openms/openms

The codebase of the OpenMS project

OpenMS

OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software. OpenMS is free software available under the three clause BSD license and runs under Windows, macOS, and Linux.

It comes with a vast variety of pre-built and ready-to-use tools for proteomics and metabolomics data analysis (TOPPTools) as well as powerful 1D, 2D and 3D visualization (TOPPView).

OpenMS offers analyses for various quantitation protocols, including label-free quantitation, SILAC, iTRAQ, TMT, SRM, SWATH, etc.

It provides built-in algorithms for de-novo identification and database search, as well as adapters to other state-of-the art tools like X!Tandem, Mascot, Comet, etc. It supports easy integration of OpenMS built tools into workflow engines like KNIME, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and a unified parameter handling via a 'common tool description' (CTD) scheme.

With pyOpenMS, OpenMS offers Python bindings to a large part of the OpenMS API to enable rapid algorithm development. OpenMS supports the Proteomics Standard Initiative (PSI) formats for MS data. The main contributors of OpenMS are currently the Eberhard-Karls-Universität in Tübingen, the Freie Universität Berlin, and the ETH Zürich.

Features

• Core C++ library under three-clause BSD licence using modern C++17
• Python bindings to the C++ API through pyOpenMS
• Major community file formats supported (mzML, mzXML, mzIdentXML, pepXML, mzTab, etc.)
• Over 150+ individual analysis tools (TOPP Tools), covering most MS and LC-MS data processing and mining tasks
• Powerful 1D, 2D and 3D visualization tools (TOPPView)
• Support for most MS identification and quantification workflows (targeted, DIA, label-free, isobaric and stable isotope)
• Support for all major platforms (Windows [XP, 7, 8, 10], macOS and Linux)

Documentation

Users and developers should start by reading the OpenMS documentation. OpenMS API reference documentation and advanced developer doxygen documentation can be browsed here.

openms.readthedocs.io documentation aims at being an entry point for users and developers alike. It is trying to be mostly version-independent and therefore only consists of one main branch. We may introduce tags for older releases in the future.

The OpenMS API reference has several endpoints:

1. nightly: OpenMS API reference and advanced developer documentation of nightly releases.
2. release/latest : OpenMS API reference and advanced developer documentation of latest stable release.
3. release/${version} : OpenMS API reference and advanced developer documentation of an older version.

Documentation for the Python bindings pyOpenMS can be found on the pyOpenMS online documentation.

Citation

Please cite:

Pfeuffer, J., Bielow, C., Wein, S. et al. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data, Nat Methods 21, 365–367 (2024). https://doi.org/10.1038/s41592-024-02197-7

The file AUTHORS contains a list of all authors who worked on OpenMS.

Licence

OpenMS is released under the three clause BSD licence.

openms's Issues

pepXML handling of PTMs [10]

Submitted by OpenMS Retreat on 2009-10-07 13:14:16

(DONE, Andreas)

FeatureFinder - allow parallel execution [12]

Submitted by OpenMS Retreat on 2009-10-07 13:18:14

(DONE for centroided, Marc)

All TOPP/UTILS segfault if /share is not found [46]

Submitted by cbielow on 2009-11-18 10:55:48

The order of instanciation of our own error handler and some object that requires files from /share is mixed up.
Our error handler should be in place to quit the app gracefully, before anything else happens...

---

Commented by cbielow on 2010-01-27 13:38:06:
File::getOpenMSDataPath() should be used if data from share is required.
The function first checks if ./share is present and quits the app gracefully with an error message otherwise.

Overflow Error in LogStream [49]

Submitted by hendrikweisser on 2009-11-19 10:01:25

---

Commented by aiche on 2009-11-19 10:02:23:
fixed in [6429] ..

generate publication ready figures in SVG format - 1D view first [27]

Submitted by OpenMS Retreat on 2009-10-09 14:03:52

---

Commented by cbielow on 2010-01-07 16:38:29:
Qt supports SVG's on all platforms (as opposed to PS - missing on Windows)

http://doc.trolltech.com/4.4/qt4-arthur.html

---

Commented by timosachsenberg on 2010-11-24 14:41:56:
1D View: done

---

Commented by cbielow on 2010-11-24 15:50:17:
How can the user change the axis labels or the font size now?!
Maybe we should publish a little guide on how to do this (maybe on our doxygen docu). The main problem with screen-shots (as done before) was not the resolution, but rather the font size and the title etc.

---

Commented by timosachsenberg on 2010-11-25 11:26:17:
Sure, would be nice to have these features.
For now, I think it's sufficient to document that 1D plots can be exported in a vector format and edited in a vector graphics program.

Feature data: add option to display unassigned identifications [9]

Submitted by OpenMS Retreat on 2009-10-07 13:08:56

(DONE, Marc)

change integer type of DataValue from UInt to Size [11]

Submitted by OpenMS Retreat on 2009-10-07 13:16:45

(DONE, Chris)

allow measurements from start point to mouse position [6]

Submitted by aiche on 2009-10-07 13:04:49

(DONE, Marc)

escape strings for writing XML [24]

Submitted by OpenMS Retreat on 2009-10-09 13:56:53

special chars like "&" e.g. in user-params are dangerous and will create an error when reading the file back in (Andreas idXML, ... ALLE)

=> implement "static String XMLFile::escape(const String&) const" which uses uses xerces::xmlformatter()

---

Commented by andreas_bertsch on 2009-10-28 16:01:33:
implemented and seems to work

---

Commented by cbielow on 2011-02-18 12:54:01:

• we currently do not to this for mzML... enquiry ongoing...

---

Commented by herrzweiblum on 2012-09-04 09:23:56:
commit 9872 for MzML: Fixed in writeUserParam function so writing invalid userparams will not be possible. To be generalised for XML

Add an update mode for parameter files using -ini and -write_ini [4]

Submitted by OpenMS Retreat on 2009-10-07 12:57:02

---

Commented by cbielow on 2009-10-13 16:12:35:
implemented in Rev 6112

new TOPP tool PrecursorMassCorrector [25]

Submitted by OpenMS Retreat on 2009-10-09 13:58:51

estimate more accurate precursor masses e.g. from survey scans (Andreas)

---

Commented by andreas_bertsch on 2009-11-14 15:19:42:
Added experimental PrecursorMassCorrector tool with test for QTof data.

Remove or SVN revision support in OpenMS or implement it properly - load it form OpenMS share [16]

Submitted by OpenMS Retreat on 2009-10-07 13:29:01

(DONE, Chris)

MapAligner parameters [36]

Submitted by lars20070 on 2009-10-28 10:46:36

Beim Schreiben des *.ini files muss der Typ angegeben werden z.B.
MapAligner -type apply_given_trafo -write_ini par.ini
Dieser Type selbst erscheint im *.ini File und ist editierbar, sollte es aber nicht.

---

Commented by groepl on 2009-11-11 16:17:11:
Hm, wo ist das Problem? So funktioniert das ...
Wenn der "type" nicht editierbar sein sollte, msste man das fr TOPP generell ndern

Show progress while RTModel runs [37]

Submitted by lars20070 on 2009-10-28 10:49:54

Progress sollte angezeigt werden.

---

Commented by andreas_bertsch on 2009-10-28 16:00:25:
changed to upcoming releases. not a trivial task

---

Commented by aiche on 2010-02-18 13:43:31:
changed title to something more meaningful

---

Commented by cbielow on 2010-10-20 21:00:29:
already done pre 1.7, i.e [7103]

link *.toppas in Installer [14]

Submitted by OpenMS Retreat on 2009-10-07 13:21:51

(Chris, DONE)

IdXMLFile seg. faults if no protein identification given [28]

Submitted by andreas_bertsch on 2009-10-13 10:59:34

seq. fault if idXML file does not contain a protein identification.
However, this is explicitely allowed in the schema

(reported by Hendrik, see open-ms-developers ML, october 12th)

---

Commented by andreas_bertsch on 2009-10-13 11:01:45:
fixed in revision 6108

FileFilter option [35]

Submitted by lars20070 on 2009-10-28 10:45:38

Weder
-select_activation High-energy collision-induced dissociation noch
-select_activation 'High-energy collision-induced dissociation'
funktioniert.

---

Commented by cbielow on 2009-10-28 12:51:15:
use
FileFilter -select_activation "High-energy collision-induced dissociation"

(note the double quotes!)

This is a "problem" of the Windows command line, not of TOPP!

---

Commented by cbielow on 2009-10-28 13:44:05:
changed output of --help
, now showing double quotes instead of single quote to "guide" user towards using dq

Integrate Logger into TOPPBase and GUI apps [50]

Submitted by aiche on 2009-11-19 10:09:37

---

Commented by cbielow on 2010-04-22 15:48:29:
technical thoughts:

• create a new baseclass "LogHandlerBase" from which TOPPBase and GUI tools will be derived
• allow to bind/unbind streams to any of the loggers via this baseclass
  • e.g. "bind(ENUM_INFO, &cout)"
• this can be used to "preconfigure" every tool (TOPP or GUI in their own constructors) and to additionally allow for interaction via command line (which should be parseable by "LogHandlerBase")
• command line syntax:
  "-LOG "
  e.g. is any of: DEBUG, INFO, ..., all
  e.g. is any of: add, remove, clear (clear makes obsolete)
  e.g. is any of: cerr, cout, ...

Q: What if we want to write every logger to a single file? Should "LogHandlerBase" manage the iostream for that and distribute it to the loggers? That might work...

---

Commented by aiche on 2010-09-02 17:14:28:
will not make it into 1.7 -> moved to 1.8

---

Commented by hendrikweisser on 2011-02-17 15:38:13:
See also ticket #181 (closed as duplicate).

TOPPASS pipeline [33]

Submitted by lars20070 on 2009-10-28 10:42:38

OMSSAAdapter output kann nicht als ID Mapper input verwendet werden. *.IdXML Schnittstelle passt nicht.

---

Commented by andreas_bertsch on 2009-10-28 15:53:07:
works with revision 6200

Build problem [42]

Submitted by chriii on 2009-11-05 16:34:31

My latest check out is some time ago (~2 month). I intended to update to the newest version and therefore to checked out contrib and OpenMS. Contrib package seemed to build without any problems but trying to compile OpenMS resulted in mysterious linking problems which I could not resolve. Finally I got the idea to recompile the contrib package but this time as root user (because I imagined the make install might need root access). Subsequence compilation of OpenMS was successful.
This might be obvious but compilation of contrib package seemed to work and did not show any problems. Thus it took my quite a long time to figure it out and make OpenMS work.
OS: Debian GNU/Linux, kernel 2.6.26-2-686

---

Commented by cbielow on 2009-11-05 18:26:36:
This probably requires some more information to tackle the issue:
It would be helpful if you could provide

• the complete console output (stout&stderr) of the cmake call to build the contrib.
• a list of the files in <contrib_buildtree>/lib when the contrib build finished
• and the specific linker errors that occurred when linking OpenMS.

Thx!

---

Commented by chriii on 2009-11-06 09:46:44:
I know i will certainly help but my intension was to make it work and therefore I did not store console output (and since I solved the problem I can not recontruct it). But I know there was just the typical stout (calling make ... calling make install ... successfully build ... etc.). After building contrib the <contrib_buildtree>/lib folder seemed to contain all necessary files. The linking error was caused by undefined references in libgsl.so.

I suppose I have libgsl installed in the system (/usr/lib) and building the contrib package rebuild libgsl in contrib folder but anyway OpenMS was linked to the older system library leading to undefined references. When building contrib packages with root privileges 'make install'-call updated the libgsl in the system (/usr/lib) solving the problem since OpenMS was now linked to the updated libgsl.

I know this description is somewhat spongy but hope it is enough to describe the problem ...

---

Commented by cbielow on 2009-11-20 12:41:58:
We're probably going to test this with a normal user account on Debian Lenny (32bit).. and see what comes up.

---

Commented by cbielow on 2009-11-20 15:20:43:
Just tested OpenMS 1.6 source package on a Debian Lenny 32 bit as non-root user using the installation instructions:
works out of the box.
The problem described could stem from updating an old contrib, instead of starting from scratch (at least for the contrib). As long as detailed info on that actually went wrong is missing, I'm closing the ticket.
Feel free to re-open it if the problem occurs again.

FilerMerger accumulates processingMethod entries [29]

Submitted by andreas_bertsch on 2009-10-23 11:30:55

Somehow, the number of software entries and processing methods explodes when using Filemerger...

---

Commented by andreas_bertsch on 2009-10-26 12:56:49:
fixed in commit 6183

TOPPView save [32]

Submitted by lars20070 on 2009-10-28 10:41:04

2D Bereich in TOPPview ausgeschnitten, dann mit Rechts Klick "save visible layer data" -> File Endung *.mzML wurde nicht angehaengen.

---

Commented by cbielow on 2009-11-09 13:40:58:
Not reproducible on Win64 with current svn version.
File ending is only omitted if "All files (*)" is selected as datatype.

---

Commented by andreas_bertsch on 2009-11-09 14:34:50:
Works on MacOSX and Windows variants. Does not work on Unix, because Qt uses a different dialog.

Qt4.4 offers simple way, however we also support Qt4.3

-> Postponed to later release

---

Commented by andreas_bertsch on 2009-11-09 14:54:18:
moved to 1.6

---

Commented by andreas_bertsch on 2009-11-13 14:48:24:
Finally fixed. If no correct file ending is given the correct one is appended, depending on the filter setting, mzXML, mzData and mzML (and also featureXML and consensusXML). If the filter setting of the peak save dialog is set to "All files (*)" mzML is written with .mzML as file ending

AndiMS for 32/64bit Windows and 64bit Linux.. [41]

Submitted by cbielow on 2009-11-04 14:22:26

currently only 32bit Linux/MacOS is working...
Maybe mzMine (Java) is worth a look... they support NetCDF (might be their own format though)

---

Commented by waldi on 2011-09-04 10:47:11:
AndiMS was removed.

---

Commented by aiche on 2011-09-04 11:49:24:
fixed in [8698], [8701], [8702]], changing resolution, milestone, ..

---

Commented by aiche on 2011-09-04 11:49:49:
we removed the support, so wontfix

different icons and icon sizes for features and consensus features (DONE, Marc) [5]

Submitted by aiche on 2009-10-07 13:02:48

dummy .. for the sake of completeness

Automatic notification in TOPPView for new Releases of OpenMS [40]

Submitted by cbielow on 2009-11-03 18:22:24

just a popup that says: new version available. Go and get it.

implement via a status file on Openms.de and Qt's http interface.

unique feature IDs for ConsensusMaps and everything else [21]

Submitted by OpenMS Retreat on 2009-10-07 13:46:19

• Problem: reordering an input featureMap internally and storing a CM will not produce correct id's in the CM which refers to the untouched FM
• Solution:
  • Feature UID: Zufalls-Size + Datum eindeutig in Datei => (map,id) unique within consensusxml
  • new member "Size id_" for each Feature
    • preserved when sorting, filtering and in file I/O
    • id is initialized to -1 (=invalid) by default, -1 not accepted upon write to file
  • "Size FeatureMap::indexToId(Size)", converts UIDs to index within vector and which checks back whether hash was valid
  • "FeatureMap::assignIDs(String method)" e.g. override
  • UIDServer for local use, unique within a run

---

Commented by groepl on 2009-10-07 15:56:56:
Mixed remarks .......

New classes: UniqueIdGenerator; UniqueIdInterface, UniqueIdIndexer

UniqueIdGenerator uses current Date and Time for initialization of a gsl random number generator. Unique ids are UInt64. Class tests and TOPP tests use a fixed moment in time for initialization for reproducible results (TOPPBase, ClassTest).

UniqueIdInterface and UniqueIdIndexer are designed as base classes.

FileConverter supports ConsensusXML to FeatureXML conversion.
Identifications are okay, groups are lost.

New UTIL UniqueIdAssigner can be used to assign new unique ids to ConsensusXML and FeatureXML (with options).

Invalid unique id is represented by 0, not Size(-1).

Sorting and filtering is no longer an issue :-)

File I/O is implemented.

However some xml schema changes are necessary. As for now (20009-10-07) both schemas have version 1.3 but were modified illegally ;-). To do: new versions 1.4 and revert 1.3 to their state of OpenMS 1.5.

Note that the containers have a unique id as well.
This interferes with the lsid approach.
Thus at the container level, the attribute name "unique_id" is used.
At the element level, the name is "id". That's kind of weird.

ConsensusXML uses the old approach internally to link from feature handles to the map list. We cannot use the unique id of the file because "labeled" methods will have the same file with different labels in their map list.

Unique ids are inconsistently written with a prefix (f_12345) or without (12345), depending on the circumstances. Sigh! In the schemas, its always an xs:string.

Note that there are cases when a unique id of a consensus feature is reused for a feature (e.g. FileConverter). In this case, the prefix will change.

---

Commented by andreas_bertsch on 2009-10-28 16:02:49:

• fix windows test
• fix warnings

---

Commented by aiche on 2009-11-16 08:42:54:
Is there any update on this issue ..

---

Commented by groepl on 2009-11-16 21:36:52:
XML Schema versions 1.4 for ConsensusXML and FeatureXML were added, and the 1.3 versions were reverted to the state of revision 4231.

Invalid UniqueIds are reported to LOG_INFO but tolerated by store().
That was necessary to deal with older files.

The test on Vista 64 Bit was fixed by Chris. Somehow UInt64 is not parsed correctly by this operating system, so he wrote a hand-crafted solution.

There are at least three related concepts. Attribute names have changed since last posting:

• unique ids (attribute name in OpenMS: "id" or "unique_id")
• ids as specified by W3C, xml:id or xs:id (attribute name in OpenMS: "id", maybe other names)
• lsid, life science identifiers (attribute name in OpenMS: "document_id")

We had to use unique_id within ConsensusXML to remain downward compatible. See xml schema version 1.4.

Usage of UniqueIdAssigner is recommended!

Change OpenMS Version from 1.5 to 1.6 [20]

Submitted by aiche on 2009-10-07 13:38:41

Maybe we could somehow automate or at least ease this process and do this for the head right after creating the release branch

---

Commented by cbielow on 2009-10-09 00:55:52:
We should not store the OpenMS version in config.h, as one would need to recompile the whole lib when the version number changes.

--> use a lean header included only where necessary (Version.C, ...)

modifying the build system to do so is easy.

---

Commented by cbielow on 2009-10-09 23:24:50:
Updated to OpenMS version tag 1.6

changing the Version number will from now on only trigger Version.C to be compiled (not the whole lib as before) (see svn [6104])

Discuss overhaul of OpenMS web site and possible migration to CMS [43]

Submitted by aiche on 2009-11-13 15:28:20

Shouldn't we migrate the OpenMS website to something more reasonable then a bunch of php Files .. this affects design and technology

---

Commented by aiche on 2011-03-28 16:19:43:
since 26.2.2011 we have a new website based on wordpress

auto-compile of contrib [48]

Submitted by cbielow on 2009-11-18 15:35:07

configuring OpenMS should trigger compilation of contrib -
disadvantage: this would need to be an in-source build, otherwise we're stuck with more param options...
maybe look at "ExternalProject: Create custom targets to build projects in external trees", which requires CMake2.8

Add Nightly coverage builds [18]

Submitted by OpenMS Retreat on 2009-10-07 13:31:30

(DONE, Stephan)

Next generation MapAligner and FeatureLinker: ConsensusXML, Splines, Hierarchical groups [45]

Submitted by groepl on 2009-11-17 17:55:45

Support for ConsensusXML is currently scarce. We should change this.

Current state is: ConsensusXML can be converted to FeatureXML using FileConverter. However, only the centroids are copied (directly from ConsensusMap to FeatureMap).

'''Topics for FeatureLinker:'''

• This tool takes FeatureXML as input. What if the input should consist of "grouped" stuff? -- ideas:
• We could copy the consensus elements into subordinate features. However, there is no equivalent of the map list in FeatureXML. We could derive FeatureMap from MetaInfoInterface and store such things there.
• In general using subordinate features would allow to support a wider range of alignment scenarios... but now we already have ConsensusXML. (-> Think about this.)
• ConsensusXML/ConsensusMap does not remember from which consensus element a peptide identification stems from! We get a mess here...
• We can flatten the groups (group of group becomes union) or compose a tree (group of group stored explicitly, thus we will have an intermediate centroid etc.). Both alternatives make sense, but it is a one-way road
• Adding visualization of subordinate features should not be too hard to implement in TOPPView

'''Topics for MapAligner:'''

• Add new method MapAlignmentAlgorithm::alignConsensusMaps(), which can be implemented (at least) in MapAlignmentAlgorithmPoseClustering and MapAlignmentAlgorithmIdentification, using similar ideas as alignFeatureMaps()
• Pose clustering should generate shift/affine/spline depending upon user choice

---

Commented by groepl on 2009-12-08 11:09:45:
Note: I have chosen map alignment / feature linking as the implementation challenge of a course on "Praxis des Programmierens" at Greifswald university.
Maybe a student will produce something useful...

http://www.alice-dsl.net/clemens.groepl/Praxis-des-Programmierens.html

---

Commented by aiche on 2011-02-24 17:25:08:
is this change in Release 1.8 or was it already in Release 1.7

---

Commented by hendrikweisser on 2011-02-25 21:39:01:
Most of the changes should be in 1.8. Don't know if some things were already addressed in 1.7.

refactor the CMake script for the revision number and change the number right after a release [15]

Submitted by OpenMS Retreat on 2009-10-07 13:24:09

(DONE, Chris)

add features and consensus features to 3D view [26]

Submitted by OpenMS Retreat on 2009-10-09 14:02:46

---

Commented by hendrikweisser on 2011-03-08 11:02:08:
I've attached an image of how this looks in Progenesis. The ability to visually compare different features in a group (consensus feature) would be cool to have, but it's currently impossible because we don't store the relevant data in the consensusXML...

Add tool version, to write_ini output => Add warning when old version [3]

Submitted by aiche on 2009-10-07 12:55:42

add new label types: all peptide IDs [7]

Submitted by aiche on 2009-10-07 13:06:00

(DONE, Marc)

Add tool description to --write_ini output [2]

Submitted by aiche on 2009-10-07 12:53:40

just for the sake of completeness

Consistent handling of ppm & absolute deltas [39]

Submitted by cbielow on 2009-11-03 18:18:28

Look at every Class/TOPP tool and decide if we also need ppm metrics for measuring distance & matches. This is especially required for new instrument types, as absolute mz deltas will usually not suffice to map in low and high m/z regions simultaneously.

CDF import broken on 64bit Linux [38]

Submitted by sneumann on 2009-11-03 10:38:48

Hi,

I couldn't find a corresponding ticket, nor sth. in the Changelog,
so here is a new ticket:

Reading netCDF files on 64bit is broken for quite a while.
Please consider fixing it, or return an error message,
instead of silently writing a broken output.

Yours,
Steffen

FileConverter -in FAM014_HHS_MS.cdf -out FAM014_HHS_MS.mzData
Progress of 'storing mzData file':
-- done (took 0.000 s) --

438894516 2009-11-03 09:43 FAM014_HHS_MS.cdf
=> 1110 2009-11-03 09:43 FAM014_HHS_MS.mzData

dchroot (i386)
FileConverter -in FAM014_HHS_MS.cdf -out FAM014_HHS_MS.mzData
Progress of 'reading ANDI/MS file':
-- done (took 17.640 s) --
Progress of 'storing mzData file':
-- done (took 3.260 s) --

391644509 Nov 3 08:49 FAM014_HHS_MS.mzData

---

Commented by andreas_bertsch on 2009-11-03 14:39:57:
Hi Steffen,

the list of supported file formats now depends on the platform. netCDF support will not be listed any more by the TOPP-tools if it is a 64Bit build. If one tries to convert a netCDF file on a platform not supporting it will see the following message:
"Invalid parameter: Input file 'source/TEST/data/ANDIFile_test.cdf' has invalid format 'CDF'. Valid formats are: 'mzData','mzXML','mzML','DTA','DTA2D','mgf','featureXML','consensusXML','ms2'."

Thanks for reporting. This fix will be contained in the upcoming release 1.6 expected to be finished this month.

Cheers,
A.

support chromatograms [1]

Submitted by cbielow on 2009-10-07 12:48:31

---

Commented by andreas_bertsch on 2009-10-26 19:40:46:
KERNEL and file adapter now support Chromatograms. TOPPView has only rudimentary implementation of chromatograms, just a extra layer with black dots

loading Dialog is usually not responding when loading big files on Windows. [8]

Submitted by OpenMS Retreat on 2009-10-07 13:07:44

Use Threading (DONE, Chris)

implement protXML [23]

Submitted by OpenMS Retreat on 2009-10-09 13:53:00

Chris, Lars ..

---

Commented by cbielow on 2010-01-22 16:41:04:
first implementation is available

Run checker.php nightly [19]

Submitted by OpenMS Retreat on 2009-10-07 13:33:09

(DONE, Andreas) ..

http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/search/errors_and_warnings.txt

Support chromatogram in TOPPView properly [31]

Submitted by andreas_bertsch on 2009-10-26 18:04:59

So far only black dots are drawn for chromatograms to visualize them. A number of function must be implemented in the Spectrum widgets and canvas classes, to produce chromatograms as nice as the 2d peak data

---

Commented by hendrikweisser on 2009-12-08 17:37:44:
I don't know if that's really comparable, but [https://brendanx-uw1.gs.washington.edu/labkey/project/home/software/Skyline/begin.view Skyline] seems to be a very nice viewer for SRM transitions and spectra. Might be worth a look for inspiration.

---

Commented by johannes_junker on 2012-09-17 11:49:39:
Solved. Chromatograms can be visualized in SpectrumWidgets. They can be browsed conveniently, and TOPP tools can be run on them.

Line numbers in errors of Textbased files [47]

Submitted by andreas_bertsch on 2009-11-18 11:40:23

If an error or a warning occurs while parsing textbase files, the line number should be printed as well.

---

Commented by cbielow on 2010-01-26 14:41:12:
Done:
(see svn Rev 6580)
dta, dta2D, FASTAFile, PepNovoOutfile, MascotGenericFile, MS2File, MSPFile, OMSSACSVFile, TextImporter (csv, msInspect, SpecArray, Kroenik)

Missing:
InspectInfile, SequestOutfile, ?

---

Commented by andreott on 2011-02-24 14:54:13:
Replying to [comment:1 cbielow]:

Done:
(see svn Rev 6580)
dta, dta2D, FASTAFile, PepNovoOutfile, MascotGenericFile, MS2File, MSPFile, OMSSACSVFile, TextImporter (csv, msInspect, SpecArray, Kroenik)

Missing:
InspectInfile, SequestOutfile, ?

Probably meant InspectrOutfile. This does not throw parse error exceptions but returns line numbers for which parsing failed. SequestOutfile obsolete? Crux?

---

Commented by hroest on 2012-09-17 11:53:43:
wont fix Inspecter and Sequest

take out tests to another project [17]

Submitted by OpenMS Retreat on 2009-10-07 13:30:29

(DONE, Chris)

TOPPASS Fehlermeldung [34]

Submitted by lars20070 on 2009-10-28 10:44:22

Fehlermeldungen traten auf: Beschwerde ueber falsch gesetzte Pfadvariabel, obwohl diese korrekt ist (TOPP tools direkt aufrufbar):
"Could not execute 'MascotAdapterOnline -write_ini /tmp/TOPPAS_MascotAdapterOnline_2009-10-21_182001_do2-oms-eminiar_29348_1_tmp.ini'!
Make sure the TOPP tools are in your $PATH variable, that you have write permission in the temporary file path, and that there is space left in the temporary file path."
Aehnliche Meldungen fuer ITRAQAnalyzer, IDMapper und TextExporter.

---

Commented by andreas_bertsch on 2009-10-28 15:55:57:
Seems to be a local problem. See hints above to solve the problem.

TOPPView warning "Cannot show projections!" [44]

Submitted by cbielow on 2009-11-17 17:28:44

TOPPView will show the above message if you delete the layer where projections where activated and still have other layers that do not support it.
Furthermore it is not possible to disable projections any longer because the button is not accessible any longer.

quickfix 1: deactivate the "auto-update" check button
quickfix 2: load a new layer which supports projections, disable them and remove the new layer.

---

Commented by cbielow on 2009-11-20 18:13:49:
fixed in Rev. 6451

---

Commented by aiche on 2010-01-12 10:41:02:
fix is available in Release 1.7 -> Milestone set to Release 1.7

FeatureFinder: use MS2 precursors for seeding , allow filling in missing features after alignment [13]

Submitted by OpenMS Retreat on 2009-10-07 13:20:03

(DONE for centroided, Marc)

• allow specification of arbitrary seed lists (RT, m/z, [charge]) e.g. from precursors
• allow forcing a feature even if no signal can be found (bad quality, baseline intensity)

MGF file conversion awfully slow on Windows (&Linux?) [30]

Submitted by cbielow on 2009-10-26 17:30:48

When using FileConverter to create an MGF file, the output file taken ages to write out.

---

Commented by cbielow on 2009-10-26 17:37:30:
solved by replacing endl with "\n" which does not trigger a flush() each time.

implement logger class with error, warning, info, debug streams [22]

Submitted by OpenMS Retreat on 2009-10-07 13:48:11

(90% DONE, Andreas, Stephan, Chris, ... ALLE)

---

Commented by aiche on 2009-10-07 13:51:34:
The logging works (somehow) using the framework from BALL. Problem is, that the LogStream sometimes disrupts the "cout/cerr" streams ..

---

Commented by aiche on 2009-10-09 12:59:07:
reimplementation based on BALL 1.3 in rev [6100] by cbielow -> problem with disrupted cout/cerr is now fixed

---

Commented by aiche on 2009-10-09 13:02:04:
we should add another logLevel called "Development" which will be disabled release versions

---

Commented by aiche on 2009-10-09 14:53:25:
fixed the problem with the killed cout/cerr streams ..

whats missing

• caching
• macros

---

Commented by aiche on 2009-10-12 14:30:03:

• implemented 1st caching draft in [6107]
• removed internal logline buffer

---

Commented by aiche on 2009-11-19 10:20:04:
implemented and integrated into Release 1.6

created follow up ticket for integration into TOPP #50, OpenMS #51 and TOPPView #52