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

[FIX] expose additional parameter on the CLI

06133849299d348676cd9399e98fd23b228025cc authored over 10 years ago by Hannes Roest <[email protected]>

[NOP] checker fix

5afaac54ae98f2bf3b00f1f9800b37f2669d9a07 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fixed failing TOPPDocumenter due to #721

1b2074fde6a0e22c43006a15caf84c5158efe4cf authored over 10 years ago by Stephan Aiche <[email protected]>

[BUILD] reduced number of warnings by disabling doc related warnings

* -Wdocumentation-unknown-command
* -Wdocumentation

f24792fd81b8ab3f629964592904f5f5c124c3e0 authored over 10 years ago by Stephan Aiche <[email protected]>

[NOP] fixed a couple of unreachable-code warnings

15fe2327e8c744a5700f191a9947db566b0d3250 authored over 10 years ago by Stephan Aiche <[email protected]>

[BUILD,NOP] made StopWatch_test run alone to avoid test timing errors

1d970b111902fe5325b34dfa116dbb928236a6c7 authored over 10 years ago by Stephan Aiche <[email protected]>

added a comment

c5022bb17d943c71661c301bd1db8e087918ec7b authored over 10 years ago by Chris Bielow <[email protected]>

[FIX] suppress plots when not requested

17d585dc5b57d259108ad1fc94b38a83eefb825f authored over 10 years ago by Chris Bielow <[email protected]>

[INTERNAL,BUILD] restructured include_directories calls

* we now distinguish between internal and SYSTEM includes and instruct the compiler to ignore s...

a04e806f8a214b62ebb12a9bb29a47fee0a61dad authored over 10 years ago by Stephan Aiche <[email protected]>

[BUILD] added clang warnings as suggested in #652

079beddfda3bc5ce34d3dcd7428563891135be44 authored over 10 years ago by Stephan Aiche <[email protected]>

fixed 'out_plot' from required to optional'

31e9189e7a45dbddcf13998a852bc3076178218b authored over 10 years ago by Chris Bielow <[email protected]>

Merge pull request #721 from aiche/feature/cleanup-iostream-include

[INTERNAL] cleanup of iostream includes

a4e0f520c930a5f93a02ffa3f3b60e4ca2c643bd authored over 10 years ago by Hannes Roest <[email protected]>

fixed gcc compile errors

9b6cf20aaceaf361751fa20e06a8886802aac917 authored over 10 years ago by Chris Bielow <[email protected]>

Merge pull request #729 from OpenMS/fix/Coverity

fix several issues reported by coverity

aad59111152461edb220296f4c7993aca788ec44 authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] removed extra semicolon

4831027ddca2de262369541491781dbc92b69abd authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] amend previous merge

- get final changes from c8ca7c1 in main branch

ec353b606df54ed3d9c520fed5d5bde603701a22 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix copy-paste error

fix Coverity

- introduced in 2011-03-13 18:48:23
112221ce92c18b8dc2b1cfbc0832b645ba0652b9

fi...

96ee74906181f13064e4fa09c47bd105295148ee authored over 10 years ago by Hannes Roest <[email protected]>

Merge branch 'feature/pyopenms_mzxml_consumer' into develop

Conflicts:
src/openms/include/OpenMS/FORMAT/HANDLERS/MzXMLHandler.h

f891cbce6eac8c252614f6394201d3679d93d0b3 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix object initialization

Coverity fix
fixes 1182336 Uninitialized scalar variable

5c41411b09cf7d4576a38a7c46d8a094d8740a8b authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix uninitialized variable

Coverity fix
fixes 1182337 Uninitialized scalar variable

2539a8bc6735ff7fbd3d409024113fcf23c76910 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] Interface needs virtual destructor

Coverity fix
fixes 1182544 Non-virtual destructor

- introduced in 2009-10-07 04:11:05
7dc2749...

430ea8a02f2ad7b7ce1f6e8b5f4563d191eb8a1a authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix non-array delete for array

- match new[] with delete[] (see inside LibSVMEncoder.cpp for the new[])

- introduced in 2006-0...

3c0e4a48a391d76a085bcdb1ad6a499eac5b2485 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] Use after free fix

Coverity fix
fixes 1182546 Use after free

- introduced in 2009-08-26 15:44:26
2d77b9b5e5afdeb...

ce283391dafb68ff7e37b34f6584c1fb31a49aac authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] Coverity fix

2c55bb610038e63d6fb92694a86d6f1aa92c9898 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix resource leak

Coverity fix
fixes 1185792 Resource leak

- introduced in 2013-10-19 14:49:51
cfdadd4ad8795200...

da8d428807eadfc306ce0a24990cc06495518598 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] Coverity fix

26a4af0c5ee9cdf06f3dea8d428111aeaac976cb authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #725 from hroest/fix/misc

Fix/misc

be982e276f93d66cff27e4e85277a6550e806ce5 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] IDPep: remove unused output files, better naming; gnuplot script now writes PDF instead of PS (better platform support); fixed some bugs which lead to SegFault when q-values are provided (from FDR upstream)

2590d44432a8a76f79e48ac0ced1861efb374c78 authored over 10 years ago by Chris Bielow <[email protected]>

[DOC] added dependencies to doc_(minimal|tutorials) to avoid building them right at the start

e2be0dae3d4316afec30efea72cf456bb08f252e authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] Windows-fix

- make OpenMP variable signed

1e38dfa0528d09583943d336de0fea826f2b3dc6 authored over 10 years ago by Hannes Roest <[email protected]>

[NOP] fix typo

44d325559229a944981d930005774c7e55ec7845 authored over 10 years ago by Hannes Roest <[email protected]>

[NOP] two small fixes in mzXML Handler

648a895c1a35be6a0df745f7c4c51519f82ffac6 authored over 10 years ago by Hannes Roest <[email protected]>

[DOC] add documentation

- add docu to structures introduced in pull #702

02b159d0397a1a2a48973ac0583eff559128d811 authored over 10 years ago by Hannes Roest <[email protected]>

[PYOPENMS] some build system cleanup

9d30ef441e52ffdd754c260547862eaeccc1da35 authored over 10 years ago by Uwe Schmitt <[email protected]>

[PYOPENMS] wrapped MzXMLFile::transform

f6138c657ee45343abe30b8364fd968e91c2a554 authored over 10 years ago by Uwe Schmitt <[email protected]>

[PYOPENMS] added Pyhton support for MzMLFile.transform()

includes Python implementation of IMSDataConsumer interface

Conflicts:

pyOpenMS/setup.py

971d1bca1e464c8d67dd8cfb5f645ed27a750c0e authored over 10 years ago by Uwe Schmitt <[email protected]>

[INTERNAL] re-added std::endl to ensure flush in IDMapper

78013bbeaf9361d24f88c9e433903361fd04be27 authored over 10 years ago by Stephan Aiche <[email protected]>

[FEATURE] Add IMSDataConsumer to mzXML Handler

c8ca7c1d9f09acff6723c18914be438db74af913 authored over 10 years ago by Hannes Roest <[email protected]>

[FEATURE] add transform to mzXMLFile

e1c54dd13ff3c398336206134951b088f558d123 authored over 10 years ago by Hannes Roest <[email protected]>

[FEATURE] add mzXML support to SwathFile

25e13bfe669168f4643e9abfdcff331be4d5e524 authored over 10 years ago by Hannes Roest <[email protected]>

[TEST] add test for OpenSwathWorkflow + mzXML

cf8d1ed6acda64db7b0e2364a29863eaa3232a25 authored over 10 years ago by Hannes Roest <[email protected]>

[INTERNAL,FIX] added missing cmath include FFPickedHelperStructs

164db6a796cac4a8e2c343048dda3cf24856de30 authored over 10 years ago by Stephan Aiche <[email protected]>

Merge branch 'develop' into feature/replace_DataProcessing

Conflicts:
src/openms/include/OpenMS/APPLICATIONS/TOPPBase.h

9d308164f2ff98a6128f2ea29544b27752953900 authored over 10 years ago by Hannes Roest <[email protected]>

[API] moved insert/extraction operator of lists to separate files

* avoids global inclusion of iostream

05a98fecb5bcc2e606a631b730b2abc7576f5d64 authored over 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL,API] removed logstream/iostream include from param

87d792bd9b50088681dc9fffa1b0dcdd2607edf7 authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] added missing includes of iostream

be49852f13cca9dc890af7093c419bbbb3b71730 authored over 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL,API] removed more references to iostream

* removed Param::checkDefaults() ostream argument and replaced it with a internal LOG_WARN

6dc5eac44acf060ad94c8491d180400227d49f2b authored over 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] moved typeAsString and precissionWrapper into separate files

* this avoids the permanent inclusion of iostream via Types.h

77867e326ba8aa0f88a870390db546f71981ab3e authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] added missing limits includes

6ca186e7b43d103a9a87ec0e6259478fc0b1805d authored over 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] some more iostream cleanups

e7d74413f85bc7e28575e245639ea437a5cf7224 authored over 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] removed (where possible) the includes of iostream

abddf52fa3deeb3b8b407dd74501e783d2c7b4be authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] change which value is taken for sort

- upper window is more reliable since it will also work with broken
SWATH files (e.g. files ge...

a5b39c1709263d86bd2790a3cefb80393ed12a01 authored over 10 years ago by Hannes Roest <[email protected]>

Update feature/fix-install-target with changes from 'develop'

Resolved Conflicts in:
tools/lnx-cibuild.sh

c20c9554add3950bacd6ca7b902f362772039ffe authored over 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #719 from aiche/fix/travis-clone-problems

[CI,FIX] fix travis contrib clone problems

261255cf4362ff189a134c8c199fb31e38c2beb4 authored over 10 years ago by Hannes Roest <[email protected]>

[BUILD] removed some more tests if HAS_XSERVER is OFF

e34126e5d1b45b9da89910244aaf95a7693329dd authored over 10 years ago by Stephan Aiche <[email protected]>

[DOC,BUILD] added new variables to linux documentation

* introduces the ENABLE_TUTORIALS variable in the mac package build

a6d7ced6ff5723e832d1d80a968a2df29ec4bd34 authored over 10 years ago by Stephan Aiche <[email protected]>

[BUILD,DOC] added HAS_XSERVER and ENABLE_TUTORIALS options to control doc generation

32f9981ae9d236ac6b338d7b4e222183892492e1 authored over 10 years ago by Stephan Aiche <[email protected]>

[BUILD,TEST] disabled tests that require a GUI if HAS_XSERVER=OFF

5d35dae1bd7ee4939ba750226cf89fcd303736ec authored over 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #702 from hroest/feature/ParallelReader

Feature/parallel reader

f381706585ada5e3818df79175a30c7e251e1759 authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #715 from uweschmitt/feature/pyopenms_wrapping_improvements_neu

Feature/pyopenms wrapping improvements neu

bd9c9bb03e8a1a9a3532df57fbf55b7fabd3898d authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix const

- use const DataProcessing object when operating on a cons
Spectrum/Chromatogram

e4edde3ae475f3e4c3135a03128597534d2ac031 authored over 10 years ago by Hannes Roest <[email protected]>

[INTERNAL] use typedef for shared_ptr

9c78c99cb5d974155c3a892e4e1665e9fb4d88fc authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #717 from cbielow/OMSSA_32bit_limit

fixed 32bit memory limitation of OMSSA by chunking input data

ca79a5b8d3d29f65c55a3f3881707214273bba2b authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #718 from hendrikweisser/fix-mascotxml-warning

[FIX] fixed misleading warning ('Removed x peptide identifications...

a8e0aef519ed23a8f8afe7a9cbc99deab647d353 authored over 10 years ago by Hannes Roest <[email protected]>

[NOP] fixed path issue while fetching search engines

43355682d1c3bb7efbe0ab99d647f44dd5d25bed authored over 10 years ago by Stephan Aiche <[email protected]>

[NOP] install only required boost libs during travis setup

91b12dbf55ee7542b6e0f10e281c7a74f0d0cef0 authored over 10 years ago by Stephan Aiche <[email protected]>

[NOP] added searchengines to travis test builds

ea747cab32134726868fd78ca63fa0a0a80658a6 authored over 10 years ago by Stephan Aiche <[email protected]>

[NOP] avoid installation of latex during before script to save some build time

9632fc4f066f3ebb8c7bcbdabbacd299a449b52a authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX,NOP] fixed travis build errors during contrib build

7759709d45117e3c4d6df38361bc3b6edb8192d4 authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] remove throwing destructor

- do not call populate in the destructor since this function might throw

373775cdc9aefc760c76932e694de9a17772d458 authored over 10 years ago by Hannes Roest <[email protected]>

typo fixed

1ed8a51057123a92d3073fda3cdc5c65a255fc2d authored over 10 years ago by Chris Bielow <[email protected]>

disable chunking by default

35017d099d4f8717ad791ea0507ab884ebb3662f authored over 10 years ago by Chris Bielow <[email protected]>

negative or 0 chunk size disables chunking

8e20ca05f67e09cd5f69a948e781ba688878e91e authored over 10 years ago by Chris Bielow <[email protected]>

[FIX] fixed misleading warning ('Removed x peptide identifications without sequence')

1e532159ad27d2651d2e9bfe89de80c5ecc5eee3 authored over 10 years ago by Hendrik Weisser <[email protected]>

fixed 32bit limitation of OMSSA by chunking input data

d3286698a8ff1ddb4c3bad1f8525e7f2ebd9d722 authored over 10 years ago by Chris Bielow <[email protected]>

[FIX] mzXML does not have chromatograms

7b04473c27102bc7b6d9a3f3e4712b059090142b authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #703 from hroest/feature/AASequence_TPP

Feature/aa sequence tpp

b02cf4e0c67befc601b67ace080c19c17f915830 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] flush data after seeing end of XML file

489ef016cec3e41f05ae28d7ed9f3cbe2b31847c authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #698 from hendrikweisser/FFId

[API,FEATURE,INTERNAL,TEST] updates to FeatureFinderIdentification and the TraceFitter classes

73ecc3b846356020b250e95615623e5ba41f32f8 authored over 10 years ago by Stephan Aiche <[email protected]>

Merge branch 'FFId' of https://github.com/hendrikweisser/OpenMS into FFId

fd9c99bf8a6679795a03eb9e75b10e9791eb1a8b authored over 10 years ago by Hendrik Weisser <[email protected]>

Merge pull request #1 from aiche/hendrik/FFId

Improved intensity profile computation

9f7eb5ccd1a87aa5332bf1f722b12d3128b1150c authored over 10 years ago by hendrikweisser <[email protected]>

Merge pull request #708 from hroest/fix/fix_buildsystem_path

[BUILD] fix build system bug related to contrib finding.

e7649835f539c14d56c077fce3ab8bf8156bd251 authored over 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #716 from hroest/fix/MRMDecoy

[NOP,TEST] clean up MRMDecoy, add more tests

bab46f34fd81428080cef903b66e47fad8544123 authored over 10 years ago by Hannes Roest <[email protected]>

[NOP,TEST] clean up MRMDecoy, add more tests

33238695e8f5425c0582e9bc0568b258f020564d authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #707 from mwalzer/feature/QCML

[FEATURE] variable stylesheet support for qcml

62bebc0cac069fcfcb603060b753fe993a7dcc2f authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #677 from uweschmitt/pyopenms_cleaner_build

[PYOPENMS] setup.py as minimal as possible + other improvements

e4439295268bacf4943903bf1f645587475c231d authored over 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] utilize computeIntensityProfile in EGH- and GaussTraceFitter

a4acda8e008850a4801a715279d5b19b25e08adb authored over 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] added computeIntensityProfile() method to FFCentroided MassTraces

* moved some code from header to source files
* is faster then the previous map implementation...

cd02227724797876f6b5bab79e7d85ca890081d8 authored over 10 years ago by Stephan Aiche <[email protected]>

[PYOPENMS,FIX] corrected ns of classes in OpenMS::Interfaces

pyopenms.Chromatogram -> pyopenms.Interfaces.Chromatogram
pyopenms.Spectrum ->...

d11c25e0f38a4e96aa5aa66f52c7536aed3b2370 authored over 10 years ago by Uwe Schmitt <[email protected]>

[PYOPENMS] added Support for definitions in KERNEL/StandardTypes.h

2bf435418e389d5daac3f7f74ad3c227e5550267 authored over 10 years ago by Uwe Schmitt <[email protected]>

[PYOPENMS] added missing inheritance in pxds/TheoreticalSpectrumGenerator.pxd

added base class DefaultParamHandler and its methods

eb0c14ab971f427619f746795abf8bb972857c0b authored over 10 years ago by Uwe Schmitt <[email protected]>

[PYOPENMS] updated some broken pxd files

5bdb5e9f65db606b83321002a716b6c3c2e4def4 authored over 10 years ago by Uwe Schmitt <[email protected]>

[PYOPENMS] added inheritance from RangeManager to kernel types

131c02cbabd9dfa38a7da65ea501de5668ef1191 authored over 10 years ago by Uwe Schmitt <[email protected]>

[PYOPENMS] added dict like Param.get method for convenience

Python class Param now has additional method get() which works
in the same way as get() ...

dfb59dc0c28a0d10b0b07c90c54782b6acd17637 authored over 10 years ago by Uwe Schmitt <[email protected]>

[PYOPENMS, FIX] fixed exception when converting DataValue

in case of invalid value type, conversion to Python raises internal
exception. replaced ...

e1853b2cc721d52d2a7a4be13e6a90584e99f0da authored over 10 years ago by Uwe Schmitt <[email protected]>

[PYOPENMS] added missing "nogil except +" decls

if a C++ method is not declared with "except +" and throws an
exception the Python inter...

f52e52a550a2baadeca013a82bb033eb73e6c009 authored over 10 years ago by Uwe Schmitt <[email protected]>

[PYOPENMS] added SpectrumAlignmentScore

cfd146afa9c1db664df75124aea5538b9a8e534b authored over 10 years ago by Uwe Schmitt <[email protected]>

[PYOPENMS] fixed namespace of Residue::AIon et al

moved ResidueType.AIon -> Residue.ResidueType.AIon
same for all other members of enum ...

c0e61affca7bc87f0203e33dd7bf1ec3f8203e05 authored over 10 years ago by Uwe Schmitt <[email protected]>

[PYOPENMS] added support for SpectrumAlignment::getSpectrumAlignment

8fdd2538ab39bb66beef9beb7f64aa7ae270ebcd authored over 10 years ago by Uwe Schmitt <[email protected]>

Merge branch 'fix-pepxml-load' into FFId

a3b20784665047a3db684a9915953d397ee15ea3 authored over 10 years ago by Hendrik Weisser <[email protected]>