jalview.git
7 years agoMerge branch 'documentation/JAL-2325_release2101' into develop
Jim Procter [Mon, 21 Nov 2016 15:40:46 +0000 (15:40 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into develop

7 years agoMerge branch 'develop' into documentation/JAL-2325_release2101
Jim Procter [Mon, 21 Nov 2016 15:40:08 +0000 (15:40 +0000)]
Merge branch 'develop' into documentation/JAL-2325_release2101

7 years agoJAL-2284 documentation for the new command-line option
Jim Procter [Mon, 21 Nov 2016 13:24:10 +0000 (13:24 +0000)]
JAL-2284 documentation for the new command-line option

7 years agoJAL-2325 post-document JAL-2284 released in 2.10.0
Jim Procter [Mon, 21 Nov 2016 13:09:37 +0000 (13:09 +0000)]
JAL-2325 post-document JAL-2284 released in 2.10.0

7 years agoJAL-2325 release notes for JAL-2317
Jim Procter [Mon, 21 Nov 2016 13:04:13 +0000 (13:04 +0000)]
JAL-2325 release notes for JAL-2317

7 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Mon, 21 Nov 2016 13:03:50 +0000 (13:03 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

7 years agoJAL-2332 bugfix to enable structure chooser opening for hen lysozyme
tcofoegbu [Mon, 21 Nov 2016 13:03:40 +0000 (13:03 +0000)]
JAL-2332 bugfix to enable structure chooser opening for hen lysozyme

7 years agoJAL-2333 test beefed up with gaps
gmungoc [Mon, 21 Nov 2016 11:58:49 +0000 (11:58 +0000)]
JAL-2333 test beefed up with gaps

7 years agoJAL-1888 JAL-2325 release 2.9.0b1 notes updated post-release
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

7 years agoJAL-2333 corrected select columns with 'contact' feature
gmungoc [Mon, 21 Nov 2016 11:35:44 +0000 (11:35 +0000)]
JAL-2333 corrected select columns with 'contact' feature

7 years agoMerge branch 'documentation/JAL-2325_release2101' into develop
Jim Procter [Mon, 21 Nov 2016 11:29:16 +0000 (11:29 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into develop

7 years agoJAL-1723 release notes and note in documentation about abbreviation of tooltip
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

7 years agoJAL-2325 update release 2.10.0 release notes for JAL-1932
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

7 years agoMerge branch 'develop' into bug/JAL-2323disulfideOverview
gmungoc [Mon, 21 Nov 2016 11:02:04 +0000 (11:02 +0000)]
Merge branch 'develop' into bug/JAL-2323disulfideOverview

Conflicts:
src/jalview/io/SequenceAnnotationReport.java

7 years agoMerge branch 'bug/JAL-98consensusMemory' into develop
Jim Procter [Fri, 18 Nov 2016 16:31:52 +0000 (16:31 +0000)]
Merge branch 'bug/JAL-98consensusMemory' into develop

7 years agoJAL-98 with the two types missing from last commit Profiles[I] ! bug/JAL-98consensusMemory
gmungoc [Fri, 18 Nov 2016 08:55:47 +0000 (08:55 +0000)]
JAL-98 with the two types missing from last commit Profiles[I] !

7 years agoJAL-2323 revert to thread-safe iteration over array field
gmungoc [Thu, 17 Nov 2016 16:08:59 +0000 (16:08 +0000)]
JAL-2323 revert to thread-safe iteration over array field

7 years agoJAL-98 ProfilesI container for profiles for columns
gmungoc [Thu, 17 Nov 2016 16:01:43 +0000 (16:01 +0000)]
JAL-98 ProfilesI container for profiles for columns

7 years agoJAL-98 javadoc, third party acknowledgements (and very small code
gmungoc [Thu, 17 Nov 2016 11:50:44 +0000 (11:50 +0000)]
JAL-98 javadoc, third party acknowledgements (and very small code
change)

7 years agoJAL-2327 disulfide bond abstracted to SequenceFeature.isContactFeature
gmungoc [Thu, 17 Nov 2016 11:05:43 +0000 (11:05 +0000)]
JAL-2327 disulfide bond abstracted to SequenceFeature.isContactFeature

7 years agoJAL-2327 add isContactFeature
gmungoc [Thu, 17 Nov 2016 11:02:34 +0000 (11:02 +0000)]
JAL-2327 add isContactFeature

7 years agoMerge branch 'features/JAL-1723_sequenceReport' into develop
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

7 years agoJAL-2296 unit test for reading Chimera attributes to Jalview features
gmungoc [Wed, 16 Nov 2016 17:01:59 +0000 (17:01 +0000)]
JAL-2296 unit test for reading Chimera attributes to Jalview features

7 years agoMerge branch 'develop' of http://source.jalview.org/git/jalview into develop
Jim Procter [Wed, 16 Nov 2016 16:10:15 +0000 (16:10 +0000)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop

7 years agoMerge branch 'documentation/JAL-2325_release2101' into develop
Jim Procter [Wed, 16 Nov 2016 16:07:22 +0000 (16:07 +0000)]
Merge branch 'documentation/JAL-2325_release2101' into develop

7 years agoJAL-2325 release notes for 2.10.1 - pass one
Jim Procter [Wed, 16 Nov 2016 16:06:38 +0000 (16:06 +0000)]
JAL-2325 release notes for 2.10.1 - pass one

7 years agoMerge remote-tracking branch 'origin/bug/JAL-2282' into develop
kiramt [Wed, 16 Nov 2016 15:55:37 +0000 (15:55 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-2282' into develop

7 years agoJAL-2282 Updated docs with information about when warning is shown bug/JAL-2282
kiramt [Wed, 16 Nov 2016 15:54:05 +0000 (15:54 +0000)]
JAL-2282 Updated docs with information about when warning is shown

7 years agoJAL-2323 render disulfide bond correctly on overview and structure
gmungoc [Wed, 16 Nov 2016 15:45:13 +0000 (15:45 +0000)]
JAL-2323 render disulfide bond correctly on overview and structure

7 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 16 Nov 2016 14:38:42 +0000 (14:38 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

7 years agoJAL-2322 JAL-2309 replaced references to isheadless variable with method call to...
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

7 years agoJAL-2318 revised documentation for above PID Threshold
Jim Procter [Wed, 16 Nov 2016 14:35:07 +0000 (14:35 +0000)]
JAL-2318 revised documentation for above PID Threshold

7 years agoMerge branch 'develop' into features/JAL-2295setChimeraAttributes
gmungoc [Wed, 16 Nov 2016 12:35:15 +0000 (12:35 +0000)]
Merge branch 'develop' into features/JAL-2295setChimeraAttributes

7 years agoJAL-2324 fix and tests for comparison of Float.NaN scores
gmungoc [Wed, 16 Nov 2016 12:34:30 +0000 (12:34 +0000)]
JAL-2324 fix and tests for comparison of Float.NaN scores

7 years agoJAL-2319 corrected reporting of SIFTS mapping
gmungoc [Wed, 16 Nov 2016 12:27:31 +0000 (12:27 +0000)]
JAL-2319 corrected reporting of SIFTS mapping

7 years agoMerge branch 'develop' into features/JAL-2295setChimeraAttributes
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

7 years agoJAL-2177 remove signature from desktop library Jmol jar
Jim Procter [Wed, 16 Nov 2016 11:20:26 +0000 (11:20 +0000)]
JAL-2177 remove signature from desktop library Jmol jar

7 years agoJAL-2296 don't copy attribute with value False
gmungoc [Wed, 16 Nov 2016 10:53:03 +0000 (10:53 +0000)]
JAL-2296 don't copy attribute with value False

7 years agoJAL-2295 don't exclude RESNUM from transfer to Chimera
gmungoc [Wed, 16 Nov 2016 10:50:37 +0000 (10:50 +0000)]
JAL-2295 don't exclude RESNUM from transfer to Chimera

7 years agoJAL-2322 Refactored unified architecture for data + html exporting for SVG & BioJS...
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

7 years agoJAL-2296 new code and refactoring for 'copy Chimera attribute to
gmungoc [Mon, 14 Nov 2016 12:31:30 +0000 (12:31 +0000)]
JAL-2296 new code and refactoring for 'copy Chimera attribute to
features'

7 years agoJAL-2295 don't copy 'Chimera' features back to Chimera
gmungoc [Mon, 14 Nov 2016 12:30:17 +0000 (12:30 +0000)]
JAL-2295 don't copy 'Chimera' features back to Chimera

7 years agoJAL-2296 parse Chimera atomspec to AtomSpec
gmungoc [Mon, 14 Nov 2016 12:29:24 +0000 (12:29 +0000)]
JAL-2296 parse Chimera atomspec to AtomSpec

7 years agoJAL-2296 report whether SequenceFeature actually added to sequence
gmungoc [Mon, 14 Nov 2016 12:28:57 +0000 (12:28 +0000)]
JAL-2296 report whether SequenceFeature actually added to sequence

7 years agoJAL-2295 JAL-2296 skeleton 'attributes to features'; renamed methods
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

7 years agoJAL-2277 Refactored out duplicated method - printUnwrapped() in HtmlSvgOutput, extern...
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

7 years agoJAL-2177 remove Jmol project signature from jar so it can be resigned
Jim Procter [Fri, 11 Nov 2016 15:28:21 +0000 (15:28 +0000)]
JAL-2177 remove Jmol project signature from jar so it can be resigned

7 years agoMerge branch 'develop' into features/JAL-2295setChimeraAttributes
gmungoc [Fri, 11 Nov 2016 14:02:39 +0000 (14:02 +0000)]
Merge branch 'develop' into features/JAL-2295setChimeraAttributes

7 years agoJAL-2295 tests now 'network-free' with local PDB and SIFTS files
gmungoc [Fri, 11 Nov 2016 13:42:52 +0000 (13:42 +0000)]
JAL-2295 tests now 'network-free' with local PDB and SIFTS files

7 years agoJAL-2295 JAL-2269 JAL-2319 mockable SIFTS file, fix to mapping details
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

7 years agoJAL-2295 improved integrity of 'isFinishedInit' flag
gmungoc [Fri, 11 Nov 2016 13:40:57 +0000 (13:40 +0000)]
JAL-2295 improved integrity of 'isFinishedInit' flag

7 years agoJAL-1270 corrected command-line args
gmungoc [Fri, 11 Nov 2016 13:40:04 +0000 (13:40 +0000)]
JAL-1270 corrected command-line args

7 years agoJAL-2295 set finishedInit to false before checking files loaded
gmungoc [Fri, 11 Nov 2016 09:15:03 +0000 (09:15 +0000)]
JAL-2295 set finishedInit to false before checking files loaded

7 years agoJAL-2295 test that verifies transfer of features to Chimera attributes
gmungoc [Fri, 11 Nov 2016 08:52:53 +0000 (08:52 +0000)]
JAL-2295 test that verifies transfer of features to Chimera attributes

7 years agoJAL-2295 sorted properties for readability
gmungoc [Fri, 11 Nov 2016 08:51:36 +0000 (08:51 +0000)]
JAL-2295 sorted properties for readability

7 years agoJAL-2295 (optionally) return Chimera command reply
gmungoc [Fri, 11 Nov 2016 08:50:57 +0000 (08:50 +0000)]
JAL-2295 (optionally) return Chimera command reply

7 years agoJAL-2295 correct test for Float.isNaN(score) !
gmungoc [Fri, 11 Nov 2016 08:50:02 +0000 (08:50 +0000)]
JAL-2295 correct test for Float.isNaN(score) !

7 years agoMerge branch 'bug/JAL-2317_jmol_chimera-chain-factorisation' into develop
tcofoegbu [Thu, 10 Nov 2016 16:11:36 +0000 (16:11 +0000)]
Merge branch 'bug/JAL-2317_jmol_chimera-chain-factorisation' into develop

7 years agoMerge branch 'develop' into bug/JAL-2317_jmol_chimera-chain-factorisation
tcofoegbu [Thu, 10 Nov 2016 15:57:41 +0000 (15:57 +0000)]
Merge branch 'develop' into bug/JAL-2317_jmol_chimera-chain-factorisation

7 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Thu, 10 Nov 2016 15:55:51 +0000 (15:55 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

7 years agoJAL-2317 Fixed Chimera command for hiding/showing distinct chains bug/JAL-2317_jmol_chimera-chain-factorisation
tcofoegbu [Thu, 10 Nov 2016 15:45:33 +0000 (15:45 +0000)]
JAL-2317 Fixed Chimera command for hiding/showing distinct chains

7 years agoJAL-2295 additional tests, stronger sanitisation of attribute name
gmungoc [Thu, 10 Nov 2016 13:01:23 +0000 (13:01 +0000)]
JAL-2295 additional tests, stronger sanitisation of attribute name

7 years agoBugfix to enable accurate chain extraction/association with models loaded in Chimera...
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.

7 years agoJAL-2320 thread to close Chimera viewer panel if Chimera shut down features/JAL-2320_closeChimeraAction
gmungoc [Thu, 10 Nov 2016 11:03:52 +0000 (11:03 +0000)]
JAL-2320 thread to close Chimera viewer panel if Chimera shut down

7 years agoJAL-2320 added getViewer() method to return Chimera or Jmol panel
gmungoc [Thu, 10 Nov 2016 11:03:14 +0000 (11:03 +0000)]
JAL-2320 added getViewer() method to return Chimera or Jmol panel

7 years agoJAL-2295 set attributes commands include feature value, sent via file
gmungoc [Wed, 9 Nov 2016 16:58:33 +0000 (16:58 +0000)]
JAL-2295 set attributes commands include feature value, sent via file

7 years agoJAL-2295 single constant for "RESNUM" feature name
gmungoc [Wed, 9 Nov 2016 16:57:46 +0000 (16:57 +0000)]
JAL-2295 single constant for "RESNUM" feature name

7 years agoJAL-2295 JAL-1596 method to pass a command script file to Chimera
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

7 years agoJAL-2301 corrected search example to match AA properties mentioned
gmungoc [Tue, 8 Nov 2016 15:53:55 +0000 (15:53 +0000)]
JAL-2301 corrected search example to match AA properties mentioned

7 years agoJAL-2301 made T hydrophobic as per the cited conservation method
gmungoc [Tue, 8 Nov 2016 15:47:30 +0000 (15:47 +0000)]
JAL-2301 made T hydrophobic as per the cited conservation method

7 years agoJAL-1961 added link to GFF3 format as well as GFF2
gmungoc [Tue, 8 Nov 2016 15:16:26 +0000 (15:16 +0000)]
JAL-1961 added link to GFF3 format as well as GFF2

7 years agoJAL-2295 feature and colour commands refactored to use AtomSpecModel
gmungoc [Tue, 8 Nov 2016 14:55:21 +0000 (14:55 +0000)]
JAL-2295 feature and colour commands refactored to use AtomSpecModel

7 years agoJAL-2295 method added to return a compact mapped range in the structure
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

7 years agoJAL-2309 Made test timeout slightly longer bug/JAL-2309
kiramt [Tue, 8 Nov 2016 14:18:48 +0000 (14:18 +0000)]
JAL-2309 Made test timeout slightly longer

7 years agoJAL-2309 Adjusted timeout on headless tests
kiramt [Tue, 8 Nov 2016 13:57:18 +0000 (13:57 +0000)]
JAL-2309 Adjusted timeout on headless tests

7 years agoJAL-2295 extracted AtomSpecModel for reuse in Chimera commands
gmungoc [Tue, 8 Nov 2016 12:42:22 +0000 (12:42 +0000)]
JAL-2295 extracted AtomSpecModel for reuse in Chimera commands

7 years agoJAL-2295 make RangeComparator a top level class for reuse
gmungoc [Tue, 8 Nov 2016 12:32:07 +0000 (12:32 +0000)]
JAL-2295 make RangeComparator a top level class for reuse

7 years agoJAL-2280 Updated spanish translation as recommended by Juan
tcofoegbu [Tue, 8 Nov 2016 11:12:42 +0000 (11:12 +0000)]
JAL-2280 Updated spanish translation as recommended by Juan

7 years agoJAL-2292 updated method calls
tcofoegbu [Tue, 8 Nov 2016 10:26:21 +0000 (10:26 +0000)]
JAL-2292 updated method calls

7 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Tue, 8 Nov 2016 10:22:05 +0000 (10:22 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

7 years agoJAL-2292 renamed method and improved implementation as suggested by Kira
tcofoegbu [Tue, 8 Nov 2016 10:21:55 +0000 (10:21 +0000)]
JAL-2292 renamed method and improved implementation as suggested by Kira

7 years agoMerge branch 'develop' into features/JAL-2295setChimeraAttributes
gmungoc [Mon, 7 Nov 2016 15:58:24 +0000 (15:58 +0000)]
Merge branch 'develop' into features/JAL-2295setChimeraAttributes

7 years agoJAL-1270 renamed helper method so it is not run as a test
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

7 years agoJAL-2272 another test case
gmungoc [Mon, 7 Nov 2016 15:41:21 +0000 (15:41 +0000)]
JAL-2272 another test case

7 years agoJAL-1805 groups=Functional added where missing
gmungoc [Mon, 7 Nov 2016 15:39:46 +0000 (15:39 +0000)]
JAL-1805 groups=Functional added where missing

7 years agoJAL-2272 unit tests added for Platform.isControlDown
gmungoc [Mon, 7 Nov 2016 15:21:01 +0000 (15:21 +0000)]
JAL-2272 unit tests added for Platform.isControlDown

7 years agoJAL-2318 updated help text
gmungoc [Mon, 7 Nov 2016 12:23:40 +0000 (12:23 +0000)]
JAL-2318 updated help text

7 years agoJAL-2282 show url links that need checked; remove 'www' from default
gmungoc [Mon, 7 Nov 2016 11:52:23 +0000 (11:52 +0000)]
JAL-2282 show url links that need checked; remove 'www' from default

7 years agoJAL-2295 handle no progress bar message properly
gmungoc [Mon, 7 Nov 2016 11:01:22 +0000 (11:01 +0000)]
JAL-2295 handle no progress bar message properly

7 years agoJAL-2295 small tidy of javadoc only
gmungoc [Mon, 7 Nov 2016 10:59:12 +0000 (10:59 +0000)]
JAL-2295 small tidy of javadoc only

7 years agoJAL-2295 (unoptimised) write Jalview features as Chimera attributes
gmungoc [Mon, 7 Nov 2016 10:58:24 +0000 (10:58 +0000)]
JAL-2295 (unoptimised) write Jalview features as Chimera attributes

7 years agoMerge remote-tracking branch 'origin/bug/JAL-2282' into develop
kiramt [Fri, 4 Nov 2016 16:44:59 +0000 (16:44 +0000)]
Merge remote-tracking branch 'origin/bug/JAL-2282' into develop

7 years agoJAL-2315 Clear sequenceURLLinks if all sequence links are removed.
kiramt [Fri, 4 Nov 2016 16:43:01 +0000 (16:43 +0000)]
JAL-2315 Clear sequenceURLLinks if all sequence links are removed.

7 years agoJAL-2292 squashed bug that breaks feature mapping for different cased residues
tcofoegbu [Fri, 4 Nov 2016 16:08:53 +0000 (16:08 +0000)]
JAL-2292 squashed bug that breaks feature mapping for different cased residues

7 years agoJAL-2292 added javadoc for compareChar(..) utility method
tcofoegbu [Fri, 4 Nov 2016 15:40:49 +0000 (15:40 +0000)]
JAL-2292 added javadoc for compareChar(..) utility method

7 years agoMerge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Fri, 4 Nov 2016 15:34:11 +0000 (15:34 +0000)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

7 years agoJAL-2195 JAL-2262 house keeping
tcofoegbu [Fri, 4 Nov 2016 15:34:01 +0000 (15:34 +0000)]
JAL-2195 JAL-2262 house keeping

7 years agoJAL-2292 fix for wrong mapping output in sequence mapping output window where sequenc...
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

7 years agoJAL-2292 Wrote utility method for comparing two char either case sensitively or insen...
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

7 years agoJAL-2292 Unit test for utility method for comparing two chars
tcofoegbu [Fri, 4 Nov 2016 15:25:21 +0000 (15:25 +0000)]
JAL-2292 Unit test for utility method for comparing two chars