Jim Procter [Tue, 22 Nov 2016 12:42:25 +0000 (12:42 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
tcofoegbu [Mon, 21 Nov 2016 17:47:27 +0000 (17:47 +0000)]
JAL-2277 bug fix for mis-alligned graphics output for scrolled annotations
Jim Procter [Mon, 21 Nov 2016 15:40:46 +0000 (15:40 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into develop
Jim Procter [Mon, 21 Nov 2016 15:40:08 +0000 (15:40 +0000)]
Merge branch 'develop' into documentation/JAL-2325_release2101
Jim Procter [Mon, 21 Nov 2016 13:24:10 +0000 (13:24 +0000)]
JAL-2284 documentation for the new command-line option
Jim Procter [Mon, 21 Nov 2016 13:09:37 +0000 (13:09 +0000)]
JAL-2325 post-document JAL-2284 released in 2.10.0
Jim Procter [Mon, 21 Nov 2016 13:04:13 +0000 (13:04 +0000)]
JAL-2325 release notes for JAL-2317
tcofoegbu [Mon, 21 Nov 2016 13:03:50 +0000 (13:03 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Mon, 21 Nov 2016 13:03:40 +0000 (13:03 +0000)]
JAL-2332 bugfix to enable structure chooser opening for hen lysozyme
Jim Procter [Mon, 21 Nov 2016 11:44:00 +0000 (11:44 +0000)]
JAL-1888 JAL-2325 release 2.9.0b1 notes updated post-release
Jim Procter [Mon, 21 Nov 2016 11:29:16 +0000 (11:29 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into develop
Jim Procter [Mon, 21 Nov 2016 11:28:01 +0000 (11:28 +0000)]
JAL-1723 release notes and note in documentation about abbreviation of tooltip
Jim Procter [Mon, 21 Nov 2016 11:14:06 +0000 (11:14 +0000)]
JAL-2325 update release 2.10.0 release notes for JAL-1932
Jim Procter [Fri, 18 Nov 2016 16:31:52 +0000 (16:31 +0000)]
Merge branch 'bug/JAL-98consensusMemory' into develop
gmungoc [Fri, 18 Nov 2016 08:55:47 +0000 (08:55 +0000)]
JAL-98 with the two types missing from last commit Profiles[I] !
gmungoc [Thu, 17 Nov 2016 16:01:43 +0000 (16:01 +0000)]
JAL-98 ProfilesI container for profiles for columns
gmungoc [Thu, 17 Nov 2016 11:50:44 +0000 (11:50 +0000)]
JAL-98 javadoc, third party acknowledgements (and very small code
change)
Jim Procter [Wed, 16 Nov 2016 17:12:43 +0000 (17:12 +0000)]
Merge branch 'features/JAL-1723_sequenceReport' into develop
Conflicts:
resources/lang/Messages.properties
resources/lang/Messages_es.properties
src/jalview/io/SequenceAnnotationReport.java
reconciled refactored report/ellipsis code with refactored URLLink code for generating dynamic links with ACCESSION_ID tokens
Jim Procter [Wed, 16 Nov 2016 16:10:15 +0000 (16:10 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Wed, 16 Nov 2016 16:07:22 +0000 (16:07 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into develop
Jim Procter [Wed, 16 Nov 2016 16:06:38 +0000 (16:06 +0000)]
JAL-2325 release notes for 2.10.1 - pass one
kiramt [Wed, 16 Nov 2016 15:55:37 +0000 (15:55 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-2282' into develop
kiramt [Wed, 16 Nov 2016 15:54:05 +0000 (15:54 +0000)]
JAL-2282 Updated docs with information about when warning is shown
tcofoegbu [Wed, 16 Nov 2016 14:38:42 +0000 (14:38 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 16 Nov 2016 14:38:32 +0000 (14:38 +0000)]
JAL-2322 JAL-2309 replaced references to isheadless variable with method call to isHeadless() in HTMLOutput class
Jim Procter [Wed, 16 Nov 2016 14:35:07 +0000 (14:35 +0000)]
JAL-2318 revised documentation for above PID Threshold
gmungoc [Wed, 16 Nov 2016 12:34:30 +0000 (12:34 +0000)]
JAL-2324 fix and tests for comparison of Float.NaN scores
gmungoc [Wed, 16 Nov 2016 12:27:31 +0000 (12:27 +0000)]
JAL-2319 corrected reporting of SIFTS mapping
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
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
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
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 [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
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
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 15:42:51 +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
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
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
kiramt [Tue, 1 Nov 2016 14:55:02 +0000 (14:55 +0000)]
JAL-2282 Refactor SequenceAnnotationReport to use refactored UrlLink
code.
kiramt [Tue, 1 Nov 2016 12:13:27 +0000 (12:13 +0000)]
JAL-2282 Merge
kiramt [Tue, 1 Nov 2016 12:07:06 +0000 (12:07 +0000)]
JAL-2282 Changed DB accession id token to $DB_ACCESSION$; updated
messages
git://source.jalview.org / jalview.git / log