Jim Procter [Mon, 24 Nov 2014 16:06:31 +0000 (16:06 +0000)]
JAL-1264 update annotation panel dimensions before refresh
Jim Procter [Mon, 24 Nov 2014 16:02:58 +0000 (16:02 +0000)]
JAL-1595 update annotation sort on opening of the 'sort' menu..
Jim Procter [Mon, 24 Nov 2014 16:01:33 +0000 (16:01 +0000)]
JAL-1595 annotation score is total number of rna helices
Jim Procter [Sun, 23 Nov 2014 20:18:05 +0000 (20:18 +0000)]
JAL-1569 interactive editing of secondary structure char for RNA secondary structure
Jim Procter [Sun, 23 Nov 2014 17:22:05 +0000 (17:22 +0000)]
Merge branch 'JAL-1569_wuss_vienna_broke' into Release_2_8_2_Branch
Jim Procter [Sun, 23 Nov 2014 16:43:54 +0000 (16:43 +0000)]
employ test and secondary structure character for determining base pairing direction for rendering rna annotation
Jim Procter [Sun, 23 Nov 2014 16:42:55 +0000 (16:42 +0000)]
JAL-1569 formatting
Jim Procter [Sun, 23 Nov 2014 16:42:01 +0000 (16:42 +0000)]
JAL-1593 allow per-sequence shading of RNA helix (stored in each annotation element's value field for a paired base)
Jim Procter [Sun, 23 Nov 2014 16:37:33 +0000 (16:37 +0000)]
JAL-1569 test for open/close RNA parenthesis character
Jim Procter [Sun, 23 Nov 2014 16:35:56 +0000 (16:35 +0000)]
JAL-1569 formatting
Jim Procter [Sun, 23 Nov 2014 16:34:42 +0000 (16:34 +0000)]
JAL-1569 refactoring of stockholm test
Jim Procter [Sun, 23 Nov 2014 16:33:59 +0000 (16:33 +0000)]
JAL-1569 consistent handling of sequence and alignment associated annotation export in stockholm
Jim Procter [Sun, 23 Nov 2014 16:32:37 +0000 (16:32 +0000)]
JAL-1569 revise tests to count number and type of annotation in each file
Jim Procter [Sun, 23 Nov 2014 16:31:26 +0000 (16:31 +0000)]
JAL-1569 formatting
Jim Procter [Sun, 23 Nov 2014 16:29:58 +0000 (16:29 +0000)]
JAL-1569 preserve input ordering for stockholm files (Hashtable implementation changed possibly ?)
Jim Procter [Sun, 23 Nov 2014 16:22:25 +0000 (16:22 +0000)]
JAL-1569 remove stdout on parsing RNA
Jim Procter [Sun, 23 Nov 2014 16:21:34 +0000 (16:21 +0000)]
JAL-1152 avoid NPE on null alignment annotation vector
gmungoc [Fri, 21 Nov 2014 14:33:08 +0000 (14:33 +0000)]
JAL-1528 found and readded Colour by Chain ('rainbow color')
gmungoc [Fri, 21 Nov 2014 14:30:33 +0000 (14:30 +0000)]
Merge branch 'Release_2_8_2_Branch' of https://source.jalview.org/git/jalview.git into Release_2_8_2_Branch
Jim Procter [Fri, 21 Nov 2014 09:01:03 +0000 (09:01 +0000)]
JAL-674 add RNA sequence associated annotation to alignment as hidden annotation
Jim Procter [Fri, 21 Nov 2014 08:59:49 +0000 (08:59 +0000)]
JAL-1569 formatting
Jim Procter [Fri, 21 Nov 2014 08:56:52 +0000 (08:56 +0000)]
JAL-1140 sensible name for seuqences in RNAML files that have no ID
Jim Procter [Fri, 21 Nov 2014 08:55:38 +0000 (08:55 +0000)]
JAL-1489 change initial value to distinguish non-rna from valid and invalid RNA structure with one call to .isValidStructure()
Jim Procter [Fri, 21 Nov 2014 08:54:11 +0000 (08:54 +0000)]
JAL-1592 JAL-1489 avoid invalid RNA structure and distinguish alignment associated from sequence associated structure lines
Jim Procter [Thu, 20 Nov 2014 14:54:01 +0000 (14:54 +0000)]
JAL-1569 rna pair code in secondary structure character of annotation
Jim Procter [Thu, 20 Nov 2014 14:52:22 +0000 (14:52 +0000)]
JAL-674 JAL-1569 mark RNA helix number in the value field
Jim Procter [Thu, 20 Nov 2014 14:49:36 +0000 (14:49 +0000)]
JAL-1569 remove log output during RNA secondary structure processing
Charles Ofoegbu [Wed, 19 Nov 2014 16:53:36 +0000 (16:53 +0000)]
JAL-1583 MSA webservice validation
gmungoc [Wed, 19 Nov 2014 12:55:39 +0000 (12:55 +0000)]
JAL-1342 new command-line parameter -jabaws <URL>
Charles Ofoegbu [Wed, 19 Nov 2014 12:20:50 +0000 (12:20 +0000)]
merge commit
Charles Ofoegbu [Wed, 19 Nov 2014 12:05:44 +0000 (12:05 +0000)]
JAL-207 pairwise alignment context patch
Charles Ofoegbu [Wed, 19 Nov 2014 11:18:37 +0000 (11:18 +0000)]
Merge branch 'bug/JAL-1522_include-installation-details-in-log' into Release_2_8_2_Branch
Charles Ofoegbu [Wed, 19 Nov 2014 11:11:41 +0000 (11:11 +0000)]
JAL-1522 included installation details in log output
Charles Ofoegbu [Tue, 18 Nov 2014 16:46:18 +0000 (16:46 +0000)]
updated classpath
Charles Ofoegbu [Tue, 18 Nov 2014 15:35:57 +0000 (15:35 +0000)]
Merge branch 'bug/JAL-998_wrap-sequence-tooltip' into Release_2_8_2_Branch
Charles Ofoegbu [Tue, 18 Nov 2014 15:32:18 +0000 (15:32 +0000)]
modified classpath
Charles Ofoegbu [Tue, 18 Nov 2014 15:28:07 +0000 (15:28 +0000)]
JAL-998 tooltip wrapping
gmungoc [Tue, 18 Nov 2014 15:15:34 +0000 (15:15 +0000)]
JAL-1349 rebuild Web Service menu after add/delete preset
gmungoc [Tue, 18 Nov 2014 15:01:30 +0000 (15:01 +0000)]
JAL-1582 removing finalize() as may have unexpected behaviour
Charles Ofoegbu [Tue, 18 Nov 2014 14:39:51 +0000 (14:39 +0000)]
JAL-1583 MSA webservice client side validation
gmungoc [Tue, 18 Nov 2014 14:11:39 +0000 (14:11 +0000)]
JAL-1582 quicker tooltip on service presets (and code formatting).
gmungoc [Tue, 18 Nov 2014 13:40:04 +0000 (13:40 +0000)]
JAL-1349 refresh menu presets after 'create' new
gmungoc [Tue, 18 Nov 2014 11:51:46 +0000 (11:51 +0000)]
JAL-1580 Chimera path tooltip, removed focusListener
gmungoc [Tue, 18 Nov 2014 11:32:25 +0000 (11:32 +0000)]
Merge branch 'Release_2_8_2_Branch' of https://source.jalview.org/git/jalview.git into Release_2_8_2_Branch
Jim Procter [Tue, 18 Nov 2014 09:56:53 +0000 (09:56 +0000)]
Merge branch 'JAL-1587_promotedisorder' into Release_2_8_2_Branch
Jim Procter [Tue, 18 Nov 2014 09:52:35 +0000 (09:52 +0000)]
JAL-674 make temperature factor, local secondary structure and service based secondary structure processing configurable
Jim Procter [Tue, 18 Nov 2014 09:44:36 +0000 (09:44 +0000)]
JAL-674 JAL-1512 JAL-1333 documentation
Jim Procter [Mon, 17 Nov 2014 17:14:23 +0000 (17:14 +0000)]
JAL-1517 JAL-1587 JAL-674 secondary structure and annotation from prediction services documentation
Jim Procter [Mon, 17 Nov 2014 17:12:54 +0000 (17:12 +0000)]
JAL-1517 release notes for 2.8.2
Charles Ofoegbu [Mon, 17 Nov 2014 16:54:16 +0000 (16:54 +0000)]
Undo changes to JabaWsServerQuery.java
Charles Ofoegbu [Mon, 17 Nov 2014 16:52:32 +0000 (16:52 +0000)]
Undo changes to JabaWsServerQuery.java
gmungoc [Mon, 17 Nov 2014 16:44:14 +0000 (16:44 +0000)]
JAL-1573 unit test added to verify Help target enum values.
gmungoc [Mon, 17 Nov 2014 16:28:32 +0000 (16:28 +0000)]
JAL-1581 Tooltip slimmed down, Help button added on panel with link to
relevant Help page.
Jim Procter [Mon, 17 Nov 2014 14:47:17 +0000 (14:47 +0000)]
JAL-1587 distinct calc IDs for JPredMSA and Jpred single sequence.
Jim Procter [Mon, 17 Nov 2014 14:43:37 +0000 (14:43 +0000)]
JAL-1587 propagate results of JABA sequence based predictors to dataset
Jim Procter [Mon, 17 Nov 2014 14:42:21 +0000 (14:42 +0000)]
imports and formatting
Jim Procter [Mon, 17 Nov 2014 14:41:56 +0000 (14:41 +0000)]
JAL-1587 propagate JPred annotation from legacy jpred service to the dataset
Jim Procter [Mon, 17 Nov 2014 14:38:37 +0000 (14:38 +0000)]
formatting
Jim Procter [Mon, 17 Nov 2014 14:38:16 +0000 (14:38 +0000)]
JAL-1587 JAL-407 instrument setDataset to add dataset sequences to existing dataset if they aren't already present
Charles Ofoegbu [Mon, 17 Nov 2014 13:47:12 +0000 (13:47 +0000)]
Merge branch 'bug/JAL-1043_warning-dialog-not-shown-for-JABA-errors' into Release_2_8_2_Branch
Charles Ofoegbu [Mon, 17 Nov 2014 13:45:23 +0000 (13:45 +0000)]
JAL-1043 patch to show warning dialog when webservice exception is thrown
gmungoc [Mon, 17 Nov 2014 13:26:47 +0000 (13:26 +0000)]
JAL-1293 hide/show sequence annotations with hide/reveal sequences
gmungoc [Mon, 17 Nov 2014 12:57:39 +0000 (12:57 +0000)]
JAL-1586 chimera file chooser added, validate on OK/change tab
Jim Procter [Mon, 17 Nov 2014 11:44:00 +0000 (11:44 +0000)]
Merge branch 'Release_2_8_2_Branch' of https://source.jalview.org/git/jalview into Release_2_8_2_Branch
Jim Procter [Mon, 17 Nov 2014 11:43:36 +0000 (11:43 +0000)]
Merge branch 'r282_portforward' into Release_2_8_2_Branch
Jim Procter [Mon, 17 Nov 2014 11:42:02 +0000 (11:42 +0000)]
JAL-1469 help documentation
Jim Procter [Mon, 17 Nov 2014 11:39:05 +0000 (11:39 +0000)]
JAL-1469 help documentation
Charles Ofoegbu [Mon, 17 Nov 2014 11:38:49 +0000 (11:38 +0000)]
Merge branch 'bug/JAL-1570_unable-to-add-JABAWS-Server-which-fails-validation' into Release_2_8_2_Branch
Charles Ofoegbu [Mon, 17 Nov 2014 11:37:08 +0000 (11:37 +0000)]
updated documentation
Jim Procter [Mon, 17 Nov 2014 11:31:23 +0000 (11:31 +0000)]
Merge branch 'mrg_dev_282' into Release_2_8_2_Branch
Jim Procter [Mon, 17 Nov 2014 11:31:13 +0000 (11:31 +0000)]
Merge branch 'Release_2_8_2_Branch' into mrg_dev_282
Charles Ofoegbu [Mon, 17 Nov 2014 10:01:53 +0000 (10:01 +0000)]
comand line support for svg generation
Release_2_8_2_Branch only for JAL-1469 -removed changes to BioJS importer
code
Conflicts:
.classpath
src/jalview/io/HtmlFile.java
gmungoc [Mon, 17 Nov 2014 11:16:59 +0000 (11:16 +0000)]
JAL-1580 size parameters dialog to height of Desktop
Charles Ofoegbu [Mon, 17 Nov 2014 11:10:08 +0000 (11:10 +0000)]
Merge branch 'bug/JAL-1570_unable-to-add-JABAWS-Server-which-fails-validation' into Release_2_8_2_Branch
Charles Ofoegbu [Mon, 17 Nov 2014 11:04:24 +0000 (11:04 +0000)]
JAL-1570 patch to enable adding a webservice which fails validation
Jim Procter [Mon, 17 Nov 2014 10:40:02 +0000 (10:40 +0000)]
Merge branch 'mrg_dev_282' into Release_2_8_2_Branch
gmungoc [Fri, 14 Nov 2014 12:53:45 +0000 (12:53 +0000)]
JAL-1528 Chimera Help doc + fixes to setting colours
gmungoc [Thu, 13 Nov 2014 12:40:33 +0000 (12:40 +0000)]
JAL-1528 new Preference CHIMERA_PATH (Preferences | Structure)
gmungoc [Thu, 13 Nov 2014 11:15:42 +0000 (11:15 +0000)]
JAL-1528 Chimera tidy errors, focus after align, close option
gmungoc [Wed, 12 Nov 2014 16:55:00 +0000 (16:55 +0000)]
JAL-1528 bug fixes and adjustments to Chimera interface
Jim Procter [Mon, 17 Nov 2014 10:25:33 +0000 (10:25 +0000)]
Jim Procter [Thu, 13 Nov 2014 16:38:00 +0000 (16:38 +0000)]
Merge branch 'features/JAL-1469_svg-output-for-figure-export' into Release_2_8_2_Branch
Conflicts:
.gitignore
src/jalview/gui/AlignmentPanel.java
Jim Procter [Thu, 13 Nov 2014 16:34:59 +0000 (16:34 +0000)]
JAL-1469 added jfreesvg to desktop dependencies
Charles Ofoegbu [Thu, 13 Nov 2014 09:38:25 +0000 (09:38 +0000)]
added jfreesvg dependency to class path
Charles Ofoegbu [Wed, 12 Nov 2014 20:07:58 +0000 (20:07 +0000)]
house-keeping
Charles Ofoegbu [Wed, 12 Nov 2014 17:54:32 +0000 (17:54 +0000)]
Added support for SVG Export
Jim Procter [Wed, 12 Nov 2014 14:56:16 +0000 (14:56 +0000)]
Merge branch 'features/typed_annotations_calcId' into Release_2_8_2_Branch
Jim Procter [Wed, 12 Nov 2014 14:55:45 +0000 (14:55 +0000)]
JAL-974 fix class contamination for jalviewLite build
Jim Procter [Wed, 12 Nov 2014 12:44:17 +0000 (12:44 +0000)]
Merge branch 'features/typed_annotations_calcId' into Release_2_8_2_Branch
Jim Procter [Wed, 12 Nov 2014 12:40:43 +0000 (12:40 +0000)]
javadoc
Jim Procter [Wed, 12 Nov 2014 12:40:24 +0000 (12:40 +0000)]
JAL-674 use the getMapping/transfer to transfer annotation when creating a mapping to a sequence
Jim Procter [Wed, 12 Nov 2014 12:39:50 +0000 (12:39 +0000)]
JAL-674 patch broken getMapping function
Jim Procter [Wed, 12 Nov 2014 12:39:05 +0000 (12:39 +0000)]
JAL-674 switch from .transfer to .liftOver for transfer of annotation
Jim Procter [Wed, 12 Nov 2014 12:37:12 +0000 (12:37 +0000)]
JAL-674 note about broken .transfer method (expect this to disappear in future!)
Jim Procter [Wed, 12 Nov 2014 12:36:36 +0000 (12:36 +0000)]
JAL-674 javadoc
Jim Procter [Wed, 12 Nov 2014 12:35:40 +0000 (12:35 +0000)]
JAL-674 new tests and deprecated tests for PDB mapping to sequence code
gmungoc [Tue, 11 Nov 2014 09:20:40 +0000 (09:20 +0000)]
JAL-1527 opening a project saved with JMol should use JMol (disregard
viewer preference).
Jim Procter [Thu, 6 Nov 2014 17:18:44 +0000 (17:18 +0000)]
Merge branch 'features/JAL-1152annotationSorting' into features/typed_annotations_calcId
gmungoc [Thu, 6 Nov 2014 14:33:26 +0000 (14:33 +0000)]
JAL-1152 use a proper RadioButton not a faked one
gmungoc [Wed, 5 Nov 2014 16:04:10 +0000 (16:04 +0000)]
JAL-674 Prefences tweaks incl help documentation for Structure tab
git://source.jalview.org / jalview.git / log