Class ConsensusXMLFile

Take care that unique ids are assigned properly by TOPP tools before calling ConsensusXMLFile::store(). There will be a message on LOG_INFO but we will make no attempt to fix the problem in this class. (all developers)

Class FalseDiscoveryRate

implement combined searches properly (Andreas)

Class FeatureFinderAlgorithmPicked

Fix output in parallel mode, change assignment of charges to threads, add parallel TOPP test (Marc)

Implement user-specified seed lists support (Marc)

Class FeatureXMLFile

Take care that unique ids are assigned properly by TOPP tools before calling FeatureXMLFile::store(). There will be a message on LOG_INFO but we will make no attempt to fix the problem in this class. (all developers)

Page FileFilter

add tests for selecting modes (port remove modes) (Andreas)

Module FileIO

Implement reading of pepXML and protXML (Andreas)

Allow reading of zipped XML files (David, Hiwi)

Class GaussTraceFitter

More docu

Class Identification

docu (Andreas)

Class IdentificationHit

docu (Andreas)

Class InclusionExclusionList

allow modifications (fixed?)

Page InspectAdapter

rewrite the Adapter! It uses old formats and coding style, e.g. mzData input allowed, no input restrictions, manual (unneccessary file checking of input files) etc... + the interface is not convenient, etc ...

Class InspectOutfile

Handle Modifications (Andreas)

Class IsotopeMarker

implement a real isotope marking here with isotopedistributions and fitting (Andreas)

Class LabeledPairFinder

Implement support for labeled MRM experiments, Q1 m/z value and charges. (Andreas)

Implement support for more than one mass delta, e.g. from missed cleavages and so on (Andreas)

Page MascotAdapter

This adapter is using antiquated internal methods and needs to be updated! E.g. use MascotGenericFile.h instead of MascotInfile.h....

Class MzMLHandler

replace hardcoded cv stuff with more flexible handling via obo r/w.

Member MzMLSpectrumDecoder::decodeBinaryDataChrom_ (std::vector< BinaryData > &data)

Duplicated code from MzMLHandler, need to clean up see MzMLHandler::fillData_()

Member MzMLSpectrumDecoder::decodeBinaryDataSpectrum_ (std::vector< BinaryData > &data)

Duplicated code from MzMLHandler, need to clean up see MzMLHandler::fillData_()

Class ProductModel< D >

This class provides new member functions, which makes Factory<BaseModel<2> >::create("ProductModel2D") pretty much useless! (Clemens)

Class ProteinIdentification

Add MetaInfoInterface to modifications => update IdXMLFile and ProteinIdentificationVisualizer (Andreas)

Page ProteinInference

Integrate Top x support, integrate parsimony approach from OpenMS::PSProteinInference class The command line parameters of this tool are:

ProteinInference -- Protein inference based on an aggregation of the scores of the identified peptides.
Version: 2.4.0-HEAD-2019-01-18 Jan 18 2019, 21:06:42, Revision: 8ddd6a9
To cite OpenMS:
  Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

Usage:
  ProteinInference <options>

Options (mandatory options marked with '*'):
  -in <file>*                                               Input file(s) (valid formats: 'idXML')
  -out <file>*                                              Output file (valid formats: 'idXML')
  -merge_runs <choice>                                      If your idXML contains multiple runs, merge them 
                                                            beforehand? (default: 'no' valid: 'no', 'all')
  -annotate_indist_groups <choice>                          If you want to annotate indistinguishable protein
                                                            groups, either for reporting or for group based
                                                            quant. later. Only works with a single ID run in
                                                            the file. (default: 'true' valid: 'true', 'false'
                                                            )
                                                            

Merging:
  -Merging:annotate_origin <choice>                         If true, adds a map_index MetaValue to the Peptid
                                                            eIDs to annotate the IDRun they came from. (defau
                                                            lt: 'true' valid: 'true', 'false')

Algorithm:
  -Algorithm:score_aggregation_method <choice>              How to aggregate scores of peptides matching to 
                                                            the same protein? (default: 'maximum' valid: 'max
                                                            imum', 'product', 'sum')
  -Algorithm:treat_charge_variants_separately <text>        If this is true, different charge variants of 
                                                            the same peptide sequence count as individual
                                                            evidences. (default: 'true')
  -Algorithm:treat_modification_variants_separately <text>  If this is true, different modification variants 
                                                            of the same peptide sequence count as individual
                                                            evidences. (default: 'true')
  -Algorithm:use_shared_peptides <text>                     If this is true, shared peptides are used as evid
                                                            ences. (default: 'true')
  -Algorithm:skip_count_annotation <text>                   If this is true, peptide counts won't be annotate
                                                            d at the proteins. (default: 'false')

                                                            
Common TOPP options:
  -ini <file>                                               Use the given TOPP INI file
  -threads <n>                                              Sets the number of threads allowed to be used by 
                                                            the TOPP tool (default: '1')
  -write_ini <file>                                         Writes the default configuration file
  --help                                                    Shows options
  --helphelp                                                Shows all options (including advanced)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+ProteinInferenceProtein inference based on an aggregation of the scores of the identified peptides.

version2.4.0-HEAD-2019-01-18 Version of the tool that generated this parameters file.

++1Instance '1' section for 'ProteinInference'

in[] input file(s)input file*.idXML

out output fileoutput file*.idXML

merge_runsno If your idXML contains multiple runs, merge them beforehand?no,all

annotate_indist_groupstrue If you want to annotate indistinguishable protein groups, either for reporting or for group based quant. later. Only works with a single ID run in the file.true,false

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue,false

forcefalse Overwrite tool specific checks.true,false

testfalse Enables the test mode (needed for internal use only)true,false

+++Merging

annotate_origintrue If true, adds a map_index MetaValue to the PeptideIDs to annotate the IDRun they came from.true,false

+++Algorithm

score_aggregation_methodmaximum How to aggregate scores of peptides matching to the same protein?maximum,product,sum

treat_charge_variants_separatelytrue If this is true, different charge variants of the same peptide sequence count as individual evidences.

treat_modification_variants_separatelytrue If this is true, different modification variants of the same peptide sequence count as individual evidences.

use_shared_peptidestrue If this is true, shared peptides are used as evidences.

skip_count_annotationfalse If this is true, peptide counts won't be annotated at the proteins.

Class ProtXMLFile

Document which metavalues of Protein/PeptideHit are filled when reading ProtXML (Chris)

Writing of protXML is currently not supported

Page RTPredict

This needs serious clean up! Combining certain input and output options will result in strange behaviour, especially when using text output/input.

Class SequestOutfile

Handle Modifications (Andreas)

Complete rewrite of the parser (and those of InsPecT and PepNovo), the code is bullshit... (Andreas)

Class Spectrum1DCanvas

Use spectrum StringDataArray with name 'label' for peak annotations (Hiwi, Johannes)

Class SpectrumCanvas

Allow reordering the layer list by drag-and-drop (Hiwi, Johannes)

Class SpectrumIdentification

docu (Andreas)

Class SpectrumWidget

Add support to store the displayed data as SVG image (HiWi)

Class TOPPBase

: replace writeLog_, writeDebug_ with a logger concept we'd need something like -VLevels [LOGGERS] to specify which loggers shall print something the '-log' flag should clone all output to the log-file (maybe with custom [LOGGERS]), which can either be specified directly or is equal to '-out' (if present) with a ".log" suffix maybe a new LOGGER type (TOPP), which is only usable on TOPP level?

Class TraceFitter

docu needs update

Class TwoDOptimization

Works only with defined types due to pointers to the data in the optimization namespace! Change that or remove templates (Alexandra)