gmungoc [Wed, 16 Sep 2015 09:26:54 +0000 (10:26 +0100)]
JAL-1859 revert to resolving full path to PDB file
gmungoc [Wed, 16 Sep 2015 09:25:43 +0000 (10:25 +0100)]
JAL-1859 refactor addProtocol, setProtocolState as resolveFileProtocol
gmungoc [Wed, 16 Sep 2015 08:01:20 +0000 (09:01 +0100)]
JAL-1859 temporary debug output
gmungoc [Tue, 15 Sep 2015 15:01:25 +0000 (16:01 +0100)]
JAL-1859 use unresolved PDB filename
gmungoc [Tue, 15 Sep 2015 15:00:52 +0000 (16:00 +0100)]
JAL-1859 strip file name from applet documentbase
gmungoc [Tue, 15 Sep 2015 11:26:34 +0000 (12:26 +0100)]
JAL-1859 refactoring / debugging added
gmungoc [Mon, 14 Sep 2015 14:50:41 +0000 (15:50 +0100)]
JAL-1865 fixed so initial state of annotation sort options matches
display
gmungoc [Mon, 14 Sep 2015 12:10:05 +0000 (13:10 +0100)]
JAL-1851 add retrieved sequence's start (-1) to match offset for start
of trimmed sequence
gmungoc [Mon, 14 Sep 2015 11:12:39 +0000 (12:12 +0100)]
JAL-1880 updated mapping tests to ensure they handle subsequence offsets
gmungoc [Mon, 14 Sep 2015 08:43:11 +0000 (09:43 +0100)]
JAL-1270 test added for separatorListToArray
gmungoc [Mon, 14 Sep 2015 08:42:07 +0000 (09:42 +0100)]
JAL-1880 handle sequence offsets properly when mapping cDNA to protein
gmungoc [Mon, 14 Sep 2015 08:39:06 +0000 (09:39 +0100)]
JAL-1684 align added alignment to match original in split frame
gmungoc [Mon, 14 Sep 2015 08:34:05 +0000 (09:34 +0100)]
JAL-1684 align added alignment to match original in split frame
gmungoc [Mon, 14 Sep 2015 08:31:45 +0000 (09:31 +0100)]
JAL-1684 ensure cDNA placed above protein in SplitFrame
Jim Procter [Fri, 11 Sep 2015 13:39:02 +0000 (14:39 +0100)]
JAL-1884 add the JNLP template to jalview_jnlp_vm.jar
Jim Procter [Thu, 10 Sep 2015 15:35:14 +0000 (16:35 +0100)]
JAL-1645 fix broken link in docs
Jim Procter [Thu, 10 Sep 2015 10:14:10 +0000 (11:14 +0100)]
JAL-1645 reformat help html - 2 spaces indents, no tabs
Jim Procter [Thu, 10 Sep 2015 10:02:54 +0000 (11:02 +0100)]
JAL-1645 licencing for help html
Jim Procter [Thu, 10 Sep 2015 10:00:58 +0000 (11:00 +0100)]
JAL-1645 licencing for doc directory files
Jim Procter [Thu, 10 Sep 2015 09:59:00 +0000 (10:59 +0100)]
JAL-1645 licencing for groovy files
Jim Procter [Thu, 10 Sep 2015 09:50:30 +0000 (10:50 +0100)]
JAL-1645 licencing for new files in test and utils
Jim Procter [Thu, 10 Sep 2015 09:34:38 +0000 (10:34 +0100)]
JAL-1645 licencing for new files in src
Jim Procter [Thu, 10 Sep 2015 03:59:59 +0000 (04:59 +0100)]
JAL-1645 source formatting and organise imports
Jim Procter [Thu, 10 Sep 2015 03:57:44 +0000 (04:57 +0100)]
JAL-1645 source formatting and organise imports
Jim Procter [Thu, 10 Sep 2015 03:40:52 +0000 (04:40 +0100)]
JAL-1684 updated example to just a fragment of the estrogen sequences
Jim Procter [Thu, 10 Sep 2015 03:31:38 +0000 (04:31 +0100)]
JAL-1645 add reference seq docs to index/etc
Jim Procter [Thu, 10 Sep 2015 03:28:45 +0000 (04:28 +0100)]
JAL-1645 formatting and updated release date
Jim Procter [Thu, 10 Sep 2015 03:27:24 +0000 (04:27 +0100)]
JAL-1645 formatting
Jim Procter [Thu, 10 Sep 2015 02:50:17 +0000 (03:50 +0100)]
JAL-736 JAL-1645 brief documentation about physicochemical property conservation tooltips
Jim Procter [Thu, 10 Sep 2015 02:42:05 +0000 (03:42 +0100)]
Merge branch 'develop' into release/2_9_documentation
Jim Procter [Thu, 10 Sep 2015 02:39:16 +0000 (03:39 +0100)]
JAL-1645 typo
Jim Procter [Thu, 10 Sep 2015 02:39:03 +0000 (03:39 +0100)]
JAL-1645 JAL-1595 sort by RNA helices docs
Jim Procter [Thu, 10 Sep 2015 02:18:39 +0000 (03:18 +0100)]
JAL-1645 more cross-links and fixing menu entries
Jim Procter [Thu, 10 Sep 2015 02:10:58 +0000 (03:10 +0100)]
JAL-1645 links from whats New page
Jim Procter [Thu, 10 Sep 2015 01:53:26 +0000 (02:53 +0100)]
JAL-1645 yet more documentation tweaks
Jim Procter [Thu, 10 Sep 2015 01:44:14 +0000 (02:44 +0100)]
JAL-1370 correct i18n message for reference sequence entry in popup menu
Jim Procter [Thu, 10 Sep 2015 01:41:38 +0000 (02:41 +0100)]
JAL-1370 detect any type of gap character in reference sequence when showing unconserved residues
Jim Procter [Thu, 10 Sep 2015 01:39:15 +0000 (02:39 +0100)]
JAL-1370 mark Jpred query sequence as reference sequence
Jim Procter [Wed, 9 Sep 2015 21:16:41 +0000 (22:16 +0100)]
JAL-1645 rejig annotation selection dialog box
Jim Procter [Wed, 9 Sep 2015 20:31:18 +0000 (21:31 +0100)]
JAL-1645 rejig biojson/biojsmsa docs
Jim Procter [Wed, 9 Sep 2015 19:53:56 +0000 (20:53 +0100)]
JAL-1645 documentation tweaks
Jim Procter [Wed, 9 Sep 2015 17:24:00 +0000 (18:24 +0100)]
JAL-1645 rejig bioJSON, export and whats new
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
gmungoc [Wed, 9 Sep 2015 14:39:33 +0000 (15:39 +0100)]
JAL-857 debug=true for Jmol example diagnosis
gmungoc [Wed, 9 Sep 2015 14:06:51 +0000 (15:06 +0100)]
JAL-857 added debug output to track down document base glitch
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
git://source.jalview.org / jalview.git / log