gmungoc [Wed, 16 Nov 2016 12:23:33 +0000 (12:23 +0000)]
Merge branch 'develop' into features/JAL-2295setChimeraAttributes
Conflicts:
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
src/jalview/gui/ChimeraViewFrame.java
gmungoc [Wed, 16 Nov 2016 10:53:03 +0000 (10:53 +0000)]
JAL-2296 don't copy attribute with value False
gmungoc [Wed, 16 Nov 2016 10:50:37 +0000 (10:50 +0000)]
JAL-2295 don't exclude RESNUM from transfer to Chimera
tcofoegbu [Mon, 14 Nov 2016 19:47:59 +0000 (19:47 +0000)]
JAL-2322 Refactored unified architecture for data + html exporting for SVG & BioJS msa exports
gmungoc [Mon, 14 Nov 2016 12:31:30 +0000 (12:31 +0000)]
JAL-2296 new code and refactoring for 'copy Chimera attribute to
features'
gmungoc [Mon, 14 Nov 2016 12:30:17 +0000 (12:30 +0000)]
JAL-2295 don't copy 'Chimera' features back to Chimera
gmungoc [Mon, 14 Nov 2016 12:29:24 +0000 (12:29 +0000)]
JAL-2296 parse Chimera atomspec to AtomSpec
gmungoc [Mon, 14 Nov 2016 12:28:57 +0000 (12:28 +0000)]
JAL-2296 report whether SequenceFeature actually added to sequence
gmungoc [Mon, 14 Nov 2016 09:43:28 +0000 (09:43 +0000)]
JAL-2295 JAL-2296 skeleton 'attributes to features'; renamed methods
with a view to pull-up
tcofoegbu [Fri, 11 Nov 2016 17:23:24 +0000 (17:23 +0000)]
JAL-2277 Refactored out duplicated method - printUnwrapped() in HtmlSvgOutput, externalised facebox script, and made other minor housekeepings
gmungoc [Fri, 11 Nov 2016 14:02:39 +0000 (14:02 +0000)]
Merge branch 'develop' into features/JAL-2295setChimeraAttributes
gmungoc [Fri, 11 Nov 2016 13:42:52 +0000 (13:42 +0000)]
JAL-2295 tests now 'network-free' with local PDB and SIFTS files
gmungoc [Fri, 11 Nov 2016 13:42:06 +0000 (13:42 +0000)]
JAL-2295 JAL-2269 JAL-2319 mockable SIFTS file, fix to mapping details
gmungoc [Fri, 11 Nov 2016 13:40:57 +0000 (13:40 +0000)]
JAL-2295 improved integrity of 'isFinishedInit' flag
gmungoc [Fri, 11 Nov 2016 13:40:04 +0000 (13:40 +0000)]
JAL-1270 corrected command-line args
gmungoc [Fri, 11 Nov 2016 09:15:03 +0000 (09:15 +0000)]
JAL-2295 set finishedInit to false before checking files loaded
gmungoc [Fri, 11 Nov 2016 08:52:53 +0000 (08:52 +0000)]
JAL-2295 test that verifies transfer of features to Chimera attributes
gmungoc [Fri, 11 Nov 2016 08:51:36 +0000 (08:51 +0000)]
JAL-2295 sorted properties for readability
gmungoc [Fri, 11 Nov 2016 08:50:57 +0000 (08:50 +0000)]
JAL-2295 (optionally) return Chimera command reply
gmungoc [Fri, 11 Nov 2016 08:50:02 +0000 (08:50 +0000)]
JAL-2295 correct test for Float.isNaN(score) !
tcofoegbu [Thu, 10 Nov 2016 16:11:36 +0000 (16:11 +0000)]
Merge branch 'bug/JAL-2317_jmol_chimera-chain-factorisation' into develop
tcofoegbu [Thu, 10 Nov 2016 15:57:41 +0000 (15:57 +0000)]
Merge branch 'develop' into bug/JAL-2317_jmol_chimera-chain-factorisation
tcofoegbu [Thu, 10 Nov 2016 15:55:51 +0000 (15:55 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Thu, 10 Nov 2016 15:45:33 +0000 (15:45 +0000)]
JAL-2317 Fixed Chimera command for hiding/showing distinct chains
gmungoc [Thu, 10 Nov 2016 13:01:23 +0000 (13:01 +0000)]
JAL-2295 additional tests, stronger sanitisation of attribute name
tcofoegbu [Thu, 10 Nov 2016 11:56:51 +0000 (11:56 +0000)]
Bugfix to enable accurate chain extraction/association with models loaded in Chimera, refactored and factorised some duplicated codes with Jmol viewer implementation.
gmungoc [Wed, 9 Nov 2016 16:58:33 +0000 (16:58 +0000)]
JAL-2295 set attributes commands include feature value, sent via file
gmungoc [Wed, 9 Nov 2016 16:57:46 +0000 (16:57 +0000)]
JAL-2295 single constant for "RESNUM" feature name
gmungoc [Tue, 8 Nov 2016 16:29:22 +0000 (16:29 +0000)]
JAL-2295 JAL-1596 method to pass a command script file to Chimera
gmungoc [Tue, 8 Nov 2016 15:53:55 +0000 (15:53 +0000)]
JAL-2301 corrected search example to match AA properties mentioned
gmungoc [Tue, 8 Nov 2016 15:47:30 +0000 (15:47 +0000)]
JAL-2301 made T hydrophobic as per the cited conservation method
gmungoc [Tue, 8 Nov 2016 15:16:26 +0000 (15:16 +0000)]
JAL-1961 added link to GFF3 format as well as GFF2
gmungoc [Tue, 8 Nov 2016 14:55:21 +0000 (14:55 +0000)]
JAL-2295 feature and colour commands refactored to use AtomSpecModel
gmungoc [Tue, 8 Nov 2016 14:54:27 +0000 (14:54 +0000)]
JAL-2295 method added to return a compact mapped range in the structure
kiramt [Tue, 8 Nov 2016 14:18:48 +0000 (14:18 +0000)]
JAL-2309 Made test timeout slightly longer
kiramt [Tue, 8 Nov 2016 13:57:18 +0000 (13:57 +0000)]
JAL-2309 Adjusted timeout on headless tests
gmungoc [Tue, 8 Nov 2016 12:42:22 +0000 (12:42 +0000)]
JAL-2295 extracted AtomSpecModel for reuse in Chimera commands
gmungoc [Tue, 8 Nov 2016 12:32:07 +0000 (12:32 +0000)]
JAL-2295 make RangeComparator a top level class for reuse
tcofoegbu [Tue, 8 Nov 2016 11:12:42 +0000 (11:12 +0000)]
JAL-2280 Updated spanish translation as recommended by Juan
tcofoegbu [Tue, 8 Nov 2016 10:26:21 +0000 (10:26 +0000)]
JAL-2292 updated method calls
tcofoegbu [Tue, 8 Nov 2016 10:22:05 +0000 (10:22 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Tue, 8 Nov 2016 10:21:55 +0000 (10:21 +0000)]
JAL-2292 renamed method and improved implementation as suggested by Kira
gmungoc [Mon, 7 Nov 2016 15:58:24 +0000 (15:58 +0000)]
Merge branch 'develop' into features/JAL-2295setChimeraAttributes
gmungoc [Mon, 7 Nov 2016 15:42:51 +0000 (15:42 +0000)]
JAL-1270 renamed helper method so it is not run as a test
gmungoc [Mon, 7 Nov 2016 15:41:21 +0000 (15:41 +0000)]
JAL-2272 another test case
gmungoc [Mon, 7 Nov 2016 15:39:46 +0000 (15:39 +0000)]
JAL-1805 groups=Functional added where missing
gmungoc [Mon, 7 Nov 2016 15:21:01 +0000 (15:21 +0000)]
JAL-2272 unit tests added for Platform.isControlDown
gmungoc [Mon, 7 Nov 2016 12:23:40 +0000 (12:23 +0000)]
JAL-2318 updated help text
gmungoc [Mon, 7 Nov 2016 11:52:23 +0000 (11:52 +0000)]
JAL-2282 show url links that need checked; remove 'www' from default
gmungoc [Mon, 7 Nov 2016 11:01:22 +0000 (11:01 +0000)]
JAL-2295 handle no progress bar message properly
gmungoc [Mon, 7 Nov 2016 10:59:12 +0000 (10:59 +0000)]
JAL-2295 small tidy of javadoc only
gmungoc [Mon, 7 Nov 2016 10:58:24 +0000 (10:58 +0000)]
JAL-2295 (unoptimised) write Jalview features as Chimera attributes
kiramt [Fri, 4 Nov 2016 16:44:59 +0000 (16:44 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-2282' into develop
kiramt [Fri, 4 Nov 2016 16:43:01 +0000 (16:43 +0000)]
JAL-2315 Clear sequenceURLLinks if all sequence links are removed.
tcofoegbu [Fri, 4 Nov 2016 16:08:53 +0000 (16:08 +0000)]
JAL-2292 squashed bug that breaks feature mapping for different cased residues
tcofoegbu [Fri, 4 Nov 2016 15:40:49 +0000 (15:40 +0000)]
JAL-2292 added javadoc for compareChar(..) utility method
tcofoegbu [Fri, 4 Nov 2016 15:34:11 +0000 (15:34 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Fri, 4 Nov 2016 15:34:01 +0000 (15:34 +0000)]
JAL-2195 JAL-2262 house keeping
tcofoegbu [Fri, 4 Nov 2016 15:30:28 +0000 (15:30 +0000)]
JAL-2292 fix for wrong mapping output in sequence mapping output window where sequence residue has different case with structure residue
tcofoegbu [Fri, 4 Nov 2016 15:26:44 +0000 (15:26 +0000)]
JAL-2292 Wrote utility method for comparing two char either case sensitively or insensitively
tcofoegbu [Fri, 4 Nov 2016 15:25:21 +0000 (15:25 +0000)]
JAL-2292 Unit test for utility method for comparing two chars
kiramt [Fri, 4 Nov 2016 14:29:55 +0000 (14:29 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-2282' into develop
kiramt [Fri, 4 Nov 2016 14:28:57 +0000 (14:28 +0000)]
JAL-2282 Better check for existing url links
gmungoc [Fri, 4 Nov 2016 14:02:41 +0000 (14:02 +0000)]
JAL-2272 right mouse button on Mac is not Cmd equivalent!
kiramt [Fri, 4 Nov 2016 13:26:13 +0000 (13:26 +0000)]
JAL-2282 Remove Cache dependency from applet
kiramt [Fri, 4 Nov 2016 11:10:36 +0000 (11:10 +0000)]
JAL-2282 Message box stays on top at Jalview open; checks for links
before deciding whether to display.
kiramt [Thu, 3 Nov 2016 20:58:08 +0000 (20:58 +0000)]
JAL-2282 Link menu disabled if there are no valid links
kiramt [Thu, 3 Nov 2016 20:22:40 +0000 (20:22 +0000)]
JAL-2282 Updated warn.url_must_contain
kiramt [Thu, 3 Nov 2016 19:40:41 +0000 (19:40 +0000)]
JAL-2282 If checkbox on warning dialog is unclicked, reset cache
settings for checking url links.
kiramt [Thu, 3 Nov 2016 19:33:16 +0000 (19:33 +0000)]
JAL-2281 Back out unit test update, as Mungo already added.
kiramt [Thu, 3 Nov 2016 19:29:51 +0000 (19:29 +0000)]
Merge remote-tracking branch 'origin/develop' into bug/JAL-2282
kiramt [Thu, 3 Nov 2016 19:19:00 +0000 (19:19 +0000)]
JAL-2308 Fixed hiddenColsTest
tcofoegbu [Thu, 3 Nov 2016 17:15:03 +0000 (17:15 +0000)]
JAL-2312 unit test for bug fix - repeated mapping generated from SIFTS when heuristic identification fails for some SIFTS entities
tcofoegbu [Thu, 3 Nov 2016 16:50:29 +0000 (16:50 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Thu, 3 Nov 2016 16:47:18 +0000 (16:47 +0000)]
JAL-2312 Bug fix for repeated mapping generation from SIFTS when heuristic identification fails for some SIFTS entities
gmungoc [Thu, 3 Nov 2016 09:24:58 +0000 (09:24 +0000)]
JAL-2281 test added to show searchRefs is now not case sensitive
kiramt [Thu, 3 Nov 2016 09:14:32 +0000 (09:14 +0000)]
JAL-2281 Minor unit test addition
gmungoc [Thu, 3 Nov 2016 09:12:25 +0000 (09:12 +0000)]
JAL-2295 step 1 new menu item to transfer Jalview attributes (no action
yet)
kiramt [Wed, 2 Nov 2016 18:03:42 +0000 (18:03 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-2282' into develop
kiramt [Wed, 2 Nov 2016 18:02:16 +0000 (18:02 +0000)]
JAL-2281 Unit test updates
kiramt [Wed, 2 Nov 2016 16:19:54 +0000 (16:19 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-2282' into develop
gmungoc [Wed, 2 Nov 2016 16:06:47 +0000 (16:06 +0000)]
JAL-2301 table formatted, and corrected to match the diagram and code
kiramt [Wed, 2 Nov 2016 15:22:45 +0000 (15:22 +0000)]
JAL-2281 Use DBRefs.selectRefs to uppercase URL link target
kiramt [Wed, 2 Nov 2016 15:01:32 +0000 (15:01 +0000)]
JAL-2282 Refactor applet too
kiramt [Wed, 2 Nov 2016 15:00:37 +0000 (15:00 +0000)]
JAL-2282 Updated and checked messages, English and Spanish
kiramt [Wed, 2 Nov 2016 14:18:52 +0000 (14:18 +0000)]
JAL-2282 Updated help documentation
gmungoc [Wed, 2 Nov 2016 12:09:49 +0000 (12:09 +0000)]
JAL-98 JAL-1854 encapsulate 'magic number' threshold 3 in Conservation
gmungoc [Wed, 2 Nov 2016 11:56:49 +0000 (11:56 +0000)]
JAL-98 ProfileI interface for Profile
gmungoc [Wed, 2 Nov 2016 11:02:57 +0000 (11:02 +0000)]
JAL-98 test updated for percentage rounded
gmungoc [Wed, 2 Nov 2016 10:05:20 +0000 (10:05 +0000)]
JAL-98 Profile and ResidueCount moved from analysis to datamodel
gmungoc [Wed, 2 Nov 2016 10:04:18 +0000 (10:04 +0000)]
JAL-98 wording "negatively conserved" now "absence conserved"
kiramt [Wed, 2 Nov 2016 10:03:15 +0000 (10:03 +0000)]
JAL-2282 Code tidy
kiramt [Wed, 2 Nov 2016 09:39:10 +0000 (09:39 +0000)]
JAL-2282 Renamed internal use of sequence id / db accession for
consistency
kiramt [Wed, 2 Nov 2016 09:28:50 +0000 (09:28 +0000)]
JAL-2282 URLLink unit tests updated
gmungoc [Tue, 1 Nov 2016 16:14:18 +0000 (16:14 +0000)]
Conservation now using ResidueCount; tests added
gmungoc [Tue, 1 Nov 2016 16:13:52 +0000 (16:13 +0000)]
JAL-98 use Integer constants; tests added for propHash values
gmungoc [Tue, 1 Nov 2016 16:12:58 +0000 (16:12 +0000)]
JAL-98 typo in javadoc
gmungoc [Tue, 1 Nov 2016 16:12:27 +0000 (16:12 +0000)]
JAL-98 simplified repeat() method
gmungoc [Tue, 1 Nov 2016 16:11:05 +0000 (16:11 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
tcofoegbu [Tue, 1 Nov 2016 15:41:32 +0000 (15:41 +0000)]
JAL-2280 refactored and improved structure file identification code for drog'n'drop on AlignFrame to StructureFile class
git://source.jalview.org / jalview.git / log