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

chore: remove commented-out code

e12d029e4f7d58c5df0fb256aecb558430437011 authored over 5 years ago by Pasquale Domenico Colaianni <[email protected]>

feat: replace string with StringList for failure messages

094db76129301fe97559303ac9f5629ec1ad69bf authored over 5 years ago by Pasquale Domenico Colaianni <[email protected]>

Merge remote-tracking branch 'origin/fix/ResidueDB' into fix/ResidueDB

bd298d3a8175931c1624f08ed15a434cd64115f8 authored over 5 years ago by timosachsenberg <[email protected]>

[FIX] removed unused and error-prone method to add custom residues on run time

e292e789e5c483b636b944e7b46a354c64fac204 authored over 5 years ago by timosachsenberg <[email protected]>

[FIX] fix AASequence string conversion

- fix bug introduced in #3969 which changes meaning of AASequence
strings

8419e6af37fb18492d6d959b915a671a078505b7 authored over 5 years ago by Hannes Roest <[email protected]>

Merge pull request #3995 from hroest/feature/pyopenms_fix

[FIX] pyOpenMS fix

8ac67c136a18791025c4f455575b4d1ef75bd242 authored over 5 years ago by Timo Sachsenberg <[email protected]>

[FIX] fix AASequence string conversion

- fix bug introduced in #3969 which changes meaning of AASequence
strings

c7adb50d9cdc53781cbb9a0bb015e657dea9ac72 authored over 5 years ago by Hannes Roest <[email protected]>

[FIX] pyOpenMS fix

a66f784ecfe827570e6b7a24c6bc8731b8ec7234 authored over 5 years ago by Hannes Roest <[email protected]>

Merge branch 'develop' into feature/aaseq_fixes

d5693489087dffb06f64c5e8115ad229ebd36ed3 authored over 5 years ago by Hannes Roest <[email protected]>

Update AASequence.cpp

74a769c36954827525079a8adfba76d59927f263 authored over 5 years ago by Timo Sachsenberg <[email protected]>

[fix] Fixed RNaseDigestion::digest performance of unspecific cleavage on long RNAs.

9d00c20ae6169bf7aeaae6611063d7e88ff243ef authored over 5 years ago by Samuel Wein <[email protected]>

Update ModificationsDB.cpp

787f11778df1492c4759512e133b65b085ec153f authored over 5 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] NucleicAcidSearchEngine: use more efficient generation of theoretical spectra

7a54d626318fcc95b7410fb1ccc30f3ab62e3af6 authored over 5 years ago by Hendrik Weisser <[email protected]>

[API] slight change in signature of function for efficient generation of multiple spectra

a7c797e8cea5e5b1abfb492e56ccc090f5b57cdf authored over 5 years ago by Hendrik Weisser <[email protected]>

[API,INTERNAL] optimized theoretical spectrum generation for nucleic acid sequences

87c8837149fa81003073acb2f7b8749eff4825bc authored over 5 years ago by Hendrik Weisser <[email protected]>

[FIX] make ModificationsDB thread safe

2456bfd2b7a88254c6f1c069b6c7381352739f8e authored over 5 years ago by timosachsenberg <[email protected]>

[FIX] remove exceptions from ModificationsDB

c5fcabfc87b30da307da33b45b24a9ea65d4a4d9 authored over 5 years ago by timosachsenberg <[email protected]>

Merge remote-tracking branch 'origin/fix/ResidueDB' into fix/ResidueDB

93d69c6b3285f25fbdadda9ad21e46b2dd93ac7a authored over 5 years ago by timosachsenberg <[email protected]>

[FIX] DOMhandler

493dfa011373c99cb047380d2bd7dad6e7e97816 authored over 5 years ago by timosachsenberg <[email protected]>

Update ModificationsDB_test.cpp

e1d796d5763446630e3c9f8582144505c6684144 authored over 5 years ago by Timo Sachsenberg <[email protected]>

[FIX] adapted use of ModificationsDB to new interface

efb4f236058163d963c0ddf91f7117ee0182c823 authored over 5 years ago by timosachsenberg <[email protected]>

DBsearchDeconvMass - adding file. in progress

461a7825cd552aa1f671771411e8a27bf3c42b8f authored over 5 years ago by JeeK <[email protected]>

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

DBsearchDeconvMass - in progress

dae49ccf7ae3a86d4fed881b500fc57840c56e3d authored over 5 years ago by JeeK <[email protected]>

Merge pull request #3977 from hroest/feature/gene

Feature/gene

8cff7009450ae1b0ef5b0cd0e13e51d80e21b728 authored over 5 years ago by Hannes Roest <[email protected]>

[FIX] make ResidueDB thread safe

5c6e53487599539aeb897140b150fbbbf3303739 authored over 5 years ago by timosachsenberg <[email protected]>

[FIX] make ResidueDB thread-safe

bbb2bc1c13d2852433bc55c2c85116d317062e5c authored over 5 years ago by timosachsenberg <[email protected]>

Update TransitionPQPFile.cpp

undo previous change

8f01e13b9b74cdc4b08f126f13a060615f8fea06 authored over 5 years ago by Hannes Roest <[email protected]>

[TEST,FIX] more updates to 'ModifiedNASequenceGenerator_test'

7d0ff88bc8c5877884d473c2c96dcd7b3f55e936 authored over 5 years ago by Hendrik Weisser <[email protected]>

[RESOURCE] moved definition of custom RNA modifications to a dedicated file; improved parsing of RNA modification data

635c9e4b5dce9720c83d2df2df472fa01ec72346 authored over 5 years ago by Hendrik Weisser <[email protected]>

[TEST,FIX] updated 'Ribonucleotide_test' to recent changes, removed dependency on 'RibonucleotideDB'

ab323945a167ea71e6b0345f848d5b3a3c588e41 authored over 5 years ago by Hendrik Weisser <[email protected]>

[FIX] initialize 'Ribonucleotide::baseloss_formula_' with a sensible (non-empty) default

8714c21f9803ab3b9ec8820290da6a7bf8829464 authored over 5 years ago by Hendrik Weisser <[email protected]>

[LOG] simplified debug output in NucleicAcidSearchEngine

5ffa8de24b71a0f81a7da1415843255dc5242ad7 authored over 5 years ago by Hendrik Weisser <[email protected]>

high mass error fixed, mass trace ppm error adopted, and code optimized..

da03187ac528fd431c3fc23a09eeebc67b5d1f17 authored over 5 years ago by kyowonjeong <[email protected]>

high mass error fixed, mass trace ppm error adopted, and code optimized..

13d7ca56a34f39c9439a4dae7eeeb85ca03bcf40 authored over 5 years ago by kyowonjeong <[email protected]>

high mass error fixed, mass trace ppm error adopted, and code optimized..

b58b1dca6e444a7a7453ff03e3687ceb5f9b2e7c authored over 5 years ago by kyowonjeong <[email protected]>

Merge pull request #3989 from OpenMS/hroest-readme

[README]

cc1257b02f203fc2ccb12f436220cccaedae3519 authored over 5 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3988 from hroest/feature/fixtest

[TEST] sort proteins

6c49dba3784f5bf101d217872841dfe870851df3 authored over 5 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #3914 from hroest/feature/pyopenms_string

Feature/pyopenms string

f3d67cb2050a501358dfbb61e7f60cc7640506aa authored over 5 years ago by Timo Sachsenberg <[email protected]>

min mass error fixed!!!!!

97220262099ec59eff9d482486506b2c6169fbba authored over 5 years ago by kyowonjeong <[email protected]>

min mass error fixed!!!!!

40402287bf648d06de5ffda595f28b09542bed35 authored over 5 years ago by kyowonjeong <[email protected]>

min mass error fixed!!!!!

293ccbac15221f6359fe0368e1de15c5614e5ab3 authored over 5 years ago by kyowonjeong <[email protected]>

[README]

make it as easy as possible to cite us

5c518e4fd24e029772318e84e3b8238b9084610b authored over 5 years ago by Hannes Roest <[email protected]>

min max charge output

c702c0742f0a128cf91a30169dee382e80548571 authored over 5 years ago by kyowonjeong <[email protected]>

min max charge output

844ad0c1deab4d8bb78f417803ed217ab4d5e979 authored over 5 years ago by kyowonjeong <[email protected]>

[TEST] sort proteins

ea68f104acb6d666f5aa414fd948237d246d16f1 authored over 5 years ago by Hannes Roest <[email protected]>

parameter optimized

88340a04e78932c7f91495ca9101b25172dde464 authored over 5 years ago by kyowonjeong <[email protected]>

[FIX] add some fixes to tutorial

70c4940eef30e2d7d72f6ace4d81e9577144a9fa authored over 5 years ago by Hannes Roest <[email protected]>

[TEST] test fixes

c9128f3b170cbd18abb41001e4cbeccd6a241fd5 authored over 5 years ago by Hannes Roest <[email protected]>

[FEATURE] DataValue conversion for unicode

0c621f79127bf74a381fcf39d0ab2c082f31e043 authored over 5 years ago by Hannes Roest <[email protected]>

parameter optimized

3be267ad39c72e25ce5c10ac759d0700855d789e authored over 5 years ago by kyowonjeong <[email protected]>

mass trace bug fixed

7a822f5a0146b3d2eabc964965e7f7575b1140ad authored over 5 years ago by kyowonjeong <[email protected]>

Merge branch 'develop' into feature/pyopenms_string

add20aa647a6f6495144e53a0d3624bcba51ca9a authored over 5 years ago by Hannes Roest <[email protected]>

mass trace merge success!!!!

3bc667f558fb4a88fd5276a5aab59495d22a4b92 authored over 5 years ago by kyowonjeong <[email protected]>

mass trace merge success!!!!

bc3c1998e33d5f7064248a0f20f193ce913b1d12 authored over 5 years ago by kyowonjeong <[email protected]>

a bit speed up..

2ed3199a19a0dc72990852a748b3a294bd8354d4 authored over 5 years ago by kyowonjeong <[email protected]>

union of mass bins across 10 spectrum.

b16d7f8812ebd702f5c356c475885cf040d83aed authored over 5 years ago by kyowonjeong <[email protected]>

harmonic artifact wash out using isotope and charge peaks

currently 2,3,5 artifacts are removed..

cb19b5760171b2be6394c153ac524bc9e57e9b4b authored over 5 years ago by kyowonjeong <[email protected]>

harmonic artifact wash out using isotope and charge peaks

currently 2,3,5 artifacts are removed..

9c0b620c7a2254df42f70b217880e9d7cc4c7cb7 authored over 5 years ago by kyowonjeong <[email protected]>

harmonic artifact wash out using isotope and charge peaks

currently 2,3,5 artifacts are removed..

e69688badc7051a1e25d7720d7d6598836744c7f authored over 5 years ago by kyowonjeong <[email protected]>

mass count bug fixed

ff75a74e26ad1170f1bd91d291b0cb1524866ca5 authored over 5 years ago by kyowonjeong <[email protected]>

Apply suggestions from code review

47b211ae79781ca9eaf8792b5926e33471776772 authored over 5 years ago by Hannes Roest <[email protected]>

Merge pull request #3985 from OpenMS/hroest-patch-5

Update Ribonucleotide.pxd

f87be33d76f1a26d34c82cab69d80fe6ddaf83a6 authored over 5 years ago by Hannes Roest <[email protected]>

Merge pull request #3984 from OpenMS/hroest-patch-4

[FIX] switch to boost regex

fb4d64e5959786d1b55b534d76269e745d653c8b authored over 5 years ago by Hannes Roest <[email protected]>

Revert "[BUILD] travis cache restart"

This reverts commit 89c5cd7f2d9d343b3d63fc6bab18e08dcd969c05.

01cc38e3a5db926624d2b73d6606274fb7958ce8 authored over 5 years ago by Hannes Roest <[email protected]>

Update Ribonucleotide.pxd

1d588486da0785daa51496f05fb9c46f66a0d311 authored over 5 years ago by Hannes Roest <[email protected]>

Merge pull request #3758 from OpenMS/feature/move_semantics

Feature/move semantics

9add291c13ec6490347253126aef3fc90f73d159 authored over 5 years ago by Timo Sachsenberg <[email protected]>

[BUILD] travis cache restart

- only build TOPP tools in order to reset the ccache and allow travis to
complete an OpenMS bu...

03d41744c77a07515a286b8cf2e491150931c693 authored over 5 years ago by Hannes Roest <[email protected]>

mass count bug fixed

0c14087f2385ff6bae6f393c9f8c5f744e087973 authored over 5 years ago by kyowonjeong <[email protected]>

mass count bug fixed

48e33b456db7fc60243f06e33dd07b6e086d2dd6 authored over 5 years ago by kyowonjeong <[email protected]>

Merge remote-tracking branch 'origin/develop' into refactor/AssayGeneratorMetabo

2724744e2327b027b54599c2e57bfc0c77d81a20 authored over 5 years ago by oliveralka <[email protected]>

[ADD] PQP support - some cleanup

966f1704c13215e0e80726c1e8e0a06405612f41 authored over 5 years ago by oliveralka <[email protected]>