Skip to content

Commit

Permalink
Merge pull request #1966 from OpenMS/feature/changelog_removed_PRs
Browse files Browse the repository at this point in the history 
[NOP] Update CHANGELOG
  • Loading branch information
@timosachsenberg
timosachsenberg committed Apr 21, 2016
2 parents d690ce5 + 1d7336c commit b12d9f6
Showing 1 changed file with 2 additions and 309 deletions.
311 changes: 2 additions & 309 deletions CHANGELOG
View file
Original file line number Diff line number Diff line change
Expand Up @@ -294,315 +294,8 @@ XTandemAdapter - default_input_file input-file
XTandemAdapter - min_precursor_charge int 1
XTandemAdapter - precursor_mass_tolerance double 1.5

merged pull requests:
#1876 [FIX,STYLE] cppcheck fixes
#1871 [BUILD SYSTEM] Disable "old-style cast" warning for clang
#1833 [FEATURE] Implemented a PeptideIndexing class
#1869 [FIX] fixed multi-identification run merging
#1844 Feature luciphor2
#1868 [FIX-#1740] MzTabExporter: modification "Phospho (ST)" throws error
#1861 OpenMS/fix/travis_ignored_variable [TRAVIS] previous line was never evaluated to true
#1866 [fix] missing include
#1864 [FIX] fixed some typos in unimod for custom modifications
#1863 OpenMS/GUI-QtStylesheets [GUI] customizable TOPP[AS/View] look and feel using Qt style sheets
#1859 fixes FileInfo TOPP test
#1830 update of HMDB to version 3.6. This resolves issue #1799
#1856 [FIX] fixed conversion of argc enzyme
#1851 FileInfo tests for mzid validation
#1853 Fix/spectra data type
#1855 [FIX] added columns for run level scores in PEP section
#1838 PeptideIndexer performance optimizations
#1845 change of N- and C-terminal characters in mzid output
#1846 Update wrapper for Percolator
#1849 [FIX] fixing duplicate measure id write in mzid, coupled to its Spect…
#1847 ModificationParams and Enzymes section in mzid moved
#1841 Fix phospho scoring
#1787 Fix ConsensusMapNormalizer
#1842 mzid validation in FileInfo switched on
#1837 [FIX] add missing include
#1835 minor improvements to TOPPView
#1832 [Feature] MS/MS precursor filtering by mass list
#1815 [FEATURE] add peak apex to output
#1821 [fix] silent conversion of incomplete strings
#1819 more convenient setting of valid strings in TOPPBase
#1818 [FIX] attempt to fix gcc6 compile error
#1816 Moves the SpectraMerger tool to the correct section
#1812 [FEATURE] add option to generate peptides of max length to digestion of
#1813 [Fix] PeptideIndexer chymotrypsin/"IL_equivalent" problem
#1809 [FIX] MSGFPlusAdapter sets MS-GF+ e-value as peptide score
#1810 [FIX] fix column count for search engine scores in mzTab
#1808 Feature/rename primary ms run
#1807 [FIX] mzIdentML handler stores scores now as float
#1802 [FIX] added search_parameter reading from comet pep.xml
#1794 [FIX] theoretical spectrum generator tries to create X_1 and C_1 ions…
#1796 [FEATURE] comet pepXML file reading
#1550 [FIX] #1509 IDFileConverter crash, unrecognised Carboxyamidomethylation modification
#1795 [INTERNAL] add another string as identifier for MS-GF+ search engine
#1782 [FIX] Refactoring of MRMDecoy
#1791 [BUILD] remove class tests from OS X build
#1778 IDFilter clean-up and extension
#1790 [FIX] nasty bug
#1784 [BUILD] make travis use third party binaries on github
#1786 [DOC] update README
#1781 [FIX] FeatureFinderMultiplex speedup
#1779 [FEATURE] add sanity check for swath windows
#1772 Fix/fix ms1 segfaults
#1776 [DOC] add documentation for the OpenSWATH output format
#1773 [BUILD] remove two tests from travis as they always seem to fail
#1767 [FIX] fix pow issue
#1766 [FIX] fix for Windows
#1766 Fix/pyfix
#1752 Feature/mz iRT correction
#1731 [FEATURE] OpenSwathAssayGenerator
#1705 [FIX-#1703] MzTabExporter: header columns doesn't match with data columns
#1751 [Feature] TheoreticalSpectrumGenerator speedup
#1692 [Fix] phospho scoring
#1753 [Fix] bounds check in spectra access
#1756 [FIX, BUILD] fix cmake warning
#1749 [FIX] gcc compile error
#1743 [REFACTORING] Remove enzyme enum in ProteinIdentification#1411
#1741 OpenMS/feature/lowess_transformation Feature/lowess transformation
#1746 [Feature] osw inmem
#1745 OpenMS/fix/hyperscore_test guide compiler in template argument resolution
#1738 [FIX]#1735 for ConsensusXMLFile
#1737 [FIX] enable Address Sanitizer in Debug mode
#1700 [FEATURE] export from mzID
#1736 [FIX] fixed #1735 added resp. test
#1733 [BUILD] use only OpenMS boost headers
#1720 [FIX] Feature/fixwindowsmzidtestfail
#1732 [BUILD] fix platform for Python 3
#1730 [BUILD] update autowrap version
#1698 [FEATURE] add HyperScore and PScore implementations
#1725 OpenMS/fix/cmake_escaping [BUILD] Update third_party_tests.cmake
#1724 OpenMS/fix/win_build_doc [DOC] Update install-win.doxygen
#1723 OpenMS/fix/mac_build_doc [DOC] mac build documentation updated
#1707 [FIX] added code for peak alignment with relative tolerances
#1721 [PARAM] changed default parameter
#1722 Feature/fix#1699
#1714 [Fix] doc fixes
#1717 [Fix] pyopenms build
#1718 [FIX,TEST] fix tests for Python 3
#1713 [FEATURE] extrapolation from fits
#1715 [FIX] allow user to turn off mass trace length check
#1712 [FEATURE, FIX] fixed bug in comparison operator, added default
#1710 Feature/spellche|ck
#1704 [FEATURE] MetaProSip deuterium label
#1702 [FEATURE] faster digestion of unmodified string
#1653 [FEATURE] OpenSWATH: UIS Scoring
#1695 [FIX] fixes mzTab to tsv R scripts and wrappers
#1675 [FIX] schema simplifications and adaptation of enzyme entry
#1690 missing macro added to struct DeltaMass
#1689 OpenMS/fix/win_compile_putenv Update File_test.cpp
#1682 label sets for MultiplexDeltaMasses
#1688 [FIX] compile errors on windows
#2 [PYOPENMS] Add missing method declaration and update inline docs
#1680 [FEATURE] retain search parameter units
#1686 [FEATURE] make OpenMS home directory configurable by environmental
#1687 Improvements/Fixes to HighResPrecursorMassCorrector
#1684 [FEATURE] Xtandem-Adapter external config
#1679 MS-GF+ adapter converts mzIdentML directly to idXML
#1669 [FEATURE] Feature/qc injectiontimes
#1681 [FIX] forgot to fix fido tests
#1677 [FEATURE] MzMLSplitter: include total number of parts in output file names
#1676 [FIX] minor fix for warnings in mzidentml parser
#1664 [FIX] Fixed missing space in FORMAT/PepXMLFile.cpp
#1673 correction of generic R script wrappers for mzTab to tsv conversion
#1674 fix MyriMatchAdapter for MyriMatch 2.2
#1667 [Feature] featureXML / consensusXML multiple evidence support
#1666 [Feature] idXML multiple evidence support
#1505 Fix/msgf mzid read
#1662 Feature/qc creator tic vs ric
#1471 Feature/search parameter units
#1665 [TEST] add test for new function getFeatureList
#1661 PhosphoScoring: marked "in"/"id" parameters as required
#1660 [FEATURE] add function that returns simple list
#1658 [Fix] annotate correct ms path
#1657 [NOP] made rewriting the SourceFile entry a parameter and private method
#1656 [FIX] changed relative path to absolute one so it is the same on every
#1654 [Fix] mgf space/tab while loading making it more robust
#1650 [FEATURE] TextExporter optionally export PeptideIdentification and PeptideHits metavalues
#1646 [FIX] adapted user parameter parser for idXML files
#1652 [Refactoring] of mass shift generation in FeatureFinderMultiplex
#1644 [FEATURE, UTIL] New utility for splitting mzML files
#1647 [FEATURE] order independent QT algorithm
#1649 [BUILD] try to fix build
#1645 [TEST] add test for corrupted ms-numpress file
#1638 [FEATURE] Feature/ms spectrum nearest peak
#1641 [FIX] handles invalid mzML without data type
#1643 [Build] Feature/enable as
#1642 [build] Feature/address sanitizer
#1640 Fix/tests
#1540 [FEATURE] Feature/set primary ms run
#1631 [FIX] Fidoadapter: improved PEP handling, removed "prob_param"
#1639 [FIX] attempt to fix SVNWrapper fail on MacOS travis
#1630 [FEATURE] minor optimizations for profile mode
#1637 OpenMS/fix/compile_warning [FIX] attempt for a quick compile warning fix
#1634 [FIX] mtd fix when MS2 are present
#1635 [FIX] DataProcessing comperator fix
#1613 poshul/OpenMS/develop [FEATURE] User defined averagines
#1627 MascotAdapterOnline: use input file name as search title
#1632 [TEST] update new files with indexed mzML
#1629 minor optimizations for profile mode
#1626 [FEATURE] more speed optimizations
#1622 [FIX] minor optimization
#695 [Feature] replace data processing
#1623 Fix/pyopenms fix
#1620 [FIX] replaced sort by stable sort in rank sorting
#1610 [FEATURE] FeatureLinkerUnlabeledQT speed and memory improvements
#1334 [FEATURE] Feature/pep xml prophets
#1355 OpenMS/feature/indexed_mzml [FEATURE] write mzML index by default
#1617 OpenMS/fix/KNIME_WIN_MSGFPlus [KNIME] Update binaries_win.ini
#1581 OpenMS/build/travis-osx [Build] travis osx
#1614 [FIX] fix bug in VS related to multiple static variable definitions in a
#1587 Helper class for spectrum look-up, used for adding RT information to ID data
#1611 [FIX] attempt to fix error C2332: 'struct' : missing tag name caused by
#1608 [build] migration to docker infrastructure in travis
#1593 [Feature] Splitter node for TOPPAS
#1605 Feature/lowess
#1607 [FIX] TOPPView: add margins around data range (2%)
#1606 [FIX] pyopenms fix
#1592 [TOPPAS] make download of TOPPAS a little more verbose
#1604 [Fix] base64 BigEndian encoding
#1602 [FEATURE] fast linear lowess
#1521 Feature/resampler ppm
#1600 [REFACTOR] Feature/alignment refactor interface
#1601 [TEST] fix
#1363 Feature/more tests
#1583 OpenMS/feature/nonroot_installdocs [DOC] installation docs if you dont have root
#1595 [Refactor] Feature/refactor ffmetabo
#1598 [Refactor] PoseClustering
#1594 [BUILD] revert changes from #1571
#1596 [FEATURE] allow output of progress for featureXML storage
#1597 [NOP] Fix/whitespace docu
#1571 [TEST] disable PeakPickerWavelet test 3 (fails on travis with gcc)
#1585 FeatureFinderMultiplex mzq output fix
#1588 Fix/mtd
#1586 Toppas filename generation
#1573 [GUI] GUI improvements for TOPPAS and TOPPView
#1579 [FIX] proper argument quoting in GenericWrapper-TTD's
#1576 Feature/set qc
#1578 [TEST] change from release to debug to fix PeakPickerWavelet test 3
#1547 [Fix] warning fix
#1569 index variable change in MapAlignerPoseClustering
#1563 [TOPP] force flag circumvents java time-outs in MSGFPlusAdapter
#1564 [NOP] minor optimization to FeatureFinderMultiplex
#1562 [DOC,TEST] for StablePairFinder / FeatureDistance
#1561 [BuildSystem] better log when configuring
#1560 [DOC] MSGFPlusAdapter error message updated
#1556 [NOP] fix name in active maintainers
#1554 [FIX] pyopenms fix
#1553 [FIX] travis CI build
#1545 [#Fix] file info segfault on empty consensusXML input
#1551 [FIX] winfix2
#1542 [FIX] attempt to fix windows
#1458 [Fix #1411] EnzymaticDigestion support for new Enzyme / EnzymeDB class
#1539 [FEATURE ]FileMerger: added option to concatenate files in RT
#1531 Refactoring of map alignment code
#1532 [FEATURE] Implement matched whitelist in FuzzyDiff
#1533 [FIX,PYOPENMS] after #1440
#1508 [FIX] IsotopeDistribution bug for gapped isotopes (e.g. Bromine)
#1529 OpenMS/fix/travis_sourceforge_epic_fail [TRAVIS] don't fail if sourceforge is down
#1520 [DOC] add documentation and Python code to Base64 test
#1526 [FEATURE] added meta info interface to featuremap
#1522 [FIX] format maxima and hires the same way
#1519 [FIX-#618] fix spelling errors
#1492 Reworking of parameters/defaults for protein FDR calculations
#1440 [FIX] Issue #1310: Fixes weight calculation for single AA ions.
#1490 [FEATURE] Better protein ID support for mzTabExporter
#1507 [DOC,FIX] as suggested by W Wolski
#1498 WindowsOS: add a convenience batch file
#1497 [FIX] added search engine information and PSM_ID
#1486 [FEATURE] IDScoreSwitcher: new UTILS tool for dealing with scores on ID data
#1495 [FIX] extended blacklisting in FeatureFinderMultiplex
#1496 [Feature] mz tab improved mod support
#1494 ConsensusID: avoid warning message
#1478 [FEATURE] TOPPAS convenience functionality
#1491 [CI] split tests for CI build into TOPP vs. class-tests
#1493 [FIX] SpectraMerger seg fault
#1489 [DOC, BINARY] add meta data for Fedora
#1488 [DOC] Added FeatureFinderIdentification to main TOPP documentation page (fixes #1487)
#1481 New ConsensusID algorithm "worst"
#1482 [DOC] Improved wording of note regarding mzid support
#1457 R script for mzTab to csv conversion
#1476 [INTERNAL] StopWatch convenience toString() op
#1475 [FIX, FEATURE] GaussFitter: return valid sigma values
#1474 [FIX, DOC, INTERNAL] Fix enzymesDB
#1470 [PARAM] SpectraMerger default params changed
#1472 fix for #1467
#1467 TOPPView: enable viewing the next data point in 1D View
#1465 [FIX] Removed invalid usage of inherited member stdev2_ undefined in …
#1464 [feature] add MedianAbsoluteDeviation to Math::
#1463 [Feature]Improvements to SpectraFilterNormalizer
#1459 [FIX] fixed wrong number of study variable columns
#1455 [FIX] fix compiler errors for GUIHelpers on mac osx
#1454 TOPPAS: small usage improvements & refactoring
#1227 [Feature] support mismatches in PeptideIndexer
#1288 [FIX] fix #1285 #1297 Explicitly model enzymes in OpenMS
#1452 [TESTS] Changed FidoAdapter tests according to changes in the Adapter.
#1442 FileInfo, field renamed
#1448 [fix] Windows compile errors
#1424 [FEATURE] Wrappers for Percolator (MS-GF+ and Mascot)
#1438 [FIX] Fixed clang compile error introduced in merge #1403
#1433 [FEATURE ] mz tab protein export
#1403 [FIX] IDPEP fails on certain datasets. Fixes #1376.
#1434 [FEATURE] Meta value export for TextExporter
#1430 [FEATURE] add FeatureFinderMultiplex to TOPPView
#1418 [FEATURE] TOPPAS: allow for custom output folder names
#1417 skip empty spectra in FeatureFinderMultiplex filtering step
#1405 [FIX] fixes pyopenms compilation
#1402 Cubic Spline -- 2nd
#1404 [FIX] fix for clang issue with default parameters containing ,
#1410 TOPPAS tool progress
#1401 Speedup (x 3-4) cubic spline 2d
#1396 [FEATURE] new flag use_noise_suppression in XTandemAdapter
#1398 [FIX] blind attempt to fix clang compile error
#1391 [FEATURE] initial merge of MetaProSIP for stable isotope probing experiments
#1394 labels in consensusXML for knockouts added
#1388 [feature] enable individual temp directory in file_post tags of TTD files
#1387 [FIX] WindowsOS compile errors
#1383 [FEATURE] TOPPAS: better error messages and suffix for output filenames
#1366 ProteinQuantifier: use peptide-level protein inference results
#1380 [DOC] minor cleanup of AMS
#1358 [Feature] Greedy resolution of groups in FidoAdapter based on Fido output
#1348 [FEATURE] protein name added to TextExporter output
#1371 [FIX, DOC] Small fixes to MSSimulator
#1362 [TEST] add csv writing test for OpenSwathWorkflow
#1346 [FEATURE] added filtering by protein accession stringlist
#1351 [FIX] TOPPAS signals
#1177 [FEATURE ]Extend peptide mapping capabilties
#1353 TOPPView: fix vertical scrollbar behaviour
#1373 [FIX] change MzTabExporter output format from csv to tsv
#1369 [Fix/warnings] in clang
#1364 OpenMS/fix/osw_fix Fix/osw fix
#1370 Fix/winfix
#1365 [FIX] (second) attempt to fix MSVS compilation errors
#1360 [FIX] attempt to fix MSVS compilation errors
#1354 Fix TOPP/UTIL documentation
#1244 [Feature] PP-Wavelet's area computation should not depend on m/z spacing
#1350 [TEST FIX] fix pyOpenMS tests
#1328 ConsensusID rewrite and extension
#1291 [FEATURE] optimized base64 string handling
#1295 Feature/mzml hotpath
#1335 [FEATURE] added ciRT to OpenSwathWorkflow
#1296 Feature/speed improvements indexed
#1349 [DOC] Extended IsobaricAnalyzer documentation
#1294 Feature/speed improvements
#1293 Feature/base64 nowhitespacecheck
#1302 [FEATURE] substantially faster indexed mzML access
#1329 AccurateMassSearch: export MassTraceIntensities to mzTab
#1276 [FEATURE] Feature/adopt pp max
#1282 [Feature] Readable numbers in TOPPView's status bar
#1129 [FEATURE] correct precursor to feature
#1345 [FIX] OpenSwathAssayGenerator: Compatibilty with VS10.0
#1344 modified logarithm for Visual Studio 10
#1337 [FEATURE] Feature/sn warnings
#1292 [Feature] base64 checks
#1338 [FEATURE] OpenSwathAssayGenerator
#1323 [FEATURE] new spectra averaging feature in SpectraMerger
#1332 [FEATURE] FFMetabo: quantify mass traces using median
#1311 [FEATURE] PeakPicker-Wavelet speedup
#1336 [Fix] toppview pen size in 2D View
#1341 sync of develop with master
Note: If you are interested in details on the number of merged pull requests or the state of individual issues.
You can simple query this information from our github repository (see e.g. https://help.github.com/articles/searching-issues/).

------------------------------------------------------------------------------------------
---- OpenMS 2.0 ----
Expand Down

0 comments on commit b12d9f6

Please sign in to comment.