Charles Ofoegbu [Fri, 31 Oct 2014 14:45:38 +0000 (14:45 +0000)]
updated gitignore
Charles Ofoegbu [Fri, 31 Oct 2014 14:34:49 +0000 (14:34 +0000)]
stash
Charles Ofoegbu [Tue, 21 Oct 2014 14:07:43 +0000 (15:07 +0100)]
Modified example query string for different Intermine descendants
Charles Ofoegbu [Tue, 21 Oct 2014 12:30:14 +0000 (13:30 +0100)]
Added support for different intermine database variants
Charles Ofoegbu [Mon, 20 Oct 2014 11:13:06 +0000 (12:13 +0100)]
Modifed the way Intermine.java parse alignment data
Charles Ofoegbu [Mon, 20 Oct 2014 09:39:17 +0000 (10:39 +0100)]
Removed dependency for Jersey webservice lib and updated code to use HttpClientUtils class.
Charles Ofoegbu [Mon, 20 Oct 2014 09:34:25 +0000 (10:34 +0100)]
Implementation of support for Intermine webservice as a source of sequence data
Charles Ofoegbu [Mon, 20 Oct 2014 08:46:50 +0000 (09:46 +0100)]
Downgraded TestAnnotate3D compatibility from Java8 to Java7
Charles Ofoegbu [Mon, 20 Oct 2014 08:39:40 +0000 (09:39 +0100)]
Modified SequenceFetcher to include Intermine as a data source
Charles Ofoegbu [Thu, 9 Oct 2014 16:11:02 +0000 (17:11 +0100)]
Updated gitignore to ignore .settings/
Charles Ofoegbu [Fri, 3 Oct 2014 15:33:03 +0000 (16:33 +0100)]
Integration of David Corsars Phylip File support
Charles Ofoegbu [Fri, 3 Oct 2014 10:50:33 +0000 (11:50 +0100)]
removed local test data
Charles Ofoegbu [Fri, 3 Oct 2014 10:45:50 +0000 (11:45 +0100)]
Local branch test
gmungoc [Thu, 18 Sep 2014 13:16:21 +0000 (14:16 +0100)]
Merge branch 'JAL-1360_Branch' into Release_2_8_2_Branch
gmungoc [Thu, 18 Sep 2014 13:12:52 +0000 (14:12 +0100)]
Merge branch 'Release_2_8_2_Branch' of https://source.jalview.org/git/jalview.git into Release_2_8_2_Branch
gmungoc [Thu, 18 Sep 2014 12:59:17 +0000 (13:59 +0100)]
JAL-1360 tweaks to match help page conventions, size image properly
gmungoc [Thu, 18 Sep 2014 12:58:40 +0000 (13:58 +0100)]
JAL-1360 consistent (bold) help page headings
gmungoc [Thu, 18 Sep 2014 10:21:04 +0000 (11:21 +0100)]
JAL-1360 Javadoc, Vector replaced with ArrayList, code formatted
gmungoc [Thu, 18 Sep 2014 10:19:17 +0000 (11:19 +0100)]
JAL-1360 Javadoc/JUnit
gmungoc [Thu, 18 Sep 2014 08:31:00 +0000 (09:31 +0100)]
JAL-1360 refactored utility method to ColorUtils class
gmungoc [Thu, 18 Sep 2014 08:29:57 +0000 (09:29 +0100)]
JAL-1544 it's --> its
gmungoc [Wed, 17 Sep 2014 15:41:54 +0000 (16:41 +0100)]
JAL-1360 updates to online help for user define colour scheme
gmungoc [Wed, 17 Sep 2014 15:41:14 +0000 (16:41 +0100)]
Correct colour for text when colour set
gmungoc [Wed, 17 Sep 2014 12:42:25 +0000 (13:42 +0100)]
JAL-1360 refactored for consistent lighter/darker for
selected/unselected button foreground
gmungoc [Wed, 17 Sep 2014 09:56:45 +0000 (10:56 +0100)]
JAL-1360 workaround for user defined colours display on Java 7
gmungoc [Mon, 15 Sep 2014 14:56:27 +0000 (15:56 +0100)]
JAL-1542 script to show aligned positions of selected column(s)
j.procter@dundee.ac.uk [Fri, 12 Sep 2014 16:38:46 +0000 (17:38 +0100)]
Merge branch 'Release_2_8_2_Branch' of https://source.jalview.org/git/jalview into Release_2_8_2_Branch
j.procter@dundee.ac.uk [Fri, 12 Sep 2014 16:33:51 +0000 (17:33 +0100)]
Merge branch 'bug/JAL-1486_flatfile' into Release_2_8_2_Branch
patch to export of selected area so that start/end numberings are correct. main file export option still needs fixing.
j.procter@dundee.ac.uk [Fri, 12 Sep 2014 16:27:47 +0000 (17:27 +0100)]
JAL-1486 JAL-1543 pushed alignment viewport->view->flat file logic into jalview.io to unify applet and application selected region export method
j.procter@dundee.ac.uk [Fri, 12 Sep 2014 16:04:38 +0000 (17:04 +0100)]
formatting and organise imports
j.procter@dundee.ac.uk [Fri, 12 Sep 2014 16:04:03 +0000 (17:04 +0100)]
JAL-1486 fix: pass selected region to jalview.io via alignment view and align viewport annotation methods
j.procter@dundee.ac.uk [Fri, 12 Sep 2014 15:58:58 +0000 (16:58 +0100)]
JAL-1199 add stockholm output to list of AppletFormatAdapter formatters
j.procter@dundee.ac.uk [Fri, 12 Sep 2014 15:56:29 +0000 (16:56 +0100)]
JAL-1486 JAL-535 refactor code for trimming alignment annotation according to selections from FormatAdapter to view model method
j.procter@dundee.ac.uk [Fri, 12 Sep 2014 15:55:14 +0000 (16:55 +0100)]
JAL-535 tidy interface definition and documentation
gmungoc [Fri, 12 Sep 2014 13:59:38 +0000 (14:59 +0100)]
JAL-1516 handle null annotations
j.procter@dundee.ac.uk [Fri, 12 Sep 2014 09:52:46 +0000 (10:52 +0100)]
JAL-1516 Annotation row score output script for jalview-discuss request from David M Garcia
j.procter@dundee.ac.uk [Tue, 22 Jul 2014 20:09:36 +0000 (21:09 +0100)]
Merge branch 'features/JAL-1333' into Release_2_8_2_Branch
j.procter@dundee.ac.uk [Tue, 22 Jul 2014 20:09:10 +0000 (21:09 +0100)]
JAL-1333 fix imports
j.procter@dundee.ac.uk [Tue, 22 Jul 2014 19:32:45 +0000 (20:32 +0100)]
Merge branch 'features/JAL-1333' into Release_2_8_2_Branch
j.procter@dundee.ac.uk [Tue, 22 Jul 2014 19:32:14 +0000 (20:32 +0100)]
JAL-1333 log4j/slf additional jars
j.procter@dundee.ac.uk [Tue, 22 Jul 2014 19:25:09 +0000 (20:25 +0100)]
JAL-1333 add log4j-slf4j bridge
j.procter@dundee.ac.uk [Tue, 22 Jul 2014 19:22:04 +0000 (20:22 +0100)]
Merge branch 'features/JAL-1333' into Release_2_8_2_Branch
j.procter@dundee.ac.uk [Tue, 22 Jul 2014 19:21:12 +0000 (20:21 +0100)]
JAL-1333 finessing log4j and slf dependencies for strucviz and jaba-client code
j.procter@dundee.ac.uk [Tue, 22 Jul 2014 19:12:48 +0000 (20:12 +0100)]
JAL-1333 JAL-1533 todo to get Chimera superposing properly we need to specify a set of atoms from each chain (or model in chimera-speak), but for chains with multiple models, each model needs to be superposed independently (potentially)
j.procter@dundee.ac.uk [Tue, 22 Jul 2014 18:37:34 +0000 (19:37 +0100)]
JAL-1333 more superposition debugging and deadlock avoidance
j.procter@dundee.ac.uk [Fri, 18 Jul 2014 12:59:26 +0000 (13:59 +0100)]
JAL-1379 Jpred JABA client test harness
j.procter@dundee.ac.uk [Fri, 18 Jul 2014 12:35:32 +0000 (13:35 +0100)]
JAL-1333 allow reuse of existing chimera for new or additional structures
j.procter@dundee.ac.uk [Fri, 18 Jul 2014 12:35:06 +0000 (13:35 +0100)]
JAL-1333 more refinements - deadlocks still possible with this version
j.procter@dundee.ac.uk [Fri, 18 Jul 2014 12:33:42 +0000 (13:33 +0100)]
JAL-674 futzing with bugs
j.procter@dundee.ac.uk [Fri, 18 Jul 2014 12:32:23 +0000 (13:32 +0100)]
JAL-795 take colour from annotation if colour is present
j.procter@dundee.ac.uk [Fri, 18 Jul 2014 12:31:32 +0000 (13:31 +0100)]
ensure the dataset is instantiated before materialising alignment viewport
j.procter@dundee.ac.uk [Fri, 18 Jul 2014 12:30:29 +0000 (13:30 +0100)]
JAL-1379 new look JPred results
j.procter@dundee.ac.uk [Fri, 18 Jul 2014 11:08:09 +0000 (12:08 +0100)]
JAL-1520 switch between Protein and non-canonical RNA secondary structure rendering styles for an annotation row
j.procter@dundee.ac.uk [Fri, 18 Jul 2014 11:00:44 +0000 (12:00 +0100)]
JAL-1028 JAL-1142 refactor test to allow reuse of secondary structure validation routine
j.procter@dundee.ac.uk [Tue, 8 Jul 2014 19:16:49 +0000 (15:16 -0400)]
JAL-1333 allow reuse of existing viewers (of a specified or currently preferred type)
j.procter@dundee.ac.uk [Tue, 8 Jul 2014 19:15:11 +0000 (15:15 -0400)]
JAL-1333 more efficient color statement
j.procter@dundee.ac.uk [Fri, 4 Jul 2014 03:09:00 +0000 (20:09 -0700)]
JAL-1333 more abstraction and refactoring and working demo of Jalview talking to Chimera
j.procter@dundee.ac.uk [Thu, 3 Jul 2014 19:53:56 +0000 (12:53 -0700)]
Merge branch 'Release_2_8_2_Branch' into features/JAL-1333
j.procter@dundee.ac.uk [Thu, 3 Jul 2014 18:27:00 +0000 (11:27 -0700)]
Merge branch 'hotfix/JAL-1530' into Release_2_8_2_Branch
Conflicts:
src/jalview/gui/PopupMenu.java
Jim Procter [Thu, 3 Jul 2014 18:23:48 +0000 (11:23 -0700)]
fixes JAL-1530
Jim Procter [Wed, 2 Jul 2014 22:51:00 +0000 (15:51 -0700)]
revalidate appears to have gone away ?? (java 1.7 upgrade perhaps ?)
Jim Procter [Wed, 2 Jul 2014 22:50:27 +0000 (15:50 -0700)]
formatting
Jim Procter [Wed, 2 Jul 2014 22:49:47 +0000 (15:49 -0700)]
JAL-1333 JAL-1527 refactors to create core structure viewer binding architecture and StructureViewer factory for creating structure views with the currently preferred viewer
Jim Procter [Wed, 2 Jul 2014 22:35:09 +0000 (15:35 -0700)]
JAL-1333 test suite for key functionality of java interface to chimera
Jim Procter [Wed, 2 Jul 2014 22:31:47 +0000 (15:31 -0700)]
JAL-1333 Chimera specific code extracted from the StructureViz library for opening and querying structure data managed by chimera
Jim Procter [Tue, 1 Jul 2014 22:28:04 +0000 (15:28 -0700)]
Merge branch 'feature/JAL-1333' into features/JAL-1333
Conflicts:
.classpath
Jim Procter [Mon, 23 Jun 2014 15:21:42 +0000 (16:21 +0100)]
Merge branch 'JAL-1526' into Release_2_8_2_Branch
Jim Procter [Mon, 23 Jun 2014 15:21:02 +0000 (16:21 +0100)]
JAL-1526 simple function to write a snapshot of the desktop.
Jim Procter [Thu, 12 Jun 2014 10:41:20 +0000 (11:41 +0100)]
Merge branch 'hotfix/JAL-1524' into Release_2_8_2_Branch
Jim Procter [Thu, 12 Jun 2014 10:41:02 +0000 (11:41 +0100)]
Merge branch 'hotfix/JAL-1524' into Release_2_8_1_Branch
Jim Procter [Thu, 12 Jun 2014 10:40:15 +0000 (11:40 +0100)]
JAL-1524 fix
Jim Procter [Tue, 10 Jun 2014 17:01:22 +0000 (18:01 +0100)]
Merge branch 'feature/JAL-1379' into Release_2_8_2_Branch
Jim Procter [Tue, 10 Jun 2014 16:26:30 +0000 (17:26 +0100)]
JAL-1379 a JPred v3.0.1 client via JABA 2.1
Jim Procter [Tue, 10 Jun 2014 16:24:41 +0000 (17:24 +0100)]
JAL-1379 allow services with an MSA interface to create an interactive service gui rather than a turnkey service gui
Jim Procter [Tue, 10 Jun 2014 16:21:56 +0000 (17:21 +0100)]
tidy source
Jim Procter [Tue, 10 Jun 2014 16:21:31 +0000 (17:21 +0100)]
JAL-1379 allow JABA2 tests to run on local or default service
Jim Procter [Tue, 10 Jun 2014 16:20:49 +0000 (17:20 +0100)]
JAL-1379 refactor Jws2 service client so dynamic services can be of any type of JABA client interface
Jim Procter [Fri, 6 Jun 2014 14:20:45 +0000 (15:20 +0100)]
JAL-1520 fix unicode translation errors.
Jim Procter [Fri, 6 Jun 2014 14:13:20 +0000 (15:13 +0100)]
JAL-1520 fix unicode translation errors.
Jim Procter [Fri, 6 Jun 2014 10:50:49 +0000 (11:50 +0100)]
JAL-1519 make the splash screen larger/more readable
Jim Procter [Fri, 6 Jun 2014 10:50:22 +0000 (11:50 +0100)]
JAL-1519 - tidy build properties management code
Jim Procter [Fri, 6 Jun 2014 10:49:38 +0000 (11:49 +0100)]
JAL-1519 fix author update issue (doh)
Jim Procter [Fri, 6 Jun 2014 09:27:30 +0000 (10:27 +0100)]
JAL-1140 Add Anne Menard to author list
Jim Procter [Fri, 6 Jun 2014 09:20:50 +0000 (10:20 +0100)]
JAL-1517 copyright and formatting
Jim Procter [Fri, 6 Jun 2014 09:20:27 +0000 (10:20 +0100)]
JAL-1518 drop Jalopy from utils directory
Jim Procter [Fri, 6 Jun 2014 09:19:11 +0000 (10:19 +0100)]
JAL-1517 copyright and formatting
Jim Procter [Fri, 6 Jun 2014 09:04:38 +0000 (10:04 +0100)]
JAL-1517 source formatting
Jim Procter [Fri, 6 Jun 2014 08:58:57 +0000 (09:58 +0100)]
JAL-1518 drop Jalopy from utils directory
Jim Procter [Fri, 6 Jun 2014 08:52:38 +0000 (09:52 +0100)]
JAL-1517 fix copyright for 2.8.2
Jim Procter [Thu, 5 Jun 2014 18:59:25 +0000 (19:59 +0100)]
JAL-1517 update copyright to version 2.8.2
Jim Procter [Thu, 5 Jun 2014 10:46:39 +0000 (11:46 +0100)]
Merge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch
JAL-1517 JAL-1503 merge 2.8.1 source code updates to 2_8_2 branch
Conflicts:
RELEASE
build.xml
src/jalview/ext/varna/VarnaCommands.java
src/jalview/io/AppletFormatAdapter.java
src/jalview/io/StockholmFile.java
Jim Procter [Wed, 4 Jun 2014 16:19:30 +0000 (17:19 +0100)]
Merge branch 'docs/2_8_1_Release' into Release_2_8_1_Branch
Jim Procter [Wed, 4 Jun 2014 16:19:00 +0000 (17:19 +0100)]
JAL-1503 typo
Jim Procter [Wed, 4 Jun 2014 16:17:13 +0000 (17:17 +0100)]
Merge branch 'develop' into Release_2_8_2_Branch
Jim Procter [Wed, 4 Jun 2014 15:45:15 +0000 (16:45 +0100)]
Merge branch 'docs/2_8_1_Release' into Release_2_8_1_Branch
Jim Procter [Wed, 4 Jun 2014 15:43:47 +0000 (16:43 +0100)]
JAL-1503 update author list for 2.8.1
Jim Procter [Wed, 4 Jun 2014 14:47:34 +0000 (15:47 +0100)]
Merge branch 'docs/2_8_1_Release' into Release_2_8_1_Branch
Jim Procter [Wed, 4 Jun 2014 14:47:03 +0000 (15:47 +0100)]
JAL-690 JAL-1503 make file associations optional for JNLP
Jim Procter [Wed, 4 Jun 2014 14:22:07 +0000 (15:22 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
Jim Procter [Wed, 4 Jun 2014 12:30:26 +0000 (13:30 +0100)]
JAL-952 fixed unresolved conflict breaking build
git://source.jalview.org / jalview.git / log