Jim Procter [Tue, 3 Jun 2014 13:34:22 +0000 (14:34 +0100)]
JAL-1503 JAL-1350 rework documentation for 2.8.1
Jim Procter [Tue, 3 Jun 2014 13:33:30 +0000 (14:33 +0100)]
JAL-1164 note that feature introduced in 2.8.0b1
Jim Procter [Tue, 3 Jun 2014 13:30:21 +0000 (14:30 +0100)]
JAL-1503 JAL-1355 documentation
Jim Procter [Tue, 3 Jun 2014 13:29:45 +0000 (14:29 +0100)]
JAL-1473 exclude score models not compatible with PCA algorithm
Jim Procter [Tue, 3 Jun 2014 13:28:44 +0000 (14:28 +0100)]
JAL-1503 gui changes (score models, flanking regions, trim retrieved sequences)
Jim Procter [Tue, 3 Jun 2014 13:27:38 +0000 (14:27 +0100)]
JAL-1503 formatting
Jim Procter [Tue, 3 Jun 2014 13:27:21 +0000 (14:27 +0100)]
JAL-1503 additional tree score functions
Jim Procter [Tue, 3 Jun 2014 13:26:59 +0000 (14:26 +0100)]
JAL-1503 PAM250 documentation
Jim Procter [Tue, 3 Jun 2014 13:26:22 +0000 (14:26 +0100)]
JAL-1503 document updated PCA interface
Jim Procter [Tue, 3 Jun 2014 13:25:23 +0000 (14:25 +0100)]
JAL-690 add .jvp as default jalview project filetype
Jim Procter [Tue, 3 Jun 2014 13:24:43 +0000 (14:24 +0100)]
JAL-1503 formatting
JAL-690 add .jvp as default javaws filetype for jalview projects
Jim Procter [Tue, 3 Jun 2014 13:23:39 +0000 (14:23 +0100)]
JAL-1503 formatting build file
Jim Procter [Tue, 3 Jun 2014 09:22:01 +0000 (10:22 +0100)]
JAL-1512 comment out for 2.8.1 release
Jim Procter [Tue, 3 Jun 2014 09:20:24 +0000 (10:20 +0100)]
JAL-1512 fix calculation once again and include score matrix documentation in comments in Jalview help
Jim Procter [Tue, 3 Jun 2014 09:14:52 +0000 (10:14 +0100)]
JAL-1473 make it easier to generate HTML documentation for similarity matrices
Jim Procter [Mon, 2 Jun 2014 15:45:40 +0000 (16:45 +0100)]
JAL-1512 rejig buggy conservation-basesd score matrix calculation
Jim Procter [Wed, 28 May 2014 14:16:48 +0000 (15:16 +0100)]
JAL-1509 use local deployJava
JAL-816 reinstate hashtable include to fix regression introduced in 2.8.0b1
Jim Procter [Wed, 28 May 2014 14:15:21 +0000 (15:15 +0100)]
fix for JAL-1510 - workaround for IE9
Jim Procter [Wed, 28 May 2014 08:02:38 +0000 (09:02 +0100)]
JAL-1507 bugfix
Jim Procter [Tue, 27 May 2014 15:06:54 +0000 (16:06 +0100)]
JAL-1509 update deployJava.js from java.com/js/deployJava.js
Jim Procter [Tue, 27 May 2014 15:03:20 +0000 (16:03 +0100)]
JAL-1507 added loop to throw dummy javascript calls out to the browser to make sure it wakes up and prompts user to allow LiveConnect
Jim Procter [Tue, 27 May 2014 15:02:12 +0000 (16:02 +0100)]
JAL-1402 conditional logic to ensure annotation & label panel/canvas components not touched in validation/layout/paint routines unless layout requires them
Jim Procter [Tue, 27 May 2014 14:59:45 +0000 (15:59 +0100)]
JAL-1508 make default font size 11pt for embedded menus. workaround - not a fix
Jim Procter [Fri, 23 May 2014 11:10:57 +0000 (12:10 +0100)]
JAL-1445 updated documentation and added link in whatsNew
Jim Procter [Fri, 23 May 2014 10:57:27 +0000 (11:57 +0100)]
JAL-1445 extend functionality to select or toggle selection for columns containing/not containing features in alignment or currently selected region
Jim Procter [Thu, 22 May 2014 14:08:19 +0000 (15:08 +0100)]
remove non-utf8 characters in help pages
Jim Procter [Thu, 22 May 2014 14:06:39 +0000 (15:06 +0100)]
JAL-1503 update version in GPL header
Jim Procter [Thu, 22 May 2014 13:34:06 +0000 (14:34 +0100)]
JAL-1355 JAL-1503 update i18n note
Jim Procter [Thu, 22 May 2014 13:33:12 +0000 (14:33 +0100)]
JAL-1503 new entry for 2.8.1 release history
Jim Procter [Thu, 22 May 2014 13:31:48 +0000 (14:31 +0100)]
JAL-1503 JAL-1355 note about internationalisation in release notes
Jim Procter [Sat, 17 May 2014 11:55:19 +0000 (12:55 +0100)]
JAL-1477 documentation and tooltips
Jim Procter [Tue, 13 May 2014 14:16:16 +0000 (15:16 +0100)]
Merge branch 'bugfix/JAL-1239' into Release_2_8_1_Branch_i18n
Jim Procter [Tue, 13 May 2014 14:13:17 +0000 (15:13 +0100)]
JAL-1239 cancelled flag should be checked and counted
Jim Procter [Tue, 13 May 2014 14:12:30 +0000 (15:12 +0100)]
JAL-1239 make doubly sure sub job status is set to complete/cancelled
Jim Procter [Mon, 12 May 2014 15:07:08 +0000 (16:07 +0100)]
Merge branch 'JAL-1397' into Release_2_8_1_Branch_i18n
Jim Procter [Mon, 12 May 2014 15:05:53 +0000 (16:05 +0100)]
Merge branch 'JAL-1397' into Release_2_8_1_Branch
Jim Procter [Mon, 12 May 2014 14:05:11 +0000 (15:05 +0100)]
JAL-1397 catch other random version strings
Jim Procter [Mon, 12 May 2014 14:04:54 +0000 (15:04 +0100)]
patch for regression introduced JAL-1397
Jim Procter [Fri, 2 May 2014 09:44:52 +0000 (10:44 +0100)]
Merge branch 'Release_2_8_1_Branch' into Release_2_8_1_Branch_i18n
Jim Procter [Fri, 2 May 2014 09:44:22 +0000 (10:44 +0100)]
Merge branch 'JAL-1397' into Release_2_8_1_Branch
Jim Procter [Fri, 2 May 2014 09:43:26 +0000 (10:43 +0100)]
JAL-1397 JAL-1066 JAL-1233 refactored annotation colours XML parsing code and support per group annotation colours
Jim Procter [Fri, 2 May 2014 09:41:03 +0000 (10:41 +0100)]
JAL-1369 JAL-1397 version check to support correct interpretation for older projects where data semantics have changed
Jim Procter [Fri, 2 May 2014 09:35:12 +0000 (10:35 +0100)]
formatting
Jim Procter [Fri, 2 May 2014 09:27:38 +0000 (10:27 +0100)]
JAL-1233 JAL-1066 fix for JAL-1397 test: allow per group colour by annotation to be stored/recovered in Jalview projects (version compatibility will be 2.8.1 and after)
Jim Procter [Thu, 1 May 2014 16:05:20 +0000 (17:05 +0100)]
JAL-1397 (probably buggy) test for recovery of background and per group alignment annotation shading
Jim Procter [Thu, 1 May 2014 14:42:07 +0000 (15:42 +0100)]
remove todo
Jim Procter [Thu, 1 May 2014 14:41:20 +0000 (15:41 +0100)]
JAL-1492 formatting and squash NPEs
Jim Procter [Thu, 1 May 2014 14:40:20 +0000 (15:40 +0100)]
JAL-1092 TODO - allow Jalview/JalviewLite to generate its own user defined colour scheme parameter strings
Jim Procter [Thu, 1 May 2014 14:38:57 +0000 (15:38 +0100)]
JAL-1492 JAL-1397 make AnnotatedCollectionI context aware so groups can be coloured based on annotation on their parent alignments.
Jim Procter [Thu, 1 May 2014 14:33:59 +0000 (15:33 +0100)]
JAL-1492 JAL-1397 JAL-643 JAL-969 pull up global and group colourscheme logic and regularise interface
Jim Procter [Thu, 1 May 2014 14:29:31 +0000 (15:29 +0100)]
JAL-1492 JAL-1397 JAL-643 JAL-969 factory method to clone and apply colour scheme to another alignment/group
Jim Procter [Thu, 1 May 2014 14:26:07 +0000 (15:26 +0100)]
JAL-1492 JAL-1397 JAL-643 JAL-969 modifiable flag on colourscheme indicating conservation shading should be applied
Jim Procter [Thu, 1 May 2014 14:24:08 +0000 (15:24 +0100)]
javadoc
Jim Procter [Thu, 1 May 2014 14:14:08 +0000 (15:14 +0100)]
properly quit so JUnit marks tests as successful
Jim Procter [Thu, 1 May 2014 14:12:07 +0000 (15:12 +0100)]
JAL-1497 check to see if tree structure is ready for display, and show a 'tree loading' message if it isn't.
Jim Procter [Thu, 1 May 2014 14:06:29 +0000 (15:06 +0100)]
fix for JAL-1495 - initialise menu entry from current state of apply to all groups flag !
Jim Procter [Thu, 1 May 2014 14:03:33 +0000 (15:03 +0100)]
fix for JAL-1494 tweaked logic to fix NPEs and modify settings for both background and all defined groups
Jim Procter [Thu, 1 May 2014 13:57:30 +0000 (14:57 +0100)]
JAL-969 remove unnecessary overrides
Jim Procter [Thu, 1 May 2014 13:33:44 +0000 (14:33 +0100)]
JAL-961 configure conservation worker from alignment viewport
Jim Procter [Thu, 1 May 2014 13:32:45 +0000 (14:32 +0100)]
JAL-961 store result of conservation analysis worker on the alignment viewport
Jim Procter [Thu, 1 May 2014 13:24:07 +0000 (14:24 +0100)]
make sure valid value for non-gapped calculation with zero symbol data
Jim Procter [Thu, 17 Oct 2013 12:44:25 +0000 (13:44 +0100)]
JAL-643 - abstracted colourscheme components to allow consensus/colouring to be propagated from background to a group
Jim Procter [Tue, 29 Apr 2014 12:25:35 +0000 (13:25 +0100)]
Merge branch 'JAL-1340_redundancy' into Release_2_8_1_Branch
Jim Procter [Mon, 28 Apr 2014 12:32:52 +0000 (13:32 +0100)]
JAL-1340 mark redundant sequences as soon as redundancy calculation has finished
Jim Procter [Mon, 28 Apr 2014 12:31:59 +0000 (13:31 +0100)]
JAL-1340 simpler and more efficient interactive highlighting of redundant sequences
Jim Procter [Mon, 28 Apr 2014 12:28:17 +0000 (13:28 +0100)]
JAL-1340 ensure slider value wide enough to see three figures
Jim Procter [Sun, 27 Apr 2014 22:15:20 +0000 (23:15 +0100)]
Merge branch 'JAL-1322' into Release_2_8_1_Branch_i18n
Jim Procter [Sun, 27 Apr 2014 22:15:11 +0000 (23:15 +0100)]
Merge branch 'JAL-1322' into Release_2_8_1_Branch
Jim Procter [Sun, 27 Apr 2014 22:14:24 +0000 (23:14 +0100)]
JAL-1322 avoid rounding error causing non functional slider and allow slider to reach maximum value for parameter
Jim Procter [Sun, 27 Apr 2014 22:13:58 +0000 (23:13 +0100)]
JAL-1322 allow slider to reach maximum value for parameter
Jim Procter [Sun, 27 Apr 2014 22:12:56 +0000 (23:12 +0100)]
JAL-1322 only update slider when return is pressed
Jim Procter [Sun, 27 Apr 2014 20:42:10 +0000 (21:42 +0100)]
Merge branch 'Release_2_8_1_Branch' into Release_2_8_1_Branch_i18n
Jim Procter [Sun, 27 Apr 2014 20:41:36 +0000 (21:41 +0100)]
Merge branch 'JAL-952_rnahelix' into Release_2_8_1_Branch
Jim Procter [Sun, 27 Apr 2014 20:41:29 +0000 (21:41 +0100)]
Merge branch 'JAL-1164_regression' into Release_2_8_1_Branch
Jim Procter [Sun, 27 Apr 2014 17:44:12 +0000 (18:44 +0100)]
workaround for JAL-1319 - catch unexpected NPE thrown by JABA client method
Jim Procter [Sun, 27 Apr 2014 17:38:13 +0000 (18:38 +0100)]
JAL-1164 (regression) reinstate 'apply disorder prediction to selection' functionality in 2.8.1+ lost during JabaCalcWorker refactoring
Jim Procter [Sun, 27 Apr 2014 15:59:31 +0000 (16:59 +0100)]
JAL-952 JAL-1268 document TCoffee and RNA helices colourschemes in applet properties
Jim Procter [Sun, 27 Apr 2014 15:22:18 +0000 (16:22 +0100)]
JAL-952 JAL-1268 document RNA Helices and T-Coffee Scores as valid colour scheme names for applet parameters
Jim Procter [Sun, 27 Apr 2014 15:17:11 +0000 (16:17 +0100)]
JAL-952 JAL-1268 add RNA Helices and T-Coffee to list of available colour schemes in jalview preferences
Jim Procter [Sun, 27 Apr 2014 15:16:41 +0000 (16:16 +0100)]
JAL-952 resolve colour scheme as 'RNA Helices'
Jim Procter [Sun, 27 Apr 2014 15:12:42 +0000 (16:12 +0100)]
JAL-952 refactor code to select annotation for colouring the alignment
Jim Procter [Sun, 27 Apr 2014 15:06:09 +0000 (16:06 +0100)]
test for JAL-952
Jim Procter [Fri, 25 Apr 2014 16:17:03 +0000 (17:17 +0100)]
Merge branch 'Release_2_8_1_Branch' into Release_2_8_1_Branch_i18n
Jim Procter [Fri, 25 Apr 2014 16:11:28 +0000 (17:11 +0100)]
Merge branch 'JAL-1177_prop_rnasecstr' into Release_2_8_1_Branch
Jim Procter [Fri, 25 Apr 2014 16:10:10 +0000 (17:10 +0100)]
fix for JAL-1268
Jim Procter [Fri, 25 Apr 2014 16:09:55 +0000 (17:09 +0100)]
test for JAL-1268
Jim Procter [Fri, 25 Apr 2014 13:27:23 +0000 (14:27 +0100)]
JAL-1177 additional saveState calls to write a dataset only jalview xml document
Jim Procter [Fri, 25 Apr 2014 13:26:04 +0000 (14:26 +0100)]
JAL-1177 patches to loader to cope with dataset only jalview xml documents
Jim Procter [Fri, 25 Apr 2014 13:24:56 +0000 (14:24 +0100)]
JAL-1177 new flag to write a dataset only jalview XML document
Jim Procter [Fri, 25 Apr 2014 13:20:42 +0000 (14:20 +0100)]
JAL-1177 allow jalview alignments to be saved that have no alignment views, to support storage of parent datasets
Jim Procter [Fri, 25 Apr 2014 12:51:34 +0000 (13:51 +0100)]
JAL-1177 propagate sequence associated annotation to dataset sequence
Jim Procter [Fri, 25 Apr 2014 12:50:47 +0000 (13:50 +0100)]
JAL-1177 refactored command line test harness
Jim Procter [Fri, 25 Apr 2014 12:49:44 +0000 (13:49 +0100)]
test for JAL-1177 store and recover RNA secondary structure for a stockholm file with sequence associated RNA structure
Jim Procter [Thu, 24 Apr 2014 16:39:58 +0000 (17:39 +0100)]
JAL-1232 fix - ensure display all columns flag is set if an RNA helix is created on an annotation row.
Jim Procter [Wed, 23 Apr 2014 16:16:09 +0000 (17:16 +0100)]
Merge branch 'JAL-1486_hiddenStartEnd' into Release_2_8_1_Branch_i18n
Jim Procter [Wed, 23 Apr 2014 16:15:57 +0000 (17:15 +0100)]
Merge branch 'JAL-1486_hiddenStartEnd' into Release_2_8_1_Branch
Jim Procter [Wed, 23 Apr 2014 16:15:04 +0000 (17:15 +0100)]
JAL-1486 todo for 2.8.2 release
Jim Procter [Wed, 23 Apr 2014 15:38:30 +0000 (16:38 +0100)]
Merge branch 'Release_2_8_1_Branch' into Release_2_8_1_Branch_i18n
Jim Procter [Wed, 23 Apr 2014 15:37:13 +0000 (16:37 +0100)]
Merge branch 'jims_marckhacks' into Release_2_8_1_Branch
Jim Procter [Mon, 21 Apr 2014 21:25:17 +0000 (22:25 +0100)]
JAL-1458 updated logo for installer
git://source.jalview.org / jalview.git / log