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Merge remote-tracking branch 'origin/releases/Release_2_10_2_Branch' into features...
[jalview.git]
/
src
/
jalview
/
io
/
2017-08-18
TZVanaalten
Merge branch 'develop' into features/hmmer
tree
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commitdiff
2017-08-18
TZVanaalten
JAL-2668 HMMFile export method moved to print method
tree
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commitdiff
2017-08-17
TZVanaalten
JAL-2599 move fillSymbol method to HMFile
tree
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commitdiff
2017-08-17
TZVanaalten
JAL-2599 some slight renaming of variables and methods
tree
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commitdiff
2017-08-17
TZVanaalten
JAL-2629 add documentation to previous work
tree
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commitdiff
2017-08-16
Jim Procter
JAL-2418 add GPL to main sources
tree
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commitdiff
2017-08-16
Jim Procter
JAL-2418 source formatting
tree
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commitdiff
2017-08-16
TZVanaalten
JAL-2629 add hmmbuild validation check which also gets...
tree
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commitdiff
2017-08-15
tzvanaalten
JAL-2629 fix file loading issues on Mac
tree
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commitdiff
2017-08-15
TZVanaalten
JAL-2629 selected HMM name now shown in HMMER menu
tree
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commitdiff
2017-08-14
TZVanaalten
JAL-2629 remove gap padding, and now has option to...
tree
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commitdiff
2017-08-14
TZVanaalten
JAL-2629 add insert sequence at method on alignment
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commitdiff
2017-08-14
TZVanaalten
JAL-2629 add padding for .sto annotations to fix issues...
tree
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commitdiff
2017-08-14
TZVanaalten
JAL-2629 fix incorrect gap insertions on HMM sequence
tree
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commitdiff
2017-08-13
TZVanaalten
JAL-2629 fix issue where HMM sequences would be too...
tree
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commitdiff
2017-08-11
TZVanaalten
JAL-2599 HMMs can now be dropped onto the desktop
tree
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commitdiff
2017-08-10
tzvanaalten
JAL-2629 fix files permission issue on Mac
tree
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commitdiff
2017-08-08
TZVanaalten
JAL-2599 fix for index issue on node lookup
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commitdiff
2017-08-07
TZVanaalten
JAL-2629 current hmmer commands are now executed in...
tree
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commitdiff
2017-08-02
TZVanaalten
JAL-2599 fix issue where parser exported map annotation...
tree
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commitdiff
2017-07-31
TZVanaalten
JAL-2629 add hmmalign command
tree
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commitdiff
2017-07-27
TZVanaalten
JAL-2629 implement hmmbuild
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commitdiff
2017-07-27
TZVanaalten
JAL-2629 moved HMM storage location to placeholder...
tree
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commitdiff
2017-07-24
tzvanaalten
JAL-2599 .hmm parser should now accept older .hmm files
tree
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commitdiff
2017-07-20
TZVanaalten
JAL-2599 add ability to process RNA HMMer files
tree
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commitdiff
2017-07-18
TZVanaalten
JAL-2599 complete documentation for HMM and HMMFile...
tree
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commitdiff
2017-07-18
TZVanaalten
JAL-2599 modified state transition probability storage
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commitdiff
2017-06-29
TZVanaalten
transferred the storage position of the HMM to annotations
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commitdiff
2017-06-22
TZVanaalten
fully integrate HMMER3 file format into Jalview
tree
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commitdiff
2017-06-20
TZVanaalten
restructure file exporter
tree
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commitdiff
2017-06-15
TZVanaalten
add HMMFile class to read and write HMM files
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 Hidden columns regions can be output to string...
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 simplifying hidden columns usage
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commitdiff
2017-06-01
Jim Procter
Merge branch 'features/JAL-1648_cache_user_inputs'...
tree
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commitdiff
2017-05-31
tcofoegbu
Fixed failing tests
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commitdiff
2017-05-29
Jim Procter
Merge branch 'features/JAL-2465_No-mapping_Jmol-structu...
tree
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commitdiff
2017-05-29
Jim Procter
JAL-2533 update javadoc
features/JAL-2465_No-mapping_Jmol-structures-loaded-via-url
tree
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commitdiff
2017-05-26
tcofoegbu
JAL-2465 Improvement to re-instate storing recently...
tree
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commitdiff
2017-05-26
tcofoegbu
JAL-2465 fix to prevent files loaded from the system...
tree
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commitdiff
2017-05-25
Jim Procter
Merge branch 'develop' into features/JAL-1648_cache_use...
tree
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commitdiff
2017-05-15
Jim Procter
Merge branch 'bug/JAL-2507_rnasecstrstockholm' into...
tree
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commitdiff
2017-05-15
Jim Procter
JAL-2507 capitalisation for annotation lines generated...
tree
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commitdiff
2017-05-15
Jim Procter
JAL-2507 case insensitive recognition of annotation...
tree
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commitdiff
2017-05-15
Jim Procter
JAL-2535 quick hack to implement posterior probabilitie...
tree
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commitdiff
2017-05-15
tcofoegbu
JAL-2520 improvement to use URL leaf name for creating...
tree
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commitdiff
2017-05-15
tcofoegbu
JAL-2533 improvement to prune off file extension when...
tree
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commitdiff
2017-05-12
Jim Procter
Merge branch 'features/JAL-2388OverviewWindow' into...
tree
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commitdiff
2017-05-11
Jim Procter
JAL-2509 JAL-2507 allow whitespace in GS annotation...
tree
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commitdiff
2017-05-09
Jim Procter
JAL-2509 extend set of brackets recognised by stockholm...
tree
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commitdiff
2017-05-09
tcofoegbu
JAL-2520 improvement to download and update structure...
tree
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commitdiff
2017-05-09
Jim Procter
JAL-2507 unpaired RNA marked as ‘ ‘ in Stockholm SS...
tree
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commitdiff
2017-05-09
Jim Procter
JAL-2507 output secondary structure regardless of prese...
tree
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commitdiff
2017-05-05
kiramt
Merge remote-tracking branch
tree
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commitdiff
2017-05-05
tcofoegbu
JAL-2484 adjusted default cache settings panel's left...
tree
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commitdiff
2017-05-05
kiramt
Merge remote-tracking branch 'origin/develop' into
features/JAL-2388hiddencolumnschanges
tree
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commitdiff
2017-05-05
kiramt
Merge remote-tracking branch 'origin/develop' into
tree
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commitdiff
2017-05-04
tcofoegbu
JAL-1648 improvements: enter key closes the popup and...
tree
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commitdiff
2017-05-04
tcofoegbu
JAL-1648 resolved CR-JAL-41 review issues
tree
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commitdiff
2017-05-04
Jim Procter
fix for JAL-2509 - don’t replace all bracket types...
tree
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commitdiff
2017-05-04
Jim Procter
fix for JAL-2507 - resolve stockholm per residue annota...
tree
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commitdiff
2017-05-02
gmungoc
JAL-2499 JAL-2403 push 'configure for view' inside...
tree
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commitdiff
2017-05-02
gmungoc
Merge branch 'develop' into features/JAL-2393customMatrices
tree
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commitdiff
2017-05-01
gmungoc
JAL-2489 JAL-2371 reinstate calls to
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commitdiff
2017-04-28
gmungoc
Merge branch 'develop' into features/JAL-2393customMatrices
tree
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commitdiff
2017-04-26
kiramt
Merge remote-tracking branch 'origin/develop' into...
tree
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commitdiff
2017-04-26
kiramt
Merge remote-tracking branch 'origin/develop' into...
tree
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commitdiff
2017-04-25
tcofoegbu
JAL-2489 bug fix
tree
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commitdiff
2017-04-25
kiramt
JAL-2388 Working hidden regions hide/show in desktop
tree
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commitdiff
2017-04-24
tcofoegbu
JAL-1648 House keeping
tree
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commitdiff
2017-04-24
kiramt
JAL-2388 Finished split of hidden columns and selected...
tree
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commitdiff
2017-04-24
tcofoegbu
JAL-1648 added unit test for AppCache
tree
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commitdiff
2017-04-24
kiramt
JAL-2388 Hidden cols separated from column selection...
tree
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commitdiff
2017-04-20
tcofoegbu
JAL-2484 minor house-keeping
tree
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commitdiff
2017-04-20
tcofoegbu
JAL-2484 minor house-keeping and code docs
tree
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commitdiff
2017-04-20
tcofoegbu
JAL-2484 added improvement to enable clearing cache...
tree
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commitdiff
2017-04-20
tcofoegbu
JAL-1648 refactored and improved caching architecture...
tree
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commitdiff
2017-04-11
tcofoegbu
JAL-1648 Fix review issue - remove usage of String...
tree
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commitdiff
2017-04-03
tcofoegbu
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2017-04-03
tcofoegbu
JAL-1648 Added improvement to persist cache items to...
tree
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commitdiff
2017-03-28
gmungoc
JAL-2416 more test coverage of matrix parser
tree
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commitdiff
2017-03-27
gmungoc
JAL-2416 parse score matrices in either NCBI or AAindex...
tree
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commitdiff
2017-03-27
gmungoc
JAL-2416 class Javadoc updates prior to parsing changes
tree
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commitdiff
2017-03-24
gmungoc
JAL-2428 simplify TreeModel constructors, add getOrigin...
tree
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commitdiff
2017-03-24
gmungoc
JAL-1632 TreeChooser renamed CalculationChooser, text...
tree
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commitdiff
2017-03-23
gmungoc
Merge branch 'develop' into features/JAL-2393customMatrices
tree
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commitdiff
2017-03-13
gmungoc
JAL-2438 FeatureColourFinder refactored from FeatureRen...
tree
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commitdiff
2017-03-06
gmungoc
JAL-2428 separate TreeModel from TreeBuilder/NJTree...
tree
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commitdiff
2017-03-01
gmungoc
Merge branch 'features/JAL-2295setChimeraAttributes...
tree
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commitdiff
2017-02-27
gmungoc
JAL-1632 similarity options on TreeChooser panel affect...
tree
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commitdiff
2017-02-21
gmungoc
JAL-2416 support roundtrip print/parse of ScoreMatrix
tree
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commitdiff
2017-02-17
gmungoc
JAL-2416 allow space in score matrix name
tree
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commitdiff
2017-02-17
gmungoc
JAL-2403 constants for "NJ", "AV"
tree
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commitdiff
2017-02-14
gmungoc
Parsing moved to (new) ScoreMatrixFile, drag and drop...
tree
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commitdiff
2017-01-26
gmungoc
Merge branch 'features/JAL-2360colourSchemeApplicabilit...
tree
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commitdiff
2017-01-26
gmungoc
Merge branch 'develop' into features/JAL-2360colourSche...
tree
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commitdiff
2017-01-26
gmungoc
JAL-2344 test fix and code tidy for review comments
tree
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commitdiff
2017-01-25
gmungoc
JAL-2344 push Cache.getProperty("LAST_DIRECTORY") insid...
tree
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commitdiff
2017-01-17
gmungoc
Merge branch 'develop' into features/JAL-2295setChimera...
tree
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commitdiff
2017-01-17
gmungoc
Merge branch 'features/JAL-2360colourSchemeApplicabilit...
tree
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commitdiff
2017-01-17
gmungoc
Merge branch 'develop' into features/JAL-2360colourSche...
tree
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commitdiff
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