Jim Procter [Wed, 9 Sep 2015 17:20:47 +0000 (18:20 +0100)]
JAL-1645 relocate developer info about BioJS MSA templates to jalview/doc.
Jim Procter [Wed, 9 Sep 2015 16:07:09 +0000 (17:07 +0100)]
JAL-1645 update 2.9 docs
Jim Procter [Wed, 9 Sep 2015 15:56:04 +0000 (16:56 +0100)]
JAL-1645 JAL-1667 revised PDB sequence fetcher docs
Jim Procter [Wed, 9 Sep 2015 15:54:45 +0000 (16:54 +0100)]
JAL-1645 update TOC for 2.9 what’s new
Jim Procter [Wed, 9 Sep 2015 15:52:51 +0000 (16:52 +0100)]
JAL-1645 update release note link to v2.9
Jim Procter [Wed, 9 Sep 2015 12:31:44 +0000 (13:31 +0100)]
JAL-1684 use Muscle protein alignment as guide for cDNA alignment reconstruction.
Jim Procter [Wed, 9 Sep 2015 11:57:03 +0000 (12:57 +0100)]
Merge branch 'release/2_9_documentation' into develop
Jim Procter [Wed, 9 Sep 2015 11:55:43 +0000 (12:55 +0100)]
JAL-1684 clarification of which alignment will be used to guide the reconstruction of the linked alignment
Jim Procter [Wed, 9 Sep 2015 11:55:16 +0000 (12:55 +0100)]
JAL-1684 aligned proteins and citation for for Estrogen cDNA/Protein
gmungoc [Wed, 9 Sep 2015 11:37:15 +0000 (12:37 +0100)]
JAL-1619 update applet.currentAlignFrame on any menu action (fixes Find
in applet split frame)
gmungoc [Wed, 9 Sep 2015 11:33:38 +0000 (12:33 +0100)]
JAL-1619 'align protein as cDNA' now leaves unmapped protein unchanged
Jim Procter [Wed, 9 Sep 2015 11:21:22 +0000 (12:21 +0100)]
JAL-1645 formatting tree distance docs
Jim Procter [Wed, 9 Sep 2015 11:20:48 +0000 (12:20 +0100)]
JAL-1483 more explicit description of feature similarity calculation
Jim Procter [Wed, 9 Sep 2015 10:54:33 +0000 (11:54 +0100)]
JAL-1483 description of the sequence feature based tree calculation
tcofoegbu [Wed, 9 Sep 2015 10:38:57 +0000 (11:38 +0100)]
house keeping
tcofoegbu [Wed, 9 Sep 2015 09:12:50 +0000 (10:12 +0100)]
updated Biojs msa help doc
tcofoegbu [Tue, 8 Sep 2015 18:52:16 +0000 (19:52 +0100)]
merge
tcofoegbu [Tue, 8 Sep 2015 18:51:52 +0000 (19:51 +0100)]
JAL-1541 doc for biojs msa
Jim Procter [Tue, 8 Sep 2015 17:02:45 +0000 (18:02 +0100)]
JAL-1645 Merge branch 'release/2_9_documentation' into develop
Jim Procter [Tue, 8 Sep 2015 17:02:26 +0000 (18:02 +0100)]
Merge branch 'develop' into release/2_9_documentation
Jim Procter [Tue, 8 Sep 2015 17:00:42 +0000 (18:00 +0100)]
JAL-1645 defictionalising release notes
Jim Procter [Tue, 8 Sep 2015 17:00:22 +0000 (18:00 +0100)]
JAL-1645 first stab at R2.9 “What’s new”
Jim Procter [Tue, 8 Sep 2015 16:59:41 +0000 (17:59 +0100)]
JAL-1645 JAL-1701 fix up split frame docs and add a bit more info about reconstructed alignments. maybe we need a screenshot here too.
Jim Procter [Tue, 8 Sep 2015 16:57:48 +0000 (17:57 +0100)]
JAL-1645 incorrect internal doc link
Jim Procter [Tue, 8 Sep 2015 16:57:06 +0000 (17:57 +0100)]
JAL-1645 update appletParameters docs for 2.9
Jim Procter [Tue, 8 Sep 2015 16:55:12 +0000 (17:55 +0100)]
JAL-1695 make enableSplitFrame applet parameter true by default
tcofoegbu [Tue, 8 Sep 2015 16:28:22 +0000 (17:28 +0100)]
updated biojson help content
tcofoegbu [Tue, 8 Sep 2015 16:02:16 +0000 (17:02 +0100)]
merge
tcofoegbu [Tue, 8 Sep 2015 16:01:41 +0000 (17:01 +0100)]
updated helpTOC to include recently added features, updated menus and outdated screenshots
gmungoc [Tue, 8 Sep 2015 15:48:41 +0000 (16:48 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Tue, 8 Sep 2015 15:48:27 +0000 (16:48 +0100)]
JAL-1859 debug output of pdb mappings (mine and SSMs)
Jim Procter [Tue, 8 Sep 2015 15:22:06 +0000 (16:22 +0100)]
Merge branch 'develop' into release/2_9_documentation
Jim Procter [Tue, 8 Sep 2015 15:20:48 +0000 (16:20 +0100)]
JAL-1626 added missing gap character and fixed typo in example file
tcofoegbu [Tue, 8 Sep 2015 13:42:04 +0000 (14:42 +0100)]
merge
tcofoegbu [Tue, 8 Sep 2015 13:40:38 +0000 (14:40 +0100)]
updated help to include BioJS option in export.html
Jim Procter [Tue, 8 Sep 2015 12:34:17 +0000 (13:34 +0100)]
Merge branch 'develop' into release/2_9_documentation
Jim Procter [Tue, 8 Sep 2015 12:33:54 +0000 (13:33 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Tue, 8 Sep 2015 12:33:34 +0000 (13:33 +0100)]
Merge branch 'develop' into release/2_9_documentation
Jim Procter [Tue, 8 Sep 2015 12:32:24 +0000 (13:32 +0100)]
JAL-1551 crlf change
tcofoegbu [Tue, 8 Sep 2015 11:56:04 +0000 (12:56 +0100)]
commited jmol/Jmol2.js diff with origin shows no change, seems to be an issue with line endings as git gave the following warning: 'CRLF will be replaced by LF'
tcofoegbu [Tue, 8 Sep 2015 10:38:42 +0000 (11:38 +0100)]
JAL-857 revert show equivalent decoration link
tcofoegbu [Tue, 8 Sep 2015 09:31:38 +0000 (10:31 +0100)]
merge
tcofoegbu [Tue, 8 Sep 2015 09:30:54 +0000 (10:30 +0100)]
JAL-857 removed 'development' as active link and added links to decorated html equivalent pages when the example pages are viewed directly
Jim Procter [Tue, 8 Sep 2015 09:30:39 +0000 (10:30 +0100)]
Merge branch 'develop' into release/2_9_documentation
Jim Procter [Tue, 8 Sep 2015 09:29:00 +0000 (10:29 +0100)]
JAL-1645 draft release notes for v2.9...
gmungoc [Tue, 8 Sep 2015 09:12:50 +0000 (10:12 +0100)]
JAL-1859 reverted to signed JalviewApplet.jar!
gmungoc [Tue, 8 Sep 2015 09:09:08 +0000 (10:09 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Tue, 8 Sep 2015 09:08:57 +0000 (10:08 +0100)]
JAL-1859 Jmol applet black background; fix _jvmols table key
tcofoegbu [Tue, 8 Sep 2015 08:09:07 +0000 (09:09 +0100)]
merge
tcofoegbu [Tue, 8 Sep 2015 08:08:26 +0000 (09:08 +0100)]
deleted jbake example directory and the old biojs template directory
gmungoc [Mon, 7 Sep 2015 20:20:48 +0000 (21:20 +0100)]
JAL-1859 Jmol linked applet updated to use Jmol2.js
Jim Procter [Mon, 7 Sep 2015 15:37:39 +0000 (16:37 +0100)]
Merge branch 'features/JAL-857_dynamic-example-files' into develop
gmungoc [Mon, 7 Sep 2015 14:34:58 +0000 (15:34 +0100)]
JAL-1636 translate stop codon as '*', mouseover * as STOP
gmungoc [Mon, 7 Sep 2015 14:33:45 +0000 (15:33 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
tcofoegbu [Mon, 7 Sep 2015 14:25:57 +0000 (15:25 +0100)]
merge
tcofoegbu [Mon, 7 Sep 2015 14:25:25 +0000 (15:25 +0100)]
JAL-1831 updated BioJSON schema
gmungoc [Mon, 7 Sep 2015 13:32:04 +0000 (14:32 +0100)]
JAL-1152 check 'autocalculated' not 'null sequenceRef'; sort by sequence
respects autocalc above/below
Jim Procter [Mon, 7 Sep 2015 13:14:30 +0000 (14:14 +0100)]
Merge branch 'features/JAL-857_dynamic-example-files' into develop
Minor tweaks due to Mungo's cleaning up of the embeddedWJmol example
Jim Procter [Mon, 7 Sep 2015 12:08:27 +0000 (13:08 +0100)]
JAL-1522 report commit id and branch in installation type (may move this to separate property in future?)
Jim Procter [Mon, 7 Sep 2015 12:06:06 +0000 (13:06 +0100)]
JAL-1522 make installation default 'applet' for the applet
Jim Procter [Mon, 7 Sep 2015 10:10:42 +0000 (11:10 +0100)]
JAL-1701 added links to example files. will probably remove them later
Jim Procter [Sun, 6 Sep 2015 16:43:04 +0000 (17:43 +0100)]
JAL-1655 transfer setting option only displayed in development version of Jalview
Jim Procter [Sun, 6 Sep 2015 16:31:21 +0000 (17:31 +0100)]
JAL-1368 JAL-1863 JAL-1304 reformatting and revision of wording, clarify RNA secondary structure example
Jim Procter [Sun, 6 Sep 2015 16:17:49 +0000 (17:17 +0100)]
JAL-1368 JAL-1628 revise documentation in line with code for VIEW_SETREF, VIEW_HIDECOLS, and VIEW_HIDE_INSERTIONS.
Jim Procter [Sun, 6 Sep 2015 13:47:57 +0000 (14:47 +0100)]
JAL-1645 JAL-1355 UI/i18n: added missing messages, moved ‘…’ into action messages for actions needing more user input, title caps for menu entries and dialog titles
Jim Procter [Sat, 5 Sep 2015 17:43:21 +0000 (18:43 +0100)]
JAL-1871 JAL-1553 don’t modify selection/view colour scheme again after OK is pressed.
Jim Procter [Sat, 5 Sep 2015 17:40:05 +0000 (18:40 +0100)]
JAL-1871 choose a new RNA Helices palette when annotation colouring is updated
Jim Procter [Sat, 5 Sep 2015 17:38:57 +0000 (18:38 +0100)]
JAL-1871 don’t change the palette every time an edit occurs
Jim Procter [Sat, 5 Sep 2015 17:37:17 +0000 (18:37 +0100)]
JAL-1871 reinstate random generation of palette when applying RNA Helices colouring
Jim Procter [Thu, 9 Jul 2015 16:21:22 +0000 (17:21 +0100)]
JAL-1869 make per-sequence RNA helix colours each time Colour By Annotation is opened
Jim Procter [Sat, 5 Sep 2015 11:34:23 +0000 (12:34 +0100)]
Merge branch 'bugfix/JAL-841_JAL-1081' into develop
Jim Procter [Sat, 5 Sep 2015 11:17:53 +0000 (12:17 +0100)]
JAL-1805 move misassigned test from Functional to Network
Jim Procter [Sat, 5 Sep 2015 09:24:36 +0000 (10:24 +0100)]
JAL-1233 tidy up and use same RNA helix colours in colour by annotation and RNA helix colouring
Jim Procter [Sat, 5 Sep 2015 09:21:45 +0000 (10:21 +0100)]
JAL-1081 JAL-891 don’t overwrite global colour scheme with base pair consensus
Jim Procter [Sat, 5 Sep 2015 09:13:54 +0000 (10:13 +0100)]
JAL-1081 JAL-841 JAL-1053 JAL-1081 use same selection criteria for secondary structure annotation employed for structure consensus and colour by helices
Jim Procter [Fri, 4 Sep 2015 16:31:52 +0000 (17:31 +0100)]
JAL-1847 Merge branch 'thiago' into develop
Jim Procter [Fri, 4 Sep 2015 16:31:35 +0000 (17:31 +0100)]
JAL-1847 added AUTOSUPERIMPOSE property which can be used to disable automatic superposition when loading multiple structures
tcofoegbu [Fri, 4 Sep 2015 16:24:16 +0000 (17:24 +0100)]
JAL-793 added ability to visualise raw BioJSON in the exported HTML using facebox
gmungoc [Fri, 4 Sep 2015 15:43:17 +0000 (16:43 +0100)]
JAL-1859 jmolFindTarget not JmolFindTarget
gmungoc [Fri, 4 Sep 2015 15:03:38 +0000 (16:03 +0100)]
JAL-1859 embedded Jmol applet example updated for Jmol 14.2 javascript
Jim Procter [Thu, 3 Sep 2015 21:19:34 +0000 (22:19 +0100)]
JAL-1863 allow RNA secondary structure rows exported by Jalview to be imported again
Jim Procter [Thu, 3 Sep 2015 21:00:18 +0000 (22:00 +0100)]
JAL-961 efficiency TODO: decouple overview updates from sequence colour broadcasts
Jim Procter [Thu, 3 Sep 2015 20:35:49 +0000 (21:35 +0100)]
JAL-1680 JAL-1576 JAL-1233 all conservation and consensus calculation triggers and applying colour schemes to subgroups are refactored to viewport model
Jim Procter [Thu, 3 Sep 2015 20:30:29 +0000 (21:30 +0100)]
JAL-1576 fix: trigger broadcast of colour change with paintAlignment(true)
Jim Procter [Thu, 3 Sep 2015 20:28:32 +0000 (21:28 +0100)]
JAL-961 TODO use workers for calculations supporting colour schemes
Jim Procter [Thu, 3 Sep 2015 20:23:42 +0000 (21:23 +0100)]
JAL-1551 source tidy
Jim Procter [Thu, 3 Sep 2015 20:21:08 +0000 (21:21 +0100)]
JAL-1550 JAL-1551 formatting
Jim Procter [Thu, 3 Sep 2015 20:20:13 +0000 (21:20 +0100)]
JAL-1233 JAL-1576 copy constructor to propagate helix colours and applyTo implementation to clone colour scheme to subgroups
tcofoegbu [Thu, 3 Sep 2015 16:07:42 +0000 (17:07 +0100)]
merge
tcofoegbu [Thu, 3 Sep 2015 16:04:49 +0000 (17:04 +0100)]
JAL-1859 JAL-857 house keeping
tcofoegbu [Thu, 3 Sep 2015 15:24:47 +0000 (16:24 +0100)]
JAL-1859 JAL-857 updated all reference of JmolApplet-12.2.4.jar to JmolApplet-14.2.14_2015.06.11.jar
tcofoegbu [Thu, 3 Sep 2015 15:11:24 +0000 (16:11 +0100)]
house keeping
tcofoegbu [Thu, 3 Sep 2015 14:01:03 +0000 (15:01 +0100)]
merge
tcofoegbu [Thu, 3 Sep 2015 14:00:34 +0000 (15:00 +0100)]
JAL-1861 disable the action buttons for 1500 millisec when the ok button is clicked
gmungoc [Thu, 3 Sep 2015 13:36:50 +0000 (14:36 +0100)]
JAL-1859 removed unneeded dependency on package not in Jmol applet lib
tcofoegbu [Thu, 3 Sep 2015 11:04:13 +0000 (12:04 +0100)]
another merge from develop
tcofoegbu [Thu, 3 Sep 2015 10:39:03 +0000 (11:39 +0100)]
updated examples index page
gmungoc [Thu, 3 Sep 2015 10:37:28 +0000 (11:37 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Thu, 3 Sep 2015 10:37:16 +0000 (11:37 +0100)]
JAL-1690 scaleProteinAsCdna new optional attribute on Viewport in
project file
tcofoegbu [Thu, 3 Sep 2015 10:33:47 +0000 (11:33 +0100)]
merge
git://source.jalview.org / jalview.git / log