more
permissive non-GPL (e.g., Apache or BSD) license.

File formats:
  - mzQuantML support (experimental)
  - mzIdentML support (experimental)
  - mzTab support (experimental)
  - Indexed mzML support
  - Support for numpress encoding in mzML
  - Major speed improvement in mzML / mzXML parsing (up to 4x for some setups)

TOPPView:
  - Support for visualizing mass fingerprinting hits from featureXML along with their raw spectra in MS1
  - Improved "Tools" -> "Goto" dialog
  - Improved display of m/z, RT, and intensity values 1D and 2D view

New tools:
  - FeatureFinderIdentification -- Detects features in MS1 data based on peptide identifications (TOPP)
  - FeatureFinderMultiplex -- Determination of peak ratios in LC-MS data (TOPP)
  - FidoAdapter -- Runs the protein inference engine Fido (TOPP)
  - LowMemPeakPickerHiRes -- Finds mass spectrometric peaks in profile mass spectra (UTIL)
  - LowMemPeakPickerHiRes_RandomAccess -- Finds mass spectrometric peaks in profile mass spectra (UTIL)
  - MRMTransitionGroupPicker (UTIL)
  - MSGFPlusAdapter -- MS/MS database search using MS-GF+ (TOPP)
  - MetaboliteSpectralMatcher -- Find potential HMDB ids within the given mass error window (UTIL)
  - OpenSwathWorkflow -- Complete workflow to run OpenSWATH (UTIL)
  - PeakPickerIterative -- Finds mass spectrometric peaks in profile mass spectra (UTIL)
  - RTAnnotator -- Annotates identification files that are missing the RT field (UTIL)
  - SimpleSearchEngine -- Annotates MS/MS spectra using SimpleSearchEngine (UTIL)
  - TopPerc -- Facilitate input to Percolator and reintegrate (UTIL)

Deprecated tools:
  - DBExporter -- Exports data from an OpenMS database to a file (TOPP)
  - DBImporter -- Imports data to an OpenMS database (TOPP)
  - FeatureFinderRaw -- Determination of peak ratios in LC-MS data (TOPP)
  - SILACAnalyzer -- Determination of peak ratios in LC-MS data (TOPP)

Status changes:
  - PhosphoScoring (UTIL -> TOPP)

Tools with major changes:
  - OpenSWATH now supports MS1 extraction and labelled workflows
  - OpenSWATHWorkflow single binary (high performance integrated workflow)
  - IsobaricAnalyzer now supports TMT 10-plex

General:
  - Removed GSL dependencies
  - Introduced low memory versions of various algorithms
  - OpenMS now offers a single interface for different implementations to access mass spectrometric data
      - in memory
      - on disk with index
      - cached on disc for fast access
    as well as a chainable, low memory sequential processor of MS data (using a separate interface)
  - pyOpenMS now supports python 3.x
  - Refactored AASequence, major speed improvement (~40x) for construction of unmodified sequences

Third party software:
  - Added Fido support
  - Added MS-GF+ support

Changes to the Build System / Package System:
  - Restructured repository layout and build system
  - Added support for Travis CI
  - Simplified pyOpenMS build system
  - Support for Visual Studio 2013


Resolved issues and merged pull requests:
  #644 Fix header macros
  #649 Fix ms numpress
  #651 [INTERNAL,API] Removal of the GSL
  #656 Repository layout restructuring
  #657 [FIX, INTERNAL]
  #658 [FIX] PeptideIndexer crashes on empty idXML (#653)
  #659 [NOP] replaced c like file ending C with cpp
  #660 [FIX] fix Cython 0.20 compatibility issue
  #661 [BUILD,PYOPENMS] simplify pyOpenMS build system
  #662 CMake and docu cleanups w.r.t. to the new layout
  #664 [BUILD] build system fixes / cleanups
  #665 Fix coverity errors
  #666 [FEATURE] ib spectra format export
  #667 [BUILD] improved handling of boost in OpenMS build system
  #668 [NOP] added support for travis-ci to OpenMS
  #669 [FIX] fixed AccurateMassSearch_test
  #673 [FEATURE,FIX] Added min/max values to go-to dialog
  #675 Checker/Test fixes and adds test for CTD writing
  #677 [PYOPENMS] setup.py as minimal as possible + other improvements
  #678 [FIX] fix how swath files are annotated
  #679 [FIX,TEST] fixed OpenSwathDecoyGenerator / MRMDecoy
  #680 [INTERNAL] Feature/CachedMzML fixes
  #684 [FIX] Bugfix for threading issue in MascotGenericFile
  #685 Typo fixes in documentation and licence files
  #688 Fix/file size limit
  #689 [FIX] disable OpenMP again for ILPDCWrapper
  #690 Fix/misc
  #691 further improvements to MGF::load()
  #693 Major speedup of String --> Double conversion
  #694 added missing index file for OMSSA test, which gets recreated when runni...
  #696 [FIX] fix RAM usage when adding dataprocessing to chromatograms
  #697 [FIX] proper usage of map in ControlledVocabulary
  #698 Updates to FeatureFinderIdentification and the ...TraceFitter classes
  #702 Feature/parallel reader
  #703 Feature/aa sequence tpp
  #705 [FIX] Propagate metadata in OpenSwathWorkflow
  #707 [FEATURE] variable stylesheet support for qcml
  #708 [BUILD] fix build system bug
  #711 [FEATURE,BUILD] fix install target
  #713 Fix for pepXML loading bug (#710)
  #715 Feature/pyopenms wrapping improvements neu
  #716 [NOP,TEST] clean up MRMDecoy, add more tests
  #717 fixed 32bit memory limitation of OMSSA by chunking input data
  #718 [FIX] fixed misleading warning ("Removed x peptide identifications...
  #719 [CI,FIX] fix travis contrib clone problems
  #721 [INTERNAL] cleanup of iostream includes
  #722 Feature/mz xml consumer
  #724 Feature/pyopenms mzxml consumer
  #725 Fix/misc
  #726 IDPosteriorErrorProbability fix
  #729 Fix/coverity
  #730 Feature/peak picker sn performance
  #734 Feature/more pyopenms improvements
  #735 [FEATURE] clang warning level
  #737 [FIX] several minor fixes
  #739 Feature/uids fileconverter
  #741 ProteinResolver fix
  #742 svn cleanup
  #743 [FIX] fixed compilation error on vs2013
  #747 Speedup OMSSA-XML parsing and some stats for OMSSA&XTandem
  #749 Feature/python3
  #750 [PYOPENMS,FIX] fixed streampos->long conversion
  #751 [FEATURE] track base name when reading pep.xml files
  #752 [FIX] fixed missing adaption PeptideIdentification::empty()
  #754 [PYOPENMS] changed extra methods on MSSpectrum
  #755 [FIX] fixed shadow warning
  #756 Unity Builds
  #760 [FIX-#618] fix spelling errors in headers
  #761 Feature/header fixes
  #764 [FEATURE] lib superhirn
  #765 Feature/db removal
  #768 [FIX] fixed warnings in CONCEPTS
  #770 [FIX] fixed some clang warnings in stream manipulation
  #771 New warnings
  #773 [BUILD,PYOPENMS] fix pyOpenMS build
  #775 [FIX] typos in the CMake file
  #776 Fix for IDPosteriorErrorProbability on Mascot search results (#740)
  #777 Memory profiling class
  #779 [FIX] replaced DoubleReal and Real by double and float.
  #780 [FIX] fix Swath window estimation
  #781 Fix/open swath fixes
  #784 [FEATURE] fix macosx pyopenms errors
  #785 [FIX] VS2013 compile fixes
  #786 [FEATURE] added openms_add_library function
  #787 [FEATURE,BUILD] move pyOpenMS to src
  #789 small fix to Win install doc for VS2013
  #790 Remove "RT"; and "MZ"; metavalues from PeptideIdentification
  #791 [FIX] forgot writtenDigits fixes in tests VS2013
  #792 [FIX] AASequence refactoring
  #794 Generic Wrapping of R scripts using GenericWrapper
  #797 [NOP,DOC] removed all remaining references to FeatureFinderRaw and SILAC...
  #798 Fix/py open ms testfix
  #799 [DOC] removed migrated pages from doxygen. replaced by link to wiki
  #800 spline interpolation of MS1 spectra
  #801 RTPredict: fixed order of parameters and doc
  #802 [FIX] fixed copy-paste mistake in error message
  #804 [FIX] MRMDecoy: Fix neutral losses for higher charge states
  #805 [PYOPENMS] added getters/setters for MZ and RT in PeptideIdentification....
  #807 cubic spline implementation
  #810 cubic spline interpolation
  #811 [NOP] add better debug information and error handling
  #812 [FIX] per cppcheck
  #813 Fix/openswath
  #814 [FEATURE] ConvertTSVToTraML: Support for SpectraST MRM Transition Lists
  #816 Feature/cached mz ml format change
  #817 [FIX] fix spline derivative for cubic spline
  #819 Feature/custom i rt
  #820 Fix/warnings
  #821 [FIX] suppress clang warnings
  #823 Feature/update numpress
  #824 Fix/coverity
  #826 Feature/funny pictures
  #827 [FIX] fixes export macro warnings
  #831 [FEATURE] fix all gcc warnings and turn warnings into errors
  #832 several pyopenms fixes + updates
  #833 Feature/visibility hidden
  #834 Fix/fix werror
  #835 Fix spline spectrum
  #836 [FIX,TEST] MRMRTNormalizer_test: Windows compatibility
  #838 [FIX] fixed uninitialized pointer warning
  #840 [FIX] fix pyOpenMS test
  #841 [BUILD] disable -Werror by default
  #842 [FIX] fix dereference of iterator
  #843 [FIX] fixes tests failing win debug mode
  #844 [FIX] evaluation at m/z in first package now possible
  #845 [FEATURE] replace String classes with StringUtils
  #846 Fix/fixes from822
  #847 peak boundaries and new cubic splines for PeakPickerHiRes
  #850 [FEATURE] modified tests to reflect X!Tandem SLEDGEHAMMER as default
  #851 Fix and tests for a bug in reading Mascot XML files
  #852 [FIX] fix windows compile error
  #854 [FIX] ConsensusID doesn't sort peptide hits before processing (idXML)
  #855 [FIX] FalseDiscoveryRate "target+decoy"; hits should be considered as targets
  #856 [FEATURE] KNIME package generation updates
  #857 Fix/py open ms fix
  #858 [FEATURE] ~40x speedup for constructions of unmodified AASequence
  #859 Feature/SystemWildMagic
  #863 [BUILD] added test for x!tandem version to enable tests only with newer ...
  #865 Work-around for special modifications in Mascot (fixes #864)
  #866 [FEATURE] git version embedding
  #867 [FIX-#861,DOC] fixed eigen 3.2.1 problems with GammaDistributionFitter
  #868 multiplex filtering
  #869 [FIX] fixed problems with negative sizeof values in CachedMzML
  #870 [FIX,DOC] doxygen 1.8.7 fixes
  #873 [FIX] fixed macosx version query
  #875 Rewrite of 'AASequence::parseString_', increasing robustness of parsing (fixes #818)
  #876 [DOC] added new doc_class_only target
  #880 PeakPickerHiRes peak boundaries fixed
  #881 [FEATURE] mzTab 1.0
  #882 [FEATURE] coding style improvements
  #884 [FIX] Convert XTandem search results into .pepXML by IDFileConverter
  #885 [NOP] added moc files to gitignore
  #888 [FIX-#887] IDFilter errornousely removed peptidhits in multiple run files
  #889 multiplex clustering
  #891 [FIX] converting uniform distributed generators with normal distributions
  #892 Enable loading of some pepXML files that used to cause crashes
  #894 [FEATURE] improved 3rd party lib finding
  #895 [FEATURE] simple search engine
  #896 added scan-polarity filter to FileFilter ...
  #897 (feature for Windows developers) added a small Windows .reg file
  #898 More compact format for MGF files (fixes #890)
  #899 [DOC] some minor documentation addition
  #901 [FIX] fix MS level for DTA file reader
  #902 [FIX,PYOPENMS] fix pyOpenMS after #875
  #903 [FIX] mzXML fix (filterLine, basePeakMz)
  #904 Feature/fix peak boundaries
  #910 [FIX] fixed unity build error introduced in #845
  #911 [FIX] FFCentroided replace exception handling with proper check
  #914 fix index in CubicSpline2d
  #916 IDMapper extension for featureMaps
  #917 AccurateMassSearchEngine annotation of input map (not only mzTab output)
  #919 [FIX] libc++ test fixes
  #920 [FIX] fixed minor problem with knime package generation and cmake versions >2.8.11
  #921 MS1 annotation in TOPPView
  #922 [FIX] build system improvements
  #923 EmpiricalFormula: fix (negative counts were casted away)
  #924 Switch to disable tracking of Git version within OpenMS
  #925 Fix/small docu improvement
  #926 Feature/spellcheck
  #927 PeptideIndexer: support for treating isoleucine/leucine as equivalent (resolves #872)
  #928 Build System
  #929 TextFile feature (skip empty lines) and docu fix
  #930 check for missing peaks
  #931 fix for evaluation at last node
  #936 [FIX] fixed the 'variable' consumption of xslt files for a QcML file.
  #938 [FEATURE] precursor scoring
  #939 [FIX] fix compile error
  #940 coding convention violations in MultiplexClustering fixed
  #943 [FIX,PYOPENMS] fix pyOpenMS after #889
  #944 [FIX,TOOLS] pyopenms parser fix
  #945 [FEATURE] pyopenms wrap improved
  #946 OPENMS_DLLAPI removed from GridBasedClustering
  #947 [FEATURE] FeatureFinderMultiplex
  #949 Fix/xml escape
  #950 Feature/traml heavylight
  #951 [FIX] add setOptions method for FileHandler
  #955 Fix/xml escape
  #958 [FIX] disallow concurrent access to the static PRNG
  #959 Feature/pyopenms copyconstr
  #960 [FEATURE] peptide group label new
  #962 [FIX] QCCalculator now computes TIC only on MS1 spectra (fixes #96)
  #964 [FIX] check for invalid charge ranges in search engine adapters (see #963)
  #965 [FEATURE] tmt 10plex support
  #966 [FEATURE] chaining consumer
  #967 [FEATURE,TEST] mssim more ground truth in id xml
  #968 [FEATURE] export PT value analogous to predicted rt value in TextExporte...
  #969 [FEATURE] add a low memory FileConverter option
  #970 [FEATURE] test if java can be executed
  #972 Fix/file cleanup
  #973 [FIX] validate presence of input file before starting executable
  #977 [FEATURE] replaced pphires ms1_only flag with ms_levels parameter
  #981 Feature/TextExporter_mzML
  #983 [FEATURE] add library check on Windows for correct lib arch
  #984 [NOP] add heavy methyl SILAC labels to unimod.xml
  #985 [FEATURE] bspline support using eol bsplines implementation
  #988 [FIX] simplified EmpiricalFormula
  #990 [FIX,FEATURE] TransformationModelInterpolated readded
  #993 Feature/sort on load (mzML, mzXML)
  #994 fixes mass traces in featureXML output
  #995 fixes CubicSpline2d constructor exceptions
  #996 allow for SplinePackages based on just two data points
  #1000 fixes problems with ">>" generated in nested C++ templates
  #1001 Fix/py open ms test
  #1002 [pyOPENMS] features
  #1003 [FIX] fixes random fails of MSSim_test
  #1006 [FEATURE] enable gui less OpenMS
  #1009 update unimod.xml with newest version from unimod.org
  #1010 [FIX] external code tests updated/fixed
  #1011 [FIX] external project doc
  #1012 [FEATURE] decreased memory footprint of Feature class by up to 44%
  #1014 TOPPView: group separator for mz,rt and int values in 1D and 2D canvas
  #1019 [FIX] fixed unitybuild problem on win32 with eol-bsplines
  #1020 [NOP] updated copyright/license header to 2014
  #1021 Feature/py open ms fixes and wraps
  #1024 sorting mass shifts in FeatureFinderMultiplex
  #1025 Fix/checker fixes
  #1026 additional example in SplineSpectrum test
  #1027 Adapter for Fido (protein inference engine), solves #808
  #1029 [FIX-#184] remove public vector/map inheritance
  #1032 fixes peak boundaries in PeakPickerHiRes (resolves #1022)
  #1034 [FIX] improve set_peaks documentation
  #1035 B-spline interpolation for peak width estimation in MultiplexClustering class
  #1036 [FEATURE,API] Removed template parameter from FeatureMap
  #1037 Fix/ TraML load/store
  #1038 Feature/py open ms wraps
  #1039 Fix/debug fix
  #1040 Fix/spellcheck
  #1044 [FIX:#1043]fixed featureXML reading spectrum_reference as String
  #1045 [FIX] fix compile issue on win32 systems
  #1046 Fix/py open ms wrap
  #1047 [FIX] first probe install path, then the build path for share/OpenMS
  #1048 Feature/peptide hit protein locations
  #1050 Re-added B-spline transformation for non-linear RT alignment in MapAlignerIdentification
  #1051 [FIX] made arguments and functions in BSpline2d const (if possible)
  #1055 [FEATURE] improved purity computation for IsobaricAnalyzer
  #1056 [FIX] UniqueIdGenerator susceptible to identical RNG seeds
  #1057 GenericWrapper doc has minor quirks
  #1058 Feature/openswathwf add
  #1059 Switch to version 2.0
  #1061 FeatureFinderIdentification: documentation, tests, parameter improvements
  #1063 Fix/accession nr
  #1065 PeakPickerHiRes docu updated
  #1067 Testing/mzid
  #1069 Fix and test for issue #1068 (bug in "AASequence::operator<" involving N-terminal modifications)
  #1070 removing zeros in profile data caused by Thermo bug
  #1072 PeakPickerHiRes: disable spacing constraints for chromatograms (fixes #1060)
  #1074 'intensity weighted mean'; averaging added to ProteinQuantifier, solves #830
  #1076 Adapter for MS-GF+ search engine
  #1077 [TESTING] download and add MSGFPlus in travis-ci
  #1078 [FEATURE] export aabefore and aaafter in peptideindexer
  #1079 Linear extrapolation (and other options) for B-spline transformation
  #1080 [NOP] refactored PeptideHit protein accession extraction to true member
  #1082 [NOP] removed index file as these are recreated by MSGF+ anyways
  #1083 Feature/mz tab fixes
  #1084 [FIX] compile fixes
  #1086 Update (indistinguishable) protein groups when filtering protein identifications (fixes #748)
  #1087 centroided input data for FeatureFinderMultiplex
  #1088 Fix FileConverter's "write_mzML_index" flag
  #1089 Fix/mzid
  #1090 Enable mzIdentML input in IDFileConverter
  #1091 Feature/mz tab cleanup
  #1092 [NOP] removed unnecessary index files
  #1094 [FIX] fixed small bugs preventing a build on windows
  #1097 [FIX] consistent use of wildmagic
  #1098 Revert "[FIX] consistent use of wildmagic"
  #1099 [FIX,BUILD] fix Windows build
  #1100 Fix/windows fix
  #1101 optimisation for knockout searches in FeatureFinderMultiplex
  #1102 Fix/fix spellcheck
  #1104 [FIX] fix compile warning from unused variables
  #1108 [FIX] fix compile warnings and increase QT min version to 4.6
  #1109 [FIX] removed support for multiple id formats in tools without
  #1115 fix some windows compile warnings
  #1116 fix segfaults in XTandemXMLFile and IsobaricChannelExtractor
  #1118 Feature/swath window loader
  #1121 [FIX] some VC 2013 static tests fixed
  #1122 Fix PeakPicker Wavelet
  #1123 [FEATURE] remove PeakType template argument from FeatureFinder
  #1124 [NOP] addendum to #1123
  #1125 optimisations in FeatureFinderMultiplex
  #1126 [FIX] intermediate fix for win32 systems
  #1127 [FEATURE] create uncrustify branch
  #1128 Fix/RT meta value related bug, removed unused comment
  #1131 Make BuildSystem's LibCheck fail-safe
  #1135 Fix/ams mz tab export
  #1136 [NOP] uncrustified
  #1137 [FIX] added -b option to create new branch
  #1140 [FIX] fixed bugs in AScore implementation and added deisotoping as
  #1141 Fix AccurateMassSearch and visualization
  #1145 Fix/spellchecks
  #1147 Fix/copyright update
  #1150 Added PhosphoScoring tool to TOPP documentation
  #1151 Changelog 2.0
  #1152 [FIX,PYOPENMS] fix and adopt pyOpenMS
  #1153 minor amendmend to last fix (better console output)
  #1154 [TEST] fix test
  #1156 [FIX-#618] fix spelling errors
  #1157 [NOP] correct version in LICENSE file
  #1158 [FIX] make identifier of multiple identification runs unique
  #1161 pyOpenMS 2.0 features
  #1162 [FIX] fixed study variable index start at 1. Added global identifiert to
  #1164 [FIX] pepXML does on some occassion contain very small fixed
  #1165 Added minimal test cases for checker.php Missing test errors
  #1169 [FIX] fixed segfault if searchparam requested on empty proteinids
  #1170 [FIX,TEST] FidoAdapter test
  #1172 [FIX] fix for the write out of mzid
  #1173 [FIX] changed path String parameter to input files
  #1174 [TRAVIS] added Fido executables and adapted to new directory structure
  #1175 [FEATURE] add ConsensusMap push_back
  #1176 [BUILD] added support for new thirdparty executables in KNIME
  #1179 [FIX] added missing option to apply e-value filtering
  #1180 [FIX] fix toolnames for KNIME packaging
  #1181 fixed minor typo in error message
  #1184 [FIX] we decided to add the missing struct mapping file and in the
  #1185 [FIX] added missing elements and spike ins
  #1186 Fix/docu qc mzid
  #1187 [FIX] AMS: export observed-Mass in mzTab as well
  #1188 [Build] Added support for new third party binaries for dmg packaging. Adapted Li...
  #1189 Feature/sn
  #1190 [TEST] fix test
  #1192 [FIX] HMDB: removed duplicates introduced by including spike ins
  #1194 [NOP] removed deprecated qc toppas workflow
  #1195 [STYLE] Changed header guards mentioned by checker.php
  #1196 [FIX] XTandemAdapter added option to disable isotope error flag
  #1198 [TEST] fix
  #1199 [TEST,FIX] changing the order of the test fixes the issue
  #1201 Fix/lp wrapper param file
  #1203 [TEST,FIX] set reasonable comparison tolerance
  #1204 Removes debug code from FeatureFinderMultiplex
  #1206 [TEST] fix test error
  #1212 [FIX] and/or extension to IDFilter: Added support for old target_decoy user param in decoy filtering.
  #1213 [DOC] improve linux install doc
  #1215 [FIX] export AMS result as valid mzTab
  #1218 [FIX] consistent use of wildmagic: TransformationModelLinear
  #1219 [FIX] Map index stored as meta value in peptide identification
  #1220 change parameter ranges in FeatureFinderMultiplex
  #1224 updated KNIME license
  #1225 [FIX][TEST] Fido replacing scores
  #1226 Ammend to pull request #1212
  #1228 [FIX, PYOPENMS] fixed pxd file
  #1229 [DOC] merged License.txt and LICENSE for more complete description
  #1230 Updated ACTIVE_MAINTAINERS with people commiting, starting in 2012. Remo...
  #1231 Added Deuterium and Tritium to Elements.xml, as LIPIDMAPS contains sum f...
  #1232 Fix amt
  #1237 [FIX] minimum value for max_length should be 0 not -Inf
  #1240 [FIX] Fix/id filter blacklist
  #1242 Fix amt
  #1243 fixes INIUpdater test
  #1246 Updated problematic FidoAdapter test (fixes #1171)
  #1247 [FIX] added missing function
  #1248 [FIX, PYOPENMS] ammend to last commit
  #1249 Documentation improvements (and minor fixes)
  #1250 Another FidoAdapter test fix
  #1253 [FIX] IsobaricAnalyzer: set charge states of consensus features
  #1254 [DOC,FIX] Updated CHANGELOG, changelog_helper.sh
  #1256 Fix MSGFPlusAdapter running in TOPPAS (mzid output)
  #1257 Clean-up of UTILS documentation
  #1261 [KNIME] adapted parameter naming for FidoAdapter in KNIME
  #1262 IDFilter reports empty results
  #1263 [FIX] moved TopPerc to UTILS and changed experimental status of MSGFPlus
  #1266 [FIX] ammend to last commit
  #1267 [FIX] fix conversion from Feature with Masstraces to MSExperiment
  #1269 IsobaricAnalyzer: documentation, warning fix
  #1270 [FIX] lexical cast is discouraged. Use of build in functions.
  #1273 [FIX][BUILD] Fixes linking issue with boost in UTILS #1272
  #1275 [FEATURE] [FIX] mass trace RT spacing
  #1283 [PYOPENMS] Better PepXMLFile write support
  #1284 [FIX] KNIME execution of MSGFPlusAdapter
  #1286 [FIX] set low memory log type correctly
  #1290 [FIX, PYOPENMS] fix python binding for MassTrace
  #1305 [FIX] Fix/id mapper statistics
  #1307 remove OS X specific code for opening folders
  #1309 [FIX] Ammend to #1284
  #1315 sync develop additions

-------------------------------------------------------------------------------------------
----                                OpenMS 1.11.1  (released 11/2013)                  ----
-------------------------------------------------------------------------------------------
Release date: November 2013

OpenMS 1.11.1 is a bugfix release resolving the following issues with OpenMS 1.11:

TOPPAS:
- fixed bug that caused TOPPAS to crash when a connection between nodes was added under certain circumstances

TOPP:
- XMLValidator can now be used on mzML files
- fixed bug in MSSimulator/EnzymaticDigestion where amino acid "U" was leading to crash
- fixed some problems with protein modifications in MascotAdapterOnline
- fixed potential problems of TOPP help screens on small screens / small terminal windows

Build system:
- fixed issues with CMake 2.8.12
- fixed potential clang compile errors

General:
- fixed issues with MIME types in KNIME

Resolved issues:
  #606 TOPPAS crashes during creation of certain edges.
  #609 MascotAdapterOnline: Problems with modifications
  #614 Amino acid "U" leads to crash in MSSimulator/EnzymaticDigestion
  #629 OpenMS is incompatible with CMake 2.8.12
  #630 Knime mime.types file should have lower case mime type names
  #633 ConsoleUtils::breakString triggers uncaught exception if terminal size is too small

------------------------------------------------------------------------------------------
----                                  OpenMS 1.11                                     ----
------------------------------------------------------------------------------------------
Release date: August 2013

OpenMS 1.11 is the first release with fully integrated Python bindings (termed pyOpenMS).
For further details, please refer to https://pypi.python.org/pypi/pyopenms

File formats:
- QcML support
- pepXML exported from Mascot (added support)
- mzTab updated to 1.0RC3
- ParamXML updated to v 1.6.2
- support for CTD schema 0.3
- full support of sourceFile tag in mzML (all source files are written, SHA1 support)

TOPPView:
- handle .mzML file with mixed spectra and chromatograms (prefer spectra)
- chromatograms of all types can be displayed (not just SRM)
- link to documentation and webpage fixed
- fix a segfault when loading empty chromatograms into TOPPView

TOPPAS:
- link to documentation and webpage fixed

TOPP tools:
- MODIFIED:
  - FeatureLinkerUnlabeledQT: performance (speed and memory) improvement
  - FeatureLinkerUnlabeled: performance (memory) improvement (now constant in number of input maps)
  - MapAlignerPoseClustering: performance (memory) improvement (now constant in number of input maps)
  - EICExtractor: critical bugfix if the input map was not sorted
  - PeptideIndexer: by default now demands that the peptide is fully tryptic ("-enzyme:specificity none" restores the old behavior)
  - FileFilter: filter MS2 spectra by consensus map feature overlap, collision energy, isolation window width
  - ProteinResolver: documentation and interface improvements
  - QCCalculator/QCEmbedder/QCExtractor: multiple improvements
  - WindowMower: speed improvement (movetype either slide or jump [faster])
- ADDED
  - AccurateMassSearch: AccurateMassSearch assembles metabolite features from singleton mass traces.
  - IsobaricAnalyzer: Extracts and normalizes isobaric labeling information from an MS experiment. This merges the previous TMTAnalyzer and ITRAQAnalyzer functionality
  - QCExtractor: Extracts a table attachment to a given qc parameter
  - QCImporter: Embed tables or pictures in QcML

General:
- Python bindings allow full access to the OpenMS API from Python
- TOPPTools now support passing of all parameters on the command line (use --helphelp)
- Better chromatogram support (for NoiseFilterGaussian, NoiseFilterSGolay, PeakPickerHiRes)

Search engine support:
- Mascot 2.4 is now supported
- OMSSAAdapter with improved memory footprint
- N-terminal modifications work now with X!Tandem

Changes to the Build System / Package System:
- shared linking works for all contrib packages with automated detection using CMake find modules
- upgrade of xerces to version 3.1.1
- upgrade of libsvm to version 3.12

Development:
- public inheritance from std::vector and std::set has been reduced in the
  OpenMS codebase (removed from ConsensusFeature, FeatureMap, ConsensusMap,
  MSExperiment)
- addition of the OpenMS/INTERFACES folder which contains proposed OpenMS
  interfaces for reading/writing spectra

Deprecated:
- TMTAnalyzer, ITRAQAnalyzer -> please use IsobaricAnalyzer instead
- Several functions provided by std::vector in the MSSpectrum interface are now
  deprecated (e.g. push_back, reserve etc.)

Resolved issues:
  #120	Improve visual representation of edges
  #151	Optimize time/memory efficiency of critical tools/algorithms
  #184	Some OpenMS classes are derived from std::vector
  #309	FileConverter puts incorrect/incomplete information in <sourceFile>
  #343	OpenMS build system should allow searching for contrib libs also in system paths (e.g., /opt/local/..)
  #382	Excessive memory usage by MapAligners and FeatureLinkers
  #398	INIFileEditor doesn't save modified values if still in edit mode
  #457	Use system libraries instead of contrib
  #465	"-debug" option in TOPP tools doesn't show LOG_DEBUG messages
  #497	Non-intuitive way to edit parameters in TOPPView/TOPPAS/INIFileEditor
  #516	TOPPAS: "Refresh parameters" complains if no input files are present
  #517	MSQuantification::load declared but not implemented
  #519	Merge ITRAQAnalyzer and TMTAnalyzer
  #520	Support linking against shared libs
  #521	Upgrade contrib libsvm
  #522	Make parameters from subsections addressable from command line
  #523	Link to OpenMS website from within TOPPAS/TOPPView broken
  #524	PeptideIndexer does not honor cleavage sites
  #525	EICExtractor will report wrong intensities if input map is not sorted
  #527	pyOpenMS compile issue with clang
  #529	Strange naming of TextExporter parameters
  #531	Upgrade xerces-c version in contrib to 3.1.1
  #533	pyOpenMS
  #534	MascotAdapterOnline does not support Mascot 2.4
  #535	mzML with Spectra and Chromatograms
  #536	MascotAdapterOnline SSL and Mascot 2.4
  #537	Invalid Doxygen XML Files
  #540	IsobaricAnalyzer
  #541	AccurateMassSearch
  #542	TOPPView: switch to 3D view should pick the data layer automatically
  #544	featureXML version at 1.4 while 1.6 is the current version
  #549	Problems converting Mascot XML to idXML
  #552	pyOpenMS build system
  #553	TOPPView's "Apply TOPP tool" functionality is broken
  #554	FeatureLinkerUnlabeled(QT) - speed/memory enhancements
  #556	Setting parameter may not take effect
  #557	XTandemAdapter/mz-out scramble
  #562	cmake doesn't check for MSBuild.exe location on Windows
  #565	XTandemAdapter fails to add terminal modifications correctly to X!Tandem search
  #569	Segfault of IDEvaluator and IDEvaluatorGUI
  #570	FeatureLinkerUnlabeledQT regression
  #574	Update ParamXMLHandler to support v1.6.2 of Param schema
  #575	Upgrade TOPPBase's CTD support to new version of CTD schema
  #576	Cython 0.19 does not compile current pyOpenMS
  #578	Add qcML CV terms
  #580	XTandemAdapter finds non-tryptic peptides although cleavage rule is set to "[RK]|{P}"
  #582	Compile error with Boost 1.46
  #583	MascotAdapterOnline with Mascot 2.4.0 may never finish
  #584	FileFilter parameter -mz (mz range to extract) applies to all MS levels and not to a specified level
  #586	ModificationsDB_test relies on raw memory addresses
  #587	MascotAdapterOnline does not support SSL connections
  #588	MascotAdapterOnline does not support connections to public MatrixScience Mascot instance
  #591	Detection of MGF format via file content fails on our own files
  #593	Parameter default of 'tab' will be returned as single space
  #598  SILACAnalyzer (no label) crash
  #603  TOPPView: showing peptide annotations of feature maps also shows feature indexes

------------------------------------------------------------------------------------------
----                                  OpenMS 1.10                                     ----
------------------------------------------------------------------------------------------
Release date: March 2013

OpenMS 1.10 is the first release integrated into KNIME (www.knime.org).
To use OpenMS in KNIME please refer to the www.OpenMS.de for additional information.

File formats:
- TraML 1.0.0 support
- Initial mzQuantML, mzIdentML and mzTab support (not fully supported)

TOPPView:
- Concurrent zoom
- SRM data visualization

New tools:
- Superhirn
- OpenSWATH
- QCCalculator
- IDRipper
- FeatureFinderMetabo
- IDEvaluation
- RNPxl

General:
- Better chromatogram support
- Decoy strings can now be prepended
- Filter modified peptides
- Many memory and speed improvements
- TMT-6plex support
- EDTA conversion from feature and consensusXML in FileConverter
- Filtering of MS2 spectra by identifications

Search engine support:
- MyriMatch adapter

Changes to the Build System / Package System:
- Cpplint coding convention check integrated into build system
- Integration of OMSSA search engine in Windows and Mac installers
- Integration of X!Tandem search engine in Windows and Mac installers
- Integration of MyriMatch search engine in Windows and Mac installers

Development:
- Style corrections of the OpenMS source base using uncrustify

Deprecated:
- Conversion of Sequest files in IDFileConverter

Resolved issues:
	#513	Commented out the functionality of smartFileNames_() (not mature enough for the 1.10 release)
	#508	allow free columns for TSV
	#473	change in/out types again to csv
	#507	TOPPDocumenter now expects the path to the executables and can generate doc for TOPPView/TOPPAS on mac osx
	#506	added custom info.plist containing the path to OMSSA/XTandem for the GUI tools
	#505	goto dialogs now act with error tolerance
	#504	Fixed XTandemXMLFile loading when no encoding is given by XTandemXML file by enforcing ISO-Latin-1 (default would be utf-8, breaking the aminoacid sequence readin). Introduced enforceEncoding(encoding) to XMLFile.
	#316	SpectraTreeTab is not cleaned up when last layer is deleted
	#283	TOPPView: Scan view widget does not clear after closing last file
	#379	MapAlignerPoseClustering: -reference:index has no effect
	#384	replace zip libraries with The Boost Iostreams Library (already in contrib)
	#280	IonizationSimulation_test can not be compiled with OpenMP support on Mac OS X	(Unit) Tests
	#368	Check Example pipelines and tutorials if they still contain the Tools using the type parameters
	#341	Move IMS Mass Decomposition Code to OpenMS and remove IMS from contrib
	#330	Remove static references to 10.5 SDK in OpenMS and contrib builds
	#135	Remove temporary files after completion
	#301	IDExtractor has no documentation
	#78		Write generic Nightly Testing Script
	#355	Adapt documentation to the changes in the contrib handling of the build system
	#348	Update TOPP tool names in documentation
	#383	iTRAQ isotope correction & simulation broken for 8plex
	#333	CMake returning incorrect configurations.
	#378	Intensity issue for simulation of MS2 signals
	#264	PrecursorIonSelector crashs (SegFault) with minimal input
	#322	PeakPicker (wavelet) writes lots of "dataProcessing" junk to mzML file
	#327	Feature width not stored in featureXML
	#372	Calculation of rank correlation coefficient buggy
	#376	Command line parser does not recognize --help and --helphelp
	#374	IonizationSimulation takes ages to complete on very high abundance peptides
	#371	FileFilter should support filtering by meta values
	#359	Remove type argument from SpectrumFilter
	#346	Implement mechanism to convert pre1.9 toppas workflows to 1.9 workflows
	#345	Implement mechanism to convert pre1.9 ini files to 1.9 workflows
	#212	Nicer formatting of parameter listings in documentation
	#356	PeakPickerWavelet fails for broad peaks
	#332	TOPPAS: QWebView for downloading pipelines does not work behind proxy
	#366	SILACLabeler should adjust all channels to have the same RT elution profiles
	#365	Sampling of RT parameters in RTSimulation can produces abnormal RT parameters
	#364	Improve handling of user input while downloading workflows from the online repository
	#363	TOPP test need to define their dependencies to avoid wrong execution
	#360	Remove type argument from FeatureFinder
	#357	IDPosteriorError Prob crashes with small number of peptides
	#354	Adapt documentation to the changes in the contrib handling of the build system
	#344	remove TOPPBase type argument from MSSimulator
	#347	Contaminant simulation might produce wrong masses when used in unintended way
	#41		AndiMS for 32/64bit Windows and 64bit Linux.
	#326	PepXMLFile: use RT of MS2 spectra for peptide RT
	#321	Update Seqan to 1.3	Build System
	#331	TOPPAS: Active tab changes all the time under MacOSX (10.6 and 10.7)
	#106	Export for Workflows as image
	#325	No HTML for Internal FAQ
	#324	DecoyDatabase should support shuffling and contaminants	TOPP
	#323	MapAligner -apply_given_trafo's "invert" option only works from commandline	TOPP
	#209	Reading Bruker XMassFile failes with invalid DateTime String
	#236	TOPP tool API change will crash existing TOPPAS pipelines
	#282	TOPPAS updateParameters() might create invalid Pipeline
	#298	"Open in TOPPView" broken for MacOSX
	#320	TOPPAS Workflows should support a short documentation
	#318	FuzzyStringComparator::compareLines_ throws exception on gcc-4.6
	#317	ostream::operator<< for MSSpectrum is not working
	#314	Crash when selecting empty window
	#227	TOPPAS tmp directory not multi-user friendly
	#178	Warn if merger node is followed by a tool for single files, not lists
	#313	MascotAdapterOnline does not support Mascot 2.3
	#312	FilterFilter should support filtering by precursor charge
	#226	Specific isotopes in ElementsDB are generated with wrong masses
	#308	AASequence(iterator, iterator) constructor is invalid, since it ignores terminal modifications
	#305	TOPPView fails while opening mzML with intensities stored in an int32 array
	#234	File forwarding/merging broken
	#303	TOPPAS, TOPPView and ExecutePipeline: looking for TOPP tools
	#302	Simulator should support picked peak Ground Truth
	#300	Allow input node recycling	TOPPAS	closed	fixed
	#299	Enable automatic static code analysis of OpenMS using cppcheck
	#205	TOPPAS crashes
	#210	TOPPAS Merger nodes are buggy
	#259	Resume button broken
	#43		Discuss overhaul of OpenMS web site and possible migration to CMS	Website, FAQs, Screencasts
	#297	Simulation: Ionization does not consider n-term to carry charge
	#295	Split OpenMS library in two or more parts
	#296	PeptideIndexer might keep 1 old ProteinAccession

------------------------------------------------------------------------------------------
----                                  OpenMS 1.9                                      ----
------------------------------------------------------------------------------------------
Release date: February 2012

OpenMS 1.9 has some major changes in TOPP tool names and usage. Therefore all .ini files
for "typed" TOPP tools (i.e. those with a "type" parameter) built with OpenMS 1.8 and below
are incompatible! To fix your old .ini and .toppas files use the new
INIUpdater tool (see its documentation and the TOPP documentation in general).

OpenMS 1.9 removed support for Mac OS X 10.5.

Documentation:
- new Quickstart tutorial
- dedicated and reworked TOPPAS tutorial

TOPPView improvements:
-MODIFIED:
  - ConsensusFeatures can now be colored using MetaValues
  - better grid line drawing/calculation, extracted AxisPainter class
  - IdentificationView:
    - added automatic labeling with peptide fragment sequence
    - theoretical spectrum is now hidden by default (labeling contains relevant information for most use cases)
    - automatic zoom to measured MS2 data range

TOPPAS improvements:
	- TOPPAS allows for interactive download of preconfigured TOPPAS pipelines from OpenMS homepage
	- "Recycling" mode for nodes, useful for database input files (see docu for details)
- more flexible pipeline design for Merger nodes
- Merger nodes (merge, merge all) renamed to "Merge" (one round) and "Collect" (all rounds)


TOPP tools:
- ADDED:
  - MapStatistics: statistics for low level quality control
  - EICExtractor: quantify known RT, m/z locations in one or many LC/MS maps and align them
  - MassTraceExtractor: annotate mass traces in centroided LC/MS maps - useful for metabolomics and top-down proteomics (use FeatureFinder tools for peptides)
  - FeatureFinderRaw: feature finding on raw data
	- FeatureFinderMetabo: feature finding for metabolites
  - IDConflictResolver: resolve ambiguous annotations of features with peptide identifications
- MODIFIED:
  - FeatureFinder: split into FeatureFinderMRM, FeatureFinderCentroided, FeatureFinderIsotopeWavelet
  - FeatureLinker: split into FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT
  - FeatureLinker tools remove unneeded data after loading featureXML files to conserve memory
  - MapAligner: split into MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, and MapRTTransformer
  - model parameters of MapAligner tools are now set in the INI file
  - MapAlignerIdentification: don't fail if parameter "min_run_occur" is set too high, warn and use possible maximum instead
  - NoiseFilter: split into NoiseFilterGaussian and NoiseFilterSGolay
  - PeakPicker: split into PeakPickerWavelet and PeakPickerHiRes
  - PILISModel: split into PILISModelCV, PILISModelTrainer, and PILISSpectraGenerator
  - MascotAdapterOnline: now supports Mascot 2.3 servers
  - ProteinQuantifier: added support for writing idXML (suitable for export to mzTab)
  - IDFileConverter: when reading pepXML, fail if the requested experiment (parameters "mz_file"/"mz_name") could not be found in the file
- REMOVED:
  - AndiMS/NetCDF is no longer supported on any platform
  - removed IDDecoyProbability tool

UTIL tools:
- ADDED:
  - INIUpdater: update INI and TOPPAS files
  - TransformationEvaluation: evaluate a (RT) transformation by applying it to a range of values
- REMOVED:
  - CaapConvert
  - UniqueIdAssigner
  - HistView

Changes to the Build System:
	- TOPPAS now requires Qt's Webkit library
	- Use CMAKE_BUILD_TYPE instead of OPENMS_BUILD_TYPE (removed)
	- Use CMAKE_FIND_ROOT_PATH instead of CONTRIB_CUSTOM_DIR (deprecated)
  - Removed AndiMS, NetCDF and dependencies
	- Removed dependency to imslib, relevant classes were moved directly to OpenMS/CHEMISTRY/MASSDECOMPOSITION/IMS
- OpenMS now supports ctests functionality for optimized and parallel testing (see ticket #363)

Fixed Issues: (see also http://sourceforge.net/apps/trac/open-ms/report)
	#341 	Move IMS Mass Decomposition Code to OpenMS and remove IMS from contrib
	#330 	Remove static references to 10.5 SDK in OpenMS and contrib builds
	#301 	IDExtractor has no documentation
	#78 	Write generic Nightly Testing Script
	#355 	Adapt documentation to the changes in the contrib handling of the build system
	#348 	Update TOPP tool names in documentation
	#333 	CMake returning incorrect configurations
	#264 	PrecursorIonSelector crashs (SegFault) with minimal input
	#280	IonizationSimulation_test can not be compiled with OpenMP support on Mac OS X
	#322 	PeakPicker (wavelet) writes lots of "dataProcessing" junk to mzML file
	#327 	Feature width not stored in featureXML
	#372 	Calculation of rank correlation coefficient buggy
	#376 	Command line parser does not recognize --help and --helphelp
	#371 	FileFilter should support filtering by meta values
	#359 	Remove type argument from SpectrumFilter
	#346 	Implement mechanism to convert pre1.9 toppas workflows to 1.9 workflows
	#345 	Implement mechanism to convert pre1.9 ini files to 1.9 workflows
	#212 	Nicer formatting of parameter listings in documentation
	#356 	PeakPickerWavelet fails for broad peaks
	#363 	TOPP test need to define their dependencies to avoid wrong execution
	#360 	Remove type argument from FeatureFinder
	#357 	IDPosteriorErrorProb crashes with small number of peptides
	#354 	Adapt documentation to the changes in the contrib handling of the build system
	#41 	AndiMS for 32/64bit Windows and 64bit Linux..
	#326 	PepXMLFile: use RT of MS2 spectra for peptide RT
	#321 	Update to Seqan 1.3
	#324 	DecoyDatabase should support shuffling and contaminants
	#323 	MapAligner -apply_given_trafo's "invert" option only works from commandline
	#209 	Reading Bruker XMassFile failes with invalid DateTime String
	#236 	TOPP tool API change will crash existing TOPPAS pipelines
	#318 	FuzzyStringComparator::compareLines_ throws exception on gcc-4.6
	#317 	ostream::operator<< for MSSpectrum is not working
	#297 	Simulation: Ionization does not consider n-term to carry charge
	#383 	Simulation: iTRAQ isotope correction & simulation broken for 8plex
	#378 	Simulation: Intensity issue for simulation of MS2 signals
	#374 	Simulation: IonizationSimulation takes ages to complete on very high abundance peptides
	#366 	Simulation: SILACLabeler should adjust all channels to have the same RT elution profiles
	#365 	Simulation: Sampling of RT parameters in RTSimulation can produces abnormal RT parameters
	#344 	Simulation: remove TOPPBase type argument from MSSimulator
	#347 	Simulation: Contaminant simulation might produce wrong masses when used in unintended way
	#303 	TOPPAS, TOPPView and ExecutePipeline: looking for TOPP tools
	#305 	TOPPView fails while opening mzML with intensities stored in an int32 array
	#314 	TOPPView: Crash when selecting empty window
	#205 	TOPPAS crashes
	#227 	TOPPAS: tmp directory not multi-user friendly
	#282 	TOPPAS: updateParameters() might create invalid Pipeline
	#332 	TOPPAS: QWebView for downloading pipelines does not work behind proxy
	#135 	TOPPAS: Remove temporary files after completion
	#320 	TOPPAS: Workflows should support a short documentation
	#298 	TOPPAS: "Open in TOPPView" broken for MacOSX
	#106 	TOPPAS: Export for Workflows as image
	#364 	TOPPAS: Improve handling of user input while downloading workflows from the online repository
	#331 	TOPPAS: Active tab changes all the time under MacOSX (10.6 and 10.7)
	#210 	TOPPAS: Merger nodes are buggy
	#259 	TOPPAS: Resume button broken
	#300 	TOPPAS: Allow input node recycling
	#234 	TOPPAS: File forwarding/merging broken
	#178 	TOPPAS: Warn if merger node is followed by a tool for single files, not lists
	#313 	MascotAdapterOnline does not support Mascot 2.3
	#312 	FilterFilter should support filtering by precursor charge
	#226 	Specific isotopes in ElementsDB are generated with wrong masses
	#308 	AASequence(iterator, iterator) constructor is invalid, since it ignores terminal modifications
	#302 	Simulator should support picked peak Ground Truth
	#299 	Enable automatic static code analysis of OpenMS using cppcheck
	#43 	Discuss overhaul of OpenMS web site and possible migration to CMS
	#295 	Split OpenMS library in two or more parts
	#296 	PeptideIndexer might keep 1 old ProteinAccession
	#379  MapAlignerPoseClustering: -reference:index has no effect


Detailed list of changes to specific OpenMS classes:
- NEW:
	- compose_f_gx_hy_t (from imslib)
	- compose_f_gx_t (from imslib)
	- IMSAlphabet (from imslib)
	- IMSAlphabetParser (from imslib)
	- IMSAlphabetTextParser (from imslib)
	- IMSElement (from imslib)
	- IMSIsotopeDistribution (from imslib)
	- IntegerMassDecomposer (from imslib)
	- MassDecomposer (from imslib)
	- RealMassDecomposer (from imslib)
	- Weights (from imslib)
  - sum/mean/median functions added to header "StatisticFunctions"
  - PeptideAndProteinQuant: contains quantification code formerly included in ProteinQuantifier (TOPP tool)
- MODIFIED:
  - AASequence: removed AASequence(ConstIterator, ConstIterator) constructor, since it ignored Terminal Modifications; since there was no way to enable correct construction from two Iterators, we removed it
  - MapAlignmentAlgorithmIdentification: don't fail (exception: InvalidParameter) if value for "min_run_occur" is too high, warn and use possible maximum instead
  - MSSimulator: "type" parameter moved to "MSSim:Labeling:type"
  - Param: added new command line parser with improved functionality
  - PepXMLFile:
    - added reading support for pepXML version 1.17
    - set RT's of peptide identifications based on MS2 spectra, not the MS1 precursors as before (flag "use_precursor_rt" switches to the old behavior)
    - fail with ParseError if a requested experiment could not be found in a pepXML file
  - ProtXMLFile: set score type for peptides
  - TOPPBase: added methods to turn Param objects into command line parameters
  - TransformationModel: simplified handling of parameters
  - TransformationModelBSpline: new option to distribute breakpoints evenly at data quantiles (instead of uniformly over the data range)
  - lots more... too much to list



------------------------------------------------------------------------------------------
----                                  OpenMS 1.8                                      ----
------------------------------------------------------------------------------------------

TOPP tools:
- MODIFIED:
  - MapAligner: separated data extraction from transformation modelling - this allows to combine different algorithms and models; new option "invert"; reworked parameters (please see the MapAligner documentation and update your INI files)
  - FeatureLinker: now able to link consensus maps; added new experimental algorithm "unabeled_qt"; improved quality calculation in "unlabeled" algorithm
  - IDMapper, FeatureLinker ("unlabeled"/"unlabeled_qt" algorithms): now consider charge states by default (use parameter "ignore_charge" if you want to avoid this)
  - FileInfo: improved formatting of output
  - TextExporter: unified output formats
  - FileConverter: added conversion to consensusXML
  - ProteinQuantifier: redefined meaning of parameter combination "top 0"/"consensus:fix_peptides"
  - ITRAQAnalyzer: isotope corrected quantitation result is written to "-out" instead of the uncorrected values
  - GenericWrapper: now supports arbitrary external programs, when a .ttd file is present (see <OpenMS>/share/OpenMS/TOOLS/EXTERNAL)

UTIL tools:

TOPPView improvements:
- NEW:
  - Identification View (load idXML through Tools->annotate with identifications)
  - 1D view now supports vector graphics export when saving an image
  - Peaks in 2D view are drawn as circles at a high zoom level
  - TOPPAS pipelines can be edited and run directly from TOPPView

TOPPAS improvements:
- MODIFIED:
  - improved stability when using longer filenames
  - minor fixes (see bug tickets below)

OpenMS library improvements:
- Stability and consistency fixes mostly (see bug tickets below)

Changes to the Build System:
- minor only


Fixed Issues:
#277 	Crash upon annotation with idXML
#271 	Filename generation in TOPPAS broken
#278 	TOPP tools update only values from INI files, not restrictions
#273 	TOPPAS appends an extra "toppas" when saving files with uppercase TOPPAS extension
#272 	TOPPAS doesn't update the tab title after saving a new pipeline
#261 	ProteinQuantifier: handling of mod. peptides during protein quantification
#153 	"Unlabeled" FeatureLinker produces quality values that make no sense
#220 	TOPPAS: mzML.gz files are not recognized as correct input
#260 	InclusionExclusionListCreator creates invalid lists for Thermo instruments
#269 	OMSSAAdapter crashes when run from directory containing spaces
#267 	bug in StablePairfinder (distances)
#266 	TOPPAS "store" button for vertex' INI files always writes default INI
#129 	TOPPAS: Allow opening files in one layer
#105 	TOPPAS: Split TOPPAS.ini into Resource and Workflow files
#262 	PrecursorIonSelector handles input/output arguments incorrectly
#100 	TOPPView memory consumption high when copying data
#257 	CLang++ crashes with "SCEVAddRecExpr operand is not loop-invariant!" on EnzymaticDigestion
#233 	TOPPView's updateLayer does not reload all data
#247 	TOPPView: crashes if file is deleted while opened
#66 	"Tools -> Go to" coordinates should default to current view
#239 	seg. fault when loading featureXML into TOPPView from the wrong context
#221 	TOPPView: when loading a new layer, the zoom should not reset
#222 	IDMapper should support mapping charge-matched entities only
#255 	TOPPView's Projection is showing only single peaks at high zoom
#253 	TOPP tools should be able to write their type into ini file, without knowing it a priori
#252 	OMSSAAdapter crashes when v2.1.7 and 'precursor_mass_tolerance_unit_ppm' are used
#251 	XTandem Adapter ignores "no_refinement" flag
#198 	add Proteowizward to Windows binary installer
#246 	TOPPView: Update Layer broken
#149 	Support external tools not derived from TOPPBase
#245 	PeptideIndexer fails on ambiguous AA's
#244 	merging by Precursor in SpectraMerger
#242 	Protein coverage should be reported
#237 	RT corrections via BSpline transformation is unreliable for sparse regions (e.g. borders and extrapolation)
#235 	TOPPAS input file name lists should be sorted
#231 	FeatureFinder has faulty Averagine model
#229 	Digestor UTIL cannot write FASTA output
#27 	generate publication ready figures in SVG format - 1D view
#215 	FeatureFinder crashes with Segmentation fault
#213 	TOPPView crashs when loading mzML and featureXML
#224 	PepXMLFile produces invalid files (mod_aminoacid_mass position is 1-based)
#225 	msInspect pepXML parser can not handle OpenMS pepXML due to massdiff attribute
#223 	TOPPAS restores wrong parameter name when deleting an input/output edge
#217 	Caching in LogStream is not thread safe
#218 	FF should work on non-sorted data, but gracefully exit on negative m/z values
#214 	MapAligner crashes on certain data
#211 	TOPPAS: IDFilter RTPredict linking not possible
#150 	TOPPAS does not use user environment to find executables
#208 	Windows: hide extra console window when starting GUI apps
#207 	Projections show wrong axis names
#179 	adapt to command/console width
#206 	Parameter names should include subsection
#204 	TOPPView "Go To" Dialog should support UniqueID's
#202 	"Open file" dialog: "readable files" should include .gz files
#191 	changing from 1D to 2D,3D View and 3D to 2D if MS1 spectra are present
#196 	NoiseFilter, PeakPicker, BaselineFilter crash on certain input-data

Detailed list of changes to specific OpenMS classes:
- NEW:
  - BaseFeature: parent of Feature and ConsensusFeature
  - FeatureGroupingAlgorithmQT, QTClusterFinder, QTCluster, GridFeature: feature grouping for unlabeled data based on QT clustering
  - FeatureDistance: distance measure for features
  - TransformationModel: different models for retention time transformations
  - SvmTheoreticalSpectrumGenerator: simulator for MS/MS spectra

- MODIFIED:
  - Feature, ConsensusFeature: moved common parts to BaseFeature
  - StablePairFinder: moved distance calculation to FeatureDistance
  - TransformationDescription: reworked, some functionality moved to TransformationModel
  - all MapAlignmentAlgorithm... classes, PoseClustering[Affine/Shift]Superimposer, TransformationXMLFile, InternalCalibration: adapted to changes in RT alignment/transformation modelling
  - FeatureGroupingAlgorithm: support linking of consensus maps; new algorithm "unlabeled_qt"
  - BaseGroupFinder: new algorithm "qt"
  - IDMapper: consider charge states for matching
  - PepXMLFile: use E-value (instead of hyperscore) as score for X! Tandem results
  - FileHandler: accept endings ".pep.xml" and ".prot.xml" for pepXML/protXML
  - FeatureMap, ConsensusMap: "clear" also clears meta data by default
  - ConsensusMap: adapted signature of "convert" for feature maps (to mirror that for peak maps)
  - Param: remove() and ::removeAll() now delete empty nodes which have no subnodes nor entries (otherwise writing paramXML breaks)
  - TheoreticalSpectrumGenerator: getSpectrum() now generates all selected ion types not only b- and y-ions

------------------------------------------------------------------------------------------
----                                  OpenMS 1.7                                      ----
------------------------------------------------------------------------------------------
Release date: Sep 5th 2010

TOPP tools:
- TOPP tool categories have been reorganized
- TOPP documentation now has a predecessor/successor tool section and uniform algorithms subsection parameter documentation
- MODIFIED:
  - IDFilter: reworked parameter names and documentation (please see the IDFilter documentation and update your INI files)
  - IDMapper: reworked parameter handling (please see the IDMapper documentation and update your INI files)
  - FileMerger: can now merge featureXML
  - IDMerger: new option to integrate data from pepXML and protXML
  - MapAligner: improved handling of reference files, added several options to the "identification" algorithm
  - SeedListGenerator: new option to use monoisotopic peptide mass instead of precursor m/z for seeds from idXML input
  - Resampler: PNG image creation functionality removed and transferred to ImageCreator UTIL
  - FeatureFinder: deprecated algorithms "simple" and "simplest"
  - FeatureLinker: deprected algorithm "identification"
- NEW:
  - ProteinQuantifier: compute protein/peptide abundances from annotated featureXML or consensusXML files
  - GenericWrapper: wrap external programs (e.g. ProteinProphet) in TOPPAS
  - ConsensusID: [rewritten] combine several peptide search engine results to improve precision and recall
  - InclusionExclusionListCreator: creates inclusion or exclusion lists for MS/MS based on identifications, feature maps or protein databases
- REMOVED:
  - TextImporter (functionality moved to FileConverter)

UTIL tools:
- MODIFIED:
  - DecoyDatabase now uses "_rev" as decoy string by default (previously: "_ref"), as required by PeptideIndexer by default
  - MSSimulator provides a framework for the simulation of labeled data (#88)
- NEW:
  - ImageCreator: creates PNG's from MS maps
  - IDSplitter: splits peptide/protein annotations off of data files (inverse operation as IDMapper)
  - MassCalculator: calculates masses and mass-to-charge ratios of peptide sequences

OpenMS library improvements:
- read protXML files
- support protein groups in ProteinIdentification/idXML
- line numbers in errors of Textbased files (most formats: dta, dta2D, FASTAFile, PepNovoOutfile, MascotGenericFile, MS2File, MSPFile, OMSSACSVFile, TextImporter (csv, msInspect, SpecArray?, Kroenik))
- FeatureFinderAlgorithmPicked is now able to fit asymmetric retention time profiles (experimental)
- added generic labeling framework to SIMULATION (#88) (experimental)

TOPPView improvements:
- basic visualization of peptide identifications in idXML
- when the amount of loaded data causes memory depletion, an error is issued and TOPPView does not crash (only a problem on 32bit systems)
- zooming beyond the last zoom stack item using the mouse wheel or CTRL+

TOPPAS improvements:
- added copy/paste for workflow items
- workflows can now include other workflows (File>Include)
- several bug fixes
- split TOPPAS in TOPPAS and PipelineExecute TOPP-tool

Changes to the Build System:
- external code support for CMake 2.8:
  External code using "include (${OpenMS_USE_FILE})" in its CMakeLists.txt cannot be configured against OpenMS 1.7, however, only minor changes are required to fix this. See the documentation for "Programming with OpenMS".
- nightly tests for external code
- SVN revision used to build the lib is remembered (finer version tracking)
- nightly coverage builds
- GUI testing (experimental)
- Visual Studio 2010 support
- building on Mac OS X requires CMake 2.8.1 due to bugs in CMake < 2.8.1

Fixed Issues:
[new tracker: http://sourceforge.net/apps/trac/open-ms/query?status=closed&group=resolution&milestone=Release+1.7]
-	#23	  implement protXML
-	#44  	TOPPView warning "Cannot show projections!"
-	#46  	All TOPP/UTILS segfault if /share is not found
-	#53  	TOPPAS select directory has save as dialog
-	#54  	TOPPAS select directory has save as dialog
-	#56  	TOPPAS context menu "open in TOPPView" does not work under MacOSX
-	#58  	Unit tests for nested classes
-	#59  	Test of external Code
-	#61  	automatic ini file Version number update
-	#62  	nightly tests for external code
-	#63  	rename methods named min() or max() to something else...
-	#64  	TOPPView - update_layer reload is incomplete
-	#69  	FileMerger needs ability to merge featureXML
-	#73  	Resampler: can't create PNGs with TOPPAS
-	#74  	Default parameters of PTModel cause infinite loop
-	#76  	Add deployment target for compatibility with older MacOSX versions
-	#77  	FuzzyDiff always returns 'true' when comparing any two PNG images
-	#81  	Terminal modification with residue specificity
-	#85	  IDMapper will crash on negative RT's or big deltas
-	#87  	Gzipped files work as input, but arrow stays red
-	#88  	Implement Labeling Framework for MSSimulator
-	#90	  Quantification on protein level
-	#91	  Simple FF crashes on very sparse data
-	#92	  Encoding of XML files (invalid multcharacter)
-	#93	  TOPPAS layer bug
-	#98	  display RT value when viewing 1D data
-	#104	Split TOPPAS in TOPPAS and PipelineExecute TOPP-tool
-	#110	"Copy&paste, include workflows in current window"
-	#121	Tool categories and menu items in context menus have arbitrary order
-	#122	Projection view: mouse-over text on RT projection says "m/z"
-	#123	Reorganize TOPP tool categories
-	#124	TOPPAS fails to load files correctly
-	#127	catch out-of-memory exceptions in TOPPView
-	#131	TOPP input files check too restrictive...
-	#132	check all system calls
-	#133	Textexporter runs indefinitely when input has no IDs and -consensus_features as output
-	#134	[Windows] failure of TOPP tools in TOPPAS due to _out and _temp directory not writeable
-	#136	TOPPView: #of Isotopes in TheoreticalSpectrumGenerator not forwarded
-	#137	Implement asymmetric elution profile shapes for model fitting in FeatureFinderAlgorithmPicked
-	#141	CMake 2.8.1 causes linker errors on Mac OS 10.6.3
-	#143	Incompatibility between String and string methods
-	#147	Internal Compiler Error with gcc 4.3
-	#152	Remove/hide deprecated algorithms
-	#154	Update TOPPAS workflows params
-	#155	linking OpenMS.so using a relative contrib directory fails
-	#156	use MSBuild instead of devenv for contrib building on Windows
-	#158	FeatureFinder (centroided) might crash on certain input
-	#159	IDMapper will crash when given empty FeatureMap
-	#161	TOPPAS Output file naming can lead to wrong "merge all" behaviour
-	#163	rework IDFilter
-	#164	DecoyDatabase creates faulty protein names by default
-	#170	TheoreticalSpectrumGenerator computes wrong prefix/suffix masses
-	#171	Remove/hide entire deprecated tools
-	#175	Internal Compiler error in BaseModel/FeatureFinder
-	#182	INIFileEditor crashes upon execution
For more minor bugfixes visit the above URL.

Detailed list of changes to specific OpenMS classes:
- ConsensusMap, FeatureHandle, ConsensusFeature:
  - element index replaced by unique id
- DPosition:
  - min() renamed to minPositive()
  - min_negative() to minNegative()
- DIntervalBase
  - min() renamed to minPosition()
  - max() renamed to maxPosition()
- String
  - removed:
     String substr(SignedSize start, SignedSize n) const;
     String substr(SignedSize start) const;
  - added:
     String substr(size_t pos = 0, size_t n = npos) const;
     String chop(Size n) const;

------------------------------------------------------------------------------------------
----                                  OpenMS 1.6                                      ----
------------------------------------------------------------------------------------------
Release date: Nov 19th 2009

Main improvements of TOPPView:
- Storing peak data is now possible in mzData, mzXML and mzML format
- Feature and consensus feature peaks are now configurable (icon and size)
- Added new label mode for feature layers: all peptide hits of a feature are displayed
- Added visualization of unassigned peptide hits for feature layers
- Measuring to arbitrary end points is now supported in 1D and 2D view
- file load progress bar stays responsive under load on Windows
- rudimentary chromatogram support

Main improvements of TOPP-Framework:
- Major update of TOPPAS
- TOPP tools now warn when used with parameter files from a different version
- Combining '-write_ini' and '-ini' option now allows to transfer settings with identical
  path and names from an old ini file into a new one.

New TOPP tools:
- SeedListGenerator
  - generates seed lists for feature detection (still experimental)
- PrecursorMassCorrector
  - update precursor m/z information of MS/MS spectra based on MS1 peptide isotope fits
    (still experimental)

Main improvements of TOPP-Tools:
- all tools:
  - gzipped and bzipped XML files (e.g. mzML) can be directly read
- FeatureFinder
  - Centroided
    - supports parallel execution now
    - supports user-specified seeds now
    - Wavelet: removed (Isotope-Wavelet is still available)
- FileMerger: accumulated processingMethod entries, which all contained the same
  information
- IDMapper
  - has new default m/z tolerance and uses ppm as new default measure! Da is still
    supported.
  - referenze m/z of ID can now be either: 1) precursor mass, 2) [new] mass of identified
    peptide
  - assigns more peptides to features with convex hulls (the deltas are used)
- InternalCalibration
  - supports calibration functions calculated seperately for each spectrum or one global
    function
  - supports peptide ids as reference peaks
  - works on peak or feature data now
- MapAligner
  - new "identification" algorithm for alignment based on identified peptides
    (still experimental)
- PeakPicker
  - support for automatic estimation of peak width
- TextImporter can now import Koenik(Hardkloer) feature files
- TextExporter
  - added option for string quoting
  - improved export of consensusXML
- PepNovoAdapter: complete rewrite of the code, including classes

New UTILS:
- UniqueIdAssigner can be used to assign unique ids to FeatureXML and ConsensusXML files

Main improvements of UTILS:


Main improvements of OpenMS C++ library:
- MGF file creation speedup (also affects some TOPP tools)
- removed FeatureFinder-Wavelet (IsotopeWavelet is still available)
- support for bzip2 and gzip compressed XML files
- chromatogram support
- comments and other strings of XML writers are now escaped to prevent reading problems
- fixed IdXMLFile segmentation fault if no protein identification given

Detailed list of changes to specific OpenMS classes
- [New classes]:
  - UniqueIdGenerator, UniqueIdInterface, UniqueIdIndexer
  - SVOutStream
  - MapAlignmentAlgorithmIdentification
  - SeedListGenerator
- [Removed classes]:
  - FeatureFinderAlgorithmWavelet
- [Renamed classes]:
  - IDTagger -> DocumentIDTagger
- String:
  - improved behaviour of split(...) method
  - added support for quoting and unquoting of strings
- ConsensusMap: added clear(...) method
- IDMapper:
  - uses bounding boxes of mass traces instead of convex hulls now
  - the given deltas are used for features with convex hulls as well
- PoseClusteringShiftSuperimposer:
  - full rewrite, uses a similar algorithm like PoseClusteringAffineSuperimposer now
- TranformationDescription:
  - added cubic b-spline transformation
  - PairsType uses DoubleReal instead of Real now, thus can be used for m/z as well
- VersionInfo:
  - includes (if available) SVN revision number that the library is build upon via support
    by the build system
  - SVN revision information is displayed in the TOPP tools help text
- PepXMLFile: improved handling of PTMs

Changes to the Build System:
- unit tests are now in a separate sub-project in <OpenMS/source/TEST/> avoiding huge
  Solution files in MSVC IDE
- new targets: test_build, tutorials_build, tutorials_exec
- SVN revision (if available) is determined and compiled into OpenMS before the library is
  built
- added real install prefix and install target to be able to do a 'make install'

Changes to OpenMS XML formats:
- FeatureXML and ConsensusXML files use unique ids now instead of running indices. New XML
  Schema versions: 1.4

Changes to the contrib package:
- updated GSL to version 1.13
- updated SVM to version 2.89
- added Z lib and bz2 lib

Bug fixes:

[old tracker: http://sourceforge.net/tracker/?func=detail&aid=2857130&group_id=90558&atid=1059012]
- [2857042]: RTModel/PTModel unable to find modification
- [2857040]: Modification names with brackets fail to parse
- [2849215]: OMSSAAdapter fails with Acetlyation not found
- [2849201]: Parameters in INI files are duplicated
- [2849439]: Compilation error with Qt 4.3.x
- [2900457]: idXML files with more than ProteinIdentification might be incorrect

[new tracker: http://sourceforge.net/apps/trac/open-ms/query?status=closed&group=resolution&milestone=Release+1.6]
- #29: FilerMerger accumulates processingMethod entries
- #28: Segfault if idXML file does not contain a protein identification.
- #24: XML formats are written with unescaped special chars like "&"

------------------------------------------------------------------------------------------
----                                  OpenMS 1.5                                      ----
------------------------------------------------------------------------------------------

Main improvements of TOPPView:
- Added new labeling options for feature data
- Fixed crash when zooming in snap-mode
- Added context menu to spectra selection bar
- Feature editing mode can be enabled/disabled in the context menu (to avoid accidental editing)
- Several minor fixes and improvements

Main improvements of TOPP:
- Made mzML 1.1.0 the default format for all TOPP tools
- Added data processing information to all output files to improve traceability
- FileFilter:
  - added 'sort_peaks' option
  - added filtering according to scan type
  - added filtering according to activation type
- FileInfo:
  - added flag for data processing output
  - corrupt data checks: sorting is checked now, improved speed
- Added new tool IDFileConverter, which can convert between identification file formats
- Added TOPPAS, a tool for visual creation and execution of TOPP pipelines (beta)
- TextImporter can now import SpecArray and msInspect feature files
- Added CompNovo, a de novo identification tool for combined CID/ETD experiments
- MapAligner uses a new algorithm for pose clustering with less parameters

Main improvements of UTILS:
- Added PeptideIndexer, assign proteins to peptides including target/decoy specification
- Added MRMPairFinder, ERPairFinder to extract ratios of labeled experiments
- Added IDMassAccurracy, given mzML files and identification, it calculates distributions of mass deviations
- Added MapAlignmentEvaluation, a tool to evaluate alignment results
- Added MSSimulator, a highly configurable simulator for mass spectrometry experiments

Main improvements of OpenMS C++ library:
- mzML 1.1.0 support
- Improved the precision of mass values in several file formats

Detailed list of changes to specific OpenMS classes
- New classes:
  - CompNovo-classes
  - StablePairFinder, which is now used by MapAligner and FeatureLinker
  - Simulation-classes
- Removed classes:
  - FeatureFinderAlgorithmWatershed
  - PeakIcon
  - FactoryProduct (replaced by DefaultParamHandler)
  - DSpectrum (all the functionalty was moved to MSSpectrum)
- Renamed and moved classes:
  - moved PersistentObject from FORMAT/ to FORMAT/DB/
  - renamed PepXMLFile to PepXMLFileMascot
- Changes to Classes:
  - MSExperiment: added 'isSorted' method
  - MSSpectrum:
    - added 'isSorted' method
    - renamed MetaDataArray to FloatDataArray
    - added IntegerDataArrays
    - added StringDataArrays
  - DataValue: added constructor for 'std::string' and QString
  - MetaInfo: 'setValue' method takes only DataValue now
  - MetaInfoInterface: 'setMetaValue' method takes only DataValue now
  - Param: 'setValue' method takes only DataValue now
  - ExperimentalSettings: moved DataProcessing to SpectrumSettings (for mzML)
  - Precursor: supports multiple dissociation methods now (for mzML)
  - MetaInfoDescription: removed comment and source file; added data processing (for MzML)
  - ElementDB: isotopes are now possible
  - EmpiricalFormula: isotopes are now possible (e.g. (2)H for deuterium)
  - ModificationsDB: switched completely to UniMod (www.unimod.org). PSI-MOD still provided for convenience
  - PepXMLFile: added new 'load' method (moved the old 'load' method to PepXMLFileMascot)
  - TextFile:
    - is now derived from StringList
    - the 'asString' method was replaced by 'concatenate' from StringList
  - MzMLFile:
    - added support for integer and string binary arrays
    - added support for compressed binary data arrays
    - loading a file with unknown CV terms in certain tags no longer causes an error
  - DBConnection:
    - The 'executeQuery' method no longer sets the internal pointer to the first record of the result.
      It is now positioned before the first record. A boolean flag can be used to switch to the old behaviour.
  - SourceFile: changed native ID type to string
  - PoseClusteringAffineSuperimposer: full rewrite, not using CGAL

Changes to the contrib package:
- Added CoinMP 1.3.3
- Added IMSlib 0.1.0
- Update Xerces-C to revision 806068 of SVN trunk

Bug fixes:
- [2778461]: mzData files containing 'supDataArray' elements no longer crash OpenMS
- [2777173]: TOPPView 2D view projections no longer forget the draw mode on repaint
- [2776386]: TOPPView snap-to-max intensity mode no longer crashes with empty spectra
- [2775912]: PeakPickerCWT no longer assigns RT=-1 to MS/MS spectra

------------------------------------------------------------------------------------------
----                                  OpenMS 1.4                                      ----
------------------------------------------------------------------------------------------

Main improvements of TOPPView:
- Drag-and-drop is now supported from the layer bar, spectrum bar and for files from the operating system
- Improved visualization of very high-resolution data
- Improved painting speed of 2D view

Main improvements of TOPP:
- Added new tool TextImporter, which can convert text files to featureXML
- TextExporter can now export peptide/protein information stored in consensusXML
- PeakPicker: reduced the number of parameters, added parallization support
- FeatureFinder: added new MRM algorithm and removed the tool 'FeatureFinderMRM'
- FileInfo: added support for idXML

Main improvements of OpenMS C++ library:
- mzML 1.1.0 RC5 support
- removed support for external memory (use the 64bit builds if you want to process large datasets)
- added support for three kinds of parallization architectures
  - OpenMP
  - Intel Threading Building Blocks
  - Nvidia Cuda

Detailed list of changes to specific OpenMS classes:
- SpectrumSettings: several precursor peaks are now supported, added product list
- Precursor: complete rewrite for better support of mzData, mzXML and mzML
- PeakPickerCWT: cleaned up interface, improved meta data handling, improved parameters, added parallelization support
- GaussFilter: cleaned up interface, improved meta data handling
- SavitzkyGolayFilter: cleaned up interface, improved meta data handling
- MorphologicalFilter: cleaned up interface
- LinearResampler: cleaned up interface
- LabeledPairFinder: estimated negative sigma values are now treated as positive values
- FeatureFinder: added new algorithm 'MRM' for MRM feature detection; replaces FeatureFinderMRM
- ExperimentalSettings: remove native ID type (for mzML support)
- SourceFile: added native ID type (for mzML support)
- File: replaced vector<String> by StringList in all methods

Bug fixes:
- [2645436]: TOPPView - Data Filter for "Size" not available
- [2645510]: OpenMS - libOpenMS.so is built but linking fails (TOPP, tests) (on Debian "Lenny")
- [2665055]: FileFilter ignores -sort option for FeatureXML and Consensus
- [2659013]: windows contrib can fail when copying compiled libraries
- [2606068]: TOPP tools with list parameters do not work with INI files
- [2690367]: Protein references missing on peptide identifications

------------------------------------------------------------------------------------------
----                                   OpenMS 1.3                                     ----
------------------------------------------------------------------------------------------

New features and improvements of OpenMS:
- The build system is now based on CMake - supporting Linux, MacOS and Windows.
- Finalized mzML implementation (version 1.1.0 RC4)
  - previously unsupported parts
  - indexed mzML
  - semantic validation (see FileInfo)
- Kernel: Replaced comparators NthPositionLess by the comparator(s) RTLess and/or MZLess.
- Kernel: Replaced methods sortByNthPosition() by the method(s) sortByRT() and/or sortByMZ().
- Improved the framework for meta data visualization.
- Several extensions to the meta data classes were made for mzML compliance.
- The macros used for unit testing in source/TEST have been revised.
- More consistent handling of single vs. double numeric precision, esp. in file output.
- Added ANALYSIS/PIP/PeakIntensityPredictor class for peak intensity prediction (contributed by Alexandra Scherbart).
- Added support for Intel Compiler versions 10 and 11
- Added support for Qt up to 4.5 rc1

New features and improvements of TOPP:
- Added SILACAnalyzer: A specialized tool for quantitation of SILAC experiments (contributed by Lars Nilse).
- Added ITRAQAnalyzer: A specialized tool for quantitation of ITRAQ experiments.
- Added IDMapper: Assigns protein/peptide identifications to features or consensus features.
- FeatureLinker: Added automated RT parameter estimation for 'labeled' algorithm.
- MapAligner: Added spectrum_alignment and apply_given_trafo, IdXML is supported.
- Resampler: This tool is now used for resampling raw data instead of resampling in NoiseFilter or BaselineFilter.
- FileInfo: The option '-v' now also does a semantic validation of mzML files.
- FileMerger: Improved interface
- ConsensusID: Now also supports consensus identification of features and consensus features.
- INIFileEditor: Support for string/int/double lists and input/output files was added.
- Added PrecursorIonSelector: A tool for result-driven precursor ion selection.
- FalseDiscoveryRate: corrected FDR calculations and added optional support for q-values
- Added MascotAdapterOnline: which allows queries to Mascot via network (together with Daniel Jameson)

New features and improvements of TOPPView:
- Added functionality for editing feature data
- Added support for consensus features (consensusXML)
- Added measuring and generic annotations to 1D view
- Several minor interface improvements and bugfixes

Changes to OpenMS XML formats:
- ParamXML:
  - Restrictions in Param .ini files are represented by 'min:max' instead
    of 'min-max' now, to avoid issues with small (1e-06) and negative numbers.
  - Replaced 'advanced' attribute by the more general 'tags' attribute.
  - Added support for float, int and string lists
- featureXML:
  - Added tag <subordinate> to store competing features that did not qualify for the final map
  - Removed <description> section
  - Added document identifier
  - Added protein and peptide information
- consensusXML:
  - Added document identifier
  - Added protein and peptide information
- idXML:
  - Added document identifier

Changes to the contrib package:
- The build system is now based on CMake - supporting Linux, MacOS and Windows.
- Updated SeqAn package to revision 2666 (this fixes the STL debug error)
- Updated xerces-c to version 3.0.0
- Updated boost to version 1.37.0
- Downgraded GSL to 1.8 (because of Mac/Windows support)

Detailed list of changes to specific OpenMS classes:
- Renamed and moved classes
  - Renamed MSMetaDataExplorer to MetaDataBrowser
  - Renamed ProcessingMethod to DataProcessing
  - Moved XMLValidator from FORMAT/ to FORMAT/VALIDATORS/
- Removed classes
  - DPeakArray (moved the functionality to the classes that inherited from it)
  - IDSpectrumMapper (replaced by IDMapper)
  - IDFeatureMapper (replaced by IDMapper)
  - FeatureXMLHandler (merged into FeatureXMLFile)
  - ConsensusXMLHandler (merged into ConsensusXMLFile)
  - PeakPicker (merged into PeakPickerCWT)
  - MorphFilter (merged into MorphologicalFilter)
  - TopHatFilter (merged into MorphologicalFilter)
- New classes
  - DATASTRUCTURES/IntList
  - DATASTRUCTURES/StringList
  - ANALYSIS/ID/IDMapper
  - ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmApplyGivenTrafo
  - ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmSpectrumAlignment
- Changes to classes
  - InstrumentSettings
    - Revisited scan modes
    - Added bool member for zoom scans (no longer a scan mode)
  - MassAnalyzer: Removed tandem scanning method. This is stored in the ScanMode of InstrumentSettings.
  - DataProcessing: Now contains Software and can handle multiple processing actions.
  - Software: Only contains name and version now.
  - SourceFile: Added MetaInfointerface and checksum type
  - ContactPerson: Added URL and address
  - Instrument:
    - Can contain multiple detectors and multiple ion sources now
    - Added Software
    - Added ion optics type
  - AcquisitionInfo: Added MetaInfoInterface
  - Acquisition: integer 'number' member was changed to a string 'identifier' (for mzML)
  - ExperimentalSettings
    - Now contains multiple SourceFiles and DataProcessings
    - ExperimentType was removed
  - SpectrumSettings
    - Added nativeID (from acquisition software)
  - DSpectrum
    - The peaks are no longer stored in a container member, but DSpectrum is derived
      from std::vector<PeakType>.
    - The container type is no longer a template argument. Peak type and allocator type
      are the new template arguments.
  - LabeledPairFinder: Added automated RT parameter estimation.
  - GaussFitter: Removed several unneeded methods.
  - GammaDistributionFitter: Removed several unneeded methods.
  - DataValue: Added support for IntList and DoubleList types
  - Param:
    - Added a new remove(key) method, that removed only exact matches.
      The old remove() method was renamed to removeAll(prefix)
    - Replaced 'advanced' flag by a generic tagging mechanism
    - Added support for IntList and DoubleList types
  - File: find(...) now throws an exception, of the file is not found.
  - DPeak and DRichPeak are metafunctions now, e.g. DPeak<1>::Type is a typedef for Peak1D.
  - VersionInfo: Added support for SVN revision info. Slight interface changes.
  - TOPPBase: Print revison info (if meaningful).
  - MetaInfo: Uses double precision now.
  - Date
    - get() now returns a string instead of modifying a string reference.
    - Made today() is static now and returns the current DateTime instead of modifying the object.
  - DateTime
    - get(), getDate() and getTime() now return a string instead of modifying a string reference.
    - Made now() is static now and returns the current Date instead of modifying the object.
  - MSExperiment: The date is now a DateTime object.
  - ProgressLogger: Nested application uses indentation.
  - XMLValidator: The output stream for error messages can now be set in the isValid(...) method
  - XMLFile: The output stream for validation error messages can now be set in the isValid(...) method
  - MzMLFile: The output stream for validation error messages can now be set in the isValid(...) method
  - IdXMLFile: Adden document identifier to the load(...) and store(...) method

------------------------------------------------------------------------------------------
----                                   OpenMS 1.2                                     ----
------------------------------------------------------------------------------------------

New features and improvements of OpenMS:
- GCC 4.3 is now supported (GCC 3.4 and 4.0 are no longer supported)
- Added support for GCC STL debug mode (configure option --enable-stl-debug)
- Complete reimplementation of map alignment and feature grouping classes.
  This affected some classes in KERNEL and nearly all classes in ANALYSIS/MAPMATCHING.
  The affected classes are not listed in detail here.
- Added meta data arrays to spectra as the new standard way of handing peak meta information
- Improved interface of SpectrumCanvas and derived classes for easier reuse outside of TOPPView
- Added support for arbitrary modifications to peptide/protein modifications (based on PSI-MOD)
- Exceptions thrown by member functions are no longer declared in the header files.
  They are however documented in the class documentation.
- Added *beta* support for the HUPO PSI format mzML
  Currently only reading is supported and some features are not implemented yet
  e.g. chromatograms, zlib compression of base64 data, base64 integer data, base64 16 bit data
- Added the UTILS package, a bundle of small helper tools.
- Changed handling of amino acid sequences and modifications. Modifications are taken from
  PSI-MOD and are fully supported via the class AASequence.
- Added new framework for generic clustering

New features and improvements of TOPP:
- Replaced 'MapAlignment', 'UnlabeledMatcher' and 'LabeledMatcher' tools by 'MapAligner' and 'FeatureLinker' tools
- Added map alignment algorithm based on spectrum similarity to 'MapAlignment'
- Added 'PTModel' and 'PTPredict' tool for prediction of proteotypic peptides
- Added XTandemAdapter with a minimal interface (shared with OMSSAAdapter) all advanced option can be set using a
  standard X!Tandem configuration file
- Changed OMSSAAdapter to same minimal interface as XTandemAdapter, advanced option are additionally available
- Added IDDecoyProbability which implements the transformation of a forward and reversed search into probability
  scores (target-decoy approach)
- Added FalseDiscoveryRate, which implements FDR calculation from forward and reversed searches at peptide
  and protein levels

New features and improvements of TOPPView:
- Major update to the user interface and functionality
- Speed improvements of the 2D view
- Many bug fixes
- Updated tutorial

Changes to OpenMS XML formats:
- Added TransformationXML which stores information about map alignment
- Removed map alignment information from ConsensusXML
- FeaturePairsXML is now deprecated (ConsensusXML is used instead)

Changes to the contrib package:
- Updated to NetCDF 3.6.3
- Updated to SeqAn 1.1 (r2416)
- Updated to CGAL 3.3.1
- Updated to GSL 1.11
- Updated to xerces-c 2.80
- Updated to boost 1.35.0
- Updated to libsvm 2.86

Detailed list of changes to specific OpenMS classes:
- Renamed and moved classes
  - Renamed 'Exception::Base' to 'Exception::BaseException'
  - Renamed all 'Peak' classes to 'RichPeak'
  - Renamed all 'RawDataPoint' classes to 'Peak'
  - Renamed 'KERNEL/DPeakConstRefArray' to 'DATASTRUCTURES/ConstRefVector'

- Removed classes
  - KERNEL/PickedPeak1D
  - DATASTRUCTURES/HashMap (replace by Map)
  - ANALYSIS/MAPMATCHING/BaseAlignment (restructuring of map alignment)
  - ANALYSIS/MAPMATCHING/BaseMapMatcher (restructuring of map alignment)
  - ANALYSIS/MAPMATCHING/BasePairFinder (restructuring of map alignment)
  - ANALYSIS/MAPMATCHING/BasePairFinder_impl (restructuring of map alignment)
  - ANALYSIS/MAPMATCHING/BasePairwiseMapMatcher_impl (restructuring of map alignment)
  - ANALYSIS/MAPMATCHING/BaseSuperImposer_impl (restructuring of map alignment
  - ANALYSIS/MAPMATCHING/ElementPair (restructuring of map alignment)
  - ANALYSIS/MAPMATCHING/Grid (restructuring of map alignment)
  - ANALYSIS/MAPMATCHING/GridCell (restructuring of map alignment)
  - ANALYSIS/MAPMATCHING/Group (restructuring of map alignment)
  - ANALYSIS/MAPMATCHING/IndexTuple (restructuring of map alignment)
  - ANALYSIS/MAPMATCHING/LinearMapping (restructuring of map alignment)
  - ANALYSIS/MAPMATCHING/MapDewarper (restructuring of map alignment)
  - ANALYSIS/MAPMATCHING/MapMatcherRegression (restructuring of map alignment)
  - ANALYSIS/MAPMATCHING/PairMatcher (restructuring of map alignment)
  - ANALYSIS/MAPMATCHING/PoseClusteringPairwiseMapMatcher (restructuring of map alignment)
  - ANALYSIS/MAPMATCHING/StarAlignment (restructuring of map alignment)
  - ANALYSIS/CLUSTERING/BinnedRep (reimplemented in BinnedSpectrum)
  - COMPARISON/SPECTRA/BinnedRepCompareFunctor (reimplemented in BinnedSpectrumCompareFunctor)
  - COMPARISON/SPECTRA/BinnedRepMutualInformation (reimplemented in BinnedMutualInformation)
  - COMPARISON/SPECTRA/BinnedRepSharedPeakCount (reimplemented in BinnedSharedPeakCount)
  - COMPARISON/SPECTRA/BinnedRepSpectrumContrastAngle (reimplemented in BinnedSpectralContrastAngle)
  - COMPARISON/SPECTRA/BinnedRepSumAgreeingIntensities (reimplemented in BinnedSumAgreeingIntensities)
  - CONCEPT/Benchmark
  - CONCEPT/HashFunction
  - FILTERING/SMOOTHING/SmoothFilter
  - FORMAT/FeaturePairsXMLFile (restructuring of map alignment)
  - FORMAT/GridFile (restructuring of map alignment)
  - FORMAT/HANDLER/FeaturePairsHandler (restructuring of map alignment)
  - FORMAT/HANDLER/GridHandler (restructuring of map alignment)
  - FORMAT/HANDLER/OMSAAXMLHandler (replaced by OMSSAXMLFile)
  - KERNEL/ConsensusPeak (restructuring of map alignment)
  - KERNEL/FeatureHandle
  - KERNEL/MSExperimentExtern
  - KERNEL/PeakIndex
  - TRANSFORMATIONS/CENTROIDING/PeakShapeType

- New classes
  - CHEMISTRY/ModificationsDB which handles the PSI-MOD modifications
  - CHEMISTRY/ModificationDefinition class, which specifies modification search options
  - CHEMISTRY/ModificationDefinitionSet class, which specifies modification search options
  - CHEMISTRY/ResidueModification which represents a PSI-MOD modification
  - ANALYSIS/ID/FalseDiscoveryRate class, which calculates FDRs on peptide and protein level
  - ANALYSIS/ID/IDDecoyProbability class, which implements a target decoy probability estimation
  - DATASTRUCTURES/Map class and replaced HashMap usage with Map
  - ANALYSIS/MAPMATCHING/BaseGroupFinder (restructuring of map alignment)
  - ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithm (restructuring of map alignment)
  - ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithmLabeled (restructuring of map alignment)
  - ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithmUnlabeled (restructuring of map alignment)
  - ANALYSIS/MAPMATCHING/LabeledPairFinder (restructuring of map alignment)
  - ANALYSIS/MAPMATCHING/MapAlignmentAlgorithm (restructuring of map alignment)
  - ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmPoseClustering (restructuring of map alignment)
  - ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmSpectrumAlignment (new map alignment type using spectral alignments)
  - ANALYSIS/MAPMATCHING/TransformationDescription (new map alignment type using spectral alignments)
  - ANALYSIS/CLUSTERING/AverageLinkage (new framework for clustering)
  - ANALYSIS/CLUSTERING/ClusterFunctor (new framework for clustering)
  - ANALYSIS/CLUSTERING/ClusterHierachical (new framework for clustering)
  - ANALYSIS/CLUSTERING/CompleteLinkage (new framework for clustering)
  - ANALYSIS/CLUSTERING/SingleLinkage (new framework for clustering)
  - COMPARISON/SPECTRA/BinnedSpectrum (Binned represenetation of a spectrum)
  - COMPARISON/SPECTRA/BinnedMutualInformation
  - COMPARISON/SPECTRA/BinnedSumAgreeingIntensities
  - COMPARISON/SPECTRA/BinnedSpectralContrastAngle
  - COMPARISON/SPECTRA/BinnedSharedPeakCount
  - COMPARISON/SPECTRA/BinnedSpectrumCompareFunctor
  - COMPARISON/SPECTRA/CompareFourierTransform
  - COMPARISON/SPECTRA/PeakAlignment
  - COMPARISON/SPECTRA/SteinScottImproveScore
  - DATASTRUCTURE/DistanceMatrix
  - FORMAT/ControlledVocabulary
  - FORMAT/HANDLER/MzMLHandler
  - FORMAT/HANDLER/UnimodXMLHandler
  - FORMAT/HANDLER/XTandemInFileXMLHandler
  - FORMAT/MSPFile
  - FORMAT/MzMLFile
  - FORMAT/OMSSACSVFile
  - FORMAT/PepXMLFile (only for Mascot output, not complete implementation of pepXML)
  - FORMAT/TransformationXMLFile
  - FORMAT/XTandemInfile
  - FORMAT/XTandemXMLFile
  - MATH/STATISTICS/GammaDistributionFitter
  - MATH/STATISTICS/GaussFitter
  - TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmIsotopeWavelet
  - TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmWavelet

- Changes to classes
  - Changed AASequence to support PSI-MOD modifications
  - Changed Residue to support PSI-MOD modifications



------------------------------------------------------------------------------------------
----                                  OpenMS 1.1.1                                    ----
------------------------------------------------------------------------------------------

Bug fixes:
- [1953335]: TOPP - TOPPView: Filter bar is not updated when deleting a layer
- [1953339]: TOPP - TOPPView: Crash when pressing cancel button of the DB password dialog
- [1948699]: TOPP - TOPPView: Opening a file from command-line containing spaces fails
- [1948080]: TOPP - MascotAdapter: Variable modification were added to fixed modifications
- [1941268]: TOPP - TOPPView: Crash when displaying files with intensity 0 peaks only
- [1941270]: TOPP - TOPPView: Recent file paths in TOPPView are wrong under certain conditions (Windows only)
- [1941273]: TOPP - TOPPView: Crash when loading an INI file without type in TOPP dialog
- [1934199]: OpenMS - SpectrumWidget: Crash when painted without layers
- [1933097]: OpenMS - TOPPBase: Invalid default values of string parameters were not handled correctly


------------------------------------------------------------------------------------------
----                                   OpenMS 1.1                                     ----
------------------------------------------------------------------------------------------

New features and improvements of OpenMS:
- Added support for Windows XP
- Improved configure
  - prefix option now works as expected
  - Fixed several bugs in handling of Qt
  - Fixed several minor bugs
- Added support for large datasets through a custom allocator
- Added support for XML schemas, which allows validation of files
- Added optional schema version tag to all OpenMS XML formats
- Removed classes: DataReducer, MaxReducer, SumReducer, SavitzkyGolaySVDFilter,
                   MSExperimentExtern, BaseMapping
- Added classes: StringList, SuffixArray, DataFilters
- Renamed/moved classes:
  - ExternalCalibraton -> TOFCalibration,
  - SavitzkyGolayQRFilter -> SavitzkyGolayFilter
  - FORMAT/Param.h -> DATASTRUCTURES/Param.h
- Refactoring of FeatureFinder framework
- Refactoring of MapAlignment framework
- Refactoring of XML parsing classes
- Refactoring of the visualization widgets
- Reorganization of the OpenMS documentation
- Lots of minor bug fixes and improvements to documentation

New features and improvements of TOPP:
- Added support for advanced parameters and parameter value restrictions
- Added file type/name checks before use of input/output files
- Improved parameter handling of the tools that offer different methods:
  FeatureFinder, NoiseFilter and SpectraFilter
- Lots of minor bug fixes and improvements to documentation
- FileFilter: Added option to sort data points according to RT and m/z
- FileInfo: Added validation of files against the XML schema, added check for corrupt data
- Added TextExporter: exports featureXML, featurePairsXML, consensusXML and idXML to text
                      files for import to other tools
- Added FeatureFinderMRM: performs peptide quantitation using Multiple-Reaction-Monitoring (MRM)

New features and improvements of TOPPView:
- Refactoring of the interface: Moved a lot of functions to context menus
- Added data filters (intensity, quality, ...)
- Lots of minor bug fixes
- Added tutorial

Detailed list of changes to specific OpenMS classes:
- BoundingBox2D
  - Added constructor from PointArrayType
- DataValue
  - Simplified to Int, DoubleReal and String types only
  - Direct cast to all data types is not possible anymore
- DefaultParamHandler
  - Added support for restrictions
  - Added support for advanced parameters
- String
  - Improved implementations of implode and substr
  - Renamed implode(...) method to concatenate(...)
- DSpectrum
  - Added method to find the nearest peak to an m/z value (findNearest)
- Feature
  - Added support for convex hulls of individual mass traces
- Param
  - Added support for value restrictions
  - Added support for advanced parameters
  - Replaced STL iterator by Param-specific iterator, which is aware of the tree strucure
  - The getValue method now throws an exception in case of a non-existing name.
    Use exists(...) to check if a parameter exists
- FileHandler
  - Added support for IdXML, ConsensusXML and mgf format
- Factory
  - Added methods to find out which products are registered
- MetaInfo/MetaInfoInterface/MetaInfoRegistry
  - Names are automatically registered now
- FileHandler
  - Renamed some of the Type enum values to make them consistent

------------------------------------------------------------------------------------------
----                                   OpenMS 1.0                                     ----
------------------------------------------------------------------------------------------
- Kernel redesign (improvement of usability)
- Removed Boost dependencies
- Qt4 port
- Experimental support for MacOS 10
- Experimental support for Windows (XP & VISTA via MinGW)
- New OpenMS and TOPP tutorial
- Redesign of protein and peptide identification datastructures
- New format for protein and peptide identification: IdXML
- Release of annotated schemas for all OpenMS XML formats
- New features and improvements of TOPPView
  - Visualization of peaks, feature and feature pairs has been speeded up
  - Meta data browsing and editing
  - TOPP tools can be invoked via TOPPView
  - Visualization of protein/peptide identification annotated to LC-MS/MS data
- New features and improvements of TOPP
  - Added INIFileEditor - A GUI editor for TOPP configuration files
  - Added ConsensusID - A tool to unify protein and petide identification from several
                        search engines
  - Added Decharger - Decharging feature maps
  - Added MapAlignment - Multiple alignment of LC-MS maps
  - Added MapNormalizer - Normalization of peak intensities
  - Added InternalCalibration - Calibration of peak m/z using reference masses
  - Added ExternalCalibration - Conversion of flight times into m/z using external
                                calibrant spectra