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Glossary:
OpenMS - Name of the project and our C++ library
TOPP - "The OpenMS Proteomics Pipeline", collection of chainable tools for flexible HPLC/MS workflows
TOPPAS - "The OpenMS Proteomics Pipeline Assistant", 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

------------------------------------------------------------------------------------------ 
----                                OpenMS 1.11.1                                     ---- 
------------------------------------------------------------------------------------------ 
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	SpectraViewWidget 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/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



------------------------------------------------------------------------------------------
----                                  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