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

Revert "Merge pull request #15 from Sharmaditi291/feature/NuXL_PD3.0"

This reverts commit ecaa62fe200295fd7e70b0c6c2418e3656f31a6a, reversing
changes made to 5d0b33ba...

cff1899c2dc2d0d747e0865946d8a4128c80a2d6 authored about 2 years ago by Arslan <[email protected]>

Merge pull request #15 from Sharmaditi291/feature/NuXL_PD3.0

Updated to PD3.0 with changes

ecaa62fe200295fd7e70b0c6c2418e3656f31a6a authored about 2 years ago by Arslan-Siraj <[email protected]>

Updated to PD3.0 with changes

6a71415bde2138c5b36df4df552db55095f8b586 authored about 2 years ago by Saditi29 <[email protected]>

2.0.3 RC2: Fixed XIC filtering param bug (no XLs)

5d0b33ba428d9b8bbe7a23b6cae27aeeaa19dc31 authored over 8 years ago by Johannes Veit <[email protected]>

Switched to VS2015, first commit after 2.0.3 RC1

cdc181d81d1a73042a099a52e6074fdcda27d83b authored over 8 years ago by Johannes Veit <[email protected]>

Interconnect all result tables (see issue #7)

3c8cb52e3fb81facb4691805036a1e0824b36a30 authored over 8 years ago by Johannes Veit <[email protected]>

Filter out unidentified features by default

28d7935d58ee64af199b968f273d24785f927ec4 authored over 8 years ago by Johannes Veit <[email protected]>

Fixed yet another cause for issue #1

feaa2fc847a90f8f8e7d7dbcee8cf6543f5f5599 authored over 8 years ago by Johannes Veit <[email protected]>

More fine-grained exception handling

1f7bbc24c5b321c90e4f3568c2ed73ea434132e2 authored over 8 years ago by Johannes Veit <[email protected]>

Fixed another cause for issue #1

64c6830e78cfbc6d02976d22213c2006793ef173 authored over 8 years ago by Johannes Veit <[email protected]>

Improved error message for "Show spectrum" exception.

485609cd5307116d158311f3f4ce5e4404deb72a authored over 8 years ago by Johannes Veit <[email protected]>

Limit protein column width (see issue #3)

0cd97039d0f4bce22f4699d8d433582c66bf3778 authored over 8 years ago by Johannes Veit <[email protected]>

Fixed issue #8

47fea27c294fc4b1e69908ea7405f8ab7207138e authored over 8 years ago by Johannes Veit <[email protected]>

Fixed issue #1

5a93b947988b3350068b464e12381550f92821da authored over 8 years ago by Johannes Veit <[email protected]>

Fixed issue #9

95483524d7632d1b4b4f275f314b924ba47fd10f authored over 8 years ago by Johannes Veit <[email protected]>

Round RNPxl scores to 4 digits (see issue #3)

f01332675fb0725690f8fee80944bd65b15dec4f authored over 8 years ago by Johannes Veit <[email protected]>

Connected RNPxl items and MS/MS spectrum infos (see issue #3)

7b51af76cb971c041014eb3b5171b85c52fa79de authored over 8 years ago by Johannes Veit <[email protected]>

Fixed issue #2

652ff1a5bcfc6d5fed5cc366ff4ffe984bb76a6d authored over 8 years ago by Johannes Veit <[email protected]>

Merge branch 'master' of https://github.com/OpenMS/PDCommunityNodes

Conflicts:
src/LFQProfilerConsensusNode.cs

e9d0b4c6b60c95061d2aa3925d398989f251be0a authored over 8 years ago by Johannes Veit <[email protected]>

Fixed issue #5

07922bd573386c059c23d6c48bb001831d2c97c4 authored over 8 years ago by Johannes Veit <[email protected]>

Fixed issue #5

e24f83764c661868bc4e901f1b7e04fc6e331dd6 authored over 8 years ago by Johannes Veit <[email protected]>

RNPxl bugfixes

c8c6509f14faffe2378f1467cf531ab16bbb2985 authored almost 9 years ago by Johannes Veit <[email protected]>

Restructured repository

16d5c5223937adc7813697b6186fb121e29cceb9 authored almost 9 years ago by Johannes Veit <[email protected]>

Changed default params, added manuals

72180c25dce0a3dc7689a80b7f9396d6742df6d2 authored almost 9 years ago by Johannes Veit <[email protected]>

add RAW file names to abundance columns

9079f2a4bc2eb37c2d98683415fef09bfadfaed7 authored almost 9 years ago by Johannes Veit <[email protected]>

Added fragment_adducts parameter to RNPxl workflow

9e1ba9dc99c89a4199d81c0b4eabefacf1c44227 authored almost 9 years ago by Johannes Veit <[email protected]>

NOP

8aa3992b192be72a3291e96339842143b66e92f6 authored almost 9 years ago by Johannes Veit <[email protected]>

Fix ZedGraph bug when saving EMF files (handles were not closed)

444f031c8e82d37a7c3295daf456d729c0efdf7a authored almost 9 years ago by Johannes Veit <[email protected]>

Fix unique peptide quant

c7d113fbb7a16a9fc3205370b4abd810a5f00a10 authored almost 9 years ago by Johannes Veit <[email protected]>

Fix bug with path names containing commas

97d292347ad18832f543a4bc486416faa0f76904 authored almost 9 years ago by Johannes Veit <[email protected]>

Removed enzyme parameter, changed some defaults

dfb96678e9f780a246bdfa9bc1f58ac8b65243fd authored almost 9 years ago by Johannes Veit <[email protected]>

Add protein FDR; hide ID conflict resolution

e62f06cd4c8d0e9a915eda83bd2eba90d4fddf88 authored almost 9 years ago by Johannes Veit <[email protected]>

Use MapAlignerIdentification, reordered some of the steps

b96c3d943fb9f32e1cde337c574067f23144fce1 authored almost 9 years ago by Johannes Veit <[email protected]>

Make ID conflict resolution optional (advanced)

e6f3fdabd9129c9cbaabd316dc45d886a5273691 authored almost 9 years ago by Johannes Veit <[email protected]>

Use IDConflictResolver

98c20beb91954615aa1993b3745fa842a9e4998e authored almost 9 years ago by Johannes Veit <[email protected]>

Better defaults, new parameters (Fido prefiltering, IDMapping via precursor/peptide)

acffd949cb4feb793b70e9cbd2ca838d44ac2a1e authored almost 9 years ago by Johannes Veit <[email protected]>

[FIX] normalization bug

3799df61348ebcd006d754233dcdbd19ca07a279 authored almost 9 years ago by Johannes Veit <[email protected]>

Merge branch 'master' of https://github.com/OpenMS/PDCommunityNodes

ffac74e05978ea6f991484b91c65488fac6b4579 authored almost 9 years ago by Johannes Veit <[email protected]>

[FEATURE] accession / description filtering for normalization

146dc82269f5a28f222f005392aae2befaf8eee3 authored almost 9 years ago by Johannes Veit <[email protected]>

[FEATURE] accession / description filtering for normalization

68b30b6a59f25976fbfa756cefab026d836f53e7 authored almost 9 years ago by Johannes Veit <[email protected]>

[FEATURE] add parameter to choose normalization method

9727bd239cc1d588bb7c944a3799051e393bb2b3 authored almost 9 years ago by Johannes Veit <[email protected]>

Fixed bug with protein-terminal modifications

3ba61d8dca111fc610b3fe934325630661fc8596 authored about 9 years ago by Johannes Veit <[email protected]>

Fix UI crash on "Show Spectrum" for spectra w/o annotation

344cec55368d55d339e55048983f3efacc77e93a authored about 9 years ago by Johannes Veit <[email protected]>

Add protein descriptions to features table

fb0ec7be9888adf0be53455f8a398b4a0d32054e authored about 9 years ago by Johannes Veit <[email protected]>

Fixed warnings

bb2e51f354e317596fdac944cbf6fe5f24f3b09c authored about 9 years ago by Johannes Veit <[email protected]>

Minor changes (comments, etc.)

82245c451adae15b9c42ea43bb466b480231055a authored about 9 years ago by Johannes Veit <[email protected]>

Removed a couple of TODOs

eb81e0cc2a40ab0d42a6ac304245a1ae78c96985 authored about 9 years ago by Johannes Veit <[email protected]>

Added minimal method docs, some more formatting

ffce2702ad5cf282e3d2e7fd3cca243c7765b938 authored about 9 years ago by Johannes Veit <[email protected]>

Merge branch 'doc-and-formatting'

Conflicts:
LFQProfilerProcessingNode.cs
OpenMSCommons.cs

974fde6372f42cbd323921b330377a06ba950a03 authored about 9 years ago by Johannes Veit <[email protected]>

Moved FixCVParams() to OpenMSCommons

9c101223054e58e8ed919232d8221d946d277510 authored about 9 years ago by Johannes Veit <[email protected]>

Refactored node logger delegates

d908d770e91e50e35a3e3857c95297e10891673e authored about 9 years ago by Johannes Veit <[email protected]>

Added protein descriptions to quantified proteins / peptides table

bb7bb63bf530c996e2d36bead9dac730dabd32bc authored about 9 years ago by Johannes Veit <[email protected]>

improved documentation, some formatting

d379e8d1e3389dda66291f5b57335daf983bcd17 authored about 9 years ago by Johannes Veit <[email protected]>

Set OPENMS_DATA_PATH correctly

b6d96c69f003e89e170980cab48540f6cafae6fc authored about 9 years ago by Johannes Veit <[email protected]>

Remove obsolete CV terms from exported mzMLs

170da870cc59e0b7136934e7a3c3e166981c18bf authored about 9 years ago by Johannes Veit <[email protected]>

Adapted idXML export to new FidoAdapter version

9cfe043ef81ee6a52b1b4f8b5f3df08ee93fbe07 authored about 9 years ago by Johannes Veit <[email protected]>

Adapted to userParam -> UserParam switch in consensusXML

cf576afaf799592ef40cd5eb5fb84c61e36a6c5c authored about 9 years ago by Johannes Veit <[email protected]>

OpenMSCommons:ModSequence now substitutes "X" AAs

c197544f3a913bc511b0e7c7d96eec947ac28f32 authored about 9 years ago by Johannes Veit <[email protected]>

refactor

aa22da33464d1d488962d8ec72a963ba5c5f14dc authored about 9 years ago by Johannes Veit <[email protected]>

Feature: multi-consensus step of batch-mode processing steps

9adba75abdcb81d5f2d9dc47015a177290b1c19b authored about 9 years ago by Johannes Veit <[email protected]>

Improved LFQProfilerConsensusNode progress bar

7d627d4811e092da351b9c589eca6ec488e0861f authored about 9 years ago by Johannes Veit <[email protected]>

Improved LFQProfilerProcessingNode progress bar

ea51501a1b3566267a15f3ea7fe5ec4b9b5fdfdd authored about 9 years ago by Johannes Veit <[email protected]>

Fixed RNPxl progress bars

ef4618283309e84fa6b7c047e5f9b616a7c567d5 authored about 9 years ago by Johannes Veit <[email protected]>

Some renaming of files and node classes

267fd23e692f0732e9d00516c1185af9825fd99a authored about 9 years ago by Johannes Veit <[email protected]>

Fixed bug (no IDs in feature table) from refactoring

4f189bfff585675fc6406ab9a9413a7b923fb6d6 authored about 9 years ago by Johannes Veit <[email protected]>

Removed OpenMSFile.cs and references

b1b66e9d5f52c9e0ac6460624547d56c3266c3b9 authored about 9 years ago by Johannes Veit <[email protected]>

Capitalized method names

4a878d17f030ed4cfafa01af895a17f770004606 authored about 9 years ago by Johannes Veit <[email protected]>

finished first round of extract method

73e3f1098937be290bba6a3902947267546a12a9 authored about 9 years ago by Johannes Veit <[email protected]>

couple of extract methods

66423606010b912f26a5f98f609457a2cb8eb04e authored about 9 years ago by Johannes Veit <[email protected]>

Added a couple of #regions

f41a13627bb753281c286c4232e8737bf9ce64ea authored about 9 years ago by Johannes Veit <[email protected]>

Use proper IDs for storing PSM IDs in XML

2a133a3f3e31166bd462c08d26958cb0b4734368 authored about 9 years ago by Johannes Veit <[email protected]>

LFQProfiler: added enzyme parameter, set specificity = none in PI

ff410dd5ab96d54464ac5fdc45abca1b3b56a2ae authored about 9 years ago by Johannes Veit <[email protected]>

RNPxl: use 3 decimals for m/z in spectrum annotations

a0ccd46f2f2ca7e681f69940789c51c519e28255 authored about 9 years ago by Johannes Veit <[email protected]>

Merge branch 'pwiz-spectrum-viewer'

142634e716689ed281583ab44d280898497423fc authored about 9 years ago by Johannes Veit <[email protected]>

Moved "Show spectrum" button to the front

3f102c15c9accfbd8b609c981e3c6fed562d9e54 authored about 9 years ago by Johannes Veit <[email protected]>

Added m/z to peak annotations

0a4b2045af800969e5ada8f523a84b8dabd58f73 authored about 9 years ago by Johannes Veit <[email protected]>

Removed unused code

defbd718e82361c88590119bfd3986a26dc8b887 authored about 9 years ago by Johannes Veit <[email protected]>

Display fragment annotations in spectrum viewer

49f63e24e25ff36a01542b92268926fcb2958cc0 authored about 9 years ago by Johannes Veit <[email protected]>

Repaired graph title

93d274f3b848e839305f33de7cb97f5cf5feb846 authored about 9 years ago by Johannes Veit <[email protected]>

Switched to using SpectrumGraphItem as CurveItem

999ee512bcac44db5df15ff785cc4541c42540f3 authored about 9 years ago by Johannes Veit <[email protected]>

Some renaming

f84500446cf6460367181d1dd35cfd739968f000 authored about 9 years ago by Johannes Veit <[email protected]>

Use MSGraphControl instead of ZedGraphControl

ecfb115470b8e699d496cf5f91de86eafc51229c authored about 9 years ago by Johannes Veit <[email protected]>

Renamed AdHocSpectrumView stuff to SpectrumView

dc255cc86b433536096c43c6150dfdefc597a0e4 authored about 9 years ago by Johannes Veit <[email protected]>

Show useful legend in spectrum vis

a4b52916624c4a0bf3ed0d8be7724e1b97d432b8 authored about 9 years ago by Johannes Veit <[email protected]>

Removed split container, made ZedGraphControl scalable

5f028808cb18ff55a5151d932a5e5c1eecdc6a91 authored about 9 years ago by Johannes Veit <[email protected]>

First steps with ZedGraph-based spectrum visualization

17aef92590a192ddf31b01df8f019c5e5416229b authored about 9 years ago by Johannes Veit <[email protected]>

Replaced old widget by ZedGraphControl

741bdeed035e7d60fba11cf4de8a89c73ee997cc authored about 9 years ago by Johannes Veit <[email protected]>

More pwiz code

72cf4c7c6abd016006afc3072ebfd309aab7ea05 authored about 9 years ago by Johannes Veit <[email protected]>

Changed enzyme parameter to StringSelectionParameter

ab078d02ad25bf1e1192e84cd9980d78c580f60c authored about 9 years ago by Johannes Veit <[email protected]>

Added some code from pwiz spectrum viewer

4510c32e6758334c256699362b50af81e4e82711 authored about 9 years ago by Johannes Veit <[email protected]>

Added "Show spectrum" button to RNPxl result rows

fe7cf793d355bc6018131a4066f35767d1e4927d authored about 9 years ago by Johannes Veit <[email protected]>

Initial commit

f44e2f5a6b69f08cf2f996d57be3d8604dc80f7b authored about 9 years ago by Johannes Veit <[email protected]>