UpcomingRelease

Upcoming Release: OpenMS 1.8

Status: closed (79 matches)

Ticket Summary Owner Type Priority Component Version

#27
generate publication ready figures in SVG format - 1D view first
all
task
major
TOPPView

#66
"Tools -> Go to" coordinates should default to current view
all
enhancement
major
TOPPView

#71
MapAlignmentAlgorithm: transforming feature map doesn't affect unassigned peptides
all
defect
minor
OpenMS - library
1.7

#84
MascotAdapterOnline reveives empty or incomplete MascotXML files
andreas_bertsch
defect
critical
TOPP
1.7

#100
rework data management
timosachsenberg
enhancement
critical
TOPPView

#102
"File changed - update layer?" only works once
all
defect
minor
TOPPView

#103
Drag and Drop for TOPPAS
johannes_junker
enhancement
major
TOPPAS
1.7

#105
Split TOPPAS.ini into Resource and Workflow files
johannes_junker
enhancement
major
TOPPAS
1.7

#107
Workflow export into ActiveBPEL
johannes_junker
enhancement
major
TOPPAS
1.7

#125
When switching between tabs, items move towards the bottom-right corner of the view
johannes_junker
defect
major
TOPPAS
1.7

#129
Allow opening files in one layer
timosachsenberg
enhancement
major
TOPPAS

#149
Support external tools not derived from TOPPBase
cbielow
enhancement
major
TOPP

#150
TOPPAS does not use user environment to find executables...
johannes_junker
defect
major
TOPPAS

#153
"Unlabeled" FeatureLinker produces quality values that make no sense
hendrikweisser
defect
minor
OpenMS - library

#160
INI files stored from TOPPAS are incomplete
johannes_junker
defect
major
TOPPAS
1.7

#162
Merge Node stops pipeline execution prematurely
johannes_junker
defect
major
TOPPAS
1.7

#168
OpenMS/TOPP fails to compile
all
defect
major
OpenMS - library

#172
Too general .svn exclusion rule
cbielow
defect
minor
Build System
1.7

#173
Error creating OpenMS export file
cbielow
defect
major
Build System
1.7

#174
Installation expects documentation to be built
cbielow
defect
major
Build System
1.7

#179
adapt to command/console width
cbielow
enhancement
minor
TOPP

#180
FileConverter silently fails when it should report "out of memory"
cbielow
defect
minor
TOPP
1.7

#181
Check output to stdout/stderr
all
defect
major
TOPP

#191
changing from 1D to 2D,3D View and 3D to 2D if MS1 spectra are present
timosachsenberg
enhancement
minor
TOPPView

#196
NoiseFilter, PeakPicker, BaselineFilter crash on certain input-data
cbielow
defect
minor
TOPP
1.7

#198
add Proteowizward to Windows binary installer
cbielow
enhancement
major
TOPP

#202
"Open file" dialog: "readable files" should include .gz files
cbielow
defect
minor
TOPPView

#204
TOPPView "Go To" Dialog should support UniqueID's
cbielow
enhancement
trivial
TOPPView

#206
Parameter names should include subsection
cbielow
defect
major
TOPPAS
1.8

#207
Projections show wrong axis names
cbielow
defect
major
TOPPView
1.7

#208
Windows: hide extra console window when starting GUI apps
cbielow
defect
major
TOPPView
1.7

#211
TOPPAS: IDFilter RTPredict link not possible
cbielow
defect
minor
TOPPAS

#213
TOPPView crashs when loading mzML and featureXML
timosachsenberg
defect
critical
TOPPView
1.8

#214
MapAligner crashes on certain data
cbielow
defect
major
OpenMS - library
1.7

#215
FeatureFinder crashes with Segmentation fault
aiche
defect
critical
OpenMS - library
1.7

#216
FileConverter stops working without any error message
aiche
defect
major
TOPP
1.7

#217
Caching in LogStream is not thread safe
aiche
defect
critical
OpenMS - library
1.7

#218
FF should work on non-sorted data, but gracefully exit on negative m/z values
cbielow
defect
major
OpenMS - library
1.7

#220
mzML.gz files are not recognized as correct input
andreott
defect
major
TOPPAS

#221
TOPPView: when loading a new layer, the zoom should not reset
all
defect
minor
TOPPView
1.7

#222
IDMapper should support mapping charge-matched entities only
all
defect
major
OpenMS - library
1.7

#223
TOPPAS restores wrong parameter name when deleting an input/output edge
cbielow
defect
major
TOPPAS

#224
PepXMLFile produces invalid files (mod_aminoacid_mass position is 1-based)
aiche
defect
blocker
OpenMS - library
1.8

#225
msInspect pepXML parser can not handle OpenMS pepXML due to massdiff attribute
aiche
enhancement
major
OpenMS - library
1.8

#229
Digestor UTIL cannot write FASTA output
cbielow
defect
trivial
UTILS
1.8

#231
FeatureFinder has faulty Averagine model
cbielow
defect
critical
OpenMS - library
1.7

#233
TOPPView's updateLayer does not reload all data
all
defect
minor
TOPPView
1.7

#235
TOPPAS input file name lists should be sorted
cbielow
enhancement
minor
TOPPAS

#237
RT corrections via BSpline transformation is unreliable for sparse regions (e.g. borders and extrapolation)
cbielow
defect
major
OpenMS - library
1.7

#239
seg. fault when loading featureXML into TOPPView from the wrong context
herrzweiblum
defect
minor
TOPPView
1.8

#241
query_charge element of MascotXML not read
all
defect
major
OpenMS - library
1.7

#242
Protein coverage should be reported
cbielow
defect
minor
(Unit) Tests

#243
(Thresholded) clustering faulty
cbielow
defect
major
OpenMS - library

#244
merging by Precursor in SpectraMerger
cbielow
defect
minor
OpenMS - library

#245
PeptideIndexer fails on ambiguous AA's
cbielow
defect
critical
OpenMS - library

#246
TOPPView: Update Layer broken
all
defect
minor
TOPPView

#247
TOPPView: crashes if file is deleted while opened
all
defect
minor
TOPPView
1.7

#249
INIFileEditor deletes certain tags in INI files
cbielow
defect
critical
OpenMS - library

#251
XTandem Adapter ignores "no_refinement" flag
cbielow
defect
major
TOPP
1.8

#252
OMSSAAdapter crashes when v2.1.7 and 'precursor_mass_tolerance_unit_ppm' are used
cbielow
defect
minor
TOPP
1.7

#253
TOPP tools should be able to write their type into ini file, without knowing it a priori
cbielow
defect
minor
TOPP

#255
TOPPView's Projection is showing only single peaks at high zoom
cbielow
defect
minor
TOPPView

#257
CLang++ crashes with "SCEVAddRecExpr operand is not loop-invariant!" on EnzymaticDigestion
cbielow
defect
major
OpenMS - library
1.8

#258
FileFilter in TOPPAS defect
all
defect
minor
TOPPAS
1.7

#260
InclusionExclusionListCreator incompatible and lacking features
cbielow
defect
critical
TOPP
1.7

#261
ProteinQuantifier: handling of mod. peptides during protein quantification
hendrikweisser
defect
major
OpenMS - library
1.7

#262
PrecursorIonSelector handles input/output arguments incorrectly
aiche
defect
major
TOPP
1.7

#263
PrecursorIonSelectionPreprocessing dbPreprocessing crashs
aiche
defect
major
OpenMS - library
1.7

#266
TOPPAS "store" button for vertex' INI files always writes default INI
cbielow
defect
major
TOPPAS
1.7

#267
bug in StablePairfinder (distances)
hendrikweisser
defect
major
OpenMS - library

#269
OMSSAAdapter crashes when run from directory containing spaces
cbielow
defect
major
TOPP

#271
Filename generation in TOPPAS broken
okohlbacher
defect
critical
TOPP
1.8

#272
TOPPAS doesn't update the tab title after saving a new pipeline
aiche
defect
major
TOPPAS
1.8

#273
TOPPAS appends an extra "toppas" when saving files with uppercase TOPPAS extension
aiche
defect
trivial
TOPPAS

#276
Param::remove() and ::removeAll() broken
cbielow
defect
major
OpenMS - library

#277
Crash upon identification annotation
cbielow
defect
major
TOPPView
1.7

#278
TOPP tools believe what the INI files tells them
cbielow
defect
critical
OpenMS - library

#279
ExecutePipeline: documentation incomplete
cbielow, nilse
defect
critical
TOPP
1.7

#281
Parameter "include_all" in ProteinQuantifier erased
all
defect
critical
TOPPAS
1.7