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

Merge pull request #713 from hendrikweisser/fix-pepxml-load

Fix for pepXML loading bug (#710)

d2fe883de745eaac5547070a9b13d899baf7ae11 authored over 10 years ago by Hannes Roest <[email protected]>

[DOC,BUILD] fixed doc installation

* removed doc from ALL
* added installation check (incl. a more helpful error message) to chec...

e5e887be0ab28efa24d0cb07dcde9a58801e0d81 authored over 10 years ago by Stephan Aiche <[email protected]>

[PYOPENMS,CMAKE] extended last commit 4d92e6

984f104d9547b983aa241cdadbca8e23f468a3f0 authored over 10 years ago by Uwe Schmitt <[email protected]>

[FIX-#710] fixed #710 - loading of pepXML files containing multiple experiments (regression)

2c7963861b3b75ef1ff289056cf2e49b79494b8e authored over 10 years ago by Hendrik Weisser <[email protected]>

[TEST] adapted test file to include data from multiple experiments

10eba5194ef323f6090a2f56e46fa1f8ca1f4090 authored over 10 years ago by Hendrik Weisser <[email protected]>

[PYOPENMS,CMAKE] running cmake removes pyOpenMS/build/ dir if exists

When working on pyopenms existing shared libraries in pyOpenMS/build
might be out of dat...

4d92e6e448b08478a69a6e7f028169a1b4853b83 authored over 10 years ago by Uwe Schmitt <[email protected]>

[PYOPENMS,FIX] fixed regression from last commit e334d31

6eb9f4f5831762a48f6800d9baff8f332899f695 authored over 10 years ago by Uwe Schmitt <[email protected]>

[PYOPENMS] new strategy for naming pyopenms distributions

+ the name now combines open-ms version + timestamp of built
of pyopenms.
(this ...

e334d310a79eb469d323905b2898d03d1673f310 authored over 10 years ago by Uwe Schmitt <[email protected]>

template for FeatureSetFinder tool

85605ebce799855dac9f279728af396ba7b20f64 authored over 10 years ago by lars20070 <[email protected]>

added some docu and exception handlling

27253e4cff89121a9085bc92195403cb2f411e94 authored over 10 years ago by Mathias Walzer <[email protected]>

[FIX] fixed checker warning (coding conventions)

e9902378178e482136c2c47110616975ed76355b authored over 10 years ago by Hendrik Weisser <[email protected]>

[INTERNAL] small simplification

054fe734d932eb22bc2b2ba5754e66f03fb7dbf5 authored over 10 years ago by Hendrik Weisser <[email protected]>

[TEST] updated test to reflect changes in GaussTraceFitter class

2bbde09b3d0f931177f63c4b5064063d0b9861b9 authored over 10 years ago by Hendrik Weisser <[email protected]>

[BUILD] fixed mac dmg package generation w.r.t. to new install scheme

* moved general package defs to separate file

1476b609482502c3bfa415e04aa46acef7b43dfe authored over 10 years ago by Stephan Aiche <[email protected]>

[DOC] updated documentation w.r.t. to the use CMAKE_INSTALL_PREFIX

* some general documentation improvements (e.g., replaced svn with git on the touched pages)

90a6a558a9f13516fa4b6ae80a3ec3b7552d6600 authored over 10 years ago by Stephan Aiche <[email protected]>

[BUILD] made install directories customisable

4d9d26fff8f96ff6daa38990cd0778d90fbe8151 authored over 10 years ago by Stephan Aiche <[email protected]>

[NOP] removed old, now obsolete installation cmake files

fc2b8e92c2ae6ef0d407be24cd8ab90be4aaab4e authored over 10 years ago by Stephan Aiche <[email protected]>

[BUILD] added installation of header alongside openms

* note that this doesn't necessarily allows compiling against the installed
headers, since t...

b1d924d841d5a3762bfa4a8cb30f06827b6b7980 authored over 10 years ago by Stephan Aiche <[email protected]>

[NOP] added xvfb to travis execution to allow gui related stuff

* since doc is now part of ALL and doc needs a GUI we need travis to run with an X Server (xvfb)

4e33621005e04c456fe225e880b49a76c7ba2873 authored over 10 years ago by Stephan Aiche <[email protected]>

[BUILD] rename file, fix comment

1f41e2e6e736b5375f57a76f64038ecd17dda39f authored over 10 years ago by Hannes Roest <[email protected]>

[BUILD] reenabled install target for OpenMS(_GUI), OpenSwathAlgo, TOPP/UTILS

* doc is now part of ALL to ensure that the documentation is ready when it is installed

42f7532027904a345d301b18ba8ee7b0a6ca82cc authored over 10 years ago by Stephan Aiche <[email protected]>

[BUILD,INTERNAL] added additional search paths in the CMAKE_INSTALL_PREFIX

* Note: Installation is completely disabled for now

090235a9c139b0cf5b0631453419f30fd26e445f authored over 10 years ago by Stephan Aiche <[email protected]>

Added MRMRTNormalizer::rm_outliers_ransac

279cf12b6c232829af1dc4bb32e7de04b131a23e authored over 10 years ago by Hannes Roest <[email protected]>

further changes

b0138310adb219fc0ffce45bd8da4a18dca49207 authored over 10 years ago by Hannes Roest <[email protected]>

[PATCH 1/2] add initial peak quality for output

6052a669807a93ee65dfe616f690c875d0207619 authored over 10 years ago by Hannes Roest <[email protected]>

[PATCH 2/2] iRT paper for Sara

be552f02bd3f68e52a90a559519cb887d1ba91ec authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] add Chauvenets criterion as a CLI flag

- possible to turn on/off the use of Chauvenets criterion

cddaa291bc339c39e9ec92787b1a8d4527ab38b8 authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #690 from hroest/fix/misc

Fix/misc

0d9c77a1a14ef6c693a49b70004bb1db4c35d396 authored over 10 years ago by Hannes Roest <[email protected]>

[INTERNAL] moved package types etc. to top-level CMakeLists.txt

132a2bb2cbda228deecff0d1fedf3dbad56be0f0 authored over 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL,NOP] moved OpenMSBuildSystem_configh.cmake into src/openms

f8bc72f42ee9aab0d54e0ddd4b6b52800081c089 authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] sequential output in multi-threaded environment

35007633828a714ffbeff75f878c33ec9084d8e3 authored over 10 years ago by Hannes Roest <[email protected]>

[FEATURE] OpenSwathWorkflow: sort windows

- option to sort by window before annotation (opt-in)

9be4796143bf539d8c7f3f64570125c46f744901 authored over 10 years ago by Hannes Roest <[email protected]>

[NOP] typo

5d0e735d674c857bfce0df22d6077aec853d5f18 authored over 10 years ago by Hannes Roest <[email protected]>

[INTERNAL] moved all path related config infos to a separate header

* the header is only included by File.cpp to avoid unnecessary access
* added some more commen...

50423104fd34ca956b3e5596f87c31ac118a9b76 authored over 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #673 from mcmenace/toppview

[FEATURE,FIX] Added min/max values to go-to dialog

d8c0222c03471637adafe37bf828df333f915c7a authored over 10 years ago by Stephan Aiche <[email protected]>

Merge remote-tracking branch 'origin/develop' into toppview

6d9ca6d4efd25c81494ece91fd456fdb38ae31dc authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[INTERNAL] removed Qt include

887fc5bfb23ab45a5f5f3d4647a9c1d643ad6a1e authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[NOP] unified lineendings in OpenMSBuildSystem_configh.cmake

8aff026cdfc473e010e09ecdf7a78c74b7eb508d authored over 10 years ago by Stephan Aiche <[email protected]>

[BUILD] fix build system bug

- use OpenMSBuildSystem_externalLibs.cmake on top level to find correct
include paths not only...

1d262a934e03de2331ed338fc68d1d895293d3fc authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #705 from hroest/fix/OpenSwathWF_MetaData

[FIX] Propagate metadata in OpenSwathWorkflow

bd7fe72d2618f5ec310a6ff77e5dbf7aad2588b8 authored over 10 years ago by Hannes Roest <[email protected]>

worked on tests for qcml

465b61eb89370c1bb5c033c5452deca4e5549e94 authored over 10 years ago by Mathias Walzer <[email protected]>

externalised qcml stylesheet to XSL/

0503bba8c0c0405be557165e649585f0fd1f8167 authored over 10 years ago by Mathias Walzer <[email protected]>

[FEATURE] fixed scroll bars for ranges outside min/max of data range

f01eaf44f763eb0d9e6c993cc42ab8666a069c34 authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[INTERNAL] removed debug info

074b28f5732fef776333c1f366e3a5d7f42feeb1 authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[GUI] renamed 'Go to' to 'Select data range'

a7996262d6d3bc9ee9a2a48c9565596dba884eac authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[API] rename 'Go to' -> 'Select data range'

ea6f4862f27e02f4da56bd4b57edfdd8996b4bd6 authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[FEATURE] added clip-checkbox to 'select data range' dialog

9a5f675eae713a816c82e47940a53bf4bcad3a49 authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[FEATURE,FIX] Added min/max values to go-to dialog, checked and corrected selected ranges

6b2a37fa83a16de20508297c209c6cd3fc145e12 authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

added MS experiment overview CV

8aa1140d86a062af61b67de69efc7223a731e29e authored over 10 years ago by Mathias Walzer <[email protected]>

[FIX] stop parsing upon error

ac53ec4eed96f7cb1e9716707d9caf4c3fe6677c authored over 10 years ago by Hannes Roest <[email protected]>

[INTERNAL] change how populateMetaData_ is called -> cleaner solution

d773abec211cd851f273cc2c2627f8b0d0000ecc authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] Propagate metadata in OpenSwathWorkflow

- correctly handle meta data and propagate from spectra to chromatogram
file
- add test for pr...

921a9e866fe4c29fbceffc60914b4d36bd52f0b3 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix TraML Reader code

be1d70da3645711f8d69147386dbdf7b0f334e57 authored over 10 years ago by Hannes Roest <[email protected]>

[FEATURE] Add parsing of TPP modifications to AASequence

- parse modifications in TPP format:

- allow parsing of modified peptides in TPP/SpectraST form...

c17753532b22139cb9500f8c2f0e40ab306978d3 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fixes suggested by Chris

- correctly handle update of shared variable
- move PeakType out of loops

b8b22900852f67e27c6eefb314a368ab9b0f1b3d authored over 10 years ago by Hannes Roest <[email protected]>

[FIX,TEST] fix typo, add test

229fc43a428ffd5f1d66a757cc6ff8d4bb20ea32 authored over 10 years ago by Hannes Roest <[email protected]>

fix some forward declarations

ef29811c6109297985f27a7b4834d4675b16fdf2 authored over 10 years ago by Hannes Roest <[email protected]>

[PYOPENMS] fix pyOpenMS code

6d6b74424720804d2779138e6ec749c75f9803e4 authored over 10 years ago by Hannes Roest <[email protected]>

[FEATURE] parallel spectra processing for mzML

- while reading, the spectra are decoded in parallel which allows for
faster read times of the...

6779c32f0537cd4279810c05e89769f275b6f699 authored over 10 years ago by Hannes Roest <[email protected]>

[FEATURE] parallel spectra processing for mzXML

- while reading, the spectra are decoded in parallel which allows for
faster read times of the...

4d7438381ed1da99b23d4494afdb008e13bd3a10 authored over 10 years ago by Hannes Roest <[email protected]>

[FEATURE] PeakFileOptions extension

- extend PeakFileOptions by an maximal_data_pool_size_ parameter which
specifies how many spec...

25b0b113935e37b1bc487fc1495ddb6082c10a88 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix sizeof for stream positions

- replace sizeof(streampos) with sizeof(streamsize) since only the
latter is guaranteed to be ...

713685e44ff2d8d0f9a3e26741bf5278544b6463 authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #696 from hroest/feature/RAM_usage_chromatograms

[FIX] fix RAM usage when adding dataprocessing to chromatograms

29f19f57d4cad31566df9ed801ba0fc26d0d6674 authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #679 from grosenberger/develop

[FIX,TEST] fixed OpenSwathDecoyGenerator / MRMDecoy

74a8b78b54a36d18be3825964278919236554b71 authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #689 from hroest/fix/OpenMP

[FIX] disable OpenMP again for ILPDCWrapper (see also #595)

54d90bdef0a679802fd11842623eea5b96116156 authored over 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #697 from timosachsenberg/feature/fix_map_usage

[FIX] proper usage of map in ControlledVocabulary

adfc4f044d60913c78883f330e3088f834be91cc authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] proper usage of map

470ef2502dbe2275eca752742d629ee2fc5e896b authored over 10 years ago by Timo Sachsenberg <[email protected]>

[FIX] fix RAM usage when adding dataprocessing to chromatograms

- instead of copying all chromatograms, add the dataprocessing directly
to each chromatogram

2d0f98f9db0b87770d97a003b7fd421debf15a0b authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] MRMDecoy: std::map replaced with boost::unordered_map

f9ec491cd49ab1eb657406648a8766442791a862 authored over 10 years ago by George Rosenberger <[email protected]>

[FIX,TEST] fixed MRMDecoy

[FIX,TEST] fixed MRMDecoy_test

[FIX,TEST] fixed OpenSwathDecoyGenerator tests

fce18bbd6a96f6b1b090aca789f470c64e791108 authored over 10 years ago by George Rosenberger <[email protected]>

[INTERNAL,TEST] increased accuracy of approximation for AUC calculation (for consistency), adapted tests

3bccfe721b1bd037587c59eb47da3f5b70b04320 authored over 10 years ago by Hendrik Weisser <[email protected]>

Merge pull request #694 from cbielow/missing_files

added missing index file for OMSSA test, which gets recreated when runni...

68b63dd2bbf51f7ccc988c7b9f5506784730629a authored over 10 years ago by cbielow <[email protected]>

Merge pull request #693 from cbielow/MGF_fix2

Major speedup of String --> Double conversion

4cdb7aff37da9b664c3131bca263636eee0ea23f authored over 10 years ago by cbielow <[email protected]>

[TEST] add new test files for OpenSwathMzMLFileCacher

ec6dcac6af1cba796637cc2e6d5fcc901d09d30e authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] bugfix in OpenSwathMzMLFileCacher

- cacher would not properly remove tag from chromatograms after
converting back from cached st...

8e46be802cc13e44040be52066d6a18a5fd72c63 authored over 10 years ago by Hannes Roest <[email protected]>

[TOOLS] adopt TOPP tools to the change in DataProcessing storage

b417e58a921ef4d38d19ce11fefd24ded947a447 authored over 10 years ago by Hannes Roest <[email protected]>

[VISUAL] adopt GUI to the change in DataProcessing storage

1c16cd568ead9f07398fcd2f1e263c5557b12ef1 authored over 10 years ago by Hannes Roest <[email protected]>

[TEST] adopt tests to the change in DataProcessing storage

45b5cdead5624a96414cf8facc82281b17576b75 authored over 10 years ago by Hannes Roest <[email protected]>

[FEATURE] adopt core library to the change in DataProcessing storage

49c8ec216c95e93bad349a05f07e61dc9a1d994f authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] correct equality

- fix equality operator (make sure that we compare the actual contents)
- this can still segfaul...

2b02bbbd56055ff2b33bd02005d623438a2f6d1f authored over 10 years ago by Hannes Roest <[email protected]>

[FEATURE] replace DataProcessing member array with shared_ptr array

- instead of storing a full DataProcessing object for each
spectrum/chromatogram, only store a s...

2d07b1b173aaac5a304c916b045f0c082dbf5f9e authored over 10 years ago by Hannes Roest <[email protected]>

[FEATURE] toInt/toFloat now also use boost::qi

5bc0fd94ceabc720b996058dace5ff3659c5b658 authored over 10 years ago by Stephan Aiche <[email protected]>

[API,FEATURE,TEST] Improved fitting of models to mass traces

- new method "getValue" to evaluate the model at a point
- more robust estimation of initial par...

5389f3df30fb0ae67e59759c6ac6635447f92560 authored over 10 years ago by Hendrik Weisser <[email protected]>

[FEATURE,PARAM] added checks for elution model validity; changed settings of OpenSWATH feature finding

47750e62d4d62409f304ed4459af12f308ebafa0 authored over 10 years ago by Hendrik Weisser <[email protected]>

Merge branch 'MGF_fix2' of https://github.com/cbielow/OpenMS into MGF_fix2

6a15db7f3d30fde195876018a3dbf2cf1cc2b9b4 authored over 10 years ago by unknown <[email protected]>

added another comment to String::toDouble()

cf479cddafdaafaf5dcedd371dda147bd647d530 authored over 10 years ago by unknown <[email protected]>

Merge pull request #675 from aiche/feature/checker-test-fixes

Checker/Test fixes and adds test for CTD writing

95709ffce78879eb18286d07608708d6555ee65d authored over 10 years ago by Stephan Aiche <[email protected]>

added missing index file for OMSSA test, which gets recreated when running the tool

318efd15e8eca07c3e71e7b8acc32fcf4bf64582 authored over 10 years ago by Chris Bielow <[email protected]>

Merge pull request #1 from aiche/MGF_fix2

[FIX] fixed missing std:: for vector

cecb4a02254bf3d27cfc009607d377b64c98f1d5 authored over 10 years ago by cbielow <[email protected]>

[FIX] fixed missing std:: for vector

* also applied uncrustify

d53eac45ba2f640573a36459efa606239216c7ab authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX,FEATURE] found blazingly fast toDouble() for Windows, making MGF parsing 700% more effective, so OMP can be removed. Should affect speed of many other parsers as well

722ec4deb62aa8cd3ad84810ad122588ce0f1e42 authored over 10 years ago by Chris Bielow <[email protected]>

Merge pull request #691 from cbielow/MGF_fix

further improvements to MGF::load()

349ec48d88083f83d2121f29c116a0be318b78a0 authored over 10 years ago by cbielow <[email protected]>

added progress functionality to MGF::load(); named OMP sections (5% performance); fixed variable name;

afede0990ea77ca190877e068cb0b30ecb3f689c authored over 10 years ago by Chris Bielow <[email protected]>

Merge pull request #688 from hroest/fix/FileSizeLimit

Fix/file size limit

eaff9322f778b85c5ec33498cabd77a18c4b225e authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix build for MSDataCachedConsumer_test after API change

ac1fac4463dd925d7e77ff2cc3ecc5a7f20ca8df authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #684 from hroest/fix/MascotGenericFile

[FIX] Bugfix for threading issue in MascotGenericFile

877a27eb53dc7374029ab200644dc96ba2f1205d authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] disable OpenMP again for ILPDCWrapper

- it was re-enabled in 0ce469d0ee54f70ee5848639f02537e5451ad44a however
the underlying issue s...

1f6b38a97e540ed689d18990694705937ea5c722 authored over 10 years ago by Hannes Roest <[email protected]>

[TEST] add test

7351c7de9772eea990ab1c69f024dde4e8b771da authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] correctly read file position from XML into std::streampos

34ad7814e3476869534a5fd0bb2ca9630f1a8db5 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] properly release xercesc resources after use

32e2760df75858fcf20cc7348d30b8cc6c07197a authored over 10 years ago by Hannes Roest <[email protected]>