OpenMS/TOPP change log

On this page you find the changlog of released OpenMS versions and planned features of future releases.

Features plannned for upcoming versions

Support for the mzIdentML format
Automatic parameter estimation for peak picking and feature finding

Version 1.6 (November 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&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 OpenMS C++ library:
- MGF file creation speedup (also affects some TOPP tools)
- removed FeatureFinder-Wavelet, Isotope-Wavelet 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
- IdXMLFile segmentation fault if no protein identification given fixed
Detailed list of changes to specific OpenMS classes:
- New classes:
  - UniqueIdGenerator, UniqueIdInterface, UniqueIdIndexer
  - SVOutStream
  - MapAlignmentAlgorithmIdentification
  - SeedListGenerator
- Removed classes:
  - FeatureFinderAlgorithmWavelet
- Renamed classes:
  - IDMapper -> DocumentIDMapper
- 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:
  - handling of PTMs now better
Changes to the Build System:
- Unit tests are now in a separate sub-project in 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 build
- 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: (New tracker)
- #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 "&"
Bug fixes: (Old tracker)
- [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
Version 1.5 (August 26th, 2009)
- 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
Version 1.4 (April 17th, 2009)
- 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 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
Version 1.3 (February 13th, 2009)
- 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 to store competing features that did not qualify for the final map
    - Removed 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.
      - 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
Version 1.2 (August 1st, 2008)
- 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:
  - Mayor 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/RAW2PEAK/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
Version 1.1.1 (Mai 5th, 2008)
- Bug fixes (see bug tracker):
  - [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
Version 1.1 (April 1st, 2008)
- New features and improvements of OpenMS
  - OpenMS running on Windows
    - compilation from source only on Windows XP
    - binary package tested on Windows 2000 (SP4), Windows XP (SP2) and Windows VISTA Business (64-bit)
  - 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
  - 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
Version 1.0 (July 1st, 2007)
- Kernel redesign (improvement of usability)
- Removed Boost dependencies
- Qt4 port
- Supported platforms: Linux, MacOS 10 (experimental)
- 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
Version 0.95 (January 20th, 2007)
- Updated TOPP - The OpenMS Proteomics Pipeline
- Added a lot of documentation
- Added a lot of tests
- Many bug fixes

OpenMS/TOPP change log

Features plannned for upcoming versions

Version 1.6 (November 19th, 2009)

Version 1.5 (August 26th, 2009)

Version 1.4 (April 17th, 2009)

Version 1.3 (February 13th, 2009)

Version 1.2 (August 1st, 2008)

Version 1.1.1 (Mai 5th, 2008)

Version 1.1 (April 1st, 2008)

Version 1.0 (July 1st, 2007)

Version 0.95 (January 20th, 2007)