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

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

and some TODO comments - due to urgent workplace shift

76f3b848eab8b61b8478ec4422c12ce258632113 authored about 10 years ago by mwalzer <[email protected]>

[TEST] tests with sine added

f4a3d4a1030bd94d630fb7652913e8399b8a16dd authored about 10 years ago by lars20070 <[email protected]>

[FIX] corrected mzid header write (id & date)

7d847ad8a6d32afdd8be2319da22f4817f53eead authored about 10 years ago by mwalzer <[email protected]>

[TEST] now non-zero intensity at right boundary of test interval

7a1de17badc3ab13f25aefc40510db75aefc3f64 authored about 10 years ago by lars20070 <[email protected]>

[Feature] added MetaInfo objects to the userparams and the other way

around for mzid write/read

691a9b1f33a06bc32373653aa5afd8306ae57553 authored about 10 years ago by mwalzer <[email protected]>

[FIX] switched to mzid stream writing, first attempt to handle a huge

family of errors with cv/user params in very custom mzid files

12f638015226747297fdd358993c1e697b55a1f0 authored about 10 years ago by mwalzer <[email protected]>

[INTERNAL] fix for evaluation at last node

7983e67c02c5bcc28da4520c4c500d21121e857b authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] minor fix

5a9b36af8df819f67794b5871e5343e9421e6874 authored about 10 years ago by lars20070 <[email protected]>

[DOC] debug removed

cfedbaf6620125870f5d5e01b48f8766b1738a37 authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] debug output fixed

5dc0e101f492c0f64dad64b9403e2b7341e25912 authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] check for -1 indices and NaN intensities added

c4028f8b05dda00f46a9bcc36d6cab9bb4faf358 authored about 10 years ago by lars20070 <[email protected]>

[FIX] mzid writing (both stream and dom) fixed technically - not

semantically

90d12ecb7ea9027fe525dabdb71b46c70c0c11e7 authored about 10 years ago by mwalzer <[email protected]>

[INTERNAL] check for -1 indices and NaN intensities added

9f7396c9bddca70dafb2a455cd80e92e448f2d71 authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] checks for -1 indices and NaN intensities added

beaeb9ff13c9f970d0c599355df2244a13556aab authored about 10 years ago by lars20070 <[email protected]>

[FIX] fixed correct number of proteinhits

a386f74c2b3d272a79f6ec898567f0b84f971e80 authored about 10 years ago by mwalzer <[email protected]>

[FIX] Fixed SpectrumIdentificationList_Ref hickup

19d919817f5b0bef22d478fe8503d097e7bfd38f authored about 10 years ago by mwalzer <[email protected]>

Merge branch 'develop' into pepXMl

a6b22bd0fcd063a5792eba77d8697d075f93c2fa authored about 10 years ago by liangoaix <[email protected]>

[TEST] add test files.

d9ba05c5dc8b7ced635ffaa2faf7311922619e2f authored about 10 years ago by liangoaix <[email protected]>

add peptideHit metaValue nextscore in XTandemFile() and remove scan_index

9841a52f213271061bd3f371779ebfb246d0e5ef authored about 10 years ago by liangoaix <[email protected]>

[FIX] Enable multiple identification runs result, multiple protein hits and FDR/q-value analysed results.

1412644773cd62c3c60adb2373358172fd6b1e6b authored about 10 years ago by liangoaix <[email protected]>

[INTERNAL] check for peak not found in filter 3

db1f13e30eaadc12c34bf7a8b4e8c353ace8d7e1 authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] check for peak not found in filter 2

e7bbb35fe2d73d0005143e0f998cb7429e160572 authored about 10 years ago by lars20070 <[email protected]>

Merge pull request #929 from cbielow/feat-TextFile

TextFile feature (skip empty lines) and docu fix

dd58d187a534746c438c2470b85a71ed2205e6ea authored about 10 years ago by cbielow <[email protected]>

TextFile feature (skip empty lines) and docu fix

f2ff8929aaa7f5cfd897c42944d7b5271b6336f5 authored about 10 years ago by Chris Bielow <[email protected]>

Merge pull request #927 from hendrikweisser/PeptideIndexer-isobaric

PeptideIndexer: support for treating isoleucine/leucine as equivalent (resolves #872)

3efd1b7672097ded53168c57746e99deded9371b authored about 10 years ago by Hannes Roest <[email protected]>

Merge pull request #928 from cbielow/AMT

[FIX,BUILD] fixes wrong parameter ordering of cmake option command

ee3270a0e3f36e7ad09cbc3e52e1f4fd57e39b69 authored about 10 years ago by Stephan Aiche <[email protected]>

capitalization (minor)

038ed1aafaa407107189d7f23d611153b4070b00 authored about 10 years ago by Chris Bielow <[email protected]>

fix order of arguments to STL_DEBUG option

9cf2fb58a06ec4c4281eafdbe6c91d174be1e507 authored about 10 years ago by Chris Bielow <[email protected]>

[TEST] test for 'PeptideIndexer -IL_equivalent'

bf5cee16500cbe9159fc2f982c4a0726abd8f1e1 authored about 10 years ago by Hendrik Weisser <[email protected]>

[FEATURE,PARAM,DOC] added option to treat isoleucine/leucine as equivalent ('-IL_equivalent'), updated doc; resolves #872

e4a2900475e9c109205ba197bc4bffa0b7f975e0 authored about 10 years ago by Hendrik Weisser <[email protected]>

[BUILD,FIX] fixed invalid option syntax introduced in 9e07f465f93f67819888d38aaeef1e582f346e55

ce9990e6b5c324e642456a63df4d46a763014caa authored about 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #924 from cbielow/git-info

[FEATURE,BUILD] added switch to disable tracking of Git version within OpenMS

1db817ca4da489f0b4fc8d01f8bd8b0d441c00a8 authored about 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] minor fix in iterator

a779953c5484794f0c5fdf70edbaa7a5f3a47627 authored about 10 years ago by lars20070 <[email protected]>

Merge pull request #926 from OpenMS/feature/spellcheck

Feature/spellcheck

242642049026065c4061d74004700a9627495a5b authored about 10 years ago by Hannes Roest <[email protected]>

Merge pull request #925 from OpenMS/fix/small_docu_improvment

Fix/small docu improvement

c7e45cedf7bf5f1769533154e06e563eff217efa authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] update correct words

7155c0a5b8ac3225d2047f5dfe61851e4ec92b8e authored about 10 years ago by Hannes Roest <[email protected]>

[FIX] typo fix

268fe7b26dbb4201404dd6dbfe7365f480385f2c authored about 10 years ago by Hannes Roest <[email protected]>

[FIX,DOCU] update documentation regarding Real and DoubleReal

f6353b6e441f982ad65c94759193972892c5cf0d authored about 10 years ago by Hannes Roest <[email protected]>

typo

small typo, small changes

7784090f12711ce6eb67729608132fef080b9c5d authored about 10 years ago by Hannes Roest <[email protected]>

update docu

write more docu for MSExperiment

since this is the central class of OpenMS, it seems more exp...

3535a4d8288f4a8cbd633f82a35507d24d525a17 authored about 10 years ago by Hannes Roest <[email protected]>

[INTERNAL] minimum distance list simplified

8c3885a99522a6e69d17e3a3a7b71a55019efe8a authored about 10 years ago by lars20070 <[email protected]>

Merge pull request #923 from cbielow/AMT

EmpiricalFormula: fix (negative counts were casted away)

6d63b3f12067c87861f0f770baf08287686dedf1 authored about 10 years ago by cbielow <[email protected]>

[API,TEST] MultiplexGrid renamed to ClusteringGrid

576c3c0752d7f5f9d773a6c0fde960185ddde061 authored about 10 years ago by lars20070 <[email protected]>

[Featrue] added DOMHandler to the FileHandler, showcased with FileInfo

e8107e7d2f5cce33c0ea85380341652d3e9da0df authored about 10 years ago by mwalzer <[email protected]>

[API,TEST] MultiplexCluster renamed to GridBasedCluster

9888c7ac9dca210bba25e8028d2df038e1dffa07 authored about 10 years ago by lars20070 <[email protected]>

Switch to disable tracking of Git version within OpenMS (during development)

9e07f465f93f67819888d38aaeef1e582f346e55 authored about 10 years ago by Chris Bielow <[email protected]>

doc fixes

ce509148042eda1e2ebfec5f4783636ce9b0c7bc authored about 10 years ago by Chris Bielow <[email protected]>

EmpricalFormula: fix (negative counts were casted away) and extension; documentation fixes

241ef16e7411aee534da1d008cfc04981724828a authored about 10 years ago by Chris Bielow <[email protected]>

Merge pull request #922 from OpenMS/fix/build-system-improvements

[FIX] build system improvements (Wm5, KNIME)

0fc3b3a1e4825c364942684f810e0c0b458ed357 authored about 10 years ago by Stephan Aiche <[email protected]>

[API] MultiplexGrid and MultiplexCluster moved to GridBasedClustering

7f1bd36322c37885e04570970771674d0e2c50d3 authored about 10 years ago by lars20070 <[email protected]>

Merge pull request #921 from cbielow/AMT

MS1 annotation in TOPPView

fd2d5a15d25ca1aacd25568123c24ad688e6f0a0 authored about 10 years ago by cbielow <[email protected]>

removed unused variable

42e27913de0a72ff3ae93f14feaaa211df23a9fb authored about 10 years ago by Chris Bielow <[email protected]>

removed unused variable

fcaa4c3a4dd2a3d5724d0f5b747c5472e48b5131 authored about 10 years ago by Chris Bielow <[email protected]>

[FIX] small fix to knime package generation

283954a4598e2ebe6a4bcdc67c510562797c1372 authored about 10 years ago by Stephan Aiche <[email protected]>

[BUILD] overhaul of wm5 find module

d08d33fd2f3e2831d4e455a75f118f6a2f90449b authored about 10 years ago by Stephan Aiche <[email protected]>

Update MRMDecoy.cpp

fix documentation

1cf61a637a63e731742f3f671382ed6dcbbd22c6 authored about 10 years ago by Hannes Roest <[email protected]>

[API] GridClustering renamed to GridBasedClustering

ddb102f0bededa966aabf377c21857cef061e6df authored about 10 years ago by lars20070 <[email protected]>

compile fix, formatting

0f54fed342d807ac20eec07ee657f997efff1296 authored about 10 years ago by Chris Bielow <[email protected]>

Merge pull request #920 from OpenMS/fix/minor-buildsystem-fix

[FIX] fixed minor problem with knime package generation and cmake versions >2.8.11

228763d224e5dd3e695b186474e25e0349b8ba6d authored about 10 years ago by Stephan Aiche <[email protected]>

[NOP] reset from DIRECTORY to PATH in favor of older cmake versions

21c53b6543bf49118a9f793146b153bb3f1e7f13 authored about 10 years ago by Stephan Aiche <[email protected]>

[FIX] fixed minor problem with knime package generation and cmake versions >2.8.11

4c516089e5f8029a832280bd5ad2cb31926dc811 authored about 10 years ago by Stephan Aiche <[email protected]>

MS1 annotation in TOPPView; docu fixes; some small efficiency improvements

749ee0a9ca32e8a624f45243be98fe45f7bfed34 authored about 10 years ago by Chris Bielow <[email protected]>

Merge pull request #919 from aiche/fix/libc++-test-fixes

[FIX] libc++/macosx test fixes

02eaec5ed8c5c0cfc038da00362e8e8e80bfc687 authored about 10 years ago by Stephan Aiche <[email protected]>

[DOC,NOP] added another comment giving some more details regarding the swapping intervals

854b3849c321938b01bd8e71d213bdca849639d9 authored about 10 years ago by Stephan Aiche <[email protected]>

[FIX] MRMDecoy uses std::random_shuffle which works well with VS and libstdc++ but not libc++

* libc++ has a different implementation of std::random_shuffle which leads to a different outpu...

11add9a163759c3cb7adadd45fdd00095e24252d authored about 10 years ago by Stephan Aiche <[email protected]>

[FIX,TEST] fixes failing SequestOutfile_test when running with libc++

* libc++ seems to handle self assignment of std::map a bit differently which leads to a failing...

ef52fe9546a76b195b973347c631d42e89a6e19a authored about 10 years ago by Stephan Aiche <[email protected]>

[FEATURE #803] add parameter setting thread to execute statement of the search engine

909392d50d2152bb4871277b5d4750ddd5eb9fae authored about 10 years ago by Petra Gutenbrunner <[email protected]>

[DOC] properties B further documented

8017856a86d2c7a0cf7d79bb1d3fef5e76a40e82 authored about 10 years ago by lars20070 <[email protected]>

[API,TEST] SILACPattern and SILACPoint removed

90468f8362fc9c12c3b3c24a6bcc094e04b40d4b authored about 10 years ago by lars20070 <[email protected]>

[API,TEST] HierarchicalClustering removed

1bc67a3d2b246101a047c086b1f919669086673b authored about 10 years ago by lars20070 <[email protected]>

[API,TEST] SILACClustering removed

4be43b6b7b1be3fa5605fe6f6aafa92bade809f9 authored about 10 years ago by lars20070 <[email protected]>

[API] small fix

3bfce5c8d0a25f9a0a58962f46425d43ca808f5b authored about 10 years ago by lars20070 <[email protected]>

[API,TEST] old clustering code restored

fd2f6124e6ea445b311370b6697b6d7368a1365e authored about 10 years ago by lars20070 <[email protected]>

[API,TEST] removed SILACClustering, HierarchicalClustering and HashGrid

ad65b8d9ba0a2e0591fb17981cfb120220735e56 authored about 10 years ago by lars20070 <[email protected]>

[API] MultiplexLocalClustering removed

d35085fdd34229d9cb65631ad4d37cdf500ed3e9 authored about 10 years ago by lars20070 <[email protected]>

[TEST] class test added

17a30a55a614034b59e38d8d6402979a22b38921 authored about 10 years ago by lars20070 <[email protected]>

[TEST] class test added

a5c7f80276d882a3b54888c4f1d1d963196b6fea authored about 10 years ago by lars20070 <[email protected]>

[INTERNAL] MultiplexLoaclClustering replaced by GridClustering

db8cc5d57b2dc7dae6f5d4cc7430e7552fa88e14 authored about 10 years ago by lars20070 <[email protected]>

[API] full functionality moved to template class GridClustering

fae14782671d343347b370680f045363e969c2e8 authored about 10 years ago by lars20070 <[email protected]>

[API] multiset distance list added

e9fa6c98637456fc98cde463c5a3bfbb0bf7cfc5 authored about 10 years ago by lars20070 <[email protected]>

[API] some functionality moved to template class GridClustering

c7f4a98e15440c1ac8cfe712d0936f79475f45f2 authored about 10 years ago by lars20070 <[email protected]>

Merge pull request #917 from cbielow/AMT

AccurateMassSearchEngine annotation of input map (not only mzTab output)

8db0b2e2e4f8b41dfdef32c1fa743d88ba550b48 authored about 10 years ago by cbielow <[email protected]>

gcc fix

b97aaef54d956a865a850e1123fa58767384a545 authored about 10 years ago by Chris Bielow <[email protected]>

mzTab-like terms for meta values; consistent use of smooth intensities (crashes otherwise, if switched off); minor fix for FuzzyStringComparator (when testing multiple times, reporting would stop after first call)

e48ee2b1aa8bab5bfde75a2e6d197fc780dacbc3 authored about 10 years ago by Chris Bielow <[email protected]>

[API] GridClustering template class added

45289907e6850119efc974468b0601dce06eefea authored about 10 years ago by lars20070 <[email protected]>

[NOP] coding style improvements

7bca5c79534cc765e0afd9b4a0b461280e817137 authored about 10 years ago by Hendrik Weisser <[email protected]>

[PARAM,DOC] added option to define max. gap length for feature detection; added comments to functions

26f6d3b9efe113d7547715d8c846fcd0c9969bd2 authored about 10 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] return fixed

e2422b82497b55c75f445f6cfc56f2cda121c47e authored about 10 years ago by lars20070 <[email protected]>

[API] Euclidean distance functor added

fcf0e70ead201dcc3efe1a5aac32bd875c24b792 authored about 10 years ago by lars20070 <[email protected]>

[API] Euclidean distance functor added

7ad6778e21cd2efe2570f2f11758d3c5924e60b7 authored about 10 years ago by lars20070 <[email protected]>

small fix

15205e395083bfe7d8524e0527a45fff50641397 authored about 10 years ago by Chris Bielow <[email protected]>

AccurateMassSearchEngine annotation of input map (not only mzTab output); cleanup of related code (const, duplicated code, inefficient code...); some more documentation

c104d5ef1366515768e7b7d4d5cdc4f16c194831 authored about 10 years ago by Chris Bielow <[email protected]>

[INTERNAL] magic number removed

9dc1b11de1a3a62cc4a5ef56164befa8af926105 authored about 10 years ago by lars20070 <[email protected]>

[FIX-#803] amino acid specific n-term modifications

If amino acid specific n-term modifications occur in the tsv output, the amino acid must be befo...

3c07dfbc69f94835b02a6a6da1dd8c342a88abab authored about 10 years ago by Petra Gutenbrunner <[email protected]>

Merge pull request #916 from cbielow/AMT

[FEATURE,BUILD] IDMapper extension for featureMaps, IDMapper speed improvements, small build sys...

2a4d2c3af0e9e1777c250ac79f416b13a0998fe2 authored about 10 years ago by Stephan Aiche <[email protected]>

better documentation of IDMapper internals

bab1df31e8c451481f8c0e4868b9cf335e8164c5 authored about 10 years ago by Chris Bielow <[email protected]>

fix MSVC warnings (mostly pragma); new IDMapper method for featureMaps; O(n) mapping for IDMapper::annotate (O(n*n) before)

456126891d97b276c9ca8e5865be4b7f513769cb authored about 10 years ago by Chris Bielow <[email protected]>

Merge pull request #914 from lars20070/fix/CubicSpline2D

[FIX] fixed index computation in CubicSpline2d::eval and CubicSpline2d::derivatives

231eecae9eaac2fc6f37d9bd0b083811ebace04d authored about 10 years ago by Stephan Aiche <[email protected]>

[DOC] comments added

fd903fe188b842537cbc2c9289e44c2d0cdafdea authored about 10 years ago by lars20070 <[email protected]>

Merge branch 'develop' into FFId

Conflicts:
src/topp/FeatureFinderIdentification.cpp

f530d1b00ba692bfab684a5a9386492811a768a5 authored about 10 years ago by Hendrik Weisser <[email protected]>