forked from OpenMS/OpenMS
-
Notifications
You must be signed in to change notification settings - Fork 0
/
CHANGELOG
1415 lines (1292 loc) · 73.4 KB
/
CHANGELOG
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
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
------------------------------------------------------------------------------------------
---- 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