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

[FIX] use std::streampos in IndexedMzML

- use std::streampos which allows to address also larger files

96dea04d92a16610ec34e909f1176f5ae568be02 authored over 10 years ago by Hannes Roest <[email protected]>

[TEST] adapt test for CachedMzML

50cce9e71035fbf0e5a771b0cd242a28c3de890c authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] use std::streampos in CachedMzML (multiple fixes)

- use std::streampos to store positions in filestreams
- check for error condition before resize...

0cca369ccc763fdf15c3ecd9992b1204eabb757b authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] catch error in seekg

- catch error when seekg cannot go to the requested position and
re-throw a sensible error mes...

f0eb43f2ca63b533f55974d9a672d36851c08f08 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX,PYOPENMS] fix pyOpenMS after #680

- also adopt header files and changed API in pyOpenMS code

a360280006a0e2818fc05f54f8d65816324e9ee7 authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #685 from cbielow/develop

Typo fixes in documentation and licence files

033411ff140e6f1bc9364831476ea324c1ee5394 authored over 10 years ago by Hannes Roest <[email protected]>

[DOC] fix typos and license links

38aa225bfbdd2506d9facd12c11a6803b42ddc58 authored over 10 years ago by Chris Bielow <[email protected]>

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

7f6cc1ce50e24f42c41f658d428eea8d29f95f36 authored over 10 years ago by Chris Bielow <[email protected]>

Merge pull request #680 from hroest/feature/CachedMzML_fixes

[INTERNAL] Feature/CachedMzML fixes

1d9746684253cb91af5c3561f6dafa8b821abbe5 authored over 10 years ago by Hannes Roest <[email protected]>

[NOP] fix compiler warnings after #666

- remove non-ASCII characters
- comment out unused parameters

95dcc28090af824e38988f4b4538d91174f81793 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] Bugfix for threading issue in MascotGenericFile

- Fixes an error introduced by multiple threads: under certain
conditions the global variable ...

638b85b91cde8a79eac6544f444689550dd34b90 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] additional fixes

- [TEST] test error conditions
- [TEST] make test faster
- fix header guards
- remove MAGIC_NUMB...

2abccc0d52524af415ff780a0e8d4f9659807b6b authored over 10 years ago by Hannes Roest <[email protected]>

[TEST] add test to CachedMzML

2b7122857248d80a4a2d9b2c6ad30b7171d8ab0f authored over 10 years ago by Hannes Roest <[email protected]>

[INTERNAL] move CachedMzML to FORMAT

fd7ac4de56b20f6d024e766500ca58f66ef2bd63 authored over 10 years ago by Hannes Roest <[email protected]>

[INTERNAL] cleanup and refactor CachedMzML

67ef638c5bd28c3f657ee7848a98daa0eaaa3ba5 authored over 10 years ago by Hannes Roest <[email protected]>

[PYOPENMS, FIX] fixed dependency decl in pyopenms.cmake

dac5e0ebd80b05ca62c02caa0b1736b2f81314b1 authored over 10 years ago by Uwe Schmitt <[email protected]>

[INTERNAL,API] gsl-removal: removed abselut refereces to 'delta_abs_error' and 'delta_rel_error'

8fe59ad1f22b7aee730248d6206291bb766f405a authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[INTERNAL] gsl-removal: added default header text

113bacd5ac738bd2dc2ce1fec4d8fe22f880dcfb authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[TEST] gsl-removal: changed relative tolerence

ff462d639d82154b205e5069679cd75fa1e8592f authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[NOP] added libs for travis

c12df8cc942d9d61aec3ababefabb24d0644dba7 authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[INTERNAL] gsl-removal: removed abselut references to epsilon_abs/rel

5d87e6ba743246dea9f17a18736792e6bf0f7431 authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[PYOPENMS, CLEANUP] reformatted pyopenms.cmake

ea900a36e5822097e369c9ca58f540de899baebb authored over 10 years ago by Uwe Schmitt <[email protected]>

[PYOPENMS] refactored build targets for pyopenms

ba2264581b29ff191a57d7249ba6b4febb80d1e6 authored over 10 years ago by Uwe Schmitt <[email protected]>

[NOP] Merge branch 'develop' into feature/checker-test-fixes

Resolved Conflicts:
src/tests/topp/CMakeLists.txt

95085073f6cda44887316767cdba703aa3881709 authored over 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #666 from aiche/feature/ib-spectra-format-export

[FEATURE] ib spectra format export

b48250afc490a20183a9cf7aecb2480ac87e71b1 authored over 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #678 from hroest/feature/SWATH_annotation

[FIX] fix how swath files are annotated

95ff308b880dc4dffd52384c67dac2d593c9f84d authored over 10 years ago by Hannes Roest <[email protected]>

[PYOPENMS] only one build target for pyopenms

building files for distribution + building extension "in place"
in one step. this is fas...

e820c1455c4860611059d46199cc1a8ffc727e47 authored over 10 years ago by Uwe Schmitt <[email protected]>

Merge pull request #665 from hroest/fix/fix_coverity

Fix coverity errors

3b30eeb5dd410e673d48d36132d82f0c8d6cea26 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix how swath files are annotated

- fix broken mapping between swath file vector and swath annotation file
(no MS1 map annotatio...

7e487576431bb7fe711a0dbe198705a96e84a893 authored over 10 years ago by Hannes Roest <[email protected]>

[PYOPENS] setup.py as minimal as possible

moved codegeneration and moving of files needed for
pyopenms distribution to new file cr...

27e64c383a9cf68398125868fff1930b272195c2 authored over 10 years ago by Uwe Schmitt <[email protected]>

[NOP] disabled IDEvaluator CTD test in travis due to missing X server

87be6feecd567e9a298a765ae5c599b3078dab0e authored over 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] gsl-removal: make boost 1.47 compatible

boost::random::uniform_int_distribution -> boost::uniform_int
boost::random::random::mt19937_64 ...

52339f6b9440bba9edfb0ed99e560f6877551da3 authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[BUILD] remove GSL from build system

61623f177bb1d3df6d3485cb9f3c8ac022f8d90a authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[INTERNAL] gsl-removal: added Eigen and WildMagic to pyOpenMS

f908c7a56da787652893eae34ef236e639ae6f7d authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[INTERNAL] gsl-removal: adaption to restructuring of the Lib layout

05b445498568f56ea259fb49667546435634bd9b authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[INTERNAL] gsl-removal: removing last references to GSL

f89ecf9987441c989ded25e3d9e9d182b2831811 authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[INTERNAL,API] gsl-removal: fixed pyOpenMS

008c54a9cbe5612bfb93e41533200cb8998fa47b authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[TEST] added write_ctd test for all topp and util tools

* the test should fail if the tools were not properly registered in ToolHandler

bc20ad5f6830e1c8b468338523c2d427cc170e07 authored over 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] gsl-removal: fixed documentation generation

82847fb9bf1e2e5d498d388c4e27aec2c37382e6 authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[INTERNAL,API] gsl-removal: made pyOpenMS compile again

7ca061b9376dd9747926f0f6c4af73d2fc7ac8aa authored over 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL,API] gsl-removal: make all unit tests work

7e9341d96fae64f756c9ffc9a3f56a394275f633 authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[INTERNAL,API] gsl-removal: use SavitzkyGolay

210ad5fffe2e49900aac14ce17b843e2a9cd2b73 authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[INTERNAL,API] gsl-removal: clean-up comments

c80b6448075eefe7c6830b393b685bbb33ec06ed authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[INTERNAL] added debug output on failure controlled with #ifdef

e45c6b60ca26a21c11585db8e8061c22c1015bcf authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[INTERNAL,API] gsl-removal: adapted ElutionPeakDetection to lowess smoothing

240866ef742dbceedebe4247c4056d2704f5efe9 authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[FIX] gsl-removal: fixed windows compiler errors and warnings

de99208e6d7bff78b7b2ee2637cdc796a4e2957e authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[FIX] fixed uninitialized member

dd5448d5ea9aa18bbf1d3d3f90adf147707a613f authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[INTERNAL,API] gsl-removal: removed SILAC(Filtering/Filter/Analyzer) and dependencies

271a5adbffd729ccf6ce3b567a643ae93179c4a5 authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[INTERNAL,API] gsl-removal: replaced GSL functions with Wm5 functions

changed PeackWidthEstimator spline
changed linear-fit
changed gsl_multifit_linear
changed quadra...

dd7c89d04d9ae88303146a739ad2b5587de4a90e authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[INTERNAL,API] gsl-removal: delete LmaGaussFitter/Model and LmaIsotopeFitter/Model

a1b6dabec7cbd45a0575b28ea0f7a3f59666e069 authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[BUILD] added wildmagic 5 as dependency to openms core

66fb11aa009861fa818962fb880fcce8839c4ab4 authored over 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL,API] gsl-removal: replace GSL function with Eigen functions

removed gsl_linalg_LU_decomp & _LU_solve
removed gsl_lanalg_SV_devomp with Eigen SVD
removed gsl...

d91d23c8b70b159e76bf15829484dbeeb4c7c7f4 authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[INTERNAL,API] gsl-removal: wrapped GSL functions

wrapped all function and replace function calles with wrapper functions
consistent namespace
...

d4d2662132304aef3d3f06a37cc80c48628725f6 authored over 10 years ago by pkelchte <pkelchte@6adb6e08-d915-0410-941f-83917bcadc18>

[BUILD] added FindEigen3 module

0378bc6781ed848df852dc3c32cce92fcb59ac07 authored over 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL,API] gsl-removal: replace GSL function using std and boost

removed gsl_pow.h
-replaced gsl power function with the std power function
moved gsl-wrapper fi...

7fd5b1cda59eab6caba620cd141fb86cafad19c5 authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[INTERNAL] adaption to use ListUtils (in commented code)

f725b556813180824599cde27e24ac6bc8cb6065 authored over 10 years ago by Hans-Christian Ehrlich <[email protected]>

[BUILD] added find code for eigen3 and included eigen3_include_dir

* eigen3 is header only so no integration into target_link_libraries required

da44a83fb6f9261c2e82d4bd218c7986626c5f95 authored over 10 years ago by Stephan Aiche <[email protected]>

[TEST,NOP] adapted checker to variable test locations and removed svn:keyword test

018453eca3e3e9a2606cf5615626464d82da1ba3 authored over 10 years ago by Stephan Aiche <[email protected]>

[TEST] fixed test dependencies and output names of OpenSwathAnalyzer_test

784d71f21ac04f6f4999efa9d2e31a280a0a3757 authored over 10 years ago by Stephan Aiche <[email protected]>

[NOP] updated feature/ib-spectra-format-export branch with changes from develop

* should allow direct merge on github
* Merge branch 'develop' into feature/ib-spectra-format-...

eb764bb87457aafda91ec01e7f7b8609aa22b348 authored over 10 years ago by Stephan Aiche <[email protected]>

[INTERNAL] use boost::shared_ptr instead of raw pointer

1eb77786e6de9ebaeb003afd485eee5f823904b1 authored over 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #668 from aiche/feature/travis-ci-support

[NOP] added support for travis-ci to OpenMS

71eeff0c70890e25bcd9e5576956b54839d6bf0f authored over 10 years ago by Stephan Aiche <[email protected]>

[NOP] re-enabled AccurateMassSearchEngine_test in travis-ci builds (see #669)

21c1e9b793be49c3cb122e611d32630818c8f76f authored over 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #667 from aiche/feature/improved-boost-handling

[BUILD] improved handling of boost in OpenMS build system

94b0e3c91d3dbad624c331a502f4a2570e5f6c16 authored over 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #669 from timosachsenberg/feature/AMSFix

[FIX] fixed AccurateMassSearch_test

90c5180f68f7cacba560e8f7d1f721b9cec1dced authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] fixed AccurateMassSearch_test

e3c2ca5989765cc57fa1c39efae20e1a6b246f80 authored over 10 years ago by Timo Sachsenberg <[email protected]>

[NOP] replaced echo 'yes' with the --yes flag of add-apt-repository

51ae27da67662540d50765716c9b0e1308ab0f3c authored over 10 years ago by Stephan Aiche <[email protected]>

[BUILD] improved handling of boost in OpenMS build system

* fixed boost compiler errors from boost1.54
* added proper dependency for MRMTransitionGrou...

fabc0be15517000e0cea2951f1b150694162188a authored over 10 years ago by Stephan Aiche <[email protected]>

[NOP] added support for travis-ci to OpenMS

* for now we ignore AccurateMassSearch_test and GzipIfstream_test

24ec553065dfab2bab17f322cc6312281214717d authored over 10 years ago by Stephan Aiche <[email protected]>

added first version of MSGFplusAdapter

d3433dc62b92d459c62fe62bec4c388db4aaa8fe authored over 10 years ago by Mathias Walzer <[email protected]>

[INTERNAL] refactored code for modify string generation

d6ad59fb891226052d675036da07bcc1df5aac97 authored over 10 years ago by Stephan Aiche <[email protected]>

[FEATURE] FileConverter now supports the conversion from cXML to ibspectra

* added conversion code to FileConverter
* added corresponding topp tests
* fixed minor issue...

96b9a1a6b8dc46d5d2a0053cbb5735603e24ec89 authored over 10 years ago by Stephan Aiche <[email protected]>

[API,FEATURE,FORMAT] added IBSpectraFile class to FORMAT

* IBSpectraFile can directly convert cXML to ibspectra format supported by isobar
* includes t...

af7ec73589d052be2d4e92ec07d59d01794ff758 authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] fix coverity 1079427 Non-array delete for scalars

304235fa9081a6b2ee7d4b6368434a1b2102b1e0 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix coverity copy-paste error

- add test cases
- fixes coverity bugs 1079407, 1079409, 1079410, 1079411

2cdb3ccdd04391ba53163bf5bd16c0ae8c17aed3 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix coverity 1079408 Copy-paste error

- fix copy paste error
- add testcase

2337aeb4ae6c25d1442c6a9c412b3e0a4cabf449 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix coverity 1079463 Explicit null dereferenced

1746f2aed2f47999bb7015354972b17c632a1f24 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix resource leak (coverity bug)

coverity 1079515 Resource leak
coverity 1079514 Resource leak

ab0e43229f84e300ea2c1efcf948ec3471d8bcd1 authored over 10 years ago by Hannes Roest <[email protected]>

[FIX] fix coverity 1080511 Uninitialized pointer read

a2567cda27576ebf006707823c63e66856deaa85 authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #664 from aiche/feature/build-system-fix

[BUILD,TEST] build system fixes / cleanups

af05c7206f8ee2f037cb923b033336eb0b7c087b authored over 10 years ago by Stephan Aiche <[email protected]>

[BUILD,TEST] adapted coding style fixes to move to src directory

* addendum to 7a3fc78aa507abe294850fba42719423f81c0d5c

5150e953b002fcf1797f26906b849ba8c07693a4 authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] addendum to 00cc0b89f1c096432c4f13b43da68ee229a6e304, missed to update the FuzzyDiff call

96322916e4f48c5ac42601a0d4be9a417427e44d authored over 10 years ago by Stephan Aiche <[email protected]>

[NOP,TEST] fixed old_files test in checker

5700325e02048863a7ee1ec6e180503853252b11 authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX,TEST] fixed test output collision in ConvertTSVToTraML tests

00cc0b89f1c096432c4f13b43da68ee229a6e304 authored over 10 years ago by Stephan Aiche <[email protected]>

[BUILD] removed all traces of svn from buildsystem

* see #648

e24db976030cbde7848671802742f8208f56b4a0 authored over 10 years ago by Stephan Aiche <[email protected]>

[BUILD] fixed 'No relevant classes found' error

743ed85be1c36f85d54593df6f860c0f9e2824dc authored over 10 years ago by Stephan Aiche <[email protected]>

[BUILD] fixed debug linker error by explicitely linking against OpenMS(GUI) instead of link_directories

84bc2936291958e3d7c98a3c7aac3f2e70a52cda authored over 10 years ago by Stephan Aiche <[email protected]>

[BUILD] moved includes.cmake to src/openms

22f0156cc7de1c3a4feb9b1031c66a55187992d3 authored over 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #659 from aiche/feature/Ctocpp

[NOP] replaced c like file ending C with cpp

3ca33daee74a669b6c719192265b8152177677e0 authored over 10 years ago by Hannes Roest <[email protected]>

[NOP] replaced c like file ending C with cpp

9bc8d670e939bc5dc77c34ba09eccb62054aad6d authored over 10 years ago by Stephan Aiche <[email protected]>

[DOC] some minor fixes to the doc build system

f73f53329579ec997cf4561036419c789a07f69b authored over 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #661 from hroest/feature/pyOpenMSbuild

[BUILD,PYOPENMS] simplify pyOpenMS build system

8b3e6709317102e7d3fe14aa8ae6ce6a72c2f9b3 authored over 10 years ago by Hannes Roest <[email protected]>

[BUILD,PYOPENMS] simplify pyOpenMS build system

- do not copy all files separately into build folder
- add gitignore statement
- add debug Pytho...

33ff86c66c877c388caa029a3805ada4acae4547 authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #662 from aiche/feature/cmake-clean-ups

CMake and docu cleanups w.r.t. to the new layout

36feabdbcec6dce4ef49ead14101e656b551631e authored over 10 years ago by Hannes Roest <[email protected]>

[DOC] removed test_build target from the documentation

* incl. further cleanups related to the repo restructuring

cc3d07d8f2c54c31571f97670550bebc0bc20ec7 authored over 10 years ago by Stephan Aiche <[email protected]>

[BUILD] minor adaptions to the build system

* removing the test_build related infos from the targets target
* updated the pyOpenMS cmake t...

714aca2728320ce25ac1e0f9f4b9068a46df5396 authored over 10 years ago by Stephan Aiche <[email protected]>

Merge pull request #660 from hroest/fix/cython0.20

[FIX] fix Cython 0.20 compatibility issue

aba32a089783618815e8c7f726f2ac26b31dbd90 authored over 10 years ago by Stephan Aiche <[email protected]>

[FIX] fix Cython 0.20 compatibility issue

- This patch makes the code work also for Cython 0.20
- Cython 0.20 seems to be pickier with emp...

32643435f91f18a2c311211a6ac2629f3bafdbb1 authored over 10 years ago by Hannes Roest <[email protected]>

Merge pull request #656 from aiche/layout-restructuring

Repository layout restructuring

7f053021bfde4af4f552d08d7519bcb03b838312 authored over 10 years ago by Hannes Roest <[email protected]>

[BUILD,TEST] moved degenerated files also to topp data since we also need them their

6c53e278922960525c00439358cac5af45218150 authored over 10 years ago by Stephan Aiche <[email protected]>