Jim Procter [Thu, 23 Jul 2015 18:03:21 +0000 (19:03 +0100)]
Merge branch 'features/JAL-1759jmolUpdate' into develop
updates from revisions due to JAL-1805
Jim Procter [Thu, 23 Jul 2015 17:52:39 +0000 (18:52 +0100)]
JAL-1759 formatting
Jim Procter [Thu, 23 Jul 2015 17:52:26 +0000 (18:52 +0100)]
JAL-1759 reinstate changes from
bdfde6ef989da0702cef90f03858f0f30e0bc83a
lost during merge.
Jim Procter [Thu, 23 Jul 2015 17:49:16 +0000 (18:49 +0100)]
JAL-1759 formatting
Jim Procter [Thu, 23 Jul 2015 16:19:57 +0000 (17:19 +0100)]
Merge branch 'develop' of source.jalview.org/git/jalview into develop
Jim Procter [Thu, 23 Jul 2015 12:15:59 +0000 (13:15 +0100)]
Merge branch 'task/JAL-1794_jettyExamplesServer' into develop
tcofoegbu [Thu, 23 Jul 2015 11:44:08 +0000 (12:44 +0100)]
Resolved merge conflict in EdtiCommandTest.java
tcofoegbu [Thu, 23 Jul 2015 11:40:24 +0000 (12:40 +0100)]
JAL-1805 modified test setup's so the are ran for groups which requires them
tcofoegbu [Thu, 23 Jul 2015 10:31:22 +0000 (11:31 +0100)]
JAL-1819 Test cases for Identify file
Jim Procter [Thu, 23 Jul 2015 10:30:56 +0000 (11:30 +0100)]
Merge branch 'bug/JAL-1819_isNaN' into develop
Jim Procter [Thu, 23 Jul 2015 10:27:57 +0000 (11:27 +0100)]
JAL-1819 commented out debugging message to stderr
Jim Procter [Thu, 23 Jul 2015 10:27:15 +0000 (11:27 +0100)]
JAL-1551 JAL-1819 formatting/imports
Jim Procter [Thu, 23 Jul 2015 10:26:11 +0000 (11:26 +0100)]
JAL-1819 use Float.isNaN() to check for NaNs!
Jim Procter [Wed, 22 Jul 2015 17:05:06 +0000 (18:05 +0100)]
JAL-1805 add group spec to the BeforeMethod setup - updated the TESTNG entry to show improvement.
Jim Procter [Wed, 22 Jul 2015 16:54:04 +0000 (17:54 +0100)]
JAL-1782 added summary test report for Release_2_9_Branch - Functional tests only
tcofoegbu [Wed, 22 Jul 2015 08:55:42 +0000 (09:55 +0100)]
JAL-1667 JAL-1668 JAL-1553 help docs update
tcofoegbu [Tue, 21 Jul 2015 17:02:03 +0000 (18:02 +0100)]
Merge
tcofoegbu [Tue, 21 Jul 2015 16:59:01 +0000 (17:59 +0100)]
JAL-1443 bugfix to prevent loading of unidentifiable gibberish data
Jim Procter [Tue, 21 Jul 2015 13:53:27 +0000 (14:53 +0100)]
Merge branch 'ismb/2015_demo' into develop
Jim Procter [Thu, 16 Jul 2015 15:19:39 +0000 (16:19 +0100)]
revision for JAL-1749 - ensure view 2D structure menu is removed when no structures are available
Jim Procter [Thu, 16 Jul 2015 15:18:19 +0000 (16:18 +0100)]
fix for JAL-1776 renamed popup menu entry
tcofoegbu [Wed, 15 Jul 2015 13:27:54 +0000 (14:27 +0100)]
updated version info in seqfetch.html
tcofoegbu [Wed, 15 Jul 2015 13:26:26 +0000 (14:26 +0100)]
JAL-1553 reviewed & updated docs
tcofoegbu [Wed, 15 Jul 2015 13:25:15 +0000 (14:25 +0100)]
JAL-1667 JAL-1668 updated reviewed and updated docs
tcofoegbu [Wed, 15 Jul 2015 13:22:53 +0000 (14:22 +0100)]
JAL-1788 updated docs
gmungoc [Wed, 15 Jul 2015 11:03:28 +0000 (12:03 +0100)]
JAL-1813 only pair up A-Z with a-z if annotation is RNA
tcofoegbu [Wed, 15 Jul 2015 10:31:47 +0000 (11:31 +0100)]
JAL-1769 updated test data
tcofoegbu [Mon, 13 Jul 2015 16:41:47 +0000 (17:41 +0100)]
JAL-1788 added help documentation for biojson
gmungoc [Sun, 12 Jul 2015 11:30:25 +0000 (12:30 +0100)]
JAL-1759 corrected jmol applet lib name
tcofoegbu [Fri, 10 Jul 2015 10:06:31 +0000 (11:06 +0100)]
JAL-1759 code fix to enable testng ant task compile and run
tcofoegbu [Thu, 9 Jul 2015 15:22:32 +0000 (16:22 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Thu, 9 Jul 2015 15:22:04 +0000 (16:22 +0100)]
JAL-1769 increased timeout period for eps generation
tcofoegbu [Thu, 9 Jul 2015 12:57:12 +0000 (13:57 +0100)]
JAL-1806 bug fix to loop through the entire data file to check for a html or rnaml tag when the data file starts with <
tcofoegbu [Thu, 9 Jul 2015 11:21:26 +0000 (12:21 +0100)]
JAL-1769 added test for commandline input operations
gmungoc [Wed, 8 Jul 2015 14:53:51 +0000 (15:53 +0100)]
JAL-1759 merge from develop
gmungoc [Wed, 8 Jul 2015 12:19:14 +0000 (13:19 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 8 Jul 2015 12:18:49 +0000 (13:18 +0100)]
JAL-1598 replaced faulty regex, amended Varna call, to get pseudo-knots
tcofoegbu [Wed, 8 Jul 2015 11:10:05 +0000 (12:10 +0100)]
JAL-1641 biojson documentation with docson
tcofoegbu [Tue, 7 Jul 2015 15:18:41 +0000 (16:18 +0100)]
JAL-1769 fixed output to jalview (.jpv) file in headless mode. Initial cause of failure: NPE while trying to save varna viewers (Desktop.destop is null in headless mode)
tcofoegbu [Tue, 7 Jul 2015 14:40:54 +0000 (15:40 +0100)]
JAL-1805 test envirionment separation
tcofoegbu [Mon, 6 Jul 2015 16:01:28 +0000 (17:01 +0100)]
Merge branch 'features/1769_headless-mode-test' into develop
tcofoegbu [Mon, 6 Jul 2015 16:00:25 +0000 (17:00 +0100)]
JAL-1641 added json schema for jalview JSON model, the schema is employed for documentation but can be more usefull for validation in the future
tcofoegbu [Mon, 6 Jul 2015 15:58:20 +0000 (16:58 +0100)]
JAL-1769 fixed headless execution mode and created test for all possible outputs
gmungoc [Mon, 6 Jul 2015 15:23:21 +0000 (16:23 +0100)]
JAL-1081 unit tests added
gmungoc [Mon, 6 Jul 2015 11:03:19 +0000 (12:03 +0100)]
JAL-1782 refactored test to ensure it passes in TestNG
gmungoc [Mon, 6 Jul 2015 11:02:33 +0000 (12:02 +0100)]
JAL-1421 generics used for leaner safer code
gmungoc [Mon, 6 Jul 2015 09:20:56 +0000 (10:20 +0100)]
JAL-1799 tweaked calculation for applet, now showing 2 not 3 seqs
gmungoc [Mon, 6 Jul 2015 08:01:52 +0000 (09:01 +0100)]
JAL-1799 equivalent logic in applet
gmungoc [Fri, 3 Jul 2015 11:00:25 +0000 (12:00 +0100)]
JAL-1759 updated Jmol version in nbproject, install anywhere,
THIRDPARTYLIBS, (but not yet appletParameters.html)
gmungoc [Fri, 3 Jul 2015 10:33:11 +0000 (11:33 +0100)]
JAL-892 jnlp, installAnywhere, build, licence references updated to 3.93
gmungoc [Fri, 3 Jul 2015 10:18:22 +0000 (11:18 +0100)]
Merge branch 'develop' into features/JAL-892varnaToProject
gmungoc [Fri, 3 Jul 2015 10:07:23 +0000 (11:07 +0100)]
JAL-892 1 second delay for correct initial rendering; code tidy up
tcofoegbu [Thu, 2 Jul 2015 15:38:40 +0000 (16:38 +0100)]
Merge branch 'bug/JAL-1443_loading-empty-file' into develop
tcofoegbu [Thu, 2 Jul 2015 15:37:56 +0000 (16:37 +0100)]
JAL-1443 data validation for empty content before loading alignment from file or clipboard
gmungoc [Thu, 2 Jul 2015 14:27:03 +0000 (15:27 +0100)]
JAL-1677 check all response lines when parsing REST server port
gmungoc [Wed, 1 Jul 2015 14:53:40 +0000 (15:53 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
gmungoc [Wed, 1 Jul 2015 14:53:27 +0000 (15:53 +0100)]
JAL-1681 more condensed tooltip where codons share same percentage
tcofoegbu [Wed, 1 Jul 2015 14:23:19 +0000 (15:23 +0100)]
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
tcofoegbu [Wed, 1 Jul 2015 14:23:11 +0000 (15:23 +0100)]
house keeping
gmungoc [Wed, 1 Jul 2015 13:29:16 +0000 (14:29 +0100)]
JAL-1802 explanatory comment added
gmungoc [Wed, 1 Jul 2015 13:15:19 +0000 (14:15 +0100)]
JAL-1802 handle slide sequences edits in split frame mode
gmungoc [Wed, 1 Jul 2015 11:05:43 +0000 (12:05 +0100)]
Merge branch 'develop' into features/JAL-1759jmolUpdate
gmungoc [Wed, 1 Jul 2015 10:48:04 +0000 (11:48 +0100)]
JAL-1799 deduct more space for decorators on Windows
gmungoc [Wed, 1 Jul 2015 08:13:22 +0000 (09:13 +0100)]
JAL-1619 align the added sequences to match what they are added to
gmungoc [Tue, 30 Jun 2015 18:16:55 +0000 (19:16 +0100)]
JAL=1759 fix Jmol state command bug; remove debug output
gmungoc [Tue, 30 Jun 2015 16:37:56 +0000 (17:37 +0100)]
JAL-1759 unused JmolPopup removed, code tidy for generics
gmungoc [Tue, 30 Jun 2015 16:36:30 +0000 (17:36 +0100)]
JAL-1759 deprecated EnfinEnvision2OneWay removed
gmungoc [Tue, 30 Jun 2015 14:41:02 +0000 (15:41 +0100)]
JAL-1759 JMol now Jmol !
gmungoc [Tue, 30 Jun 2015 14:40:14 +0000 (15:40 +0100)]
JAL-1759 unused field / methods removed
tcofoegbu [Tue, 30 Jun 2015 11:42:25 +0000 (12:42 +0100)]
Merge branch 'features/JAL-1641_JSON-tests-and-docs' into develop
tcofoegbu [Tue, 30 Jun 2015 11:40:21 +0000 (12:40 +0100)]
JAL-1641 round trip test/refactoring
gmungoc [Tue, 30 Jun 2015 11:14:45 +0000 (12:14 +0100)]
JAL-1691 trackpad scrolling goes to full width even with short sequences
gmungoc [Mon, 29 Jun 2015 15:31:40 +0000 (16:31 +0100)]
JAL-1799 adjusted annotation height calculation
gmungoc [Mon, 29 Jun 2015 09:21:38 +0000 (10:21 +0100)]
JAL-1759 correct conversion of Jmol Chain.chainId (int) to string +
tests
tcofoegbu [Fri, 26 Jun 2015 16:06:05 +0000 (17:06 +0100)]
JAL-1641 fixed broken functionalities after refactor
gmungoc [Fri, 26 Jun 2015 15:59:39 +0000 (16:59 +0100)]
JAL-1782 BeforeMethod added to fix test in NG
gmungoc [Fri, 26 Jun 2015 14:50:57 +0000 (15:50 +0100)]
Merge branch 'develop' into features/JAL-892varnaToProject
gmungoc [Fri, 26 Jun 2015 14:44:20 +0000 (15:44 +0100)]
JAL-1759 changed to non-deprecated Viewer.renderScreenImage()
gmungoc [Fri, 26 Jun 2015 13:37:19 +0000 (14:37 +0100)]
Merge branch 'develop' into features/JAL-1759jmolUpdate
Conflicts:
.classpath
src/jalview/appletgui/AlignFrame.java
test/jalview/io/NewickFileTests.java
gmungoc [Fri, 26 Jun 2015 11:06:51 +0000 (12:06 +0100)]
JAL-1759 updates for Jmol 14.2.14_25.06.11
tcofoegbu [Fri, 26 Jun 2015 09:42:27 +0000 (10:42 +0100)]
merge
tcofoegbu [Fri, 26 Jun 2015 09:41:32 +0000 (10:41 +0100)]
JAL-1780 improvement to ensure export settings dialog is not invoked if there's noting to configure and clean ups
Jim Procter [Thu, 25 Jun 2015 15:20:41 +0000 (16:20 +0100)]
JAL-1794 simple file server class - configured for 8080 in current working directory
Jim Procter [Thu, 25 Jun 2015 10:13:09 +0000 (11:13 +0100)]
JAL-1691 avoid NPE when original split frame has been closed before the alignment completes. See JAL-1792 for enhancement on this code.
Jim Procter [Thu, 25 Jun 2015 10:06:45 +0000 (11:06 +0100)]
JAL-1780 JAL-653 JAL-1892 brackets in wrong place broke ‘add to file’ for splitframe/cdna/protein
also formatted file for clarity
Jim Procter [Wed, 24 Jun 2015 20:51:35 +0000 (21:51 +0100)]
Merge branch 'features/JAL-1370_patchshowunconserved' into develop
Jim Procter [Wed, 24 Jun 2015 15:36:48 +0000 (16:36 +0100)]
JAL-1790 fix: javac.source=1.7 and javac.target=1.7 variables for all javac tasks in build.xml
Jim Procter [Wed, 24 Jun 2015 15:18:12 +0000 (16:18 +0100)]
JAL-653 JAL-1780 JAL-1892 fix jalviewLite compilation
Jim Procter [Wed, 24 Jun 2015 14:11:45 +0000 (15:11 +0100)]
Merge branch 'merge/develop_JAL-1780_JAL-653_JAL-1892' into develop
Jim Procter [Tue, 23 Jun 2015 12:26:11 +0000 (13:26 +0100)]
JAL-1780 JAL-653 jim forgot to put the conditional action in!
Jim Procter [Tue, 23 Jun 2015 08:48:13 +0000 (09:48 +0100)]
JAL-1782 JAL-1780 JAL-653 JAL-1892 update patched refactored test suite with TestNG
Jim Procter [Mon, 22 Jun 2015 18:43:33 +0000 (19:43 +0100)]
JAL-1270 fix logic in stockholm test allowing annotation.description to be equivalent if both are null, or one or both is an empty string, or a whitespace string
Jim Procter [Mon, 22 Jun 2015 18:21:59 +0000 (19:21 +0100)]
JAL-653 JAL-1780 JAL-1140 added RNAML example alignment file
Jim Procter [Mon, 22 Jun 2015 18:21:07 +0000 (19:21 +0100)]
JAL-653 JAL-1780 dropped unnecessary refs
Jim Procter [Mon, 22 Jun 2015 18:12:07 +0000 (19:12 +0100)]
JAL-1780 JAL-653 Format/AppletFormat import and export pipeline regularised, uses AlignmentI where possible, and allows configuration via Alignment Panel and ExportSettings interface references
Jim Procter [Mon, 22 Jun 2015 17:26:23 +0000 (18:26 +0100)]
JAL-653 JAL-1780 reorder imports
gmungoc [Mon, 22 Jun 2015 13:05:12 +0000 (14:05 +0100)]
JAL-892 tidy Varna panel names; JAL-1789 simplified mouseover
gmungoc [Mon, 22 Jun 2015 12:34:58 +0000 (13:34 +0100)]
JAL-893 upgrade to VARNAv3-93.jar
Jim Procter [Fri, 19 Jun 2015 16:45:50 +0000 (17:45 +0100)]
JAL-653 JAL-1780 refactor getGroups so HTMLfile/JSONfile adopt same pattern as other parsers
Jim Procter [Fri, 19 Jun 2015 16:44:27 +0000 (17:44 +0100)]
JAL-1780 JAL-653 organise imports
git://source.jalview.org / jalview.git / log