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

Update sign_bins_and_libs.rb

7eb486f07632b4857ba47d4b2c90eedbc7566664 authored almost 5 years ago by jpfeuffer <[email protected]>

Update sign_bins_and_libs.rb

76c5d2908c45586ece3241afc76dfcaf26f741a6 authored almost 5 years ago by jpfeuffer <[email protected]>

Create sign_bins_and_libs.rb

e046ab788c3ad8f3a4c55491e8dc2765cb7e8425 authored almost 5 years ago by jpfeuffer <[email protected]>

Update package_dragndrop_dmg.cmake

f1615bdad31b17b8e31254b40ee94aa7befaa0f9 authored almost 5 years ago by jpfeuffer <[email protected]>

Merge pull request #4367 from cbielow/opt_include

minor documentation

961bbe93b24c5c5f7c79c4af261e92672ed069d8 authored almost 5 years ago by Timo Sachsenberg <[email protected]>

fix shadow warning

e56f2b69809d3a7c03eb420bcdcd34a2403b3a71 authored almost 5 years ago by Chris Bielow <[email protected]>

Merge pull request #4368 from enetz/fix/XLMS_ResLinkedFrag

[FEATURE] two fixes for the OpenPepXL pipeline

f3f398d2c91ad6c3180764dfa7bce3201f550ea9 authored almost 5 years ago by Timo Sachsenberg <[email protected]>

make QC more robust to missing data in mzML (assume CID)

0603ac8f1038ad1bab8152a490a3db2c149b03fa authored almost 5 years ago by Chris Bielow <[email protected]>

NOOP

c475ada5a795c56721f7c5a7de510a5a9e8005a4 authored almost 5 years ago by Chris Bielow <[email protected]>

better docs for AMS

667073e3f267723e876e5e1a87c66ef532e4b0ea authored almost 5 years ago by Chris Bielow <[email protected]>

Merge pull request #4363 from enetz/fix/XLMS_ResLinkedFrag

[FIX] fixed two minor issues in OpenPepXL

f34134255325add47db55511a54755c08b977fe8 authored almost 5 years ago by Timo Sachsenberg <[email protected]>

[PARAM, IO] OPXL: changed order and descriptions of output files

The order and descriptions are more in line with XFDR now and the new order reflects the likely ...

497ec11b6a107c5e68dda8719d25fa2fca1bd394 authored almost 5 years ago by enetz <[email protected]>

[TEST] updated OpenPepXLLF test file

47d0b8632ac2e6fcfd4cdca089386ebc1371a8ee authored almost 5 years ago by enetz <[email protected]>

[FEATURE] OpenPepXL: filter out some types of loop-links

These are types of loop-links that we would usually not trust after a manual validation of the s...

332f1ec14966d4c40de4d70e7968a62a50a10fed authored almost 5 years ago by enetz <[email protected]>

[TEST] updated test file

4b34c0b6f732b83b37bac409eb6cd6598e942855 authored almost 5 years ago by enetz <[email protected]>

Update notarize_app.sh

35b21e3f1711c7f01a6756853fa96f7174e88b97 authored almost 5 years ago by jpfeuffer <[email protected]>

Isotope selection refined.

9238ec7e11f1085155840c40c040f01cf054c84a authored almost 5 years ago by kyowonjeong <[email protected]>

Isotope selection refined.

94db6dcd92c87b453362e3a68dbd7d1bfe3b597b authored almost 5 years ago by kyowonjeong <[email protected]>

[TEST, COMMENT] added example calculation

7f6f5c6f55b7d13221dd4fbba8a52abdbf5d479d authored almost 5 years ago by enetz <[email protected]>

[FIX] OpenPepXL: do not add Residue-Linked ions for terminal links and mono-links

813f38f2b622c587cff2999048112fcd2e40bb1e authored almost 5 years ago by enetz <[email protected]>

[TEST] update OpenPepXLLF test file

f270465abb71a73ab469675df7abb9ea55567d91 authored almost 5 years ago by enetz <[email protected]>

[TEST] update theoretical spectra generation tests

2a44dd8699541e0454cb0c8538ac889364c394e4 authored almost 5 years ago by enetz <[email protected]>

[FIX] OpenPepXL: avoid cross-linking modified residues

6a58d2b55e0ac880eaf3d8c325a83f234a87a35a authored almost 5 years ago by enetz <[email protected]>

[FIX] OpenPepXL: fix mass calculation of a rare fragment type

a8959cac6d5c16acd912b9944d0db6ca6c8e0892 authored almost 5 years ago by enetz <[email protected]>

[FIX] OpenPepXL: fix mass calculation of a rare fragment type

9f14b3315aee2e3ca61c12bbb494152b0fdd24e4 authored almost 5 years ago by enetz <[email protected]>

Merge pull request #4295 from poshul/TMTpro

Added support for 16plexed TMT

f531f2fda5833ce1be284c50e798a0b999c0528d authored almost 5 years ago by Timo Sachsenberg <[email protected]>

Isotope selection refined.

a219e040318bcf80f298439cb66e4a0e54b2d9f9 authored almost 5 years ago by kyowonjeong <[email protected]>

Update add_mac_bundle.cmake

9f59a65001e4e92fe815975d1068f3bcf16a3520 authored almost 5 years ago by jpfeuffer <[email protected]>

Include zipping and removing in notarization script

d13eb65db2bd0562421acbaf33a612203ac9f727 authored almost 5 years ago by jpfeuffer <[email protected]>

Isotope selection refined.

1655059c1a22ea673426503568b7654bbe7d9fe1 authored almost 5 years ago by kyowonjeong <[email protected]>

Merge pull request #4360 from cbielow/opt_include

[FEATURE] InternalCalibration fallback when no calibration points

fbaecf95c307f301bccbbd6ebf4180a9aaf84e34 authored almost 5 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] allow -force for InternalCalibration (writing unmodified mzML when no calibration curve could be found)

c074a397b498c5dd614cd3e6f7bf8803964e419b authored almost 5 years ago by Chris Bielow <[email protected]>

Try adding notarization to DMG

63132d98f4adfe458ce82a6c3e960139563571da authored almost 5 years ago by jpfeuffer <[email protected]>

Add ThermoRawFileParser to packaging

db7d2520e3ee21f25b97f4751a50d87678e86474 authored almost 5 years ago by jpfeuffer <[email protected]>

Merge pull request #4356 from cbielow/opt_include

PeptideIndexer does not match all peptides to DB

14e71545e40358ff488a2622b5c97e31f4149ec3 authored almost 5 years ago by Oliver Alka <[email protected]>

Merge pull request #4355 from OpenMS/fix/thermoRFP_extension

[FIX] add exe file format to thermo raw file parser.exe parameter

3bf32aec5510faed51846a4673d33b7ea8d9cc18 authored almost 5 years ago by Oliver Alka <[email protected]>

[FIX] tests, [ADD] python bindings

be4b2856d2f6d6c2c90abe7e1ff7dfa2f413e1ea authored almost 5 years ago by oliveralka <[email protected]>

Merge pull request #4354 from timosachsenberg/feature/single_table_experimental_design

alternativly allow exeperimental design in a single table

17bf82129fbadd0a9058e01523b281c1112a47c5 authored almost 5 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4338 from oliveralka/fix/convertermode

[FIX] Remove Sirius Tmp structure in converter mode

f859b5a210131fd1c7d644719b5f8082d587637b authored almost 5 years ago by Oliver Alka <[email protected]>

fix tests

a15f5aaf16b9262caa85cb48ab1b0962410a02ee authored almost 5 years ago by Chris Bielow <[email protected]>

added filetype exe

87f0bea6f643cfb1fa0aea025a23ffb7889ff2a4 authored almost 5 years ago by timosachsenberg <[email protected]>

fix test

2878aac0dd28d5e5fdf8b48512dc4cbd95f9e994 authored almost 5 years ago by Chris Bielow <[email protected]>

[FIX] incorporate ambiguous amino acids into enzyme regex rules

845f05352272208f85ecb15899658839e5eddc26 authored almost 5 years ago by Chris Bielow <[email protected]>

removing restriction on x!tandem special cutting rule: cutting sites are now also valid in semi-tryptic and none, since peptides like

D.PTDDIYNRQDFGWSFAGYGAPIMEDD.P would otherwise not be found in semi-tryptic

47f95b5e89ee49fee977fd02a78ddcd3c22f3c2b authored almost 5 years ago by Chris Bielow <[email protected]>

remove warning

e731e762df1fd7b1cf5cdafff4e3c4ca21529c63 authored almost 5 years ago by Chris Bielow <[email protected]>

NOOP

4598b9c3d14c13726de33fa54d393fb361b493cf authored almost 5 years ago by Chris Bielow <[email protected]>

add exe file format to thermo raw file parser.exe parameter

10741d072a9eb84f50fe98e9a2b457dda1c990ba authored almost 5 years ago by Timo Sachsenberg <[email protected]>

alternativly allow exeperimental design in a signle table

e7a89d2ed00bfc71bde01b00ecd23ee17230cde2 authored almost 5 years ago by timosachsenberg <[email protected]>

[FIX] sort includes

4987f15ee74dfb6988179d1be720d50cc250cf5f authored almost 5 years ago by oliveralka <[email protected]>

Merge pull request #4351 from OpenMS/fix/order_fileconverter

[FIX] FileConverter: changes default output to mzML in KNIME

52cdec4ef735c2519b103005b84c4c74f28c803e authored almost 5 years ago by Timo Sachsenberg <[email protected]>

Update FileConverter.cpp

7dc2d4ecc42bae0daa73db48f1fbbcdee6363af6 authored almost 5 years ago by Timo Sachsenberg <[email protected]>

[FIX] FileConverter: changes default output to mzML in KNIME

b6b79aad9e45e65f05c40c28d9617241bb9a226a authored almost 5 years ago by Timo Sachsenberg <[email protected]>

[FIX] error LNK2019, windows

b01a2b980128eebc056bb5e86471ecea527548f3 authored almost 5 years ago by oliveralka <[email protected]>

[FIX] QDir; variable debug_threshold

b29cd122bd20732d35d2d813e48624456527ccc8 authored almost 5 years ago by oliveralka <[email protected]>

[FIX] includes, definitions in c'tor; d'tor, const getter const

595017accc15e22e516cf17d88de5aefc2946b7e authored almost 5 years ago by oliveralka <[email protected]>

Merge pull request #4342 from hendrikweisser/primary-run-raw

Support for raw files as primary MS runs (solves #4332)

782ded35ff32f586695e90505ba558a768d32258 authored almost 5 years ago by Timo Sachsenberg <[email protected]>

[TEST] updated tests of third party tools to support MS run information from raw files

6a9bd6e20e124e49df26ae541224726c0f0473a5 authored almost 5 years ago by Hendrik Weisser <[email protected]>

[API] updated Python bindings for class ProteinIdentification

793badf7b8832a574a389df04276df9f334e7f80 authored almost 5 years ago by Hendrik Weisser <[email protected]>

[TEST] updated tests to support MS run information from raw files

2d374e9a9b37f85df244d42775bd12d694f3f445 authored almost 5 years ago by Hendrik Weisser <[email protected]>

[TEST] NucleicAcidSearchEngine: in test mode, only store input filenames, not paths

86608e3d786dc8bc690083aabdf537041224bc5e authored almost 5 years ago by Hendrik Weisser <[email protected]>

[FEATURE] IdentificationDataConverter: better support for MS run information (raw/mzML files)

83d12384a1dec719625a0a720740cd8b5043b685 authored almost 5 years ago by Hendrik Weisser <[email protected]>

[FIX] move function in constructor; getter; fix pxd

70ec4d75940098faa6929c05637d63cbb870a7d6 authored almost 5 years ago by oliveralka <[email protected]>

[FEATURE] ProteinIdentification: support for raw files as primary MS runs

aeb3a4732f6980b09b45581d884c4acb38c57824 authored almost 5 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] use appropriate separator when creating paths for primary MS runs

78b730cc1768aa38b0e229574cb14808aa2c1de9 authored almost 5 years ago by Hendrik Weisser <[email protected]>

[API,INTERNAL] ProteinIdentification: simplified handling of primary MS run information; removed redundant overload for 'getPrimaryMSRunPath()'

aeddf67fc84b2d0fd8566ae5bbdccd6739bdf203 authored almost 5 years ago by Hendrik Weisser <[email protected]>

Merge pull request #4340 from cbielow/opt_include

[FIX] removing superfluous includes to improve compilation time

92126d291f2b00fe9be72f7dcf8c6a4fec024a71 authored almost 5 years ago by Timo Sachsenberg <[email protected]>

fix

f68b53e6e3d5defc182e23d561f83a34cb5d89ab authored almost 5 years ago by Chris Bielow <[email protected]>

apple clang fixes

4ebfa2ab94285b7c5ca12cacc724dbe2e7f80103 authored almost 5 years ago by Chris Bielow <[email protected]>

[NOP] more whitespace clean-up

351fc01cea1ee90dbe0df2386d216b0bb5a1855e authored almost 5 years ago by Hendrik Weisser <[email protected]>

[NOP] whitespace clean-up

10cf0451e1c54f347f59ced4cdf6dad41e6cca65 authored almost 5 years ago by Hendrik Weisser <[email protected]>

more fixes

cd4b0f7763042305a2f242e284d1af675a691da7 authored almost 5 years ago by Chris Bielow <[email protected]>

fix includes

2ecd4aab7b1096dc4bb6382b0eb491e5d52dbb31 authored almost 5 years ago by Chris Bielow <[email protected]>

MS2 have precursor charge mass information now.

379c03b89ac3a56a2a52428ec79ca7770749ed57 authored almost 5 years ago by kyowonjeong <[email protected]>

amend

67ac7885dd4597f70e5c178a0283d14868682212 authored almost 5 years ago by Chris Bielow <[email protected]>

[TEST] RAII des

f78f7186fe3cacd89565db4271b19a32483f8159 authored almost 5 years ago by oliveralka <[email protected]>

[FIX] removing superfluous includes to improve compilation time

eeb03758b5b617acc690dc6ad8ccaf834425df72 authored almost 5 years ago by Chris Bielow <[email protected]>

Merge remote-tracking branch 'upstream/develop' into fix/convertermode

deaf377846c5bfab2e2fed3b86ef50839450bdcc authored almost 5 years ago by oliveralka <[email protected]>

Merge pull request #4323 from cbielow/fix_swath

Fix swath

16b913ad8d6afa988431f77dce1a5dcc589958b9 authored almost 5 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4334 from OpenMS/hroest-patch-1

[FIX] Python 3 fix

e0df9f1de28e16e2d3a4b5783a3813c0bda96a92 authored almost 5 years ago by Timo Sachsenberg <[email protected]>

Merge branch 'develop' into fix/convertermode

671536518d861c36a778ff67746784ab24625203 authored almost 5 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #4336 from cbielow/TOPPBase_exefile

[FEATURE] TOPP tools can use input files which are looked up on PATH …

e574864597b047fdf0c347d852110a22273a25a7 authored almost 5 years ago by jpfeuffer <[email protected]>

fix python bindings

61f50a877aa1bb9e21d1c623544a4b2f45bd366f authored almost 5 years ago by Chris Bielow <[email protected]>

fix Qt requirement

7e7d809e97538b540c8a812a799756e85df4b8f7 authored almost 5 years ago by Chris Bielow <[email protected]>

[FIX] use const ref

b7108cdb6cb025ec17e5236828562e2b245ba62a authored almost 5 years ago by oliveralka <[email protected]>

[FIX] remove SiriusTmp converter mode

63fd896c4b3062663f6b5d23669311ab8c540d5b authored almost 5 years ago by oliveralka <[email protected]>

doc fix

439c10baf0e6def72deb43f3bbcd3f7f3609e132 authored almost 5 years ago by Chris Bielow <[email protected]>

[INTERNAL] fix doxygen

4b92400c71963dcd7034bf4ace17ddf1e1c98488 authored almost 5 years ago by Chris Bielow <[email protected]>

fixes

aaf603522922f1ac0c93cc5e8165bc61d25d4cb5 authored almost 5 years ago by Chris Bielow <[email protected]>

[FEATURE] TOPP tools can use input files which are looked up on PATH (see TOPPBasE::registerInputFile())

0c519b2e97956a2e3a6eb60713e90a2d608187aa authored almost 5 years ago by Chris Bielow <[email protected]>

[NOP] whitespace clean-up

e41cd19694be26096ff37702fd20ad015abffe5e authored almost 5 years ago by Hendrik Weisser <[email protected]>

[FIX] Python 3 fix

in preparation for newer autowrap versions, we need to fix relative imports

580903be9ecd2aaa882c64e8e6d744fa45fc0e70 authored almost 5 years ago by Hannes Roest <[email protected]>

Merge pull request #4333 from cbielow/TOPPBase_exefile

[INTERNAL] #include cleanup

c84678d801199a5f50148b3d9eff672c1d060468 authored almost 5 years ago by Chris Bielow <[email protected]>

fix tests

51699df2e62b5982474449ea75edc108ddf0b85e authored almost 5 years ago by Chris Bielow <[email protected]>

include cleanup

547d2950e850221fd444047fd19e23e107a60603 authored almost 5 years ago by Chris Bielow <[email protected]>

Merge remote-tracking branch 'JeeH-K/feature/TDdeconv' into feature/TDdeconv

11487223e36be16c39c0eef69e815d920ddc88e1 authored almost 5 years ago by kyowonjeong <[email protected]>

MS2 under construction - MS2 seems to work but did not check for large masses.

820ac14e20648c9c31977afd1fb75b749c419f68 authored almost 5 years ago by kyowonjeong <[email protected]>

[FIX] ID data conversion: better treatment of missing primary files, RT, m/z

230162f1fa296f8652d8bb2ffae6f78c00e0f306 authored almost 5 years ago by Hendrik Weisser <[email protected]>

[NOP] whitespace clean-up

78bb21e75cd04dce98e395b51e252eb36bea9bbf authored almost 5 years ago by Hendrik Weisser <[email protected]>

[FIX,TEST] OMSFile: fix problems with database keys and referencing (keys are too long for int)

ed66484293a5b12f20a9215f6f13eadd38120025 authored almost 5 years ago by Hendrik Weisser <[email protected]>

[FEATURE,IO] added option to convert from/to .oms (SQLite database) format to IDFileConverter

2891383cf7b73fcd87a7c253f438fba66b2af464 authored almost 5 years ago by Hendrik Weisser <[email protected]>