github.com/OpenMS/OpenMS commits | Ecosyste.ms: OpenCollective

[INTERNAL] flags changed to bool

a682aadfe40582c1381c53a26fee73ab11f836ed authored about 10 years ago by lars20070 <[email protected]>

[FIX] validate presence of input file before starting executable

5da6d82e885ae7114b18cb3d70c99cb3e03c09d1 authored about 10 years ago by Hannes Roest <[email protected]>

[NOP] remove print statement introduced in #938 by mistake

31cae73441bb1fb9332eb785c4feb63eec86e8ac authored about 10 years ago by Hannes Roest <[email protected]>

[FIX,URGENT] fixed error in knime binaries.ini for lnx systems

287c02646a078f3304cb2bf717000ce3cffbdaab authored about 10 years ago by Stephan Aiche <[email protected]>

[FEATURE] cleanup of transform functions for mzXML

4b419f73ca786e395c0892eee8ead3cc7fdf57fa authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] cleanup of transform functions for mzML

01a82adaa2e677cfacee0d56dbd5641f884f6e2f authored about 10 years ago by Hannes Roest <[email protected]>

[NOP] renamed Java class to JavaInfo

0ad0d38ebf76e134731366722a9a7fb01d39dfbe authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] test if java can be executed

cea8db25f0f9dec2b406200c0652dbd4e985e140 authored about 10 years ago by Timo Sachsenberg <[email protected]>

[DOC,NOP] fixed some copy and paste errors

598664ab86064ac4fc4ca43cb571a5251a275cbf authored about 10 years ago by Stephan Aiche <[email protected]>

[TEST,INTERNAL] added test access getMS2Identifications before a simulation was performed

* fixed segfault if getMS2Identifications but no simulation was performed

c1abd32b04703210ed0714ee523e01c7887e7164 authored about 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] move last definitions from header file

f19b307351251c58444c7035bd019100f2a1045f authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] add a low memory FileConverter option

- add a low memory option for mzXML/mzML -> mzML conversion
- add an indexed mzML option to prod...

b395845c05d091045c6af31236f480b956221066 authored about 10 years ago by Hannes Roest <[email protected]>

[TEST] extended MSSim test

919f1e4055457d808d2828ce61d4ceed2463320b authored about 10 years ago by Stephan Aiche <[email protected]>

[DOC] better error handling in TOPPDocumenter

fe5facda34f7b53f19d650680b62f9cf79c8b5fc authored about 10 years ago by Stephan Aiche <[email protected]>

improved export of ms2 ground truth

* all hits are exported in idXML scored/sorted by their intensity contribution

8a88d43de58844fbb7b2a181a7f35d0ca96cab3a authored about 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] move code to cpp file

3653689c41e8cc030c7f6648398d095823f5bf85 authored about 10 years ago by Hannes Roest <[email protected]>

Merge pull request #938 from OpenMS/feature/precursorScoring

[FEATURE] precursor scoring

ceacc013454b87ee293da41a99b71346ec2371b9 authored about 10 years ago by Stephan Aiche <[email protected]>

[TEST] add test for MSDataChainingConsumer

d43c05838f6b068d00db77d6ff16c0b8934c93d7 authored about 10 years ago by Hannes Roest <[email protected]>

[DOC] add documentation for chaining

bbfbceb31010558465213049b75ce8621d90f2fb authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] add chaining consumer

- allows to chain multiple consumers

3b56abb63dd514ea3cde0f6119cf171f516dc588 authored about 10 years ago by Hannes Roest <[email protected]>

[NOP] added explicit d'tor for IsobaricAnalyzer freeing the quant methods

ac61482732a202a5214a397d8b8a814d74fe6c7c authored about 10 years ago by Stephan Aiche <[email protected]>

[PYOPENMS] adapted pyopenms to tmt10plex related changes

0722b7e07a3d177b290b9c2d4b54a6da8107712a authored about 10 years ago by Stephan Aiche <[email protected]>

[DOC] fixed copy/paste errors in documentation

6262deb1c2a5892eecdace9965b97332b196cbd7 authored about 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #964 from aiche/fix/invalid-charge-ranges

[FIX] check for invalid charge ranges in search engine adapters (see #963)

e9147e9e01abad8af7a24fa9abdef92e30364046 authored about 10 years ago by Stephan Aiche <[email protected]>

[TEST] added an extra test for tmt10plex channel extraction, since some of the reporters are only 0.006 Th apart

02369e3723e6ea68cb0968d9d4ff5015eddf9c99 authored about 10 years ago by Stephan Aiche <[email protected]>

[FEATURE] added tmt10plex to IsobaricAnalyzer

29723353c42c501e1c1060da11e1a7dcdaa04850 authored about 10 years ago by Stephan Aiche <[email protected]>

[FEATURE] added tmt10plex quantitation method

8990c92127b83a895168747cbeb638bce32048e7 authored about 10 years ago by Stephan Aiche <[email protected]>

[FEATURE,API] extended IsobaricChannelInformation

* switched from int to String for channel name for coming support of TMT 10plex
* added specif...

79e040450a9f29ff9fc911a6adfdbed565aa3ee8 authored about 10 years ago by Stephan Aiche <[email protected]>

fixed "shadow local variable" warning

625984e1f7fdee95f1ba06d3785ced7d85ceedbd authored about 10 years ago by Stephan Aiche <[email protected]>

final commit of TopPerc

0992be41bad2cceda96ee5d17ba3255f085538db authored about 10 years ago by Andreas Simon <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into FFId

08a709c8f4fb88f7e9e42e5885e75e22db73d86b authored about 10 years ago by Hendrik Weisser <[email protected]>

[TEST] added TOPP test for search engine adapters to test the fix

67d9f5706516d36031d5002679345ff9d579e6ea authored about 10 years ago by Stephan Aiche <[email protected]>

[FIX-#963] added charge check to (OMSSA|XTandem|MyriMatch)Adapter

0bb9a6d83970faffc4c748eb49a6455bf3d2e83d authored about 10 years ago by Stephan Aiche <[email protected]>

Merge branch 'develop' of https://github.com/OpenMS/OpenMS into FFId

452057bd32b712f6c508cfc126a1b317b524335d authored about 10 years ago by Hendrik Weisser <[email protected]>

[FIX,URGENT] fixed knime binaries.ini for mac-osx knime package

d9ea5549f5c34ffb1856205ee9d432c2e0d797ca authored about 10 years ago by Stephan Aiche <[email protected]>

[FIX] fix test after correctly escaping mzML

16db46e75edfc04929a008afa727eb1e3bb71a09 authored about 10 years ago by Hannes Roest <[email protected]>

Merge pull request #962 from mwalzer/feature/QCML

[FIX] QCCalculator now computes TIC only on MS1 spectra (fixes #96)

62ebf6fc19ea4f4bd3dbd4818e571b3642a26b32 authored about 10 years ago by Stephan Aiche <[email protected]>

resolved conflicts after merge with remote

fa69cb828e4ee903991b173ed0861bc35ae4dde3 authored about 10 years ago by mwalzer <[email protected]>

[FIX]#961

f48ca97808f5f28f4498368ce4fe1aaa71cfd0f5 authored about 10 years ago by mwalzer <[email protected]>

Merge pull request #959 from hroest/feature/pyopenms_copyconstr

[FEATURE] pyopenms copyconstr

05c6de47aa98447be83db098f38fe29f06e28fa2 authored about 10 years ago by Stephan Aiche <[email protected]>

[TEST] adopt tests

cb111bf14276d07d866ab2ea659ff3a86ec0c227 authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] also adopt decoy generation (MRMDecoy)

- decoys should have a different peptide group label than targets

c1e895daa2d4389c944a9e6fceb64dbc4a6d9958 authored about 10 years ago by Hannes Roest <[email protected]>

[TEST] adopt tests

4308f5f7d60982ef9f73931b7d0fa914088253b7 authored about 10 years ago by Hannes Roest <[email protected]>

[BUILD] needs new autowrap version

ab61a6bc4a7e90d69cf321c97a04f715f15e75db authored about 10 years ago by Hannes Roest <[email protected]>

[PYOPENMS] fix copy constructors

e9dc67066a9631e16f1b4ff954a5a92ae3b2ea75 authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] output peptide group label in csv

7d25fd4c6fea0dddc1f5763d0540f5a427ac5a57 authored about 10 years ago by Hannes Roest <[email protected]>

[INTERNAL] changed default parameters

2182bb62a724e62914271900a647a92691a709e0 authored about 10 years ago by lars20070 <[email protected]>

[TEST] unused variable from test removed

2c8f3480eed9b70b581daae0d9c26dbe7649030c authored about 10 years ago by lars20070 <[email protected]>

[TEST] unused variable from test removed

a549775e8e023e4393ef077c793d1b7b11ee6447 authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] small simplification

ec3dbfa18f6dd7006008e68b2669740b0d33570c authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] replaced postfix by prefix

66b0601cfde566de6283f464ab95dfa646d56506 authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] member variables initialised in constructor

e7fc5526c0954d9efc6a1548a9cfa7396321fade authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] removed unused variables

6d78bfccb0d066f3484ea684ad5e9c4b5d0f7a04 authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] replaces some exceptions by preconditions

3f77f037fe2e28855f6a71bd2197fa006f6128a6 authored about 10 years ago by lars20070 <[email protected]>

[PARAM,FEATURE] added option to include zero-intensity points to constrain the model fitting

9a8f00ebf63f6331c29925e4b6fd963e9f6b4e0c authored about 10 years ago by Hendrik Weisser <[email protected]>

[TEST] added test files for FidoAdapter

61a28ecd9c5a6d1d35e2c4b213b0438d80dccd93 authored about 10 years ago by Hendrik Weisser <[email protected]>

[TEST] FeatureFinderMultiplex TOPP test fixed

423b55df3242325515565c4cc0a2872ddad8b71e authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] warning for unsupported knock-out and n>4

9ce1950b1c339c0482b74d51f3e963295e9cdc00 authored about 10 years ago by lars20070 <[email protected]>

[COMMENT] refactoring

184c36b0cc4ea9102404325df5c697e57d9341c5 authored about 10 years ago by lars20070 <[email protected]>

[COMMENT] comments removed

9e6c5fb898071726838580320d589bf529bc6f74 authored about 10 years ago by lars20070 <[email protected]>

[FIX,PYOPENMS] ammend 4c54109ac

- also make peptide group label accessible from Python

f42bea2ad39f8ffb4d0b2c5e977ef5ca8a33fa75 authored about 10 years ago by Hannes Roest <[email protected]>

[NOP] change macro name

- to prevent a name clash with the OpenMS PRECONDITION

6611957c0e953ea55baec7f99324545145e0c7c7 authored about 10 years ago by Hannes Roest <[email protected]>

[NOP] remove dead code

69885ef9d86802ddde76cfa34f9a563c3b97adb5 authored about 10 years ago by Hannes Roest <[email protected]>

[API] label description fixed

a3562acae4324897b8f192ab1e60fb1c88a27770 authored about 10 years ago by lars20070 <[email protected]>

[API] samples_labels_ moved to member

3aafdf17f956ac2cd5af02b2b3ad52a729f91661 authored about 10 years ago by lars20070 <[email protected]>

Merge pull request #958 from hroest/fix/threadsafe_uniqueid

[FIX] disallow concurrent access to the static PRNG (fixes #956)

e58fca531ce7cbda233b92cc28e6203e14b5346a authored about 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #955 from hroest/fix/xml_escape

[FIX] xml escape in mzML handler

01f4dbc7b6ce95d973fd72dbbe75cb5fa6ced355 authored about 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] vector initialization optimised

4c88f674bc2d0f447e927b27c97fdc02501e90c7 authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] further check for empty profile intensity vector

cdcb7ce7c133d4f4467f0cbc925f0e7f240c5a1a authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] added a check for empty profile intensity vector

d65e502338e8957369f728a1f6b7fca433bc0e14 authored about 10 years ago by lars20070 <[email protected]>

[DOC] documentation for peptide intensity correction added

f356821b46cc5e95789fc92a328ed9f4b6c31e25 authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] vector constructor changed

1beac055ed5b8f99e94dd40bbaf4e25f45991a3a authored about 10 years ago by lars20070 <[email protected]>

[FIX] last fix of mzML files

37a88d5f9d4d8561a4b68bf7309bb1d83d474f92 authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] disallow concurrent access to the static PRNG

- otherwise the same random number might be produce twice which could
lead to all kinds of apo...

dad0b983d970d45ab231c344c393767c25383bcf authored about 10 years ago by Hannes Roest <[email protected]>

[TEST] add test which checks that the produced file can read again by OpenMS

0d8524ed02b39d750a4465fe6b37dcca34319f1b authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] partial fix of #24

- fix all direct string writing in MzMLHandler<MapType>::writeHeader_
with writeXMLEscape

c3b2505788f7014f2362210aab98a67ab1cec837 authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE #802] Add parameter to define the java param XX:MaxPermSize, needed for conversion to tsv

modified: ../src/topp/MSGFPlusAdapter.cpp

0b4e0198980b855b04e783ac1dee3e0ac500235f authored about 10 years ago by Petra Gutenbrunner <[email protected]>

Merge pull request #949 from hroest/fix/xml_escape

Fix/xml escape

4c7512994bc5ad8a2e499a4d9495463d5cd29857 authored about 10 years ago by Hannes Roest <[email protected]>

Merge pull request #950 from hroest/feature/traml_heavylight

Feature/traml heavylight

45b20724cc9b19c4c22af5932bc3476e49d1b2c5 authored about 10 years ago by Hannes Roest <[email protected]>

Merge remote-tracking branch 'upstream/develop' into feature/FeatureFinderMultiplex

06068e2c341d219072c699a2ea3ce199f80fec96 authored about 10 years ago by lars20070 <[email protected]>

[DOC] adopt and extend documentation

d4b0b8103b85d974e210c4337df5240ca0254104 authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] store peptide group label also in LightPeptide

4c54109ac9388ff691305463b1017e22fb881f0f authored about 10 years ago by Hannes Roest <[email protected]>

[CLEANUP] store peptide group label as string

da8631d622c75c4baec0a8a74295255ebb862530 authored about 10 years ago by Hannes Roest <[email protected]>

[TEST] tests work

- adopt tests to reflect changes made in TransitionTSVReader

7608c47b3a64595d1aa72aa3c3d456fe65215208 authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] allow proper handling of heavy/light in TraML

- change headers to include PeptideGroupLabel and LabelType (remove
GroupLabel which was ambig...

c03266c082fa0eec8714da908538eecfdb50a5fe authored about 10 years ago by Hannes Roest <[email protected]>

Modified XTandemXMLFile for proper use of XTandemAdapter to run TopPerc on XTandemFiles

5679d3b703bf449581f1e822093bc3b616599f2f authored about 10 years ago by Andreas Simon <[email protected]>

Merge pull request #951 from hroest/fix/FileHandlerSetOptions

[API,PYOPENMS] add setOptions method for FileHandler

8b68056bb5f939e18a9790d7b639ec559b77fc39 authored about 10 years ago by Stephan Aiche <[email protected]>

[FIX] add setOptions method for FileHandler

e1b260278eda39b5727fde1ae381fde87636120d authored about 10 years ago by Hannes Roest <[email protected]>

[TEST] add test with some juicy XML to escape

aa3d9ae01ea7e8dd3ad6600053c9fbdc078ff642 authored about 10 years ago by Hannes Roest <[email protected]>

[NOP] move

5167268d42383b4042d10e35d372550bb3abb958 authored about 10 years ago by Hannes Roest <[email protected]>

[FIX,TEST] fix test after fixing xml-escape

89377095d8a3d2f6f187776221614df9f44da6a0 authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] partial fix for #24 - XML escape

71733d20fd1c1858b24b7bd0923b92a28a0765e2 authored about 10 years ago by Hannes Roest <[email protected]>

Updated Mathias Handler and TopPerc can write mzid now

90138299c9f77c4d90eb339b928d97054b4bd3b1 authored about 10 years ago by Andreas Simon <[email protected]>

[FIX]final after rebase fix

d09ca354d8c5b61cabca5ba52192046c29b1e6ad authored about 10 years ago by mwalzer <[email protected]>

[FIX] try to fix rebase conflict

276cea2ce6ab8c90449649d2a45a1b022f849147 authored about 10 years ago by mwalzer <[email protected]>

[FIX] fixed mzid searchdatabase read/write

4ba910aa4515e91e602c73cbdb73ba5ae41848d7 authored about 10 years ago by mwalzer <[email protected]>

[FIX] fixed correct number of peptideevidences

df9fa2048f5131441a6cadc0aaffeadae7cfdd16 authored about 10 years ago by mwalzer <[email protected]>

[FIX] added generic fragmentation table entry in mzid

c111d0d44da4ff054d74749d9de44fc903d499d9 authored about 10 years ago by mwalzer <[email protected]>

[FIX] mzid AdditionalSearchParams are written, redundant pepevidence

fixed, broke spectrumidentificationresult - see FIXMEs

0c48dbabd631d907758d119130332051d689543b authored about 10 years ago by mwalzer <[email protected]>

[UNKNOWN] just added debug hack in FileInfo (toberemoved! afterwards)

and some TODO comments - due to urgent workplace shift

4dc6651e61172f37a3b1bd1e99a49f866a49dd86 authored about 10 years ago by mwalzer <[email protected]>