git://source.jalview.org
/
jalview.git
/ history
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
first
⋅
prev
⋅
next
JAL-2629 adjust placement and optionality of arguments/options
[jalview.git]
/
src
/
jalview
/
io
/
2017-08-16
Jim Procter
JAL-2418 add GPL to main sources
tree
|
commitdiff
2017-08-16
Jim Procter
JAL-2418 source formatting
tree
|
commitdiff
2017-08-16
TZVanaalten
JAL-2629 add hmmbuild validation check which also gets...
tree
|
commitdiff
2017-08-15
tzvanaalten
JAL-2629 fix file loading issues on Mac
tree
|
commitdiff
2017-08-15
TZVanaalten
JAL-2629 selected HMM name now shown in HMMER menu
tree
|
commitdiff
2017-08-14
TZVanaalten
JAL-2629 remove gap padding, and now has option to...
tree
|
commitdiff
2017-08-14
TZVanaalten
JAL-2629 add insert sequence at method on alignment
tree
|
commitdiff
2017-08-14
TZVanaalten
JAL-2629 add padding for .sto annotations to fix issues...
tree
|
commitdiff
2017-08-14
TZVanaalten
JAL-2629 fix incorrect gap insertions on HMM sequence
tree
|
commitdiff
2017-08-13
TZVanaalten
JAL-2629 fix issue where HMM sequences would be too...
tree
|
commitdiff
2017-08-11
TZVanaalten
JAL-2599 HMMs can now be dropped onto the desktop
tree
|
commitdiff
2017-08-10
tzvanaalten
JAL-2629 fix files permission issue on Mac
tree
|
commitdiff
2017-08-08
TZVanaalten
JAL-2599 fix for index issue on node lookup
tree
|
commitdiff
2017-08-07
TZVanaalten
JAL-2629 current hmmer commands are now executed in...
tree
|
commitdiff
2017-08-02
TZVanaalten
JAL-2599 fix issue where parser exported map annotation...
tree
|
commitdiff
2017-07-31
TZVanaalten
JAL-2629 add hmmalign command
tree
|
commitdiff
2017-07-27
TZVanaalten
JAL-2629 implement hmmbuild
tree
|
commitdiff
2017-07-27
TZVanaalten
JAL-2629 moved HMM storage location to placeholder...
tree
|
commitdiff
2017-07-24
gmungoc
spike branch updated from latest features/JAL-2446
tree
|
commitdiff
2017-07-24
tzvanaalten
JAL-2599 .hmm parser should now accept older .hmm files
tree
|
commitdiff
2017-07-20
TZVanaalten
JAL-2599 add ability to process RNA HMMer files
tree
|
commitdiff
2017-07-18
TZVanaalten
JAL-2599 complete documentation for HMM and HMMFile...
tree
|
commitdiff
2017-07-18
TZVanaalten
JAL-2599 modified state transition probability storage
tree
|
commitdiff
2017-06-29
TZVanaalten
transferred the storage position of the HMM to annotations
tree
|
commitdiff
2017-06-27
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
|
commitdiff
2017-06-22
TZVanaalten
fully integrate HMMER3 file format into Jalview
tree
|
commitdiff
2017-06-20
TZVanaalten
restructure file exporter
tree
|
commitdiff
2017-06-15
TZVanaalten
add HMMFile class to read and write HMM files
tree
|
commitdiff
2017-06-14
gmungoc
JAL-2598 Sequence.getSequence return a copy of the...
tree
|
commitdiff
2017-06-09
gmungoc
JAL-2446 merged to spike branch
tree
|
commitdiff
2017-06-07
kiramt
JAL-2591 Hidden columns regions can be output to string...
tree
|
commitdiff
2017-06-07
kiramt
JAL-2591 simplifying hidden columns usage
tree
|
commitdiff
2017-06-02
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
|
commitdiff
2017-06-01
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
|
commitdiff
2017-06-01
Jim Procter
Merge branch 'features/JAL-1648_cache_user_inputs'...
tree
|
commitdiff
2017-05-31
tcofoegbu
Fixed failing tests
tree
|
commitdiff
2017-05-30
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
|
commitdiff
2017-05-29
Jim Procter
Merge branch 'features/JAL-2465_No-mapping_Jmol-structu...
tree
|
commitdiff
2017-05-29
Jim Procter
JAL-2533 update javadoc
features/JAL-2465_No-mapping_Jmol-structures-loaded-via-url
tree
|
commitdiff
2017-05-26
tcofoegbu
JAL-2465 Improvement to re-instate storing recently...
tree
|
commitdiff
2017-05-26
tcofoegbu
JAL-2465 fix to prevent files loaded from the system...
tree
|
commitdiff
2017-05-25
gmungoc
JAL-2557 removal of Sequence.sequenceFeatures
tree
|
commitdiff
2017-05-25
Jim Procter
Merge branch 'develop' into features/JAL-1648_cache_use...
tree
|
commitdiff
2017-05-25
gmungoc
JAL-2050 make SequenceFeature.score final, adjust const...
tree
|
commitdiff
2017-05-25
gmungoc
JAL-2490 test coverage of empty and null feature group...
tree
|
commitdiff
2017-05-23
gmungoc
JAL-2490 find features for export as GFF, JAL-2548...
tree
|
commitdiff
2017-05-23
gmungoc
JAL-2490 tidy code and tests for feature export in...
tree
|
commitdiff
2017-05-23
gmungoc
JAL-2490 improved lookup of features for Export Feature...
tree
|
commitdiff
2017-05-22
gmungoc
JAL-2505 use setter not direct access to sf.description
tree
|
commitdiff
2017-05-22
gmungoc
JAL-2543 identify as JSON before HTML
tree
|
commitdiff
2017-05-22
gmungoc
JAL-2546 JAL-2490 efficient lookup of features, correct...
tree
|
commitdiff
2017-05-19
gmungoc
JAL-2490 refactored test for 'hasFeatures'
tree
|
commitdiff
2017-05-16
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
|
commitdiff
2017-05-16
gmungoc
JAL-2505 refactor to set type and group in SequenceFeat...
tree
|
commitdiff
2017-05-15
Jim Procter
Merge branch 'bug/JAL-2507_rnasecstrstockholm' into...
tree
|
commitdiff
2017-05-15
Jim Procter
JAL-2507 capitalisation for annotation lines generated...
tree
|
commitdiff
2017-05-15
Jim Procter
JAL-2507 case insensitive recognition of annotation...
tree
|
commitdiff
2017-05-15
Jim Procter
JAL-2535 quick hack to implement posterior probabilitie...
tree
|
commitdiff
2017-05-15
tcofoegbu
JAL-2520 improvement to use URL leaf name for creating...
tree
|
commitdiff
2017-05-15
tcofoegbu
JAL-2533 improvement to prune off file extension when...
tree
|
commitdiff
2017-05-15
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
|
commitdiff
2017-05-12
Jim Procter
Merge branch 'features/JAL-2388OverviewWindow' into...
tree
|
commitdiff
2017-05-11
Jim Procter
JAL-2509 JAL-2507 allow whitespace in GS annotation...
tree
|
commitdiff
2017-05-09
Jim Procter
JAL-2509 extend set of brackets recognised by stockholm...
tree
|
commitdiff
2017-05-09
tcofoegbu
JAL-2520 improvement to download and update structure...
tree
|
commitdiff
2017-05-09
Jim Procter
JAL-2507 unpaired RNA marked as ‘ ‘ in Stockholm SS...
tree
|
commitdiff
2017-05-09
Jim Procter
JAL-2507 output secondary structure regardless of prese...
tree
|
commitdiff
2017-05-09
gmungoc
JAL-2505 use constructors to set (what will be) final...
tree
|
commitdiff
2017-05-08
gmungoc
JAL-2505 set type,desc,begin,end,group,score in Sequenc...
tree
|
commitdiff
2017-05-08
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
|
commitdiff
2017-05-05
kiramt
Merge remote-tracking branch
tree
|
commitdiff
2017-05-05
tcofoegbu
JAL-2484 adjusted default cache settings panel's left...
tree
|
commitdiff
2017-05-05
kiramt
Merge remote-tracking branch 'origin/develop' into
features/JAL-2388hiddencolumnschanges
tree
|
commitdiff
2017-05-05
kiramt
Merge remote-tracking branch 'origin/develop' into
tree
|
commitdiff
2017-05-04
tcofoegbu
JAL-1648 improvements: enter key closes the popup and...
tree
|
commitdiff
2017-05-04
tcofoegbu
JAL-1648 resolved CR-JAL-41 review issues
tree
|
commitdiff
2017-05-04
Jim Procter
fix for JAL-2509 - don’t replace all bracket types...
tree
|
commitdiff
2017-05-04
Jim Procter
fix for JAL-2507 - resolve stockholm per residue annota...
tree
|
commitdiff
2017-05-02
gmungoc
JAL-2499 JAL-2403 push 'configure for view' inside...
tree
|
commitdiff
2017-05-02
gmungoc
Merge branch 'develop' into features/JAL-2393customMatrices
tree
|
commitdiff
2017-05-01
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
|
commitdiff
2017-05-01
gmungoc
JAL-2489 JAL-2371 reinstate calls to
tree
|
commitdiff
2017-04-28
gmungoc
Merge branch 'develop' into features/JAL-2393customMatrices
tree
|
commitdiff
2017-04-27
gmungoc
JAL-2492 use SequenceFeatures.getNonPositionalFeatures()
tree
|
commitdiff
2017-04-26
kiramt
Merge remote-tracking branch 'origin/develop' into...
tree
|
commitdiff
2017-04-26
kiramt
Merge remote-tracking branch 'origin/develop' into...
tree
|
commitdiff
2017-04-26
gmungoc
JAL-2490 findFeaturesAtRes with performant feature...
tree
|
commitdiff
2017-04-25
tcofoegbu
JAL-2489 bug fix
tree
|
commitdiff
2017-04-25
kiramt
JAL-2388 Working hidden regions hide/show in desktop
tree
|
commitdiff
2017-04-24
tcofoegbu
JAL-1648 House keeping
tree
|
commitdiff
2017-04-24
kiramt
JAL-2388 Finished split of hidden columns and selected...
tree
|
commitdiff
2017-04-24
tcofoegbu
JAL-1648 added unit test for AppCache
tree
|
commitdiff
2017-04-24
kiramt
JAL-2388 Hidden cols separated from column selection...
tree
|
commitdiff
2017-04-20
tcofoegbu
JAL-2484 minor house-keeping
tree
|
commitdiff
2017-04-20
tcofoegbu
JAL-2484 minor house-keeping and code docs
tree
|
commitdiff
2017-04-20
tcofoegbu
JAL-2484 added improvement to enable clearing cache...
tree
|
commitdiff
2017-04-20
tcofoegbu
JAL-1648 refactored and improved caching architecture...
tree
|
commitdiff
2017-04-11
tcofoegbu
JAL-1648 Fix review issue - remove usage of String...
tree
|
commitdiff
2017-04-03
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
|
commitdiff
2017-04-03
tcofoegbu
JAL-1648 Added improvement to persist cache items to...
tree
|
commitdiff
next