File: CHANGELOG

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openms 2.4.0-real-1
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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
Parameters - list of algorithm or TOPP tool parameters that changed in this release

------------------------------------------------------------------------------------------
----                                OpenMS 2.4                                        ----
------------------------------------------------------------------------------------------
OpenMS 2.4 introduces changes from 322 pull requests including new features and bug fixes.

Notable changes since version 2.3 are:

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

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

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

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

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- RNPxl -- Tool for RNP cross linking experiment analysis (UTIL) (superseded by RNPxlSearch)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

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

Major changes in functionality:
- None   

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

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

Changed tool parameters:

Tool name	Added/removed	Parameter name	Type	Default value	Restrictions	Supported formats
AccurateMassSearch	+	out	output-file			*.mzTab
AccurateMassSearch	-	out	output-file			*.tsv
CometAdapter	+	allowed_missed_cleavages	int	0	0:5	
CometAdapter	+	enzyme	string	Trypsin	glutamyl endopeptidase,Arg-C,Asp-N,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P,unspecific cleavage,Trypsin	
CometAdapter	+	fragment_bin_offset	double	0	0:1	
CometAdapter	+	fragment_bin_tolerance	double	0.02	0.01:	
CometAdapter	+	isotope_error	string	off	off,0/1,0/1/2,-1/0/1/2/3,-8/-4/0/4/8	
CometAdapter	+	mass_offsets	double			
CometAdapter	+	max_fragment_charge	int	3	1:5	
CometAdapter	+	max_precursor_charge	int	5	1:9	
CometAdapter	+	minimum_intensity	double	0	0:	
CometAdapter	+	override_charge	string	keep known search unknown	keep any known,ignore known,ignore outside range,keep known search unknown	
CometAdapter	+	remove_precursor_peak	string	no	no,yes,charge_reduced,phosphate_loss	
CometAdapter	+	remove_precursor_tolerance	double	1.5		
CometAdapter	+	require_variable_mod	string	false	true,false	
CometAdapter	+	spectrum_batch_size	int	20000	0:	
CometAdapter	-	allowed_missed_cleavages	int	1		
CometAdapter	-	enzyme	string	Trypsin	unspecific cleavage,Lys-N,Lys-C,Chymotrypsin,CNBr,glutamyl endopeptidase,PepsinA,Arg-C,Trypsin/P,Trypsin,Asp-N	
CometAdapter	-	fragment_bin_offset	double	0.25		
CometAdapter	-	fragment_bin_tolerance	double	1.0005		
CometAdapter	-	isotope_error	string	off	off,-1/0/1/2/3,-8/-4/0/4/8	
CometAdapter	-	mass_offsets	double	0		
CometAdapter	-	max_fragment_charge	int	3		
CometAdapter	-	max_precursor_charge	string	0+		
CometAdapter	-	minimum_intensity	int	0		
CometAdapter	-	override_charge	string	keep any known	keep any known,ignore known,ignore outside range,keep known search unknown	
CometAdapter	-	remove_precursor_peak	string	no	no,yes,all	
CometAdapter	-	remove_precursor_tolerance	int	1		
CometAdapter	-	spectrum_batch_size	int	1000		
DecoyDatabase	+	Decoy:keepPeptideCTerm	string	true	true,false	
DecoyDatabase	+	Decoy:keepPeptideNTerm	string	true	true,false	
DecoyDatabase	+	Decoy:non_shuffle_pattern	string			
DecoyDatabase	+	enzyme	string	Trypsin	Trypsin,Arg-C,Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin/P,Chymotrypsin,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C/P	
DecoyDatabase	+	seed	string	1		
DecoyDatabase	+	shuffle_max_attempts	int	30		
DecoyDatabase	+	shuffle_sequence_identity_threshold	double	0.5		
Digestor	+	FASTA:ID	string	parent	parent,number,both	
Digestor	+	FASTA:description	string	remove	remove,keep	
Digestor	+	enzyme	string	Trypsin	Asp-N,Trypsin,Arg-C/P,Chymotrypsin/P,CNBr,Arg-C,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Asp-N/B,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Asp-N_ambic,Chymotrypsin	
Digestor	-	enzyme	string	Trypsin	glutamyl endopeptidase,2-iodobenzoate,no cleavage,unspecific cleavage,Arg-C,Lys-C,Trypsin,Asp-N/B,Asp-N,Asp-N_ambic,V8-DE,CNBr,leukocyte elastase,proline endopeptidase,Lys-N,Lys-C/P,Arg-C/P,Chymotrypsin,Formic_acid,Chymotrypsin/P,V8-E,Alpha-lytic protease,PepsinA,TrypChymo,Trypsin/P	
DigestorMotif	+	enzyme	string	Trypsin	Trypsin,Arg-C/P,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,Asp-N,Arg-C,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,iodosobenzoate,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Asp-N_ambic,unspecific cleavage,Chymotrypsin,Asp-N/B,Chymotrypsin/P	
DigestorMotif	-	enzyme	string	Trypsin	Asp-N_ambic,Trypsin,Asp-N/B,Chymotrypsin/P,Chymotrypsin,Trypsin/P,V8-DE,V8-E,PepsinA,TrypChymo,glutamyl endopeptidase,Lys-C/P,Formic_acid,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,Lys-C,Lys-N,Arg-C,2-iodobenzoate,no cleavage,unspecific cleavage,Arg-C/P,Asp-N,CNBr	
FalseDiscoveryRate	+	algorithm:add_decoy_proteins	string	false	true,false	
FeatureFinderIdentification	+	debug	int	0	0:	
FeatureFinderIdentification	-	debug	int	0		
FeatureFinderMetabo	+	algorithm:ffm:remove_single_traces	string	false	false,true	
FeatureFinderMultiplex	+	algorithm:averagine_similarity_scaling	double	0.95	0:1	
FeatureFinderMultiplex	+	algorithm:rt_band	double	0	0:	
FeatureFinderMultiplex	+	out	output-file			*.featureXML
FeatureFinderMultiplex	+	out_multiplets	output-file			*.consensusXML
FeatureFinderMultiplex	-	algorithm:averagine_similarity_scaling	double	0.75	0:1	
FeatureFinderMultiplex	-	out	output-file			*.consensusXML
FeatureFinderMultiplex	-	out_features	output-file			*.featureXML
FeatureFinderMultiplex	-	out_mzq	output-file			*.mzq
FeatureLinkerUnlabeled	+	algorithm:ignore_adduct	string	true	true,false	
FeatureLinkerUnlabeledKD	+	algorithm:ignore_adduct	string	true	true,false	
FeatureLinkerUnlabeledQT	+	algorithm:ignore_adduct	string	true	true,false	
FileConverter	+	convert_to_chromatograms	string	false	true,false	
FileFilter	+	id:sequence_comparison_method	string	substring	substring,exact	
FileFilter	+	peak_options:indexed_file	string	true	true,false	
FileFilter	+	peak_options:numpress:float_da	string	none	none,linear,pic,slof	
FileFilter	+	peak_options:numpress:lossy_mass_accuracy	double	-1		
FileFilter	+	spectra:blackorwhitelist:blacklist	string	true	false,true	
FileFilter	+	spectra:blackorwhitelist:file	input-file			*.mzML
FileFilter	+	spectra:blackorwhitelist:mz	double	0.01		
FileFilter	+	spectra:blackorwhitelist:rt	double	0.01		
FileFilter	+	spectra:blackorwhitelist:similarity_threshold	double	-1	-1:1	
FileFilter	+	spectra:blackorwhitelist:use_ppm_tolerance	string	false		
FileFilter	-	peak_options:indexed_file	string	false	true,false	
FileFilter	-	peak_options:numpress:intensity_error	double	0.0001		
FileFilter	-	peak_options:numpress:masstime_error	double	0.0001		
IDConflictResolver	+	resolve_between_features	string	off	off,highest_intensity	
IDFileConverter	+	in	input-file			*.pepXML,*.protXML,*.mascotXML,*.omssaXML,*.xml,*.psms,*.tsv,*.idXML,*.mzid,*.xquest.xml
IDFileConverter	+	out	output-file			*.idXML,*.mzid,*.pepXML,*.FASTA,*.xquest.xml
IDFileConverter	+	out_type	string		idXML,mzid,pepXML,FASTA,xquest.xml	
IDFileConverter	-	in	input-file			*.pepXML,*.protXML,*.mascotXML,*.omssaXML,*.xml,*.psms,*.tsv,*.idXML,*.mzid
IDFileConverter	-	out	output-file			*.idXML,*.mzid,*.pepXML,*.FASTA
IDFileConverter	-	out_type	string		idXML,mzid,pepXML,FASTA	
IDFilter	+	in_silico_digestion:enzyme	string	Trypsin	Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin/P,Chymotrypsin,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Trypsin,Arg-C,Arg-C/P,no cleavage,unspecific cleavage	
IDFilter	+	in_silico_digestion:fasta	input-file			*.fasta
IDFilter	+	in_silico_digestion:methionine_cleavage	string	false	true,false	
IDFilter	+	in_silico_digestion:missed_cleavages	int	-1	-1:	
IDFilter	+	in_silico_digestion:specificity	string	full	full,semi,none	
IDFilter	+	missed_cleavages:enzyme	string	Trypsin	Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin/P,Chymotrypsin,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Trypsin,Arg-C,Arg-C/P,no cleavage,unspecific cleavage	
IDFilter	+	missed_cleavages:number_of_missed_cleavages	string	:		
IDFilter	-	digest:enzyme	string	Trypsin	Lys-C,V8-E,Trypsin/P,no cleavage,V8-DE,CNBr,Lys-C/P,Formic_acid,unspecific cleavage,Alpha-lytic protease,2-iodobenzoate,Asp-N/B,Arg-C/P,proline endopeptidase,TrypChymo,Arg-C,leukocyte elastase,Chymotrypsin/P,Asp-N,Chymotrypsin,Trypsin,PepsinA,Asp-N_ambic,glutamyl endopeptidase,Lys-N	
IDFilter	-	digest:fasta	input-file			*.fasta
IDFilter	-	digest:methionine_cleavage	string	false	true,false	
IDFilter	-	digest:missed_cleavages	int	-1	-1:	
IDFilter	-	digest:specificity	string	full	full,semi,none	
IsobaricAnalyzer	-	id_pool	string			
MRMMapper	+	algorithm:error_on_unmapped	string	false	true,false	
MRMMapper	+	algorithm:map_multiple_assays	string	false	true,false	
MRMMapper	+	algorithm:precursor_tolerance	double	0.1		
MRMMapper	+	algorithm:product_tolerance	double	0.1		
MRMMapper	-	allow_multiple_mappings	string	false	true,false	
MRMMapper	-	no-strict	string	false	true,false	
MRMMapper	-	precursor_tolerance	double	0.1		
MRMMapper	-	product_tolerance	double	0.1		
MRMTransitionGroupPicker	+	algorithm:PeakIntegrator:baseline_type	string	base_to_base	base_to_base,vertical_division,vertical_division_min,vertical_division_max	
MRMTransitionGroupPicker	+	algorithm:PeakIntegrator:fit_EMG	string	false	false,true	
MRMTransitionGroupPicker	+	algorithm:PeakIntegrator:integration_type	string	intensity_sum	intensity_sum,simpson,trapezoid	
MRMTransitionGroupPicker	+	algorithm:background_subtraction	string	none	none,original,exact	
MRMTransitionGroupPicker	+	algorithm:boundary_selection_method	string	largest	largest,widest	
MRMTransitionGroupPicker	+	algorithm:compute_peak_shape_metrics	string	false	true,false	
MRMTransitionGroupPicker	+	algorithm:compute_total_mi	string	false	true,false	
MRMTransitionGroupPicker	+	algorithm:peak_integration	string	original	original,smoothed	
MRMTransitionGroupPicker	+	algorithm:use_consensus	string	true	true,false	
MRMTransitionGroupPicker	-	algorithm:background_subtraction	string	none	none,smoothed,original	
MSGFPlusAdapter	+	add_features	string	true	true,false	
MSGFPlusAdapter	+	protocol	string	automatic	automatic,phospho,iTRAQ,iTRAQ_phospho,TMT,none	
MSGFPlusAdapter	-	add_features	string	false	true,false	
MSGFPlusAdapter	-	protocol	string	none	none,phospho,iTRAQ,iTRAQ_phospho,TMT	
MSSimulator	+	algorithm:MSSim:Digestion:enzyme	string	Trypsin	Trypsin,Asp-N/B,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,CNBr,Formic_acid,Lys-C,unspecific cleavage,Chymotrypsin,Asp-N_ambic,Arg-C/P,Chymotrypsin/P,Asp-N,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Arg-C	
MSSimulator	-	algorithm:MSSim:Digestion:enzyme	string	Trypsin	PepsinA,2-iodobenzoate,no cleavage,Arg-C,Lys-C,Trypsin,Asp-N/B,Asp-N,Asp-N_ambic,CNBr,Alpha-lytic protease,glutamyl endopeptidase,Lys-N,Lys-C/P,Chymotrypsin,Formic_acid,Chymotrypsin/P,Arg-C/P,leukocyte elastase,proline endopeptidase,TrypChymo,Trypsin/P,V8-DE,V8-E,unspecific cleavage	
MapAlignerIdentification	+	model:linear:x_datum_max	double	1e+15		
MapAlignerIdentification	+	model:linear:x_datum_min	double	1e-15		
MapAlignerIdentification	+	model:linear:x_weight	string		1/x,1/x2,ln(x),	
MapAlignerIdentification	+	model:linear:y_datum_max	double	1e+15		
MapAlignerIdentification	+	model:linear:y_datum_min	double	1e-15		
MapAlignerIdentification	+	model:linear:y_weight	string		1/y,1/y2,ln(y),	
MapAlignerPoseClustering	+	algorithm:pairfinder:ignore_adduct	string	true	true,false	
MapAlignerPoseClustering	+	in	input-file			*.featureXML,*.mzML
MapAlignerPoseClustering	+	out	output-file			*.featureXML,*.mzML
MapAlignerPoseClustering	+	reference:file	input-file			*.featureXML,*.mzML
MapAlignerPoseClustering	-	in	input-file			*.mzML,*.featureXML
MapAlignerPoseClustering	-	out	output-file			*.mzML,*.featureXML
MapAlignerPoseClustering	-	reference:file	input-file			*.mzML,*.featureXML
MapAlignerSpectrum	+	model:linear:x_datum_max	double	1e+15		
MapAlignerSpectrum	+	model:linear:x_datum_min	double	1e-15		
MapAlignerSpectrum	+	model:linear:x_weight	string		1/x,1/x2,ln(x),	
MapAlignerSpectrum	+	model:linear:y_datum_max	double	1e+15		
MapAlignerSpectrum	+	model:linear:y_datum_min	double	1e-15		
MapAlignerSpectrum	+	model:linear:y_weight	string		1/y,1/y2,ln(y),	
MapRTTransformer	+	model:linear:x_datum_max	double	1e+15		
MapRTTransformer	+	model:linear:x_datum_min	double	1e-15		
MapRTTransformer	+	model:linear:x_weight	string		1/x,1/x2,ln(x),	
MapRTTransformer	+	model:linear:y_datum_max	double	1e+15		
MapRTTransformer	+	model:linear:y_datum_min	double	1e-15		
MapRTTransformer	+	model:linear:y_weight	string		1/y,1/y2,ln(y),	
MetaboliteAdductDecharger	+	algorithm:MetaboliteFeatureDeconvolution:max_minority_bound	int	3	0:	
MetaboliteAdductDecharger	+	algorithm:MetaboliteFeatureDeconvolution:max_neutrals	int	1		
MetaboliteAdductDecharger	+	algorithm:MetaboliteFeatureDeconvolution:use_minority_bound	string	true		
MetaboliteAdductDecharger	-	algorithm:MetaboliteFeatureDeconvolution:max_minority_bound	int	2	0:	
MetaboliteAdductDecharger	-	algorithm:MetaboliteFeatureDeconvolution:max_neutrals	int	0		
MetaboliteSpectralMatcher	+	out	output-file			*.mzTab
MetaboliteSpectralMatcher	-	out	output-file			*.tsv
MzTabExporter	+	out	output-file			*.mzTab
MzTabExporter	-	out	output-file			*.tsv
OMSSAAdapter	+	enzyme	string	Trypsin	glutamyl endopeptidase,no cleavage,unspecific cleavage,Asp-N_ambic,Chymotrypsin,CNBr,Formic_acid,Lys-C,Arg-C,Asp-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,Trypsin	
OMSSAAdapter	-	enzyme	string	Trypsin	Trypsin,Arg-C,PepsinA,TrypChymo,Trypsin/P,glutamyl endopeptidase,no cleavage,Asp-N,Lys-C,Lys-C/P,Chymotrypsin,CNBr,Formic_acid,unspecific cleavage,Asp-N_ambic	
OpenPepXL	+	algorithm:deisotope	string	auto	true,false,auto	
OpenPepXL	+	ions:a_ions	string	false	true,false	
OpenPepXL	+	ions:b_ions	string	true	true,false	
OpenPepXL	+	ions:c_ions	string	false	true,false	
OpenPepXL	+	ions:neutral_losses	string	true	true,false	
OpenPepXL	+	ions:x_ions	string	false	true,false	
OpenPepXL	+	ions:y_ions	string	true	true,false	
OpenPepXL	+	ions:z_ions	string	false	true,false	
OpenPepXL	+	out_xquest_specxml	output-file			*.xml,*.spec.xml
OpenPepXL	+	out_xquestxml	output-file			*.xml,*.xquest.xml
OpenPepXL	+	peptide:enzyme	string	Trypsin	Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Arg-C/P,Trypsin,Arg-C,unspecific cleavage	
OpenPepXL	+	precursor:corrections	int			
OpenPepXL	-	out_xquest_specxml	output-file			*.xml
OpenPepXL	-	out_xquestxml	output-file			*.xml
OpenPepXL	-	peptide:enzyme	string	Trypsin	unspecific cleavage,no cleavage,TrypChymo,Lys-C,Lys-N,2-iodobenzoate,V8-E,PepsinA,proline endopeptidase,Trypsin/P,glutamyl endopeptidase,Alpha-lytic protease,V8-DE,Formic_acid,leukocyte elastase,Lys-C/P,Chymotrypsin/P,CNBr,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Arg-C/P,Trypsin,Arg-C	
OpenPepXLLF	+	algorithm:deisotope	string	auto	true,false,auto	
OpenPepXLLF	+	algorithm:number_of_scored_candidates	int	10000		
OpenPepXLLF	+	algorithm:pre_scoring	string	false	true,false	
OpenPepXLLF	+	ions:a_ions	string	false	true,false	
OpenPepXLLF	+	ions:b_ions	string	true	true,false	
OpenPepXLLF	+	ions:c_ions	string	false	true,false	
OpenPepXLLF	+	ions:neutral_losses	string	true	true,false	
OpenPepXLLF	+	ions:x_ions	string	false	true,false	
OpenPepXLLF	+	ions:y_ions	string	true	true,false	
OpenPepXLLF	+	ions:z_ions	string	false	true,false	
OpenPepXLLF	+	out_xquest_specxml	output-file			*.xml,*.spec.xml
OpenPepXLLF	+	out_xquestxml	output-file			*.xml,*.xquest.xml
OpenPepXLLF	+	peptide:enzyme	string	Trypsin	Chymotrypsin/P,Asp-N_ambic,Chymotrypsin,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Arg-C/P,Arg-C,unspecific cleavage,Trypsin,Asp-N/B,Asp-N	
OpenPepXLLF	+	precursor:corrections	int			
OpenPepXLLF	-	out_xquest_specxml	output-file			*.xml
OpenPepXLLF	-	out_xquestxml	output-file			*.xml
OpenPepXLLF	-	peptide:enzyme	string	Trypsin	Arg-C/P,Asp-N,V8-DE,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,Lys-C,Lys-N,Asp-N/B,Asp-N_ambic,Chymotrypsin/P,CNBr,Formic_acid,Chymotrypsin,Arg-C,Trypsin,2-iodobenzoate,no cleavage,unspecific cleavage,leukocyte elastase,Alpha-lytic protease,glutamyl endopeptidase,V8-E,proline endopeptidase	
OpenSwathAnalyzer	+	algorithm:DIAScoring:dia_extraction_unit	string	Th	Th,ppm	
OpenSwathAnalyzer	+	algorithm:Scores:use_mi_score	string	false	true,false	
OpenSwathAnalyzer	+	algorithm:Scores:use_ms1_mi	string	false	true,false	
OpenSwathAnalyzer	+	algorithm:Scores:use_total_mi_score	string	false	true,false	
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:PeakIntegrator:baseline_type	string	base_to_base	base_to_base,vertical_division,vertical_division_min,vertical_division_max	
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:PeakIntegrator:fit_EMG	string	false	false,true	
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:PeakIntegrator:integration_type	string	intensity_sum	intensity_sum,simpson,trapezoid	
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:background_subtraction	string	none	none,original,exact	
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:boundary_selection_method	string	largest	largest,widest	
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:compute_peak_shape_metrics	string	false	true,false	
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:compute_total_mi	string	false	true,false	
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:peak_integration	string	original	original,smoothed	
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:use_consensus	string	true	true,false	
OpenSwathAnalyzer	+	algorithm:scoring_model	string	default	default,single_transition	
OpenSwathAnalyzer	-	algorithm:TransitionGroupPicker:background_subtraction	string	none	none,smoothed,original	
OpenSwathAssayGenerator	+	disable_identification_ms2_precursors	string	false	true,false	
OpenSwathAssayGenerator	+	disable_identification_specific_losses	string	false	true,false	
OpenSwathAssayGenerator	+	enable_ipf	string	false	true,false	
OpenSwathAssayGenerator	+	enable_swath_specifity	string	false	true,false	
OpenSwathAssayGenerator	+	in	input-file			*.tsv,*.mrm,*.pqp,*.TraML
OpenSwathAssayGenerator	+	in_type	string		tsv,mrm,pqp,TraML	
OpenSwathAssayGenerator	+	max_num_alternative_localizations	int	10000		
OpenSwathAssayGenerator	+	out	output-file			*.tsv,*.pqp,*.TraML
OpenSwathAssayGenerator	+	out_type	string		tsv,pqp,TraML	
OpenSwathAssayGenerator	+	unimod_file	input-file			*.xml
OpenSwathAssayGenerator	-	enable_identification_ms2_precursors	string	false	true,false	
OpenSwathAssayGenerator	-	enable_identification_specific_losses	string	false	true,false	
OpenSwathAssayGenerator	-	enable_ms1_uis_scoring	string	false	true,false	
OpenSwathAssayGenerator	-	enable_ms2_uis_scoring	string	false	true,false	
OpenSwathAssayGenerator	-	enable_reannotation	string	false	true,false	
OpenSwathAssayGenerator	-	in	input-file			*.traML
OpenSwathAssayGenerator	-	max_num_alternative_localizations	int	20		
OpenSwathAssayGenerator	-	out	output-file			*.traML
OpenSwathChromatogramExtractor	+	ion_mobility_window	double	-1		
OpenSwathDecoyGenerator	+	aim_decoy_fraction	double	1		
OpenSwathDecoyGenerator	+	in	input-file			*.tsv,*.mrm,*.pqp,*.TraML
OpenSwathDecoyGenerator	+	in_type	string		tsv,mrm,pqp,TraML	
OpenSwathDecoyGenerator	+	method	string	shuffle	shuffle,pseudo-reverse,reverse,shift	
OpenSwathDecoyGenerator	+	min_decoy_fraction	double	0.8		
OpenSwathDecoyGenerator	+	out	output-file			*.tsv,*.pqp,*.TraML
OpenSwathDecoyGenerator	+	out_type	string		tsv,pqp,TraML	
OpenSwathDecoyGenerator	+	product_mz_threshold	double	0.025		
OpenSwathDecoyGenerator	+	separate	string	false	true,false	
OpenSwathDecoyGenerator	+	shift_precursor_mz_shift	double	0		
OpenSwathDecoyGenerator	+	shift_product_mz_shift	double	20		
OpenSwathDecoyGenerator	+	shuffle_max_attempts	int	30		
OpenSwathDecoyGenerator	+	shuffle_sequence_identity_threshold	double	0.5		
OpenSwathDecoyGenerator	+	switchKR	string	true	true,false	
OpenSwathDecoyGenerator	-	append	string	false	true,false	
OpenSwathDecoyGenerator	-	exclude_similar	string	false	true,false	
OpenSwathDecoyGenerator	-	identity_threshold	double	0.7		
OpenSwathDecoyGenerator	-	in	input-file			*.traML
OpenSwathDecoyGenerator	-	max_attempts	int	10		
OpenSwathDecoyGenerator	-	method	string	shuffle		
OpenSwathDecoyGenerator	-	mz_shift	double	20		
OpenSwathDecoyGenerator	-	mz_threshold	double	0.05		
OpenSwathDecoyGenerator	-	out	output-file			*.traML
OpenSwathDecoyGenerator	-	precursor_mass_shift	double	0		
OpenSwathDecoyGenerator	-	remove_CNterm_mods	string	false	true,false	
OpenSwathDecoyGenerator	-	remove_unannotated	string	false	true,false	
OpenSwathDecoyGenerator	-	similarity_threshold	double	-1		
OpenSwathMzMLFileCacher	+	full_meta	string	true	true,false	
OpenSwathMzMLFileCacher	+	lossy_compression	string	true	true,false	
OpenSwathMzMLFileCacher	+	lossy_mass_accuracy	double	-1		
OpenSwathMzMLFileCacher	+	lowmem_batchsize	int	500	0:	
OpenSwathMzMLFileCacher	+	process_lowmemory	string	false	true,false	
OpenSwathRTNormalizer	+	algorithm:DIAScoring:dia_extraction_unit	string	Th	Th,ppm	
OpenSwathRTNormalizer	+	algorithm:Scores:use_mi_score	string	false	true,false	
OpenSwathRTNormalizer	+	algorithm:Scores:use_ms1_mi	string	false	true,false	
OpenSwathRTNormalizer	+	algorithm:Scores:use_total_mi_score	string	false	true,false	
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:PeakIntegrator:baseline_type	string	base_to_base	base_to_base,vertical_division,vertical_division_min,vertical_division_max	
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:PeakIntegrator:fit_EMG	string	false	false,true	
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:PeakIntegrator:integration_type	string	intensity_sum	intensity_sum,simpson,trapezoid	
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:background_subtraction	string	none	none,original,exact	
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:boundary_selection_method	string	largest	largest,widest	
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:compute_peak_shape_metrics	string	false	true,false	
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:compute_total_mi	string	false	true,false	
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:peak_integration	string	original	original,smoothed	
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:use_consensus	string	true	true,false	
OpenSwathRTNormalizer	+	algorithm:scoring_model	string	default	default,single_transition	
OpenSwathRTNormalizer	-	algorithm:TransitionGroupPicker:background_subtraction	string	none	none,smoothed,original	
OpenSwathWorkflow	+	Debugging:irt_mzml	string			
OpenSwathWorkflow	+	Debugging:irt_trafo	string			
OpenSwathWorkflow	+	Scoring:DIAScoring:dia_extraction_unit	string	Th	Th,ppm	
OpenSwathWorkflow	+	Scoring:Scores:use_mi_score	string	false	true,false	
OpenSwathWorkflow	+	Scoring:Scores:use_ms1_mi	string	false	true,false	
OpenSwathWorkflow	+	Scoring:Scores:use_total_mi_score	string	false	true,false	
OpenSwathWorkflow	+	Scoring:TransitionGroupPicker:PeakIntegrator:baseline_type	string	base_to_base	base_to_base,vertical_division,vertical_division_min,vertical_division_max	
OpenSwathWorkflow	+	Scoring:TransitionGroupPicker:PeakIntegrator:fit_EMG	string	false	false,true	
OpenSwathWorkflow	+	Scoring:TransitionGroupPicker:PeakIntegrator:integration_type	string	intensity_sum	intensity_sum,simpson,trapezoid	
OpenSwathWorkflow	+	Scoring:TransitionGroupPicker:background_subtraction	string	none	none,original,exact	
OpenSwathWorkflow	+	Scoring:TransitionGroupPicker:boundary_selection_method	string	largest	largest,widest	
OpenSwathWorkflow	+	Scoring:TransitionGroupPicker:compute_peak_shape_metrics	string	false	true,false	
OpenSwathWorkflow	+	Scoring:TransitionGroupPicker:compute_total_mi	string	false	true,false	
OpenSwathWorkflow	+	Scoring:TransitionGroupPicker:peak_integration	string	original	original,smoothed	
OpenSwathWorkflow	+	Scoring:TransitionGroupPicker:use_consensus	string	true	true,false	
OpenSwathWorkflow	+	Scoring:scoring_model	string	default	default,single_transition	
OpenSwathWorkflow	+	Scoring:uis_threshold_sn	int	0		
OpenSwathWorkflow	+	in	input-file			*.mzML,*.mzXML,*.sqMass
OpenSwathWorkflow	+	ion_mobility_window	double	-1		
OpenSwathWorkflow	-	Scoring:TransitionGroupPicker:background_subtraction	string	none	none,smoothed,original	
OpenSwathWorkflow	-	Scoring:uis_threshold_sn	int	-1		
OpenSwathWorkflow	-	in	input-file			*.mzML,*.mzXML
PeptideIndexer	+	aaa_max	int	3	0:10	
PeptideIndexer	+	decoy_string	string			
PeptideIndexer	+	enzyme:name	string	Trypsin	Chymotrypsin/P,CNBr,Formic_acid,Arg-C/P,Asp-N/B,Asp-N_ambic,Chymotrypsin,Arg-C,Asp-N,Trypsin,Lys-C,Lys-N,Lys-C/P,PepsinA,elastase-trypsin-chymotrypsin,TrypChymo,V8-DE,Trypsin/P,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,no cleavage,unspecific cleavage	
PeptideIndexer	+	mismatches_max	int	0	0:10	
PeptideIndexer	+	missing_decoy_action	string	error	error,warn,silent	
PeptideIndexer	-	aaa_max	int	4	0:	
PeptideIndexer	-	decoy_string	string	DECOY_		
PeptideIndexer	-	enzyme:name	string	Trypsin	Asp-N/B,Arg-C/P,Trypsin,V8-DE,CNBr,Arg-C,TrypChymo,Lys-N,leukocyte elastase,Alpha-lytic protease,Asp-N_ambic,Chymotrypsin/P,Formic_acid,PepsinA,V8-E,proline endopeptidase,Asp-N,Lys-C,Chymotrypsin,Trypsin/P,Lys-C/P,no cleavage,unspecific cleavage,glutamyl endopeptidase,2-iodobenzoate	
PeptideIndexer	-	filter_aaa_proteins	string	false	true,false	
PeptideIndexer	-	full_tolerant_search	string	false	true,false	
PeptideIndexer	-	mismatches_max	int	0	0:	
PeptideIndexer	-	missing_decoy_action	string	error	error,warn	
PercolatorAdapter	+	in_osw	input-file			*.OSW
PercolatorAdapter	+	ipf_max_peakgroup_pep	double	0.7		
PercolatorAdapter	+	ipf_max_transition_isotope_overlap	double	0.5		
PercolatorAdapter	+	ipf_min_transition_sn	double	0		
PercolatorAdapter	+	osw_level	string	ms2		
PercolatorAdapter	+	out	output-file			*.mzid,*.idXML,*.osw
PercolatorAdapter	+	out_pin	output-file			*.tab
PercolatorAdapter	+	out_type	string		mzid,idXML,osw	
PercolatorAdapter	+	score_type	string	q-value	q-value,pep,svm	
PercolatorAdapter	+	train-best-positive	string	false	true,false	
PercolatorAdapter	-	mzid_out	output-file			*.mzid
PercolatorAdapter	-	out	output-file			*.idXML
PhosphoScoring	+	fragment_mass_tolerance	double	0.05	0:	
PhosphoScoring	+	max_num_perm	int	16384	0:	
PhosphoScoring	+	max_peptide_length	int	40	0:	
PhosphoScoring	+	out	output-file			
PhosphoScoring	+	unambiguous_score	int	1000		
PhosphoScoring	-	fragment_mass_tolerance	double	0.05		
PhosphoScoring	-	max_num_perm	int	16384	1:	
PhosphoScoring	-	max_peptide_length	int	40	1:	
PhosphoScoring	-	out	output-file			*.idXML
RNPxlSearch	+	RNPxl:can_cross_link	string	U		
RNPxlSearch	+	RNPxl:decoys	string	false	true,false	
RNPxlSearch	+	RNPxl:scoring	string	fast	fast,slow	
RNPxlSearch	+	peptide:enzyme	string	Trypsin	Arg-C/P,Trypsin,Arg-C,Asp-N/B,Asp-N,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,Asp-N_ambic,Chymotrypsin/P,Chymotrypsin,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage	
RNPxlSearch	+	peptide:max_size	int	1000000		
RNPxlSearch	-	RNPxl:restrictions	string			
RNPxlSearch	-	peptide:enzyme	string	Trypsin	glutamyl endopeptidase,Alpha-lytic protease,Asp-N,Lys-C,V8-DE,Lys-C/P,PepsinA,V8-E,Asp-N/B,CNBr,proline endopeptidase,unspecific cleavage,Lys-N,2-iodobenzoate,leukocyte elastase,Asp-N_ambic,Formic_acid,Arg-C/P,Arg-C,Chymotrypsin,TrypChymo,Trypsin/P,Trypsin,no cleavage,Chymotrypsin/P	
SimpleSearchEngine	+	enzyme	string	Trypsin	staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,iodosobenzoate,2-iodobenzoate,PepsinA + P,Clostripain/P,Arg-C/P,Trypsin,Arg-C,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin/P,Chymotrypsin,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,cyanogen-bromide	
SimpleSearchEngine	+	peptide:motif	string			
SimpleSearchEngine	-	enzyme	string	Trypsin	Asp-N/B,V8-E,Chymotrypsin/P,Asp-N_ambic,Lys-C,Alpha-lytic protease,leukocyte elastase,unspecific cleavage,Chymotrypsin,V8-DE,Trypsin,Arg-C,2-iodobenzoate,glutamyl endopeptidase,Lys-N,Lys-C/P,TrypChymo,proline endopeptidase,Asp-N,no cleavage,Formic_acid,CNBr,Arg-C/P,PepsinA,Trypsin/P	
SiriusAdapter	+	compound_timeout	int	10		
SiriusAdapter	+	elements	string	CHNOP[5]S[8]Cl[1]		
SiriusAdapter	+	feature_only	string	false	true,false	
SiriusAdapter	+	filter_by_num_masstraces	int	1	1:	
SiriusAdapter	+	in_featureinfo	input-file			*.featurexml
SiriusAdapter	+	ion_tree	string	false	true,false	
SiriusAdapter	+	isotope_pattern_iterations	int	3		
SiriusAdapter	+	most_intense_ms2	string	false	true,false	
SiriusAdapter	+	no_masstrace_info_isotope_pattern	string	false	true,false	
SiriusAdapter	+	out_fingerid	output-file			*.mzTab
SiriusAdapter	+	out_sirius	output-file			*.mzTab
SiriusAdapter	+	precursor_mz_tolerance	double	0.005		
SiriusAdapter	+	precursor_mz_tolerance_unit	string	Da	Da,ppm	
SiriusAdapter	+	precursor_rt_tolerance	double	5		
SiriusAdapter	+	top_n_hits	int	10		
SiriusAdapter	+	tree_timeout	int	0		
SiriusAdapter	-	elements	string	CHNOP[5]S		
SiriusAdapter	-	iontree	string	false	true,false	
SiriusAdapter	-	number	int	10		
SiriusAdapter	-	out_fingerid	output-file			*.tsv
SiriusAdapter	-	out_sirius	output-file			*.tsv
SpecLibSearcher	+	fragment:mass_tolerance	double	10		
SpecLibSearcher	+	modifications:fixed	string		...	
SpecLibSearcher	+	modifications:variable	string		...	
SpecLibSearcher	+	modifications:variable_max_per_peptide	int	2		
SpecLibSearcher	+	precursor:isotopes	int			
SpecLibSearcher	+	precursor:mass_tolerance	double	10		
SpecLibSearcher	+	precursor:mass_tolerance_unit	string	ppm	ppm,Da	
SpecLibSearcher	+	precursor:max_charge	int	5		
SpecLibSearcher	+	precursor:min_charge	int	2		
SpecLibSearcher	+	report:top_hits	int	10		
SpecLibSearcher	-	fixed_modifications	string		...	
SpecLibSearcher	-	precursor_mass_tolerance	double	3		
SpecLibSearcher	-	round_precursor_to_integer	int	10		
SpecLibSearcher	-	top_hits	int	10		
SpecLibSearcher	-	variable_modifications	string		...	
XFDR	+	decoy_string	string	DECOY_		
XFDR	+	in	input-file			*.xml,*.idXML,*.mzid,*.xquest.xml
XFDR	+	in_type	string		xml,idXML,mzid,xquest.xml	
XFDR	+	out_xquest	output-file			*.xquest.xml
XFDR	-	in	input-file			*.xml,*.idXML,*.mzid
XFDR	-	in_type	string		xml,idXML,mzid	
XTandemAdapter	+	enzyme	string	Trypsin	Trypsin,Arg-C/P,Asp-N_ambic,PepsinA,TrypChymo,Asp-N,Lys-N,Lys-C/P,unspecific cleavage,Lys-C,2-iodobenzoate,Asp-N/B,Arg-C,V8-DE,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Trypsin/P,V8-E,leukocyte elastase,Alpha-lytic protease,glutamyl endopeptidase	
XTandemAdapter	-	enzyme	string	Trypsin	glutamyl endopeptidase,Formic_acid,TrypChymo,Arg-C/P,Lys-C,Alpha-lytic protease,2-iodobenzoate,CNBr,leukocyte elastase,unspecific cleavage,Lys-C/P,Chymotrypsin/P,Chymotrypsin,Asp-N_ambic,Asp-N,V8-E,Lys-N,Asp-N/B,Trypsin,Arg-C,Trypsin/P,PepsinA,V8-DE

------------------------------------------------------------------------------------------
----                                OpenMS 2.3                                        ----
------------------------------------------------------------------------------------------
OpenMS 2.3 introduces a considerable number of new features and bug fixes.

Notable changes since version 2.2 are:

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

Deprecated and removed tools:
  - None

Renamed tool:
  - LowMemPeakPickerHiRes_RandomAccess was renamed to LowMemPeakPickerHiResRandomAccess

Major changes in functionality:
  - Experimental design
    - Add support for fractions
  - FeatureLinkerUnlabeledKD
    - m/z and retention time tolerances for warping and linking are now separate parameters 
  - IsobaricAnalyzer
    - Support for TMT11plex (https://www.thermofisher.com/order/catalog/product/A34808)
  - FileInfo
    - For idXML files, the tool computes the average length of contained peptides
  - TopPerc
    - Renamed in PercolatorAdapter (still experimental)
  - OpenSWATH:
    - RT normalization now allows more models
    - Add S/N ratio for each ion trace
  - Support for C++11 (requires a compiler that supports C++11)
    
Library:
  - TOPP tools report their peak memory usage when using -debug 1 (or higher)
  - idXML files can now be written faster (about 10%)
  - pyOpenMS bindings for DataArrayByName getters
  - Python build are now split in compilation units and can thus run in parallel
  - FASTA files can now be written
  - Allow String values to be passed to EnzymaticDigestion::isValidProduct

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

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

Tool name	Added/removed	Parameter name	Type	Default value	Restrictions	Supported formats
AccurateMassSearch	+	negative_adducts	input-file	CHEMISTRY/NegativeAdducts.tsv		*.tsv
AccurateMassSearch	+	out	output-file			*.tsv
AccurateMassSearch	+	positive_adducts	input-file	CHEMISTRY/PositiveAdducts.tsv		*.tsv
AccurateMassSearch	-	negative_adducts_file	input-file	CHEMISTRY/NegativeAdducts.tsv		*.tsv
AccurateMassSearch	-	out	output-file			*.csv
AccurateMassSearch	-	positive_adducts_file	input-file	CHEMISTRY/PositiveAdducts.tsv		*.tsv
Digestor	+	enzyme	string	Trypsin	Arg-C/P,glutamyl endopeptidase,2-iodobenzoate,no cleavage,unspecific cleavage,Arg-C,Lys-N,Chymotrypsin,Asp-N/B,Asp-N_ambic,CNBr,Formic_acid,proline endopeptidase,Lys-C/P,Chymotrypsin/P,Asp-N,Lys-C,Trypsin,V8-DE,V8-E,Alpha-lytic protease,leukocyte elastase,PepsinA,TrypChymo,Trypsin/P	
Digestor	-	enzyme	string	Trypsin	Asp-N,PepsinA,TrypChymo,Trypsin,Lys-C,Lys-C/P,Asp-N_ambic,Formic_acid,CNBr,Chymotrypsin,Arg-C,Trypsin/P,V8-DE,V8-E,2-iodobenzoate,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,no cleavage,unspecific cleavage	
DigestorMotif	+	enzyme	string	Trypsin	Chymotrypsin,CNBr,Asp-N_ambic,Lys-N,2-iodobenzoate,no cleavage,Trypsin/P,V8-DE,Arg-C/P,Formic_acid,Lys-C/P,Lys-C,Arg-C,Alpha-lytic protease,glutamyl endopeptidase,V8-E,proline endopeptidase,leukocyte elastase,unspecific cleavage,Asp-N/B,TrypChymo,Asp-N,Chymotrypsin/P,PepsinA,Trypsin	
DigestorMotif	-	enzyme	string	Trypsin	Formic_acid,Lys-C,Lys-C/P,PepsinA,TrypChymo,leukocyte elastase,proline endopeptidase,2-iodobenzoate,glutamyl endopeptidase,Asp-N,Asp-N_ambic,Chymotrypsin,unspecific cleavage,Arg-C,V8-E,no cleavage,Trypsin,Trypsin/P,V8-DE,CNBr	
FeatureFinderMetabo	+	out_chrom	output-file			*.mzML
FeatureLinkerUnlabeled	+	design	input-file			*.tsv
FeatureLinkerUnlabeledKD	+	algorithm:link:mz_tol	double	10	0:	
FeatureLinkerUnlabeledKD	+	algorithm:link:rt_tol	double	30	0:	
FeatureLinkerUnlabeledKD	+	algorithm:warp:enabled	string	true	true,false	
FeatureLinkerUnlabeledKD	+	algorithm:warp:max_nr_conflicts	int	0	-1:	
FeatureLinkerUnlabeledKD	+	algorithm:warp:max_pairwise_log_fc	double	0.5		
FeatureLinkerUnlabeledKD	+	algorithm:warp:min_rel_cc_size	double	0.5	0:1	
FeatureLinkerUnlabeledKD	+	algorithm:warp:mz_tol	double	5	0:	
FeatureLinkerUnlabeledKD	+	algorithm:warp:rt_tol	double	100	0:	
FeatureLinkerUnlabeledKD	+	design	input-file			*.tsv
FeatureLinkerUnlabeledKD	-	algorithm:max_nr_conflicts	int	0	-1:	
FeatureLinkerUnlabeledKD	-	algorithm:max_pairwise_log_fc	double	0.5		
FeatureLinkerUnlabeledKD	-	algorithm:min_rel_cc_size	double	0.5	0:1	
FeatureLinkerUnlabeledKD	-	algorithm:mz_tol	double	15	0:	
FeatureLinkerUnlabeledKD	-	algorithm:rt_tol	double	60	0:	
FeatureLinkerUnlabeledKD	-	algorithm:warp	string	true	true,false	
FeatureLinkerUnlabeledQT	+	design	input-file			*.tsv
FileInfo	+	in	input-file			*.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid,*.trafoXML,*.fasta
FileInfo	-	in	input-file			*.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid,*.trafoXML
FileMerger	+	in	input-file			*.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.fid,*.traML,*.FASTA
FileMerger	+	in_type	string		mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,fid,traML,FASTA	
FileMerger	-	in	input-file			*.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.fid,*.traML
FileMerger	-	in_type	string		mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,fid,traML	
IDFileConverter	+	add_ionmatch_annotation	double	0		
IDFilter	+	digest:enzyme	string	Trypsin	unspecific cleavage,PepsinA,Trypsin/P,Lys-N,2-iodobenzoate,no cleavage,glutamyl endopeptidase,Asp-N,Lys-C/P,Lys-C,CNBr,Asp-N_ambic,leukocyte elastase,V8-DE,Arg-C,Trypsin,V8-E,Alpha-lytic protease,proline endopeptidase,Asp-N/B,Arg-C/P,Formic_acid,Chymotrypsin/P,TrypChymo,Chymotrypsin	
IDFilter	-	digest:enzyme	string	Trypsin	proline endopeptidase,2-iodobenzoate,CNBr,Arg-C,Chymotrypsin,Asp-N_ambic,Asp-N,Formic_acid,glutamyl endopeptidase,no cleavage,leukocyte elastase,V8-E,Lys-C/P,unspecific cleavage,TrypChymo,Trypsin/P,Lys-C,Trypsin,V8-DE,PepsinA	
IsobaricAnalyzer	+	tmt11plex:channel_126_description	string			
IsobaricAnalyzer	+	tmt11plex:channel_127C_description	string			
IsobaricAnalyzer	+	tmt11plex:channel_127N_description	string			
IsobaricAnalyzer	+	tmt11plex:channel_128C_description	string			
IsobaricAnalyzer	+	tmt11plex:channel_128N_description	string			
IsobaricAnalyzer	+	tmt11plex:channel_129C_description	string			
IsobaricAnalyzer	+	tmt11plex:channel_129N_description	string			
IsobaricAnalyzer	+	tmt11plex:channel_130C_description	string			
IsobaricAnalyzer	+	tmt11plex:channel_130N_description	string			
IsobaricAnalyzer	+	tmt11plex:channel_131C_description	string			
IsobaricAnalyzer	+	tmt11plex:channel_131N_description	string			
IsobaricAnalyzer	+	tmt11plex:correction_matrix	string			
IsobaricAnalyzer	+	tmt11plex:reference_channel	string	126	126,127N,127C,128N,128C,129N,129C,130N,130C,131N,131C	
IsobaricAnalyzer	+	type	string	itraq4plex	itraq4plex,itraq8plex,tmt10plex,tmt11plex,tmt6plex	
IsobaricAnalyzer	-	type	string	itraq4plex	itraq4plex,itraq8plex,tmt10plex,tmt6plex	
MRMMapper	+	allow_multiple_mappings	string	false	true,false	
MRMTransitionGroupPicker	+	algorithm:PeakPickerMRM:method	string	corrected	legacy,corrected,crawdad	
MRMTransitionGroupPicker	+	algorithm:PeakPickerMRM:peak_width	double	-1		
MRMTransitionGroupPicker	+	algorithm:resample_boundary	double	15		
MRMTransitionGroupPicker	-	algorithm:PeakPickerMRM:method	string	legacy	legacy,corrected,crawdad	
MRMTransitionGroupPicker	-	algorithm:PeakPickerMRM:peak_width	double	40		
MSGFPlusAdapter	+	enzyme	string	Trypsin/P	Alpha-lytic protease,Arg-C/P,Asp-N/B,Chymotrypsin/P,Lys-C/P,Lys-N,Trypsin/P,glutamyl endopeptidase,no cleavage,unspecific cleavage	
MSGFPlusAdapter	+	precursor_mass_tolerance	double	10		
MSGFPlusAdapter	-	enzyme	string	trypsin	unspecific,trypsin,chymotrypsin,LysC,LysN,GluC,ArgC,AspN,alphaLP,no_cleavage	
MSGFPlusAdapter	-	precursor_mass_tolerance	double	20		
MSSimulator	+	algorithm:MSSim:Digestion:enzyme	string	Trypsin	no cleavage,unspecific cleavage,glutamyl endopeptidase,Arg-C,Formic_acid,Asp-N_ambic,Asp-N,Asp-N/B,V8-DE,proline endopeptidase,Alpha-lytic protease,Lys-C,Lys-N,Chymotrypsin,Arg-C/P,CNBr,Chymotrypsin/P,Trypsin,Trypsin/P,V8-E,2-iodobenzoate,leukocyte elastase,Lys-C/P,PepsinA,TrypChymo	
MSSimulator	-	algorithm:MSSim:Digestion:enzyme	string	Trypsin	Lys-C,Lys-C/P,Trypsin,CNBr,Formic_acid,Asp-N,Chymotrypsin,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,2-iodobenzoate,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,no cleavage,unspecific cleavage,Asp-N_ambic,Arg-C	
MapAlignerIdentification	+	design	input-file			*.tsv
MyriMatchAdapter	+	precursor_mass_tolerance	double	10		
MyriMatchAdapter	+	precursor_mass_tolerance_unit	string	ppm	Da,ppm	
MyriMatchAdapter	-	precursor_mass_tolerance	double	1.5		
MyriMatchAdapter	-	precursor_mass_tolerance_unit	string	Da	Da,ppm	
OMSSAAdapter	+	enzyme	string	Trypsin	Trypsin,Lys-C/P,Lys-C,Arg-C,CNBr,PepsinA,no cleavage,glutamyl endopeptidase,Chymotrypsin,Formic_acid,Asp-N,Asp-N_ambic,Trypsin/P,unspecific cleavage,TrypChymo	
OMSSAAdapter	+	precursor_error_units	string	ppm	Da,ppm	
OMSSAAdapter	+	precursor_mass_tolerance	double	10		
OMSSAAdapter	-	enzyme	string	Trypsin	Trypsin,Asp-N_ambic,unspecific cleavage,Chymotrypsin,glutamyl endopeptidase,no cleavage,TrypChymo,Trypsin/P,CNBr,Formic_acid,Arg-C,Asp-N,Lys-C,Lys-C/P,PepsinA	
OMSSAAdapter	-	precursor_mass_tolerance	double	1.5		
OMSSAAdapter	-	precursor_mass_tolerance_unit_ppm	string	false	true,false	
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:method	string	corrected	legacy,corrected,crawdad	
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width	double	-1		
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:resample_boundary	double	15		
OpenSwathAnalyzer	-	algorithm:TransitionGroupPicker:PeakPickerMRM:method	string	legacy	legacy,corrected,crawdad	
OpenSwathAnalyzer	-	algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width	double	40		
OpenSwathRTNormalizer	+	RTNormalization:RANSACMaxIterations	int	1000		
OpenSwathRTNormalizer	+	RTNormalization:RANSACMaxPercentRTThreshold	int	3		
OpenSwathRTNormalizer	+	RTNormalization:RANSACSamplingSize	int	10		
OpenSwathRTNormalizer	+	RTNormalization:outlierMethod	string	iter_residual	iter_residual,iter_jackknife,ransac,none	
OpenSwathRTNormalizer	+	RTNormalization:useIterativeChauvenet	string	false	true,false	
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:method	string	corrected	legacy,corrected,crawdad	
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width	double	-1		
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:resample_boundary	double	15		
OpenSwathRTNormalizer	-	algorithm:TransitionGroupPicker:PeakPickerMRM:method	string	legacy	legacy,corrected,crawdad	
OpenSwathRTNormalizer	-	algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width	double	40		
OpenSwathRTNormalizer	-	outlierDetection:RANSACMaxIterations	int	1000		
OpenSwathRTNormalizer	-	outlierDetection:RANSACMaxPercentRTThreshold	int	3		
OpenSwathRTNormalizer	-	outlierDetection:RANSACSamplingSize	int	10		
OpenSwathRTNormalizer	-	outlierDetection:outlierMethod	string	iter_residual	iter_residual,iter_jackknife,ransac,none	
OpenSwathRTNormalizer	-	outlierDetection:useIterativeChauvenet	string	false	true,false	
OpenSwathWorkflow	+	RTNormalization:InitialQualityCutoff	double	0.5		
OpenSwathWorkflow	+	RTNormalization:MinBinsFilled	int	8		
OpenSwathWorkflow	+	RTNormalization:MinPeptidesPerBin	int	1		
OpenSwathWorkflow	+	RTNormalization:NrRTBins	int	10		
OpenSwathWorkflow	+	RTNormalization:OverallQualityCutoff	double	5.5		
OpenSwathWorkflow	+	RTNormalization:RANSACMaxIterations	int	1000		
OpenSwathWorkflow	+	RTNormalization:RANSACMaxPercentRTThreshold	int	3		
OpenSwathWorkflow	+	RTNormalization:RANSACSamplingSize	int	10		
OpenSwathWorkflow	+	RTNormalization:alignmentMethod	string	linear	linear,interpolated,lowess,b_spline	
OpenSwathWorkflow	+	RTNormalization:b_spline:num_nodes	int	5	0:	
OpenSwathWorkflow	+	RTNormalization:estimateBestPeptides	string	false	true,false	
OpenSwathWorkflow	+	RTNormalization:lowess:span	double	0.666666666666667	0:1	
OpenSwathWorkflow	+	RTNormalization:outlierMethod	string	iter_residual	iter_residual,iter_jackknife,ransac,none	
OpenSwathWorkflow	+	RTNormalization:useIterativeChauvenet	string	false	true,false	
OpenSwathWorkflow	+	Scoring:TransitionGroupPicker:resample_boundary	double	15		
OpenSwathWorkflow	-	outlierDetection:InitialQualityCutoff	double	0.5		
OpenSwathWorkflow	-	outlierDetection:MinBinsFilled	int	8		
OpenSwathWorkflow	-	outlierDetection:MinPeptidesPerBin	int	1		
OpenSwathWorkflow	-	outlierDetection:NrRTBins	int	10		
OpenSwathWorkflow	-	outlierDetection:OverallQualityCutoff	double	5.5		
OpenSwathWorkflow	-	outlierDetection:RANSACMaxIterations	int	1000		
OpenSwathWorkflow	-	outlierDetection:RANSACMaxPercentRTThreshold	int	3		
OpenSwathWorkflow	-	outlierDetection:RANSACSamplingSize	int	10		
OpenSwathWorkflow	-	outlierDetection:estimateBestPeptides	string	false	true,false	
OpenSwathWorkflow	-	outlierDetection:outlierMethod	string	iter_residual	iter_residual,iter_jackknife,ransac,none	
OpenSwathWorkflow	-	outlierDetection:useIterativeChauvenet	string	false	true,false	
PeptideIndexer	+	enzyme:name	string	Trypsin	proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,Asp-N,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,Asp-N_ambic,Asp-N/B,2-iodobenzoate,no cleavage,unspecific cleavage,Arg-C/P,Arg-C,Trypsin	
PeptideIndexer	-	enzyme:name	string	Trypsin	Lys-C/P,Trypsin,Formic_acid,Lys-C,Arg-C,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,2-iodobenzoate,glutamyl endopeptidase,no cleavage,unspecific cleavage,Chymotrypsin,CNBr,Asp-N,Asp-N_ambic	
RNPxlSearch	+	peptide:enzyme	string	Trypsin	Trypsin,proline endopeptidase,Alpha-lytic protease,Lys-C/P,leukocyte elastase,Chymotrypsin,no cleavage,Chymotrypsin/P,Lys-N,Asp-N_ambic,PepsinA,Arg-C/P,V8-DE,V8-E,Trypsin/P,unspecific cleavage,2-iodobenzoate,CNBr,Formic_acid,Asp-N,Lys-C,Asp-N/B,Arg-C,glutamyl endopeptidase,TrypChymo	
RNPxlSearch	+	precursor:isotopes	int			
RNPxlSearch	-	peptide:enzyme	string	Trypsin	Lys-C,Trypsin,Formic_acid,Lys-C/P,PepsinA,glutamyl endopeptidase,no cleavage,Chymotrypsin,CNBr,2-iodobenzoate,leukocyte elastase,proline endopeptidase,Asp-N,Arg-C,TrypChymo,Trypsin/P,V8-DE,V8-E,unspecific cleavage,Asp-N_ambic	
SimpleSearchEngine	+	enzyme	string	Trypsin	Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,proline endopeptidase,leukocyte elastase,unspecific cleavage,Asp-N/B,Chymotrypsin,Trypsin,Asp-N_ambic,Formic_acid,Lys-N,CNBr,Chymotrypsin/P,Arg-C/P,Asp-N,Lys-C,no cleavage,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,Arg-C	
SimpleSearchEngine	+	precursor:isotopes	int			
SimpleSearchEngine	-	enzyme	string	Trypsin	glutamyl endopeptidase,no cleavage,unspecific cleavage,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,2-iodobenzoate,Asp-N,Asp-N_ambic,Chymotrypsin,Arg-C,Lys-C/P,PepsinA,CNBr,Formic_acid,Lys-C,Trypsin	
XTandemAdapter	+	enzyme	string	Trypsin	Trypsin/P,Arg-C/P,V8-DE,Formic_acid,Asp-N,Chymotrypsin/P,CNBr,Lys-C/P,unspecific cleavage,Asp-N/B,Lys-C,Chymotrypsin,PepsinA,Lys-N,Trypsin,glutamyl endopeptidase,2-iodobenzoate,leukocyte elastase,Alpha-lytic protease,V8-E,Arg-C,TrypChymo,Asp-N_ambic	
XTandemAdapter	-	enzyme	string	Trypsin	Trypsin,Formic_acid,Lys-C,Chymotrypsin,CNBr,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,2-iodobenzoate,leukocyte elastase,glutamyl endopeptidase,unspecific cleavage,Asp-N_ambic,Asp-N,Arg-C	


------------------------------------------------------------------------------------------
----                                OpenMS 2.2                                        ----
------------------------------------------------------------------------------------------
OpenMS 2.2 introduces a considerable number of new features and bug fixes.

Notable changes since version 2.1 are:

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

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

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

Third-party software:
  
Changed tool parameters:

Tool name	Added/removed	Parameter name	Type	Default value	Restrictions	Supported formats
DecoyDatabase   +       only_decoy      string  false   true,false
DecoyDatabase   -       append  string  true    true,false
Digestor        +       enzyme  string  Trypsin CNBr,proline endopeptidase,TrypChymo,no cleavage,V8-E,leukocyte elastase,Trypsin/P,Lys-C,Formic_acid,glutamyl endopeptidase,Lys-C/P,2-iodobenzoate,Trypsin,V8-DE,Chymotrypsin,PepsinA,Asp-N_ambic,unspecific cleavage,Asp-N,Arg-C
Digestor        -       enzyme  string  Trypsin Trypsin,V8-E,leukocyte elastase,Lys-C,Asp-N_ambic,no cleavage,unspecific cleavage,Chymotrypsin,Arg-C,V8-DE,Lys-C/P,2-iodobenzoate,proline endopeptidase,glutamyl endopeptidase,CNBr,TrypChymo,Trypsin/P,Asp-N,PepsinA,Formic_acid
DigestorMotif   +       enzyme  string  Trypsin Lys-C,leukocyte elastase,Formic_acid,CNBr,2-iodobenzoate,V8-DE,Trypsin,Lys-C/P,PepsinA,unspecific cleavage,TrypChymo,glutamyl endopeptidase,Arg-C,Asp-N,Chymotrypsin,V8-E,no cleavage,proline endopeptidase,Trypsin/P,Asp-N_ambic
DigestorMotif   -       enzyme  string  Trypsin PepsinA,glutamyl endopeptidase,Lys-C,Chymotrypsin,unspecific cleavage,CNBr,Lys-C/P,V8-DE,leukocyte elastase,no cleavage,Asp-N_ambic,Trypsin,proline endopeptidase,2-iodobenzoate,TrypChymo,Trypsin/P,V8-E,Asp-N,Arg-C,Formic_acid
FalseDiscoveryRate      +       FDR:PSM double  1       0:1
FalseDiscoveryRate      +       FDR:protein     double  1       0:1
FalseDiscoveryRate      +       PSM     string  true    true,false
FalseDiscoveryRate      +       protein string  true    true,false
FalseDiscoveryRate      -       in_decoy        input-file                      *.idXML
FalseDiscoveryRate      -       in_target       input-file                      *.idXML
FalseDiscoveryRate      -       peptides_only   string  false   true,false
FalseDiscoveryRate      -       proteins_only   string  false   true,false
FeatureFinderIdentification     +       candidates_in   input-file                      *.featureXML
FeatureFinderIdentification     +       candidates_out  output-file                     *.featureXML
FeatureFinderIdentification     +       detect:mapping_tolerance        double  0       0:
FeatureFinderIdentification     +       detect:min_peak_width   double  0.2     0:
FeatureFinderIdentification     +       detect:peak_width       double  60      0:
FeatureFinderIdentification     +       detect:signal_to_noise  double  0.8     0.1:
FeatureFinderIdentification     +       extract:isotope_pmin    double  0       0:1
FeatureFinderIdentification     +       extract:n_isotopes      int     2       2:
FeatureFinderIdentification     +       extract:rt_quantile     double  0.95    0:1
FeatureFinderIdentification     +       extract:rt_window       double  0       0:
FeatureFinderIdentification     +       id_ext  input-file                      *.idXML
FeatureFinderIdentification     +       model:check:min_area    double  1       0:
FeatureFinderIdentification     +       svm:cache_size  double  100     1:
FeatureFinderIdentification     +       svm:epsilon     double  0.001   0:
FeatureFinderIdentification     +       svm:kernel      string  RBF     RBF,linear
FeatureFinderIdentification     +       svm:log2_C      double
FeatureFinderIdentification     +       svm:log2_gamma  double
FeatureFinderIdentification     +       svm:min_prob    double  0       0:1
FeatureFinderIdentification     +       svm:no_selection        string  false   true,false
FeatureFinderIdentification     +       svm:no_shrinking        string  false   true,false
FeatureFinderIdentification     +       svm:predictors  string  peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score
FeatureFinderIdentification     +       svm:samples     int     0       0:
FeatureFinderIdentification     +       svm:xval        int     5       1:
FeatureFinderIdentification     +       svm:xval_out    output-file                     *.csv
FeatureFinderIdentification     -       detect:all_features     string  false   true,false
FeatureFinderIdentification     -       detect:peak_width       double  30      0:
FeatureFinderIdentification     -       extract:isotope_pmin    double  0.03    0:1
FeatureFinderIdentification     -       extract:reference_rt    string  adapt   adapt,score,intensity,median,all
FeatureFinderIdentification     -       extract:rt_window       double  60      0:
FeatureFinderIdentification     -       trafo_out       output-file                     *.trafoXML
FeatureFinderMultiplex  +       algorithm:spectrum_type string  automatic       profile,centroid,automatic
FeatureLinkerUnlabeled  +       algorithm:distance_intensity:log_transform      string  disabled        enabled,disabled
FeatureLinkerUnlabeledQT        +       algorithm:distance_intensity:log_transform      string  disabled        enabled,disabled
FeatureLinkerUnlabeledQT        +       algorithm:nr_partitions int     100     1:
FeatureLinkerUnlabeledQT        -       algorithm:nr_partitions int     1       1:
FileConverter   +       force_MaxQuant_compatibility    string  false   true,false
FileConverter   +       lossy_compression       string  false   true,false
FileConverter   +       lossy_mass_accuracy     double  -1
FileConverter   +       write_scan_index        string  true    true,false
FileConverter   -       write_mzML_index        string  false   true,false
FileFilter      +       peak_options:zlib_compression   string  false   true,false
FileInfo        +       in      input-file                      *.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid,*.trafoXML
FileInfo        +       in_type string          mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,fid,mzid,trafoXML
FileInfo        -       in      input-file                      *.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid
FileInfo        -       in_type string          mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,fid,mzid
HighResPrecursorMassCorrector   +       highest_intensity_peak:mz_tolerance     double  0
IDFileConverter +       no_spectra_data_override        string  false   true,false
IDFilter        +       digest:enzyme   string  Trypsin unspecific cleavage,Arg-C,Trypsin,Formic_acid,proline endopeptidase,TrypChymo,V8-E,Asp-N_ambic,glutamyl endopeptidase,CNBr,PepsinA,2-iodobenzoate,Chymotrypsin,Lys-C/P,Asp-N,Lys-C,Trypsin/P,leukocyte elastase,no cleavage,V8-DE
IDFilter        +       digest:fasta    input-file                      *.fasta
IDFilter        +       digest:methionine_cleavage      string  false   true,false
IDFilter        +       digest:missed_cleavages int     -1      -1:
IDFilter        +       digest:specificity      string  full    full,semi,none
IDMapper        +       spectra:in      input-file                      *.mzML
IsobaricAnalyzer        +       extraction:reporter_mass_shift  double  0.002   0.0001:0.5
IsobaricAnalyzer        -       extraction:reporter_mass_shift  double  0.1     1e-08:0.5
LowMemPeakPickerHiRes   +       algorithm:report_FWHM_unit      string  relative        relative,absolute
LowMemPeakPickerHiRes   +       algorithm:signal_to_noise       double  0       0:
LowMemPeakPickerHiRes   -       algorithm:report_FWHM_unit      string  relative(ppm)   absolute,relative(ppm)
LowMemPeakPickerHiRes   -       algorithm:signal_to_noise       double  1       0:
LowMemPeakPickerHiRes_RandomAccess      +       algorithm:report_FWHM_unit      string  relative        relative,absolute
LowMemPeakPickerHiRes_RandomAccess      +       algorithm:signal_to_noise       double  0       0:
LowMemPeakPickerHiRes_RandomAccess      -       algorithm:report_FWHM_unit      string  relative(ppm)   absolute,relative(ppm)
LowMemPeakPickerHiRes_RandomAccess      -       algorithm:signal_to_noise       double  1       0:
LuciphorAdapter +       java_memory     int     3500
LuciphorAdapter +       java_permgen    int     0
MRMTransitionGroupPicker        +       algorithm:compute_peak_quality  string  false   true,false
MRMTransitionGroupPicker        +       algorithm:recalculate_peaks     string  false   true,false
MRMTransitionGroupPicker        +       algorithm:use_precursors        string  false   true,false
MRMTransitionGroupPicker        -       algorithm:compute_peak_quality  string  false
MRMTransitionGroupPicker        -       algorithm:recalculate_peaks     string  false
MSSimulator     +       algorithm:MSSim:Digestion:enzyme        string  Trypsin unspecific cleavage,Lys-C,Formic_acid,no cleavage,Chymotrypsin,V8-DE,glutamyl endopeptidase,V8-E,Trypsin,Asp-N,CNBr,Trypsin/P,TrypChymo,PepsinA,Arg-C,leukocyte elastase,Lys-C/P,proline endopeptidase,Asp-N_ambic,2-iodobenzoate
MSSimulator     +       algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_all_precursor_charges      string  false   true,false
MSSimulator     -       algorithm:MSSim:Digestion:enzyme        string  Trypsin Asp-N,leukocyte elastase,proline endopeptidase,Lys-C,Lys-C/P,V8-DE,Asp-N_ambic,Formic_acid,no cleavage,Chymotrypsin,glutamyl endopeptidase,2-iodobenzoate,CNBr,unspecific cleavage,V8-E,TrypChymo,Arg-C,Trypsin,Trypsin/P,PepsinA
MapAlignerPoseClustering        +       algorithm:pairfinder:distance_intensity:log_transform   string  disabled        enabled,disabled
MetaboliteSpectralMatcher       +       database        input-file      CHEMISTRY/MetaboliteSpectralDB.mzML             *.mzML
MetaboliteSpectralMatcher       +       out     output-file                     *.tsv
MetaboliteSpectralMatcher       -       out     output-file                     *.csv
OMSSAAdapter    +       enzyme  string  Trypsin Trypsin,TrypChymo,Lys-C/P,PepsinA,glutamyl endopeptidase,Asp-N,Lys-C,CNBr,Trypsin/P,Asp-N_ambic,Chymotrypsin,no cleavage,unspecific cleavage,Arg-C,Formic_acid
OMSSAAdapter    -       enzyme  string  Trypsin Trypsin,Lys-C/P,CNBr,Lys-C,Chymotrypsin,unspecific cleavage,no cleavage,Trypsin/P,Formic_acid,Asp-N_ambic,TrypChymo,PepsinA,glutamyl endopeptidase,Asp-N,Arg-C
OpenSwathAnalyzer       +       algorithm:Scores:use_sonar_scores       string  false   true,false
OpenSwathAnalyzer       +       algorithm:TransitionGroupPicker:compute_peak_quality    string  false   true,false
OpenSwathAnalyzer       +       algorithm:TransitionGroupPicker:recalculate_peaks       string  false   true,false
OpenSwathAnalyzer       +       algorithm:TransitionGroupPicker:use_precursors  string  false   true,false
OpenSwathAnalyzer       -       algorithm:TransitionGroupPicker:compute_peak_quality    string  false
OpenSwathAnalyzer       -       algorithm:TransitionGroupPicker:recalculate_peaks       string  false
OpenSwathMzMLFileCacher +       in      input-file                      *.mzML,*.sqMass
OpenSwathMzMLFileCacher +       in_type string          mzML,sqMass
OpenSwathMzMLFileCacher +       out     output-file                     *.mzML,*.sqMass
OpenSwathMzMLFileCacher +       out_type        string          mzML,sqMass
OpenSwathMzMLFileCacher -       in      input-file                      *.mzML
OpenSwathMzMLFileCacher -       out     output-file
OpenSwathRTNormalizer   +       algorithm:Scores:use_sonar_scores       string  false   true,false
OpenSwathRTNormalizer   +       algorithm:TransitionGroupPicker:compute_peak_quality    string  false   true,false
OpenSwathRTNormalizer   +       algorithm:TransitionGroupPicker:recalculate_peaks       string  false   true,false
OpenSwathRTNormalizer   +       algorithm:TransitionGroupPicker:use_precursors  string  false   true,false
OpenSwathRTNormalizer   -       algorithm:TransitionGroupPicker:compute_peak_quality    string  false
OpenSwathRTNormalizer   -       algorithm:TransitionGroupPicker:recalculate_peaks       string  false
OpenSwathWorkflow       +       Library:force_invalid_mods      string  false   true,false
OpenSwathWorkflow       +       Library:override_group_label_check      string  false   true,false
OpenSwathWorkflow       +       Library:retentionTimeInterpretation     string  iRT     iRT,seconds,minutes
OpenSwathWorkflow       +       Scoring:Scores:use_sonar_scores string  false   true,false
OpenSwathWorkflow       +       Scoring:TransitionGroupPicker:compute_peak_quality      string  true    true,false
OpenSwathWorkflow       +       Scoring:TransitionGroupPicker:recalculate_peaks string  true    true,false
OpenSwathWorkflow       +       Scoring:TransitionGroupPicker:use_precursors    string  false   true,false
OpenSwathWorkflow       +       irt_mz_extraction_window        double  0.05
OpenSwathWorkflow       +       out_chrom       output-file                     *.mzML,*.sqMass
OpenSwathWorkflow       +       out_osw output-file                     *.osw
OpenSwathWorkflow       +       out_tsv output-file                     *.tsv
OpenSwathWorkflow       +       ppm_irtwindow   string  false   true,false
OpenSwathWorkflow       +       readOptions     string  normal  normal,cache,cacheWorkingInMemory,workingInMemory
OpenSwathWorkflow       +       sonar   string  false   true,false
OpenSwathWorkflow       +       tr      input-file                      *.traML,*.tsv,*.pqp
OpenSwathWorkflow       +       tr_type string          traML,tsv,pqp
OpenSwathWorkflow       -       Scoring:TransitionGroupPicker:compute_peak_quality      string  true
OpenSwathWorkflow       -       Scoring:TransitionGroupPicker:recalculate_peaks string  true
OpenSwathWorkflow       -       out_chrom       output-file                     *.mzML
OpenSwathWorkflow       -       out_tsv string
OpenSwathWorkflow       -       readOptions     string  normal  normal,cache,cacheWorkingInMemory
OpenSwathWorkflow       -       tr      input-file                      *.traML,*.tsv,*.csv
OpenSwathWorkflow       -       tr_type string          traML,tsv,csv
PeakPickerHiRes +       algorithm:report_FWHM_unit      string  relative        relative,absolute
PeakPickerHiRes +       algorithm:signal_to_noise       double  0       0:
PeakPickerHiRes -       algorithm:report_FWHM_unit      string  relative(ppm)   absolute,relative(ppm)
PeakPickerHiRes -       algorithm:signal_to_noise       double  1       0:
PeptideIndexer  +       enzyme:name     string  Trypsin V8-E,Chymotrypsin,glutamyl endopeptidase,Formic_acid,proline endopeptidase,Trypsin/P,CNBr,Asp-N_ambic,Asp-N,Arg-C,Lys-C/P,PepsinA,Trypsin,2-iodobenzoate,V8-DE,TrypChymo,unspecific cleavage,no cleavage,leukocyte elastase,Lys-C
PeptideIndexer  -       enzyme:name     string  Trypsin Asp-N_ambic,V8-E,Arg-C,CNBr,Formic_acid,Asp-N,no cleavage,leukocyte elastase,proline endopeptidase,Trypsin/P,Trypsin,glutamyl endopeptidase,2-iodobenzoate,V8-DE,PepsinA,Lys-C,unspecific cleavage,Chymotrypsin,Lys-C/P,TrypChymo
RTModel +       out_oligo_params        output-file                     *.paramXML
RTModel +       out_oligo_trainset      output-file                     *.txt
RTPredict       +       in_oligo_params input-file                      *.paramXML
RTPredict       +       in_oligo_trainset       input-file                      *.txt
SimpleSearchEngine      +       enzyme  string  Trypsin TrypChymo,V8-E,2-iodobenzoate,proline endopeptidase,PepsinA,Lys-C,no cleavage,CNBr,leukocyte elastase,Formic_acid,Chymotrypsin,glutamyl endopeptidase,Trypsin/P,Trypsin,unspecific cleavage,Arg-C,Lys-C/P,Asp-N,V8-DE,Asp-N_ambic
SimpleSearchEngine      -       enzyme  string  Trypsin Trypsin/P,no cleavage,leukocyte elastase,PepsinA,2-iodobenzoate,Lys-C/P,Lys-C,V8-E,Formic_acid,Chymotrypsin,V8-DE,TrypChymo,unspecific cleavage,Asp-N,proline endopeptidase,Arg-C,Trypsin,CNBr,Asp-N_ambic,glutamyl endopeptidase
XTandemAdapter  +       default_config_file     input-file                      *.xml
XTandemAdapter  +       enzyme  string  Trypsin Asp-N_ambic,V8-E,unspecific cleavage,V8-DE,PepsinA,Trypsin/P,Lys-C,glutamyl endopeptidase,2-iodobenzoate,Lys-C/P,Arg-C,Formic_acid,CNBr,TrypChymo,Chymotrypsin,Asp-N,Trypsin,leukocyte elastase
XTandemAdapter  +       max_precursor_charge    int     4       0:
XTandemAdapter  +       no_isotope_error        string  false   true,false
XTandemAdapter  +       xml_out output-file                     *.xml
XTandemAdapter  -       allow_isotope_error     string  yes     yes,no
XTandemAdapter  -       cleavage_site   string  Trypsin Lys-C/P,CNBr,Arg-C,Chymotrypsin,PepsinA,2-iodobenzoate,Trypsin/P,TrypChymo,V8-DE,Asp-N,Asp-N_ambic,Lys-C,unspecific cleavage,Formic_acid,Trypsin,V8-E,leukocyte elastase,glutamyl endopeptidase
XTandemAdapter  -       default_config_file     input-file      CHEMISTRY/XTandem_default_input.xml             *.xml
XTandemAdapter  -       max_precursor_charge    int     4
XTandemAdapter  -       min_precursor_charge    int     2
XTandemAdapter  -       refinement      string  false   true,false
XTandemAdapter  -       use_noise_suppression   string  false   true,false

------------------------------------------------------------------------------------------
----                                OpenMS 2.1                                        ----
------------------------------------------------------------------------------------------
OpenMS 2.1 introduces a considerable number of new features and bug fixes.

Notable changes since version 2.0.1 are:

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

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

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

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

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

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

Changed tool parameters:

Tool name	Added/removed	Parameter name	Type	Default value	Restrictions	Supported formats
AccurateMassSearch	+	db:mapping	input-file			*.tsv
AccurateMassSearch	+	db:struct	input-file			*.tsv
AccurateMassSearch	-	db:mapping	input-file	CHEMISTRY/HMDBMappingFile.tsv		*.tsv
AccurateMassSearch	-	db:struct	input-file	CHEMISTRY/HMDB2StructMapping.tsv		*.tsv
DecoyDatabase	+	append	string	true	true,false	
DecoyDatabase	+	decoy_string	string	DECOY_		
DecoyDatabase	+	decoy_string_position	string	prefix	prefix,suffix	
DecoyDatabase	+	method	string	reverse	reverse,shuffle	
DecoyDatabase	-	append	string	false	true,false	
DecoyDatabase	-	decoy_string	string	_rev		
DecoyDatabase	-	decoy_string_position	string	suffix	prefix,suffix	
DecoyDatabase	-	shuffle	string	false	true,false	
FeatureFinderMetabo	+	algorithm:ffm:isotope_filtering_model	string	metabolites (5% RMS)	metabolites (2% RMS),metabolites (5% RMS),peptides,none	
FeatureFinderMetabo	+	algorithm:ffm:mz_scoring_13C	string	false	false,true	
FeatureFinderMetabo	+	algorithm:ffm:report_convex_hulls	string	false	false,true	
FeatureFinderMetabo	+	algorithm:mtd:quant_method	string	area	area,median	
FeatureFinderMetabo	-	algorithm:ffm:disable_isotope_filtering	string	false	false,true	
FeatureFinderMetabo	-	algorithm:ffm:isotope_model	string	metabolites	metabolites,peptides	
FeatureFinderMetabo	-	algorithm:ffm:isotope_noisemodel	string	5%RMS	5%RMS,2%RMS	
FeatureFinderMetabo	-	algorithm:ffm:quant_method	string	area	area,median	
FeatureFinderMultiplex	+	labels:Leu3	double	3.01883	0:	
FileConverter	+	in	input-file			*.mzData,*.mzXML,*.mzML,*.cachedMzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.ms2,*.fid,*.tsv,*.peplist,*.kroenik,*.edta
FileConverter	+	in_type	string		mzData,mzXML,mzML,cachedMzML,dta,dta2d,mgf,featureXML,consensusXML,ms2,fid,tsv,peplist,kroenik,edta	
FileConverter	+	out	output-file			*.mzData,*.mzXML,*.mzML,*.cachedMzML,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.edta,*.csv
FileConverter	+	out_type	string		mzData,mzXML,mzML,cachedMzML,dta2d,mgf,featureXML,consensusXML,edta,csv	
FileConverter	-	in	input-file			*.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.ms2,*.fid,*.tsv,*.peplist,*.kroenik,*.edta
FileConverter	-	in_type	string		mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,ms2,fid,tsv,peplist,kroenik,edta	
FileConverter	-	out	output-file			*.mzData,*.mzXML,*.mzML,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.edta,*.csv
FileConverter	-	out_type	string		mzData,mzXML,mzML,dta2d,mgf,featureXML,consensusXML,edta,csv	
InternalCalibration	+	RANSAC:enabled	string	false	true,false	
InternalCalibration	+	RANSAC:iter	int	70		
InternalCalibration	+	RANSAC:pc_inliers	int	30	1:99	
InternalCalibration	+	RANSAC:threshold	double	10		
InternalCalibration	+	RT_chunking	double	300		
InternalCalibration	+	cal:id_in	input-file			*.idXML,*.featureXML
InternalCalibration	+	cal:lock_fail_out	output-file			*.mzML
InternalCalibration	+	cal:lock_in	input-file			*.csv
InternalCalibration	+	cal:lock_out	output-file			*.mzML
InternalCalibration	+	cal:lock_require_iso	string	false	true,false	
InternalCalibration	+	cal:lock_require_mono	string	false	true,false	
InternalCalibration	+	cal:model_type	string	linear_weighted	linear,linear_weighted,quadratic,quadratic_weighted	
InternalCalibration	+	goodness:MAD	double	1		
InternalCalibration	+	goodness:median	double	4		
InternalCalibration	+	in	input-file			*.mzML
InternalCalibration	+	ms_level	int			
InternalCalibration	+	out	output-file			*.mzML
InternalCalibration	+	ppm_match_tolerance	double	25		
InternalCalibration	+	quality_control:models	output-file			*.csv
InternalCalibration	+	quality_control:models_plot	output-file			*.png
InternalCalibration	+	quality_control:residuals	output-file			*.csv
InternalCalibration	+	quality_control:residuals_plot	output-file			*.png
InternalCalibration	-	algorithm:mz_tolerance	double	1	0:	
InternalCalibration	-	algorithm:mz_tolerance_unit	string	Da	Da,ppm	
InternalCalibration	-	algorithm:rt_tolerance	int	10		
InternalCalibration	-	in	input-file			*.mzML,*.featureXML
InternalCalibration	-	out	output-file			*.mzML,*.featureXML
InternalCalibration	-	ref_peaks	input-file			*.csv,*.idXML
InternalCalibration	-	trafo	output-file			*.trafoXML
InternalCalibration	-	type	string	spectrumwise	spectrumwise,global	
LowMemPeakPickerHiRes	+	algorithm:report_FWHM	string	false	true,false	
LowMemPeakPickerHiRes	+	algorithm:report_FWHM_unit	string	relative(ppm)	absolute,relative(ppm)	
LowMemPeakPickerHiRes_RandomAccess	+	algorithm:report_FWHM	string	false	true,false	
LowMemPeakPickerHiRes_RandomAccess	+	algorithm:report_FWHM_unit	string	relative(ppm)	absolute,relative(ppm)	
LuciphorAdapter	+	java_executable	input-file	java		
LuciphorAdapter	-	selection_method	string	Peptide Prophet probability	Peptide Prophet probability,Mascot Ion Score,-log(E-value),X!Tandem Hyperscore,Sequest Xcorr	
MSGFPlusAdapter	+	java_executable	input-file	java		
MapAlignerIdentification	+	model:lowess:delta	double	-1		
MapAlignerIdentification	+	model:lowess:extrapolation_type	string	four-point-linear	two-point-linear,four-point-linear,global-linear	
MapAlignerIdentification	+	model:lowess:interpolation_type	string	cspline	linear,cspline,akima	
MapAlignerIdentification	+	model:lowess:num_iterations	int	3	0:	
MapAlignerIdentification	+	model:lowess:span	double	0.666666666666667	0:1	
MapAlignerIdentification	-	algorithm:peptide_score_threshold	double	0		
MapAlignerSpectrum	+	model:lowess:delta	double	-1		
MapAlignerSpectrum	+	model:lowess:extrapolation_type	string	four-point-linear	two-point-linear,four-point-linear,global-linear	
MapAlignerSpectrum	+	model:lowess:interpolation_type	string	cspline	linear,cspline,akima	
MapAlignerSpectrum	+	model:lowess:num_iterations	int	3	0:	
MapAlignerSpectrum	+	model:lowess:span	double	0.666666666666667	0:1	
MapRTTransformer	+	model:lowess:delta	double	-1		
MapRTTransformer	+	model:lowess:extrapolation_type	string	four-point-linear	two-point-linear,four-point-linear,global-linear	
MapRTTransformer	+	model:lowess:interpolation_type	string	cspline	linear,cspline,akima	
MapRTTransformer	+	model:lowess:num_iterations	int	3	0:	
MapRTTransformer	+	model:lowess:span	double	0.666666666666667	0:1	
MascotAdapterOnline	+	Mascot_server:export_params	string	_ignoreionsscorebelow=0&_sigthreshold=0.99&_showsubsets=1&show_same_sets=1&report=0&percolate=0&query_master=0		
MascotAdapterOnline	-	Mascot_server:export_params	string	_sigthreshold=0.99&_showsubsets=1&show_same_sets=1&report=0&percolate=0&query_master=0		
MassTraceExtractor	+	algorithm:mtd:quant_method	string	area	area,median	
MetaProSIP	+	labeling_element	string	C	C,N,H,O	
MetaProSIP	+	pattern_18O_TIC_threshold	double	0.95		
MetaProSIP	-	labeling_element	string	C	C,N,H	
OpenSwathAssayGenerator	+	enable_identification_ms2_precursors	string	false	true,false	
PeakPickerHiRes	+	algorithm:report_FWHM	string	false	true,false	
PeakPickerHiRes	+	algorithm:report_FWHM_unit	string	relative(ppm)	absolute,relative(ppm)	
PeptideIndexer	+	decoy_string	string	DECOY_		
PeptideIndexer	+	decoy_string_position	string	prefix	prefix,suffix	
PeptideIndexer	-	decoy_string	string	_rev		
PeptideIndexer	-	prefix	string	false	true,false	

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

Notable changes are:

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

Databases:
  - HMDB has been updated to version 3.6

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

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

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

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

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

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

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


Changed tool parameters:

Tool name	Added/removed	Parameter name	Type	Default value	Restrictions	Supported formats
AccurateMassSearch	+	algorithm:mzTab:exportIsotopeIntensities	int	0	0:	
AccurateMassSearch	-	algorithm:report_mode	string	all	all,top3,best	
ConsensusID	+	algorithm	string	PEPMatrix	PEPMatrix,PEPIons,best,worst,average,ranks	
ConsensusID	-	algorithm:algorithm	string	PEPMatrix	ranked,average,PEPMatrix,PEPIons,Minimum	
ConsensusID	+	PEPIons:mass_tolerance	double	0.5	0:	
ConsensusID	+	PEPIons:min_shared	int	2	1:	
ConsensusID	+	PEPMatrix:matrix	string	identity	identity,PAM30MS	
ConsensusID	+	PEPMatrix:penalty	int	5	1:	
ConsensusID	+	filter:considered_hits	int	0	0:	
ConsensusID	+	filter:count_empty	string	false	true,false	
ConsensusID	+	filter:min_support	double	0	0:1	
ConsensusID	-	algorithm:PEPIons:MinNumberOfFragments	int	2	0:	
ConsensusID	-	algorithm:PEPIons:common	double	1.1	0:1.1	
ConsensusID	-	algorithm:PEPMatrix:common	double	1.1	0:1.1	
ConsensusID	-	algorithm:PEPMatrix:penalty	int	5		
ConsensusID	-	algorithm:considered_hits	int	10	1:	
ConsensusID	-	algorithm:number_of_runs	int	0	0:	
ConsensusID	-	min_length	int	6	1:	
ConsensusID	-	use_all_hits	string	false	true,false	
ConsensusMapNormalizer	+	accession_filter	string			
ConsensusMapNormalizer	+	algorithm_type	string	robust_regression	robust_regression,median,median_shift,quantile	
ConsensusMapNormalizer	+	description_filter	string			
ConsensusMapNormalizer	-	algorithm_type	string	robust_regression	robust_regression,median,quantile	
Digestor	+	enzyme	string	Trypsin	V8-DE,V8-E,2-iodobenzoate,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,no cleavage,unspecific cleavage,Arg-C,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,CNBr,Formic_acid,Lys-C,Asp-N_ambic,Chymotrypsin,Asp-N,Trypsin	
Digestor	-	enzyme	string	Trypsin	Trypsin,none	
DigestorMotif	+	enzyme	string	Trypsin	Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,Formic_acid,Lys-C,Trypsin,Chymotrypsin,CNBr,leukocyte elastase,proline endopeptidase,2-iodobenzoate,glutamyl endopeptidase,no cleavage,unspecific cleavage,Arg-C,Asp-N_ambic,Asp-N	
DigestorMotif	-	enzyme	string	Trypsin		
FalseDiscoveryRate	+	algorithm:no_qvalues	string	false	true,false	
FalseDiscoveryRate	+	in_decoy	input-file			*.idXML
FalseDiscoveryRate	+	in_target	input-file			*.idXML
FalseDiscoveryRate	-	algorithm:decoy_string	string	_rev		
FalseDiscoveryRate	-	algorithm:q_value	string	true	true,false	
FalseDiscoveryRate	-	fwd_in	input-file			*.idXML
FalseDiscoveryRate	-	rev_in	input-file			*.idXML
FeatureFinderMetabo	+	algorithm:ffm:enable_RT_filtering	string	true	false,true	
FeatureFinderMetabo	+	algorithm:ffm:quant_method	string	area	area,median	
FeatureFinderMetabo	+	algorithm:mtd:max_trace_length	double	-1		
FeatureFinderMetabo	-	algorithm:mtd:max_trace_length	double	300		
FeatureFinderMultiplex	+	algorithm:averagine_type	string	peptide	peptide,RNA,DNA	
FeatureLinkerUnlabeledQT	+	algorithm:nr_partitions	int	1	1:	
FidoAdapter	+	greedy_group_resolution	string	false	true,false	
FidoAdapter	-	prob_param	string	Posterior Probability_score		
FileFilter	+	algorithm:SignalToNoise:write_log_messages	string	true	true,false	
FileFilter	+	peak_options:pc_mz_list	double			
FileFilter	+	peak_options:pc_mz_range	string	:		
FileFilter	-	pc_mz	string	:		
FileMerger	+	raw:ms_level	int	0		
FileMerger	+	rt_concat:gap	double	0		
FileMerger	+	rt_concat:trafo_out	output-file			*.trafoXML
FileMerger	-	raw:ms_level	int	2		
FileMerger	-	raw:user_ms_level	string	false	true,false	
FuzzyDiff	+	matched_whitelist	string			
HighResPrecursorMassCorrector	+	feature:assign_all_matching	string	false	true,false	
HighResPrecursorMassCorrector	+	feature:believe_charge	string	false	true,false	
HighResPrecursorMassCorrector	+	feature:in	input-file			*.featureXML
HighResPrecursorMassCorrector	+	feature:keep_original	string	false	true,false	
HighResPrecursorMassCorrector	+	feature:max_trace	int	2		
HighResPrecursorMassCorrector	+	feature:mz_tolerance	double	5		
HighResPrecursorMassCorrector	+	feature:mz_tolerance_unit	string	ppm	Da,ppm	
HighResPrecursorMassCorrector	+	feature:rt_tolerance	double	0		
HighResPrecursorMassCorrector	+	nearest_peak:mz_tolerance	double	0		
HighResPrecursorMassCorrector	+	nearest_peak:mz_tolerance_unit	string	ppm	Da,ppm	
IDFileConverter	+	in	input-file			*.pepXML,*.protXML,*.mascotXML,*.omssaXML,*.xml,*.psms,*.tsv,*.idXML,*.mzid
IDFileConverter	+	score_type	string	qvalue	qvalue,PEP,score	
IDFileConverter	-	in	input-file			*.pepXML,*.protXML,*.mascotXML,*.omssaXML,*.xml,*.idXML,*.mzid
IDFileConverter	-	use_precursor_data	string	false	true,false	
IDFilter	+	blacklist:modifications	string		...	
IDFilter	+	blacklist:protein_accessions	string			
IDFilter	+	blacklist:proteins	input-file			*.fasta
IDFilter	+	charge	string	:		
IDFilter	+	length	string	:		
IDFilter	+	whitelist:ignore_modifications	string	false	true,false	
IDFilter	+	whitelist:modifications	string		...	
IDFilter	+	whitelist:peptides	input-file			*.idXML
IDFilter	+	whitelist:protein_accessions	string			
IDFilter	-	max_length	int	0	0:	
IDFilter	-	min_charge	int	1	1:	
IDFilter	-	min_length	int	0	0:	
IDFilter	-	precursor:allow_missing	string	false	true,false	
IDFilter	-	whitelist:by_seq_only	string	false	true,false	
IDPosteriorErrorProbability	+	fit_algorithm:max_nr_iterations	int	1000		
IDPosteriorErrorProbability	-	smallest_e_value	double	1e-19		
LowMemPeakPickerHiRes	+	algorithm:SignalToNoise:write_log_messages	string	true	true,false	
LowMemPeakPickerHiRes_RandomAccess	+	algorithm:SignalToNoise:write_log_messages	string	true	true,false	
MRMTransitionGroupPicker	+	algorithm:PeakPickerMRM:use_gauss	string	true	false,true	
MRMTransitionGroupPicker	+	algorithm:PeakPickerMRM:write_sn_log_messages	string	true	true,false	
MRMTransitionGroupPicker	-	algorithm:PeakPickerMRM:use_gauss	string	true		
MSGFPlusAdapter	+	legacy_conversion	string	false	true,false	
MSSimulator	+	algorithm:MSSim:Digestion:enzyme	string	Trypsin	leukocyte elastase,proline endopeptidase,2-iodobenzoate,glutamyl endopeptidase,no cleavage,unspecific cleavage,Arg-C,Formic_acid,Lys-C,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,Chymotrypsin,CNBr,Asp-N,Asp-N_ambic,Trypsin	
MSSimulator	+	algorithm:MSSim:RawTandemSignal:Precursor:min_mz_peak_distance	double	2	0.0001:	
MSSimulator	+	algorithm:MSSim:RawTandemSignal:Precursor:mz_isolation_window	double	2	0:	
MSSimulator	-	algorithm:MSSim:Digestion:enzyme	string	Trypsin	Trypsin,none	
MSSimulator	-	algorithm:MSSim:RawTandemSignal:Precursor:min_peak_distance	double	3	0:	
MSSimulator	-	algorithm:MSSim:RawTandemSignal:Precursor:selection_window	double	2	0:	
MapAlignerIdentification	+	model:interpolated:extrapolation_type	string	two-point-linear	two-point-linear,four-point-linear,global-linear	
MapAlignerSpectrum	+	model:interpolated:extrapolation_type	string	two-point-linear	two-point-linear,four-point-linear,global-linear	
MapRTTransformer	+	in	input-file			*.mzML,*.featureXML,*.consensusXML,*.idXML
MapRTTransformer	+	model:interpolated:extrapolation_type	string	two-point-linear	two-point-linear,four-point-linear,global-linear	
MapRTTransformer	+	out	output-file			*.mzML,*.featureXML,*.consensusXML,*.idXML
MapRTTransformer	+	store_original_rt	string	false	true,false	
MapRTTransformer	+	trafo_in	input-file			*.trafoXML
MapRTTransformer	+	trafo_out	output-file			*.trafoXML
MapRTTransformer	-	in	input-file			*.mzML,*.featureXML,*.consensusXML,*.idXML
MapRTTransformer	-	out	output-file			*.mzML,*.featureXML,*.consensusXML,*.idXML
MapRTTransformer	-	trafo_in	input-file			*.trafoXML
MapRTTransformer	-	trafo_out	output-file			*.trafoXML
MascotAdapterOnline	+	Mascot_server:skip_export	string	false	true,false	
MassTraceExtractor	+	algorithm:mtd:max_trace_length	double	-1		
MassTraceExtractor	-	algorithm:mtd:max_trace_length	double	300		
MyriMatchAdapter	+	SpectrumListFilters	string			
MyriMatchAdapter	+	ignoreConfigErrors	string	false	true,false	
MyriMatchAdapter	-	max_precursor_charge	int	3		
MyriMatchAdapter	-	min_precursor_charge	int	1		
MzTabExporter	+	in	input-file			*.featureXML,*.consensusXML,*.idXML,*.mzid
MzTabExporter	+	out	output-file			*.tsv
MzTabExporter	-	in_consensus	input-file			*.consensusXML
MzTabExporter	-	in_feature	input-file			*.featureXML
MzTabExporter	-	in_id	input-file			*.idXML
MzTabExporter	-	out	output-file			*.csv
OMSSAAdapter	+	enzyme	string	Trypsin	Trypsin,TrypChymo,Trypsin/P,Lys-C/P,PepsinA,Asp-N_ambic,Formic_acid,Arg-C,unspecific cleavage,CNBr,no cleavage,glutamyl endopeptidase,Lys-C,Chymotrypsin,Asp-N	
OMSSAAdapter	-	e	int	0		
OpenSwathAnalyzer	+	algorithm:Scores:use_uis_scores	string	false	true,false	
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss	string	true	false,true	
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages	string	true	true,false	
OpenSwathAnalyzer	+	algorithm:uis_threshold_peak_area	int	0		
OpenSwathAnalyzer	+	algorithm:uis_threshold_sn	int	-1		
OpenSwathAnalyzer	+	model:type	string	linear	linear,b_spline,interpolated,lowess	
OpenSwathAnalyzer	-	algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss	string	true		
OpenSwathAnalyzer	-	model:type	string	linear	linear,b_spline,interpolated	
OpenSwathChromatogramExtractor	+	model:type	string	linear	linear,b_spline,interpolated,lowess	
OpenSwathChromatogramExtractor	-	model:type	string	linear	linear,b_spline,interpolated	
OpenSwathDecoyGenerator	+	allowed_fragment_charges	string	1,2,3,4		
OpenSwathDecoyGenerator	+	allowed_fragment_types	string	b,y		
OpenSwathDecoyGenerator	+	enable_detection_specific_losses	string	false	true,false	
OpenSwathDecoyGenerator	+	enable_detection_unspecific_losses	string	false	true,false	
OpenSwathDecoyGenerator	-	enable_losses	string	false	true,false	
OpenSwathDecoyGenerator	-	theoretical	string	false	true,false	
OpenSwathRTNormalizer	+	algorithm:Scores:use_uis_scores	string	false	true,false	
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss	string	true	false,true	
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages	string	true	true,false	
OpenSwathRTNormalizer	+	algorithm:uis_threshold_peak_area	int	0		
OpenSwathRTNormalizer	+	algorithm:uis_threshold_sn	int	-1		
OpenSwathRTNormalizer	+	outlierDetection:outlierMethod	string	iter_residual	iter_residual,iter_jackknife,ransac,none	
OpenSwathRTNormalizer	+	outlierDetection:useIterativeChauvenet	string	false	true,false	
OpenSwathRTNormalizer	-	algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss	string	true		
OpenSwathRTNormalizer	-	outlierDetection:outlierMethod	string	iter_residual		
OpenSwathRTNormalizer	-	outlierDetection:useIterativeChauvenet	string	false		
OpenSwathWorkflow	+	Scoring:Scores:use_uis_scores	string	false	true,false	
OpenSwathWorkflow	+	Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss	string	false	false,true	
OpenSwathWorkflow	+	Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages	string	false	true,false	
OpenSwathWorkflow	+	Scoring:TransitionGroupPicker:background_subtraction	string	none	none,smoothed,original	
OpenSwathWorkflow	+	Scoring:uis_threshold_peak_area	int	0		
OpenSwathWorkflow	+	Scoring:uis_threshold_sn	int	-1		
OpenSwathWorkflow	+	enable_uis_scoring	string	false	true,false	
OpenSwathWorkflow	+	mz_correction_function	string	none	none,unweighted_regression,weighted_regression,quadratic_regression,weighted_quadratic_regression,weighted_quadratic_regression_delta_ppm,quadratic_regression_delta_ppm	
OpenSwathWorkflow	+	outlierDetection:InitialQualityCutoff	double	0.5		
OpenSwathWorkflow	+	outlierDetection:MinBinsFilled	int	8		
OpenSwathWorkflow	+	outlierDetection:MinPeptidesPerBin	int	1		
OpenSwathWorkflow	+	outlierDetection:NrRTBins	int	10		
OpenSwathWorkflow	+	outlierDetection:OverallQualityCutoff	double	5.5		
OpenSwathWorkflow	+	outlierDetection:RANSACMaxIterations	int	1000		
OpenSwathWorkflow	+	outlierDetection:RANSACMaxPercentRTThreshold	int	3		
OpenSwathWorkflow	+	outlierDetection:RANSACSamplingSize	int	10		
OpenSwathWorkflow	+	outlierDetection:estimateBestPeptides	string	false	true,false	
OpenSwathWorkflow	+	outlierDetection:outlierMethod	string	iter_residual	iter_residual,iter_jackknife,ransac,none	
OpenSwathWorkflow	+	outlierDetection:useIterativeChauvenet	string	false	true,false	
OpenSwathWorkflow	+	readOptions	string	normal	normal,cache,cacheWorkingInMemory	
OpenSwathWorkflow	-	Scoring:EMGScoring:deltaRelError	double	0.1		
OpenSwathWorkflow	-	Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss	string	false		
OpenSwathWorkflow	-	readOptions	string	normal	normal,cache	
PeakPickerHiRes	+	algorithm:SignalToNoise:write_log_messages	string	true	true,false	
PeptideIndexer	+	enzyme:name	string	Trypsin	Chymotrypsin,CNBr,Formic_acid,Lys-C,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,2-iodobenzoate,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,no cleavage,unspecific cleavage,Trypsin,Arg-C,Asp-N,Asp-N_ambic	
PeptideIndexer	+	filter_aaa_proteins	string	false	true,false	
PeptideIndexer	+	mismatches_max	int	0	0:	
PeptideIndexer	+	write_protein_description	string	false	true,false	
PeptideIndexer	-	annotate_proteins	string	false	true,false	
PeptideIndexer	-	enzyme:name	string	Trypsin	Trypsin	
PhosphoScoring	+	max_num_perm	int	16384	1:	
PhosphoScoring	+	max_peptide_length	int	40	1:	
RTEvaluation	-	sequences_file	input-file			*.fasta
Resampler	+	align_sampling	string	false	true,false	
Resampler	+	min_int_cutoff	double	-1		
Resampler	+	ppm	string	false	true,false	
SimpleSearchEngine	+	enzyme	string	Trypsin	Asp-N_ambic,Trypsin,PepsinA,TrypChymo,Arg-C,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,2-iodobenzoate,glutamyl endopeptidase,no cleavage,Lys-C/P,Asp-N,CNBr,Formic_acid,Lys-C,unspecific cleavage,Chymotrypsin	
SimpleSearchEngine	+	peptide:max_size	int	40		
SpectraMerger	+	algorithm:average_gaussian:cutoff	double	0.01	0:1	
SpectraMerger	+	algorithm:average_gaussian:ms_level	int	1	1:	
SpectraMerger	+	algorithm:average_gaussian:rt_FWHM	double	5	0:100000000000	
SpectraMerger	+	algorithm:average_gaussian:spectrum_type	string	automatic	profile,centroid,automatic	
SpectraMerger	+	algorithm:average_tophat:ms_level	int	1	1:	
SpectraMerger	+	algorithm:average_tophat:rt_range	double	5	0:100000000000	
SpectraMerger	+	algorithm:average_tophat:rt_unit	string	scans	scans,seconds	
SpectraMerger	+	algorithm:average_tophat:spectrum_type	string	automatic	profile,centroid,automatic	
SpectraMerger	+	algorithm:mz_binning_width	double	5	0:	
SpectraMerger	+	algorithm:mz_binning_width_unit	string	ppm	Da,ppm	
SpectraMerger	+	merging_method	string	average_gaussian	average_gaussian,average_tophat,precursor_method,block_method	
SpectraMerger	-	algorithm:mz_binning_width	double	0.0001	0:	
SpectraMerger	-	algorithm:mz_binning_width_unit	string	Da	Da,ppm	
SpectraMerger	-	merging_method	string	block_method	precursor_method,block_method	
TextExporter	+	feature:add_metavalues	int	-1	-1:100	
TextExporter	+	id:add_hit_metavalues	int	-1	-1:100	
TextExporter	+	id:add_metavalues	int	-1	-1:100	
XTandemAdapter	+	cleavage_site	string	Trypsin	Trypsin,Asp-N_ambic,Lys-C/P,PepsinA,V8-E,unspecific cleavage,Asp-N,TrypChymo,leukocyte elastase,Formic_acid,Trypsin/P,V8-DE,CNBr,2-iodobenzoate,glutamyl endopeptidase,Lys-C,Chymotrypsin,Arg-C	
XTandemAdapter	+	default_config_file	input-file	CHEMISTRY/XTandem_default_input.xml		
XTandemAdapter	+	ignore_adapter_param	string	false	true,false	
XTandemAdapter	+	min_precursor_charge	int	2		
XTandemAdapter	+	precursor_mass_tolerance	double	10		
XTandemAdapter	+	use_noise_suppression	string	false	true,false	
XTandemAdapter	-	cleavage_site	string	[RK]|{P}		
XTandemAdapter	-	default_input_file	input-file			
XTandemAdapter	-	min_precursor_charge	int	1		
XTandemAdapter	-	precursor_mass_tolerance	double	1.5		

Note: If you are interested in details on the number of merged pull requests or the state of individual issues. 
      You can simple query this information from our github repository (see e.g. https://help.github.com/articles/searching-issues/). 

------------------------------------------------------------------------------------------
----                                OpenMS 2.0                                        ----
------------------------------------------------------------------------------------------
Release date: February 2015

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

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

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

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

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

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

Status changes:
  - PhosphoScoring (UTIL -> TOPP)

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

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

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

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

Changed parameters:

Tool name	Added/removed	Parameter name	Type	Default value	Restrictions	Supported formats
AccurateMassSearch	+	algorithm:ionization_mode	string	positive	positive,negative,auto	
AccurateMassSearch	+	algorithm:keep_unidentified_masses	string	false	false,true	
AccurateMassSearch	+	db:mapping	input-file	CHEMISTRY/HMDBMappingFile.tsv		*.tsv
AccurateMassSearch	+	db:struct	input-file	CHEMISTRY/HMDB2StructMapping.tsv		*.tsv
AccurateMassSearch	+	force	string	false	true,false	
AccurateMassSearch	+	negative_adducts_file	input-file	CHEMISTRY/NegativeAdducts.tsv		*.tsv
AccurateMassSearch	+	out_annotation	output-file			*.featureXML,*.consensusXML
AccurateMassSearch	+	positive_adducts_file	input-file	CHEMISTRY/PositiveAdducts.tsv		*.tsv
AccurateMassSearch	-	algorithm:ionization_mode	string	positive	positive,negative	
AccurateMassSearch	-	algorithm:negative_adducts_file	string			
AccurateMassSearch	-	algorithm:positive_adducts_file	string			
AdditiveSeries	+	force	string	false	true,false	
BaselineFilter	+	force	string	false	true,false	
CVInspector	+	force	string	false	true,false	
CompNovo	+	force	string	false	true,false	
CompNovoCID	+	force	string	false	true,false	
ConsensusID	+	force	string	false	true,false	
ConsensusMapNormalizer	+	force	string	false	true,false	
ConvertTSVToTraML	+	algorithm:override_group_label_check	string	false	true,false	
ConvertTSVToTraML	+	algorithm:retentionTimeInterpretation	string	iRT	iRT,seconds,minutes	
ConvertTSVToTraML	+	force	string	false	true,false	
ConvertTSVToTraML	+	in	input-file			*.tsv,*.csv,*.mrm
ConvertTSVToTraML	+	in_type	string		tsv,csv,mrm	
ConvertTSVToTraML	-	in	input-file			*.csv
ConvertTraMLToTSV	+	force	string	false	true,false	
DTAExtractor	+	force	string	false	true,false	
DeMeanderize	+	force	string	false	true,false	
Decharger	+	force	string	false	true,false	
DecoyDatabase	+	force	string	false	true,false	
Digestor	+	force	string	false	true,false	
DigestorMotif	+	force	string	false	true,false	
EICExtractor	+	auto_rt:FHWM	double	5		
EICExtractor	+	auto_rt:SNThreshold	double	5		
EICExtractor	+	auto_rt:enabled	string	false	true,false	
EICExtractor	+	auto_rt:out_debug_TIC	output-file			*.mzML
EICExtractor	+	force	string	false	true,false	
EICExtractor	+	in_header	input-file			*.txt
EICExtractor	+	out	output-file			*.csv
EICExtractor	+	out_separator	string	,		
EICExtractor	-	out	output-file			*.txt
EICExtractor	-	out_detail	output-file			*.txt
ERPairFinder	+	force	string	false	true,false	
ExecutePipeline	+	force	string	false	true,false	
FFEval	+	force	string	false	true,false	
FalseDiscoveryRate	+	force	string	false	true,false	
FeatureFinderCentroided	+	force	string	false	true,false	
FeatureFinderCentroided	+	out_mzq	output-file			*.mzq
FeatureFinderCentroided	-	algorithm:fit:epsilon_abs	double	0.0001	0:	
FeatureFinderCentroided	-	algorithm:fit:epsilon_rel	double	0.0001	0:	
FeatureFinderIsotopeWavelet	+	force	string	false	true,false	
FeatureFinderMRM	+	force	string	false	true,false	
FeatureFinderMetabo	+	algorithm:epd:enabled	string	true	true,false	
FeatureFinderMetabo	+	force	string	false	true,false	
FeatureFinderSuperHirn	+	force	string	false	true,false	
FeatureLinkerLabeled	+	force	string	false	true,false	
FeatureLinkerUnlabeled	+	force	string	false	true,false	
FeatureLinkerUnlabeledQT	+	force	string	false	true,false	
FileConverter	+	MGF_compact	string	false	true,false	
FileConverter	+	UID_postprocessing	string	ensure	none,ensure,reassign	
FileConverter	+	force	string	false	true,false	
FileConverter	+	out	output-file			*.mzData,*.mzXML,*.mzML,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.edta,*.csv
FileConverter	+	out_type	string		mzData,mzXML,mzML,dta2d,mgf,featureXML,consensusXML,edta,csv	
FileConverter	+	process_lowmemory	string	false	true,false	
FileConverter	+	write_mzML_index	string	false	true,false	
FileConverter	-	out	output-file			*.mzData,*.mzXML,*.mzML,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.edta
FileConverter	-	out_type	string		mzData,mzXML,mzML,dta2d,mgf,featureXML,consensusXML,edta	
FileFilter	+	force	string	false	true,false	
FileFilter	+	peak_options:indexed_file	string	false	true,false	
FileFilter	+	peak_options:numpress:intensity	string	none	none,linear,pic,slof	
FileFilter	+	peak_options:numpress:intensity_error	double	0.0001		
FileFilter	+	peak_options:numpress:masstime	string	none	none,linear,pic,slof	
FileFilter	+	peak_options:numpress:masstime_error	double	0.0001		
FileFilter	+	spectra:select_polarity	string		unknown,positive,negative	
FileInfo	+	force	string	false	true,false	
FileInfo	+	i	string	false	true,false	
FileInfo	+	in	input-file			*.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid
FileInfo	+	in_type	string		mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,fid,mzid	
FileInfo	-	in	input-file			*.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid
FileInfo	-	in_type	string		mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,fid	
FileMerger	+	force	string	false	true,false	
FuzzyDiff	+	force	string	false	true,false	
HighResPrecursorMassCorrector	+	force	string	false	true,false	
IDConflictResolver	+	force	string	false	true,false	
IDDecoyProbability	+	force	string	false	true,false	
IDEvaluator	+	force	string	false	true,false	
IDEvaluatorGUI	+	force	string	false	true,false	
IDExtractor	+	force	string	false	true,false	
IDFileConverter	+	force	string	false	true,false	
IDFileConverter	+	in	input-file			*.pepXML,*.protXML,*.mascotXML,*.omssaXML,*.xml,*.idXML,*.mzid
IDFileConverter	+	peptideprophet_analyzed	string	false	true,false	
IDFileConverter	-	in	input-file			*.pepXML,*.protXML,*.mascotXML,*.omssaXML,*.idXML
IDFilter	+	blacklist:ignore_modifications	string	false	true,false	
IDFilter	+	delete_unreferenced_peptide_hits	string	false	true,false	
IDFilter	+	force	string	false	true,false	
IDFilter	+	max_length	int	0	0:	
IDFilter	+	precursor:allow_missing	string	false	true,false	
IDFilter	+	precursor:mz	string	:		
IDFilter	+	precursor:rt	string	:		
IDFilter	+	remove_decoys	string	false	true,false	
IDFilter	-	max_length	int	0	:0	
IDMapper	+	consensus:annotate_ids_with_subelements	string	false	true,false	
IDMapper	+	force	string	false	true,false	
IDMapper	+	id	input-file			*.mzid,*.idXML
IDMapper	-	id	input-file			*.idXML
IDMassAccuracy	+	force	string	false	true,false	
IDMerger	+	add_to	input-file			*.idXML
IDMerger	+	force	string	false	true,false	
IDPosteriorErrorProbability	+	force	string	false	true,false	
IDPosteriorErrorProbability	+	out_plot	output-file			*.txt
IDPosteriorErrorProbability	-	fit_algorithm:output_name	output-file			
IDPosteriorErrorProbability	-	fit_algorithm:output_plots	string	false	true,false	
IDPosteriorErrorProbability	-	output_name	output-file			*.txt
IDRTCalibration	+	force	string	false	true,false	
IDRipper	+	force	string	false	true,false	
IDSplitter	+	force	string	false	true,false	
INIUpdater	+	force	string	false	true,false	
ITRAQAnalyzer	+	force	string	false	true,false	
ImageCreator	+	force	string	false	true,false	
InclusionExclusionListCreator	+	algorithm:PrecursorSelection:feature_based:max_number_precursors_per_feature	int	1	1:	
InclusionExclusionListCreator	+	algorithm:PrecursorSelection:feature_based:no_intensity_normalization	string	false	true,false	
InclusionExclusionListCreator	+	force	string	false	true,false	
InclusionExclusionListCreator	-	algorithm:PrecursorSelection:min_peak_distance	double	3	0:	
InclusionExclusionListCreator	-	algorithm:PrecursorSelection:selection_window	double	2	0:	
InspectAdapter	+	force	string	false	true,false	
InternalCalibration	+	force	string	false	true,false	
IsobaricAnalyzer	+	extraction:precursor_isotope_deviation	double	10	0:	
IsobaricAnalyzer	+	extraction:purity_interpolation	string	true	true,false	
IsobaricAnalyzer	+	force	string	false	true,false	
IsobaricAnalyzer	+	tmt10plex:channel_126_description	string			
IsobaricAnalyzer	+	tmt10plex:channel_127C_description	string			
IsobaricAnalyzer	+	tmt10plex:channel_127N_description	string			
IsobaricAnalyzer	+	tmt10plex:channel_128C_description	string			
IsobaricAnalyzer	+	tmt10plex:channel_128N_description	string			
IsobaricAnalyzer	+	tmt10plex:channel_129C_description	string			
IsobaricAnalyzer	+	tmt10plex:channel_129N_description	string			
IsobaricAnalyzer	+	tmt10plex:channel_130C_description	string			
IsobaricAnalyzer	+	tmt10plex:channel_130N_description	string			
IsobaricAnalyzer	+	tmt10plex:channel_131_description	string			
IsobaricAnalyzer	+	tmt10plex:correction_matrix	string			
IsobaricAnalyzer	+	tmt10plex:reference_channel	string	126	126,127N,127C,128N,128C,129N,129C,130N,130C,131	
IsobaricAnalyzer	+	type	string	itraq4plex	itraq4plex,itraq8plex,tmt10plex,tmt6plex	
IsobaricAnalyzer	-	extraction:precursor_isotope_deviation	double	0.02	0:	
IsobaricAnalyzer	-	type	string	itraq4plex	itraq4plex,itraq8plex,tmt6plex	
LabeledEval	+	force	string	false	true,false	
MRMMapper	+	force	string	false	true,false	
MRMPairFinder	+	force	string	false	true,false	
MSSimulator	+	force	string	false	true,false	
MSSimulator	+	in	input-file			*.FASTA
MSSimulator	+	out_id	output-file			*.idXML
MSSimulator	-	in	input-file			*.fasta
MapAlignerIdentification	+	force	string	false	true,false	
MapAlignerIdentification	+	model:b_spline:boundary_condition	int	2	0:2	
MapAlignerIdentification	+	model:b_spline:extrapolate	string	linear	linear,b_spline,constant,global_linear	
MapAlignerIdentification	+	model:b_spline:num_nodes	int	5	0:	
MapAlignerIdentification	+	model:b_spline:wavelength	double	0	0:	
MapAlignerIdentification	-	model:b_spline:break_positions	string	uniform	uniform,quantiles	
MapAlignerIdentification	-	model:b_spline:num_breakpoints	int	5	2:	
MapAlignerPoseClustering	+	force	string	false	true,false	
MapAlignerSpectrum	+	force	string	false	true,false	
MapAlignerSpectrum	+	model:b_spline:boundary_condition	int	2	0:2	
MapAlignerSpectrum	+	model:b_spline:extrapolate	string	linear	linear,b_spline,constant,global_linear	
MapAlignerSpectrum	+	model:b_spline:num_nodes	int	5	0:	
MapAlignerSpectrum	+	model:b_spline:wavelength	double	0	0:	
MapAlignerSpectrum	-	model:b_spline:break_positions	string	uniform	uniform,quantiles	
MapAlignerSpectrum	-	model:b_spline:num_breakpoints	int	5	2:	
MapAlignmentEvaluation	+	force	string	false	true,false	
MapNormalizer	+	force	string	false	true,false	
MapRTTransformer	+	force	string	false	true,false	
MapRTTransformer	+	model:b_spline:boundary_condition	int	2	0:2	
MapRTTransformer	+	model:b_spline:extrapolate	string	linear	linear,b_spline,constant,global_linear	
MapRTTransformer	+	model:b_spline:num_nodes	int	5	0:	
MapRTTransformer	+	model:b_spline:wavelength	double	0	0:	
MapRTTransformer	-	model:b_spline:break_positions	string	uniform	uniform,quantiles	
MapRTTransformer	-	model:b_spline:num_breakpoints	int	5	2:	
MapStatistics	+	force	string	false	true,false	
MascotAdapter	+	force	string	false	true,false	
MascotAdapterOnline	+	Mascot_parameters:special_modifications	string	Cation:Na (DE),Deamidated (NQ),Oxidation (HW),Phospho (ST),Sulfo (ST)		
MascotAdapterOnline	+	Mascot_server:export_params	string	_sigthreshold=0.99&_showsubsets=1&show_same_sets=1&report=0&percolate=0&query_master=0		
MascotAdapterOnline	+	force	string	false	true,false	
MascotAdapterOnline	-	Mascot_server:max_hits	int	0	0:	
MascotAdapterOnline	-	Mascot_server:query_master	string	false	true,false	
MassCalculator	+	force	string	false	true,false	
MassTraceExtractor	+	force	string	false	true,false	
MyriMatchAdapter	+	CleavageRules	string		Trypsin,Trypsin/P,Arg-C,Asp-N,Asp-N_ambic,CNBr,Chymotrypsin,Formic_acid,Lys-C,Lys-C/P,PepsinA,TrypChymo,V8-DE,V8-E,glutamyl endopeptidase,leukocyte elastase,no cleavage,proline endopeptidase,unspecific cleavage	
MyriMatchAdapter	+	MonoisotopeAdjustmentSet	string	0		
MyriMatchAdapter	+	force	string	false	true,false	
MyriMatchAdapter	-	CleavageRules	string		Trypsin,Trypsin/P,Chymotrypsin,TrypChymo,Lys-C,Lys-C/P,Asp-N,PepsinA,CNBr,Formic_acid,NoEnzyme	
MyriMatchAdapter	-	MonoisotopeAdjustmentSet	string	[-1,2]		
MzTabExporter	+	force	string	false	true,false	
MzTabExporter	+	in_consensus	input-file			*.consensusXML
MzTabExporter	+	in_feature	input-file			*.featureXML
MzTabExporter	+	in_id	input-file			*.idXML
MzTabExporter	-	in	input-file			*.idXML
NoiseFilterGaussian	+	force	string	false	true,false	
NoiseFilterGaussian	+	processOption	string	inmemory	inmemory,lowmemory	
NoiseFilterSGolay	+	force	string	false	true,false	
NoiseFilterSGolay	+	processOption	string	inmemory	inmemory,lowmemory	
OMSSAAdapter	+	chunk_size	int	0		
OMSSAAdapter	+	force	string	false	true,false	
OpenSwathAnalyzer	+	algorithm:DIAScoring:peak_before_mono_max_ppm_diff	double	20	0:	
OpenSwathAnalyzer	+	algorithm:Scores:use_dia_scores	string	true	true,false	
OpenSwathAnalyzer	+	algorithm:Scores:use_ms1_correlation	string	false	true,false	
OpenSwathAnalyzer	+	algorithm:Scores:use_ms1_fullscan	string	false	true,false	
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width	double	50		
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:method	string	legacy	legacy,corrected,crawdad	
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width	double	40		
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks	string	false	false,true	
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length	int	15		
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order	int	3		
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise	double	1	0:	
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count	int	30		
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len	double	1000		
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss	string	true		
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:compute_peak_quality	string	false		
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:min_peak_width	double	-1		
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:minimal_quality	double	-10000		
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:recalculate_peaks	string	false		
OpenSwathAnalyzer	+	algorithm:TransitionGroupPicker:recalculate_peaks_max_z	double	1		
OpenSwathAnalyzer	+	force	string	false	true,false	
OpenSwathAnalyzer	-	algorithm:EMGScoring:deltaAbsError	double	0.0001		
OpenSwathAnalyzer	-	algorithm:EMGScoring:deltaRelError	double	0.0001		
OpenSwathAnalyzer	-	algorithm:TransitionGroupPicker:gauss_width	double	50		
OpenSwathAnalyzer	-	algorithm:TransitionGroupPicker:peak_width	double	40	0:	
OpenSwathAnalyzer	-	algorithm:TransitionGroupPicker:sgolay_frame_length	int	15		
OpenSwathAnalyzer	-	algorithm:TransitionGroupPicker:sgolay_polynomial_order	int	3		
OpenSwathAnalyzer	-	algorithm:TransitionGroupPicker:signal_to_noise	double	1	0:	
OpenSwathAnalyzer	-	algorithm:TransitionGroupPicker:sn_bin_count	int	30		
OpenSwathAnalyzer	-	algorithm:TransitionGroupPicker:sn_win_len	double	1000		
OpenSwathAnalyzer	-	algorithm:TransitionGroupPicker:use_gauss	string	true		
OpenSwathAnalyzer	-	model:interpolation_type	string	cspline		
OpenSwathAnalyzer	-	model:num_breakpoints	int	5	2:	
OpenSwathChromatogramExtractor	+	extract_MS1	string	false	true,false	
OpenSwathChromatogramExtractor	+	force	string	false	true,false	
OpenSwathChromatogramExtractor	+	mz_window	double	0.05	0:	
OpenSwathChromatogramExtractor	+	rt_window	double	-1		
OpenSwathChromatogramExtractor	-	extraction_window	double	0.05	0:	
OpenSwathChromatogramExtractor	-	model:interpolation_type	string	cspline		
OpenSwathChromatogramExtractor	-	model:num_breakpoints	int	5	2:	
OpenSwathChromatogramExtractor	-	rt_extraction_window	double	-1		
OpenSwathConfidenceScoring	+	force	string	false	true,false	
OpenSwathDIAPreScoring	+	force	string	false	true,false	
OpenSwathDecoyGenerator	+	enable_losses	string	false	true,false	
OpenSwathDecoyGenerator	+	force	string	false	true,false	
OpenSwathDecoyGenerator	+	mz_threshold	double	0.05		
OpenSwathDecoyGenerator	+	remove_unannotated	string	false	true,false	
OpenSwathDecoyGenerator	-	max_transitions	int	6		
OpenSwathDecoyGenerator	-	min_transitions	int	2		
OpenSwathDecoyGenerator	-	mz_threshold	double	0.8		
OpenSwathFeatureXMLToTSV	+	force	string	false	true,false	
OpenSwathMzMLFileCacher	+	force	string	false	true,false	
OpenSwathRTNormalizer	+	algorithm:DIAScoring:dia_byseries_intensity_min	double	300	0:	
OpenSwathRTNormalizer	+	algorithm:DIAScoring:dia_byseries_ppm_diff	double	10	0:	
OpenSwathRTNormalizer	+	algorithm:DIAScoring:dia_centroided	string	false	true,false	
OpenSwathRTNormalizer	+	algorithm:DIAScoring:dia_extraction_window	double	0.05	0:	
OpenSwathRTNormalizer	+	algorithm:DIAScoring:dia_nr_charges	int	4	0:	
OpenSwathRTNormalizer	+	algorithm:DIAScoring:dia_nr_isotopes	int	4	0:	
OpenSwathRTNormalizer	+	algorithm:DIAScoring:peak_before_mono_max_ppm_diff	double	20	0:	
OpenSwathRTNormalizer	+	algorithm:EMGScoring:interpolation_step	double	0.2		
OpenSwathRTNormalizer	+	algorithm:EMGScoring:max_iteration	int	500		
OpenSwathRTNormalizer	+	algorithm:EMGScoring:statistics:mean	double	1		
OpenSwathRTNormalizer	+	algorithm:EMGScoring:statistics:variance	double	1		
OpenSwathRTNormalizer	+	algorithm:EMGScoring:tolerance_stdev_bounding_box	double	3		
OpenSwathRTNormalizer	+	algorithm:Scores:use_coelution_score	string	true	true,false	
OpenSwathRTNormalizer	+	algorithm:Scores:use_dia_scores	string	true	true,false	
OpenSwathRTNormalizer	+	algorithm:Scores:use_elution_model_score	string	true	true,false	
OpenSwathRTNormalizer	+	algorithm:Scores:use_intensity_score	string	true	true,false	
OpenSwathRTNormalizer	+	algorithm:Scores:use_library_score	string	true	true,false	
OpenSwathRTNormalizer	+	algorithm:Scores:use_ms1_correlation	string	false	true,false	
OpenSwathRTNormalizer	+	algorithm:Scores:use_ms1_fullscan	string	false	true,false	
OpenSwathRTNormalizer	+	algorithm:Scores:use_nr_peaks_score	string	true	true,false	
OpenSwathRTNormalizer	+	algorithm:Scores:use_rt_score	string	true	true,false	
OpenSwathRTNormalizer	+	algorithm:Scores:use_shape_score	string	true	true,false	
OpenSwathRTNormalizer	+	algorithm:Scores:use_sn_score	string	true	true,false	
OpenSwathRTNormalizer	+	algorithm:Scores:use_total_xic_score	string	true	true,false	
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width	double	50		
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:method	string	legacy	legacy,corrected,crawdad	
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width	double	40		
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks	string	false	false,true	
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length	int	15		
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order	int	3		
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise	double	1	0:	
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count	int	30		
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len	double	1000		
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss	string	true		
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:background_subtraction	string	none	none,smoothed,original	
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:compute_peak_quality	string	false		
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:min_peak_width	double	-1		
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:minimal_quality	double	-10000		
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:recalculate_peaks	string	false		
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:recalculate_peaks_max_z	double	1		
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:stop_after_feature	int	-1		
OpenSwathRTNormalizer	+	algorithm:TransitionGroupPicker:stop_after_intensity_ratio	double	0.0001		
OpenSwathRTNormalizer	+	algorithm:add_up_spectra	int	1	1:	
OpenSwathRTNormalizer	+	algorithm:quantification_cutoff	double	0	0:	
OpenSwathRTNormalizer	+	algorithm:rt_extraction_window	double	-1		
OpenSwathRTNormalizer	+	algorithm:rt_normalization_factor	double	1		
OpenSwathRTNormalizer	+	algorithm:spacing_for_spectra_resampling	double	0.005	0:	
OpenSwathRTNormalizer	+	algorithm:stop_report_after_feature	int	-1		
OpenSwathRTNormalizer	+	algorithm:write_convex_hull	string	false	true,false	
OpenSwathRTNormalizer	+	estimateBestPeptides	string	false	true,false	
OpenSwathRTNormalizer	+	force	string	false	true,false	
OpenSwathRTNormalizer	+	outlierDetection:RANSACMaxIterations	int	1000		
OpenSwathRTNormalizer	+	outlierDetection:RANSACMaxPercentRTThreshold	int	3		
OpenSwathRTNormalizer	+	outlierDetection:RANSACSamplingSize	int	10		
OpenSwathRTNormalizer	+	outlierDetection:outlierMethod	string	iter_residual		
OpenSwathRTNormalizer	+	outlierDetection:useIterativeChauvenet	string	false		
OpenSwathRTNormalizer	+	peptideEstimation:InitialQualityCutoff	double	0.5		
OpenSwathRTNormalizer	+	peptideEstimation:MinBinsFilled	int	8		
OpenSwathRTNormalizer	+	peptideEstimation:MinPeptidesPerBin	int	1		
OpenSwathRTNormalizer	+	peptideEstimation:NrRTBins	int	10		
OpenSwathRTNormalizer	+	peptideEstimation:OverallQualityCutoff	double	5.5		
OpenSwathRewriteToFeatureXML	+	force	string	false	true,false	
PILISIdentification	+	force	string	false	true,false	
PILISModelCV	+	force	string	false	true,false	
PILISModelTrainer	+	force	string	false	true,false	
PILISSpectraGenerator	+	force	string	false	true,false	
PTModel	+	force	string	false	true,false	
PTPredict	+	force	string	false	true,false	
PeakPickerHiRes	+	algorithm:SignalToNoise:auto_max_percentile	int	95	0:100	
PeakPickerHiRes	+	algorithm:SignalToNoise:auto_max_stdev_factor	double	3	0:999	
PeakPickerHiRes	+	algorithm:SignalToNoise:auto_mode	int	0	-1:1	
PeakPickerHiRes	+	algorithm:SignalToNoise:bin_count	int	30	3:	
PeakPickerHiRes	+	algorithm:SignalToNoise:max_intensity	int	-1	-1:	
PeakPickerHiRes	+	algorithm:SignalToNoise:min_required_elements	int	10	1:	
PeakPickerHiRes	+	algorithm:SignalToNoise:noise_for_empty_window	double	1e+20		
PeakPickerHiRes	+	algorithm:SignalToNoise:win_len	double	200	1:	
PeakPickerHiRes	+	algorithm:missing	int	1	0:	
PeakPickerHiRes	+	algorithm:ms_levels	int		1:	
PeakPickerHiRes	+	algorithm:spacing_difference	double	1.5	0:	
PeakPickerHiRes	+	algorithm:spacing_difference_gap	double	4	0:	
PeakPickerHiRes	+	force	string	false	true,false	
PeakPickerHiRes	+	processOption	string	inmemory	inmemory,lowmemory	
PeakPickerHiRes	-	algorithm:ms1_only	string	false	true,false	
PeakPickerWavelet	+	algorithm:optimization:iterations	int	400	1:	
PeakPickerWavelet	+	force	string	false	true,false	
PeakPickerWavelet	-	algorithm:optimization:delta_abs_error	double	9.99999974737875e-05	0:	
PeakPickerWavelet	-	algorithm:optimization:delta_rel_error	double	9.99999974737875e-05	0:	
PeakPickerWavelet	-	algorithm:optimization:iterations	int	15	1:	
PepNovoAdapter	+	force	string	false	true,false	
PeptideIndexer	+	IL_equivalent	string	false	true,false	
PeptideIndexer	+	annotate_proteins	string	false	true,false	
PeptideIndexer	+	force	string	false	true,false	
PeptideIndexer	+	write_protein_sequence	string	false	true,false	
PeptideIndexer	-	write_protein_sequence	string	false	true,false	
PhosphoScoring	+	force	string	false	true,false	
PhosphoScoring	+	fragment_mass_tolerance	double	0.05		
PhosphoScoring	+	fragment_mass_unit	string	Da	Da,ppm	
PhosphoScoring	+	out	output-file			*.idXML
PhosphoScoring	-	fragment_mass_tolerance	double	0.5		
PhosphoScoring	-	out	output-file			
PrecursorIonSelector	+	algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature	int	1	1:	
PrecursorIonSelector	+	algorithm:MIPFormulation:feature_based:no_intensity_normalization	string	false	true,false	
PrecursorIonSelector	+	force	string	false	true,false	
PrecursorIonSelector	+	ids	input-file			*.idXML
PrecursorIonSelector	-	ids	string			
PrecursorMassCorrector	+	force	string	false	true,false	
ProteinInference	+	force	string	false	true,false	
ProteinQuantifier	+	average	string	median	median,mean,weighted_mean,sum	
ProteinQuantifier	+	force	string	false	true,false	
ProteinQuantifier	+	protein_groups	input-file			*.idXML
ProteinQuantifier	-	average	string	median	median,mean,sum	
ProteinQuantifier	-	mzTab_out	output-file			*.csv
ProteinQuantifier	-	protxml	input-file			*.idXML
ProteinResolver	+	force	string	false	true,false	
QCCalculator	+	force	string	false	true,false	
QCEmbedder	+	force	string	false	true,false	
QCExporter	+	force	string	false	true,false	
QCExtractor	+	force	string	false	true,false	
QCImporter	+	force	string	false	true,false	
QCMerger	+	force	string	false	true,false	
QCShrinker	+	force	string	false	true,false	
RNPxl	+	continue	string	false	true,false	
RNPxl	+	force	string	false	true,false	
RNPxlXICFilter	+	force	string	false	true,false	
RTEvaluation	+	force	string	false	true,false	
RTModel	+	force	string	false	true,false	
RTPredict	+	force	string	false	true,false	
Resampler	+	force	string	false	true,false	
SeedListGenerator	+	force	string	false	true,false	
SemanticValidator	+	cv	input-file			*.obo
SemanticValidator	+	force	string	false	true,false	
SemanticValidator	+	in	input-file			*.analysisXML,*.mzML,*.TraML,*.mzid,*.mzData,*.xml
SemanticValidator	-	in	input-file			*.analysisXML,*.mzML
SequenceCoverageCalculator	+	force	string	false	true,false	
SpecLibCreator	+	force	string	false	true,false	
SpecLibSearcher	+	compare_function	string	ZhangSimilarityScore	PeakAlignment,SpectrumAlignmentScore,SpectrumCheapDPCorr,SpectrumPrecursorComparator,SteinScottImproveScore,ZhangSimilarityScore	
SpecLibSearcher	+	force	string	false	true,false	
SpecLibSearcher	-	compare_function	string	ZhangSimilarityScore	CompareFouriertransform,PeakAlignment,SpectrumAlignmentScore,SpectrumCheapDPCorr,SpectrumPrecursorComparator,SteinScottImproveScore,ZhangSimilarityScore	
SpectraFilterBernNorm	+	force	string	false	true,false	
SpectraFilterMarkerMower	+	force	string	false	true,false	
SpectraFilterNLargest	+	force	string	false	true,false	
SpectraFilterNormalizer	+	force	string	false	true,false	
SpectraFilterParentPeakMower	+	force	string	false	true,false	
SpectraFilterScaler	+	force	string	false	true,false	
SpectraFilterSqrtMower	+	force	string	false	true,false	
SpectraFilterThresholdMower	+	force	string	false	true,false	
SpectraFilterWindowMower	+	force	string	false	true,false	
SpectraMerger	+	force	string	false	true,false	
SvmTheoreticalSpectrumGeneratorTrainer	+	force	string	false	true,false	
TMTAnalyzer	+	force	string	false	true,false	
TOFCalibration	+	algorithm:PeakPicker:optimization:iterations	int	400	1:	
TOFCalibration	+	force	string	false	true,false	
TOFCalibration	-	algorithm:PeakPicker:optimization:delta_abs_error	double	9.99999974737875e-05	0:	
TOFCalibration	-	algorithm:PeakPicker:optimization:delta_rel_error	double	9.99999974737875e-05	0:	
TOFCalibration	-	algorithm:PeakPicker:optimization:iterations	int	15	1:	
TextExporter	+	force	string	false	true,false	
TransformationEvaluation	+	force	string	false	true,false	
XMLValidator	+	force	string	false	true,false	
XMLValidator	+	in	input-file			*.mzML,*.mzData,*.featureXML,*.mzid,*.idXML,*.consensusXML,*.mzXML,*.ini,*.pepXML,*.TraML,*.xml
XMLValidator	-	in	input-file			*.mzML,*.mzData,*.featureXML,*.idXML,*.consensusXML,*.mzXML,*.ini,*.pepXML
XTandemAdapter	+	allow_isotope_error	string	yes	yes,no	
XTandemAdapter	+	force	string	false	true,false	
XTandemAdapter	+	output_results	string	all	all,valid,stochastic	

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

------------------------------------------------------------------------------------------
----                                OpenMS 1.11.1                                     ----
------------------------------------------------------------------------------------------
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