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Home Page: https://www.openms.de
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The codebase of the OpenMS project
Home Page: https://www.openms.de
License: Other
Submitted by aiche on 2009-10-07 13:06:00
(DONE, Marc)
Submitted by OpenMS Retreat on 2009-10-07 13:30:29
(DONE, Chris)
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:
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
Submitted by OpenMS Retreat on 2009-10-07 13:18:14
(DONE for centroided, Marc)
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
Submitted by OpenMS Retreat on 2009-10-07 13:16:45
(DONE, Chris)
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.
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...
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
Submitted by OpenMS Retreat on 2009-10-07 13:20:03
(DONE for centroided, Marc)
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.
Submitted by OpenMS Retreat on 2009-10-07 13:14:16
(DONE, Andreas)
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.
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:'''
'''Topics for MapAligner:'''
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.
Submitted by OpenMS Retreat on 2009-10-07 13:46:19
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:
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:
We had to use unique_id within ConsensusXML to remain downward compatible. See xml schema version 1.4.
Usage of UniqueIdAssigner is recommended!
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
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.
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.
Submitted by aiche on 2009-10-07 12:53:40
just for the sake of completeness
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.
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.
Submitted by OpenMS Retreat on 2009-10-07 13:31:30
(DONE, Stephan)
Submitted by OpenMS Retreat on 2009-10-07 13:07:44
Use Threading (DONE, Chris)
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
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
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
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]
Submitted by OpenMS Retreat on 2009-10-07 13:08:56
(DONE, Marc)
Submitted by OpenMS Retreat on 2009-10-07 13:21:51
(Chris, DONE)
Submitted by aiche on 2009-10-07 13:04:49
(DONE, Marc)
Submitted by aiche on 2009-10-07 12:55:42
Submitted by aiche on 2009-11-19 10:09:37
Commented by cbielow on 2010-04-22 15:48:29:
technical thoughts:
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).
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
Submitted by OpenMS Retreat on 2009-10-07 13:24:09
(DONE, Chris)
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.
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
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.
Submitted by hendrikweisser on 2009-11-19 10:01:25
Commented by aiche on 2009-11-19 10:02:23:
fixed in [6429] ..
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
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.
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
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
Submitted by aiche on 2009-10-07 13:02:48
dummy .. for the sake of completeness
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
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
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
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])
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
Commented by aiche on 2009-10-12 14:30:03:
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
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
Submitted by OpenMS Retreat on 2009-10-07 13:29:01
(DONE, Chris)
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
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