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

[INTERNAL] allow for SplinePackages with just two data points

018182bc8f67c20412367e2e6c80cc928d6ff53e authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] allow for SplinePackages with just two data points

8a3a242b3245c4b650b28b9011188a64ba5d0eb9 authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] typo fixed

441c9d089668d6d5b98a32bbaedfa8bf410a2b7f authored about 10 years ago by lars20070 <[email protected]>

[FIX] MzIdentML fixed RT as cv missing linebreak write

d38bc7f2edf51d33e6156682990798521ac4e9f9 authored about 10 years ago by mwalzer <[email protected]>

[INTERNAL] CubicSpline2d constructors now require two or more datapoints

575f09e7f47196b3a2fc115d8be7849c303839e3 authored about 10 years ago by lars20070 <[email protected]>

[FIX] MzIdentML SpectrumIdentificationItems now under the same SpectrumIdentificationResult if from the same PeptideIdentification

625f8b3d04b3231bb5a77733fafb91264634e3ec authored about 10 years ago by mwalzer <[email protected]>

[FEATURE] sort spectra and chromatograms on loading (mzML, mzXML)

7a955640c08b43e4402f843254fbafcb475d1b1c authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FIX] fixed mzidentml read for xtandem results, fixed retention time keeping (not explicit in schema 1.1 - opt. in 1.2), now as cv of SpectrumIdentificationResult, evened out spectrum id capture

c12613efa611f352f3790cbe466a2cfacc1c08e1 authored about 10 years ago by mwalzer <[email protected]>

[FEATURE] added mzid capabilites to IDFilter

74f8b2c8f711e3e4d19d4dd6bf0892f8ceed018d authored about 10 years ago by mwalzer <[email protected]>

[FEATURE] added mzid capabilites to XTandemAdapter

d4bfe2387636feee07d0be08017ffc1c3c0962ce authored about 10 years ago by mwalzer <[email protected]>

[FIX] fixed mzidentml write fpr xtandem results, added percolator as 'searchengine', fixed retention time keeping (not explicit in schema 1.1 - opt. in 1.2), now as cv of SpectrumIdentificationResult, evened out spectrum id capture

9964aa884e6070881852e99868780acb7f03d54f authored about 10 years ago by mwalzer <[email protected]>

[FIX,PYOPENMS] pyOpenMS fix after #988

590ebf1112ca1fec1fdb2b5857111b05abf4cdca authored about 10 years ago by Hannes Roest <[email protected]>

[FIX,PYOPENMS] pyOpenMS fix

8141aed1227d399b0fa1ec066736e4760f9853e6 authored about 10 years ago by Hannes Roest <[email protected]>

[TEST] FeatureFinderMultiplex TOPP test fixed

b1e45dd8c25bf38d5d133f0b4454b033f296392c authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] bounding boxes of mass traces corrected

d3446e18b920bbd1db01dde4cd77a4f82ad56157 authored about 10 years ago by lars20070 <[email protected]>

[FEATURE] added nX method to BSpline2d wrapper class

63fbba0decb78307528b30aa85c407d629a0b130 authored about 10 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #988 from timosachsenberg/feature/EmpiricalFormula_refactoring

[FIX,FEATURE,API] simplified EmpiricalFormula

9c929806c2c5ba867be476e3e035d6e1ae504bec authored about 10 years ago by Stephan Aiche <[email protected]>

minor fix for lib arch check (removed invalid space in regex)

4c72821bd5b302946506974eb60c56b557ec9f36 authored about 10 years ago by Chris Bielow <[email protected]>

[FIX] replaced string conversion by appropriate test

ddba6db7d9969e465d4365d3289381499407405e authored about 10 years ago by Timo Sachsenberg <[email protected]>

[INTERNAL] made typedef more OpenMS like

a6ddfac790b20cef4b44f24b1092585d75fdd09d authored about 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] further cleanup and speed-improvements of EmpiricalFormula

7afff081fc492cd15954233948cf3b6486e59c42 authored about 10 years ago by Stephan Aiche <[email protected]>

[FIX] simplified EmpiricalFormula

f9cfd1269c268a72c835c2d0da3f0094cd78adae authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FIX]made sure start/end positions get read and written if available in mzidentml

a29fd981c92297cc7bc03b98692f8f6d88d540b2 authored about 10 years ago by mwalzer <[email protected]>

[BUILD] fixed small error in install targets

201a3f3a4d188acae499bf040cafefda0789df9a authored about 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #7 from timosachsenberg/feature/eol-bsplines

[FEATURE] wrapped diagnostic ok() function of eol-bspline

f18f8dc17181080e7e512f7a323e11e346c868d1 authored about 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #2 from AndSi/feature/TopPerc

testing pull rq from AndSi:feature/TopPerc to mwalzer:testing/MZID

133ede9830009d2861d964c5405730aee6d51e5e authored about 10 years ago by Mathias Walzer <[email protected]>

[FEATURE] wrapped diagnostic ok() function of eol-bspline

9f5ec3b9fa6f1cbf58db880ffc48394a91961b02 authored about 10 years ago by Timo Sachsenberg <[email protected]>

[PYOPENMS] fixes IsobaricQuantifierStatistics pxd

0418bcc2eabae2c846ed20ea8a756cf274081c18 authored about 10 years ago by Stephan Aiche <[email protected]>

[NOP] removed unnecessary include

d9268826e2355425f4412aeed652a40d739d93f0 authored about 10 years ago by Stephan Aiche <[email protected]>

[FEATURE,TEST] restructured/added/extended tests for TransformationModels

* the new tests ensure gsl compliance for the TransformationModelInterpolated

9189fe8cd37df4c3923223a3b0834ecd3366f877 authored about 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #969 from OpenMS/feature/LowMemFileConversion

[FEATURE] add a low memory FileConverter option

4684ebbe8a7eec06fcfa2f557f7462ef147c76c4 authored about 10 years ago by Stephan Aiche <[email protected]>

[FIX] fixed metadata write, now as cv if in obo - also fixed score read (cast error with DataValue)

1c1926372bcfbeed83a8877aa4969e497b0b1211 authored about 10 years ago by mwalzer <[email protected]>

[FIX] set score from evalue to first search engine specific score for peptides and set setHigherScoreBetter(true) for mzid readin

48d01e88bb7abbcc7033c20c3d4dd201f9a7b68e authored about 10 years ago by mwalzer <[email protected]>

[FIX] added setHigherScoreBetter(false) and score_type_ e-value for mzid readin

22518790181bedac7f0f9efcbbf7da92fe6b0c9f authored about 10 years ago by mwalzer <[email protected]>

tested under Windows (success); added some TODO's (e.g. current calling method not robust against spaces in path)

a0dbe35608e048dc7df1865afe69b01582d45a37 authored about 10 years ago by Chris Bielow <[email protected]>

[FEATURE] added basic linear interpolation

57c14343baa13936761d41a74ac162b953ceb910 authored about 10 years ago by Stephan Aiche <[email protected]>

[FEATURE] added Akima interpolation

50f06f6ff3835ff78d173a11b250de6028b51716 authored about 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] some more code cleanups

7502fbe0c228a96138290d415bed95a2fc7ef6d2 authored about 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] moved interpolation implementation into a separate class so we can add the missing ones more easily

cfdd6094e0194bb82d41338a89f7c29726455980 authored about 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #984 from lars20070/fix/methylSILAC

[NOP] add heavy methyl SILAC labels to unimod.xml

15aee66ff708cba896f65679c541e793fd817222 authored about 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #983 from cbielow/feature/lib-arch-check

[FEATURE,BUILD] add library check on Windows for correct lib arch

aab80b50ab2fc9578ad41f6fa07d94837b6f9104 authored about 10 years ago by Stephan Aiche <[email protected]>

[FEATURE] add library check on Windows for correct lib arch (avoid nasty linker errors)

b5a1c04d07678a35fa85aedede29650eb8d358aa authored about 10 years ago by Chris Bielow <[email protected]>

[BUILD,TEST] updated cppcheck module

3a1145423022986ba6e650ec43431d1533cdd97a authored about 10 years ago by Stephan Aiche <[email protected]>

[TEST] added ignore for 3rdparty parts of OpenMS

561344ca2ddf93ba4b5c0a70d75c1166229f0920 authored about 10 years ago by Stephan Aiche <[email protected]>

[TEST] fixed unused variable warning/error in BSpline test

6d001c1037c1930be2647589b3c7355d25c0fd36 authored about 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #977 from aiche/feature/pphires-customizable-mslevels

[FEATURE] replaced pphires ms1_only flag with ms_levels parameter

d8dac15caaf38f04a45c09b2a1b059f6902743c8 authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] potential quick fix for #986

7c2d1ed42924adfce65e8430243a9f110565e35f authored about 10 years ago by mwalzer <[email protected]>

[FIX] fixed use of undeclared identifier error in eol-bspline

see http://clang.llvm.org/compatibility.html#dep_lookup_bases

8b0065765ad9238d86a64ee807a89e054b5c2a2c authored about 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] moved TransformationModel implementations to individual files

963803b2405d6b21ea21c3453572564145934390 authored about 10 years ago by Stephan Aiche <[email protected]>

[TOOL] fixed create_class.rb script w.r.t. to new directory/build-system layout

1cd2b45b0218d84c9419a2dca7a178f89347efc8 authored about 10 years ago by Stephan Aiche <[email protected]>

[RESOURCE] site R added to unimod #199 and #510

d17cce6a6177b492f32fab30383f42a565fe8023 authored about 10 years ago by lars20070 <[email protected]>

Merge pull request #6 from timosachsenberg/feature/eol-bspline

[TEST] added bspline derivative and coefficent test

cdccfc857c248f9ba01ae5d1de1a135299e479ae authored about 10 years ago by Stephan Aiche <[email protected]>

[TEST] added bspline coefficent test

8cbc0a4a642987826e51b240780eecd85a73f74e authored about 10 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5 from timosachsenberg/feature/eol-bspline

[TEST] extended tests for BSpline2d

f1b1d60dfe41490767cd45c87595836312ce2120 authored about 10 years ago by Stephan Aiche <[email protected]>

AccurateMassSearch improvements

565bafe52691df8bc61c949331a313e2e4898508 authored about 10 years ago by Chris Bielow <[email protected]>

[TEST] extended tests for BSpline2d

30439b7c16c2511ec5abad00b3e03adc908f7d52 authored about 10 years ago by Timo Sachsenberg <[email protected]>

[Feature] Added mzid read capabilities to FalseDiscoveryRate

abea458c316f6314ec72b76dd57e5844d36ad506 authored about 10 years ago by mwalzer <[email protected]>

[FEATURE] export PT value analogous to predicted rt value in TextExporter

f26645e19d4d11c90f6a10a66b1851017bbf4631 authored about 10 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #981 from timosachsenberg/feature/TextExporter_mzML

Feature/TextExporter_mzML

ea65eb43bd862849b1ac3cc090d2f83f967adb3a authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] FeatureFinderMultiplex tests fixed (ignore local file pathin xml)

34b1d3ba0db457cdba5320c9854b98cf062a8a56 authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FIX] fixed missing namespace

1de3e1f4b82ea47350039d1a851e0a2e218154ee authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FEATURE] added level, rt, prec. mz, number of peaks to export of normal spectra

f3ef3cc3b38db6f99c45559011d5a4c6f036629f authored about 10 years ago by Timo Sachsenberg <[email protected]>

[FIX] fixed msvc/gcc45 compile issue in MSSim_test

0d33fa16faf272f77e8ff1f0e9e230dcc5b9a149 authored about 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #966 from hroest/feature/ChainingConsumer

[FEATURE] chaining consumer

08c99a5a8d38002715bba61b64c642d8064f1684 authored about 10 years ago by Stephan Aiche <[email protected]>

[PARAM] parameter renaming: 'detect:mode': 'filtered' is now 'detect:algorithm': 'iso_match'

8bfa5666cb59f2fca179b9a70f435097c9151190 authored about 10 years ago by Hendrik Weisser <[email protected]>

[FIX,LOG] fixed bug in 'filtered' feature detection (selection of matching points); added debug output; cosmetic changes

c909ea686ef443768942d7d2ca566121cee22ae4 authored about 10 years ago by Hendrik Weisser <[email protected]>

[FIX,PARAM] use 'max_gap' parameter for feature detection; removed unneeded parameter 'fraction' of 'findNextExtremum_'

09ebbbbeea7741e76870c672902bbe7892e86433 authored about 10 years ago by Hendrik Weisser <[email protected]>

Merge pull request #967 from aiche/feature/mssim-more-ground-truth-in-idXML

[FEATURE,TEST] mssim more ground truth in id xml

b19c163cb8b2920b1f816ec521379e758072267f authored about 10 years ago by Hannes Roest <[email protected]>

[PARAM] changed default value for 'add_zeros' parameter (decreasing its influence)

68d2fd59473a3fcd51d7639e710b55b366c750ee authored about 10 years ago by Hendrik Weisser <[email protected]>

Merge pull request #972 from hroest/fix/FileCleanup

Fix/file cleanup

b62adfa7537d9690eb72b49a525f06b3cde2891d authored about 10 years ago by Hannes Roest <[email protected]>

[NOP] fixed cppcheck performance warnings

1dc92ef785d2562a7d20150ab78d5833ba9fa139 authored about 10 years ago by Stephan Aiche <[email protected]>

wrapped bspline2d functionality and added test stub

e76ffa5c76f1e4a7a520d16fb009ab02bdc410a6 authored about 10 years ago by Timo Sachsenberg <[email protected]>

[INTERNAL] added BSpline2d draft to test eol-bspline usage

509ae5e0713d0a61e1a0936b26cb12ffac46bd94 authored about 10 years ago by Stephan Aiche <[email protected]>

[BUILD] added eol-bspline to openms as PRIVATE dependency

876966e7efaf4364ec96992da99e695fed1a4815 authored about 10 years ago by Stephan Aiche <[email protected]>

[DOC] updates to mac install documentation

5c2dbad4fb6409d9a5e85627d33dc69a781af7dc authored about 10 years ago by Stephan Aiche <[email protected]>

[BUILD] added eol-bspline sources to src/openms/3rdparty

697fb70b86236600e46a9ada5b0e96b1b84dd659 authored about 10 years ago by Stephan Aiche <[email protected]>

[BUILD] added PRIVATE_INCLUDES argument to openms_add_library

* PRIVATE_INCLUDES will not be exported

0901f767a41934be80a10bd4afe12efcf1bb77df authored about 10 years ago by Stephan Aiche <[email protected]>

[DOC] documented param change in changelog

cbf7a86ce1bdc328a67719443de6d92aac3865aa authored about 10 years ago by Stephan Aiche <[email protected]>

[PARAM,TOPP] removed ms1_only parameter and replaced with ms_levels

d78263fccf86bb1b9a3fc3de216b37afa339534a authored about 10 years ago by Stephan Aiche <[email protected]>

[FEATURE] added option to PPHiRes to specify which ms levels should be picked

77d1f1588daa6a8bb91b2216874f0895b16c192b authored about 10 years ago by Stephan Aiche <[email protected]>

[TEST] added test for selecting spec levels when picking

58dc599db9102e45f573ecbdbfc70b06245566b4 authored about 10 years ago by Stephan Aiche <[email protected]>

[HOTFIX] fixed invalid path in sources.cmake

59057cceb8a0ca60aad4f18a11ecf97ce55201d9 authored about 10 years ago by Stephan Aiche <[email protected]>

[HOTFIX] fixed win compile error in FFMultiplex

e89278137b3c9bde69e6bb422e082ebba21e6d22 authored about 10 years ago by Stephan Aiche <[email protected]>

[TEST] add test data

1db3948ae5044dd8ad89aefa61ca4fff7829822f authored about 10 years ago by Hannes Roest <[email protected]>

[TEST] add test

d0a6277151caec6ccb0452df7554dbd75b734e48 authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] add util to cluster mass traces

0f22f1a76b174bbb069436ecda63a7c157257ec8 authored about 10 years ago by Hannes Roest <[email protected]>

[FEATURE] add masstrace correlator code to OpenMS library

f9dcdbe96404b8b56523327cd0a4cc97a07f7960 authored about 10 years ago by Hannes Roest <[email protected]>

[NOP] small fix of OpenSwath error message

882739c553e0ebfe192636f559e78974dd546630 authored about 10 years ago by Hannes Roest <[email protected]>

Merge pull request #960 from hroest/feature/peptide_group_label_new

[FEATURE] peptide group label new

d0d69dd5695c5901052c322fe70fb33d305128b3 authored about 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #947 from lars20070/feature/FeatureFinderMultiplex

[FEATURE] FeatureFinderMultiplex

201842f267fb1b4daccca5f295d7111f5f1dce2f authored about 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #970 from timosachsenberg/feature/DetectJava

[FEATURE] test if java can be executed

d21522489392777daaacac1e062b52c6b136a668 authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] Python fix

4909c3ab3a528325e719c14986c50b4b70fb6610 authored about 10 years ago by Hannes Roest <[email protected]>

Merge pull request #973 from hroest/fix/InputFileFix

[FIX] validate presence of input file before starting executable

9b69778f94c910a3153f84eb9f1809649c954a39 authored about 10 years ago by Hannes Roest <[email protected]>

[DOC] fix docu

fix error in the docu

3aa60ec1c9e6b9eee26ef291f622c369f59bd28e authored about 10 years ago by Hannes Roest <[email protected]>

[STYLE] style fix

e71e09700695ac2a30a4cee82000a893e75205ec authored about 10 years ago by Hannes Roest <[email protected]>

Merge pull request #965 from aiche/feature/tmt-10plex-support

[FEATURE] tmt 10plex support

8de54091d2b071fe963845329755e95b9c5ddfc4 authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] add LOG_INFO

b8b425001a0add2ec27cb87af33e093b8edbad48 authored about 10 years ago by Hannes Roest <[email protected]>

[NOP] whitespace changes

3dc96d729dcef93617a99adc9bf02951e8e09b0e authored about 10 years ago by Hannes Roest <[email protected]>

[NOP] whitespace changes

b268504740b411ca6a5ec865fe549d6bcf2b0765 authored about 10 years ago by Hannes Roest <[email protected]>

[INTERNAL] flags changed to bool

ee6e9ec4e777623423f75633f8e38f1014e07f2d authored about 10 years ago by lars20070 <[email protected]>