Jim Procter [Fri, 17 Jan 2014 08:26:33 +0000 (08:26 +0000)]
JAL-957 first attempt to build examples with jbake
Jim Procter [Tue, 14 Jan 2014 11:34:14 +0000 (11:34 +0000)]
Merge branch 'WIP_fix_JAL-1423' into Release_2_8_Branch
Jim Procter [Tue, 14 Jan 2014 11:31:35 +0000 (11:31 +0000)]
JAL-1400 specify minimum 1.6 JRE
Jalview build Manager [Mon, 13 Jan 2014 18:15:53 +0000 (18:15 +0000)]
Merge branch 'Release_2_8_Branch' into WIP_fix_JAL-1423
Conflicts:
examples/linkedapplets_ng.html
Jalview build Manager [Mon, 13 Jan 2014 18:09:37 +0000 (18:09 +0000)]
JAL-1400 sign the applet with manifest attributes for Java 1.6 and Java 1.7
Jalview build Manager [Mon, 13 Jan 2014 18:08:44 +0000 (18:08 +0000)]
JAL-1400 signed applets generally run with all permissions since 2014
Jim Procter [Mon, 13 Jan 2014 14:05:51 +0000 (14:05 +0000)]
Merge branch 'JAL-1422_srs' into Release_2_8_Branch
Conflicts:
examples/linkedapplets_ng.html
Jim Procter [Mon, 13 Jan 2014 14:01:20 +0000 (14:01 +0000)]
JAL-1422 update any existing configuration to replace SRS with EMBL-EBI Search link
Jim Procter [Mon, 13 Jan 2014 14:00:44 +0000 (14:00 +0000)]
JAL-1422 change default link to EMBL-EBI Search
Jim Procter [Mon, 13 Jan 2014 13:59:55 +0000 (13:59 +0000)]
JAL-1422 remove SRS and expasy links and replace with EMBL-EBI Search and Uniprot links in applet examples
Jim Procter [Tue, 7 Jan 2014 12:22:54 +0000 (12:22 +0000)]
Merge branch 'fix_JAL-1423' into Release_2_8_Branch
Jim Procter [Tue, 7 Jan 2014 12:22:28 +0000 (12:22 +0000)]
JAL-1423 - console error reporting and graceful handling for corrupt DAS local source entries
Jim Procter [Tue, 26 Nov 2013 16:21:17 +0000 (16:21 +0000)]
Merge branch 'JAL-1400_signapplet' into Release_2_8_Branch
Jim Procter [Tue, 26 Nov 2013 16:20:50 +0000 (16:20 +0000)]
JAL-1400 update manifest in the JmolApplet jar
Jim Procter [Tue, 26 Nov 2013 15:54:07 +0000 (15:54 +0000)]
Merge branch 'JAL-1400_signapplet' into Release_2_8_Branch
Jim Procter [Tue, 26 Nov 2013 15:53:14 +0000 (15:53 +0000)]
JAL-1400 disable 'Permissions' in manifest to see if it helps
Jim Procter [Tue, 26 Nov 2013 15:35:36 +0000 (15:35 +0000)]
Merge branch 'JAL-1400_signapplet' into Release_2_8_Branch
Jim Procter [Tue, 26 Nov 2013 15:35:07 +0000 (15:35 +0000)]
sandbox permissions
Jim Procter [Tue, 26 Nov 2013 15:34:44 +0000 (15:34 +0000)]
new required parameter for deploying the applet
Jim Procter [Tue, 26 Nov 2013 15:16:47 +0000 (15:16 +0000)]
Merge branch 'JAL-1400_signapplet' into Release_2_8_Branch
Jim Procter [Tue, 26 Nov 2013 15:14:57 +0000 (15:14 +0000)]
JAL-1400 add codebase and caller allowable codebase
Jim Procter [Mon, 25 Nov 2013 18:30:19 +0000 (18:30 +0000)]
Merge branch 'JAL-1139_proguard' into Release_2_8_Branch
Jim Procter [Mon, 25 Nov 2013 18:29:28 +0000 (18:29 +0000)]
JAL-1139 specified SHA1WithRSA for sig algorithm and removed Jmols original selfsigned certs
Jim Procter [Mon, 25 Nov 2013 16:54:05 +0000 (16:54 +0000)]
adivce from ant.apache.org/manual/Tasks/signjar.html re
building on Java 7 for deployment in Java 6
JAL-1139
Jim Procter [Mon, 25 Nov 2013 16:44:17 +0000 (16:44 +0000)]
Merge branch 'JAL-1139_proguard' into Release_2_8_Branch
Jim Procter [Mon, 25 Nov 2013 16:43:39 +0000 (16:43 +0000)]
JAL-1139 need to explicitly specify SHA1 for java 6 launch
Jim Procter [Mon, 25 Nov 2013 16:26:44 +0000 (16:26 +0000)]
Merge branch 'JAL-1139_proguard' into Release_2_8_Branch
Jim Procter [Mon, 25 Nov 2013 16:25:56 +0000 (16:25 +0000)]
JAL-1139 supress dependency warnings from proguard
Jim Procter [Mon, 25 Nov 2013 16:18:26 +0000 (16:18 +0000)]
Merge branch 'JAL-1139_proguard' into Release_2_8_Branch
Jim Procter [Mon, 25 Nov 2013 16:17:39 +0000 (16:17 +0000)]
JAL-1139 latest version of proguard needed for Java 1.7 builds
Jim Procter [Thu, 7 Nov 2013 13:58:31 +0000 (13:58 +0000)]
Merge branch 'JAL-1286' into Release_2_8_Branch
Jim Procter [Thu, 7 Nov 2013 13:49:15 +0000 (13:49 +0000)]
JAL-1286 additional tests to ensure that non-GZ files with a .gz at end
are read in correctly
Jim Procter [Thu, 7 Nov 2013 13:43:30 +0000 (13:43 +0000)]
JAL-1286 check if local file ends with .gz and opens as a gzip stream
Jim Procter [Thu, 7 Nov 2013 13:42:35 +0000 (13:42 +0000)]
JAL-1286 test input of gzip stream from local file
Jim Procter [Tue, 5 Nov 2013 17:33:29 +0000 (17:33 +0000)]
JAL-1400 found a fix for the sandbox exception - need a 'permissions' parameter
http://stackoverflow.com/questions/
18914650/can-you-sign-a-java-applet-but-keep-it-in-the-sandbox-not-give-it-full-access-t
http://docs.oracle.com/javase/tutorial/deployment/applet/html.html
Jim Procter [Tue, 5 Nov 2013 17:26:55 +0000 (17:26 +0000)]
experiment with reinstating the sandbox permissions
Jim Procter [Tue, 5 Nov 2013 17:07:20 +0000 (17:07 +0000)]
JAL-1400 try putting explicit domain for jalviewLite applet
Jim Procter [Mon, 21 Oct 2013 16:52:51 +0000 (17:52 +0100)]
JAL-1400 Always create indices for jar before signing
Jim Procter [Mon, 21 Oct 2013 16:54:12 +0000 (17:54 +0100)]
JAL-1400 sign everything !
Jim Procter [Mon, 21 Oct 2013 16:53:45 +0000 (17:53 +0100)]
JAL-1400 explicit security settings for applet
Jim Procter [Mon, 21 Oct 2013 16:53:25 +0000 (17:53 +0100)]
JAL-1400 explicit security permissions for Desktop
Jalview build Manager [Fri, 1 Nov 2013 17:02:37 +0000 (17:02 +0000)]
JAL-1403 make sure MacOS installer searchers for the Apple Java install, otherwise it silently fails due to a JVM not being found.
Jalview build Manager [Wed, 23 Oct 2013 10:37:12 +0000 (11:37 +0100)]
JAL-1403 updated paths to IA 2013 and additional build parameter to disable the update thread so builds happen quicker
Jalview build Manager [Wed, 23 Oct 2013 10:36:24 +0000 (11:36 +0100)]
JAL-1403 upgraded the InstallAnywhere build file to IA Professional 2013
Jim Procter [Fri, 11 Oct 2013 16:22:59 +0000 (17:22 +0100)]
Merge branch 'JAL-1164_disorderforselection' into Release_2_8_Branch
Jim Procter [Fri, 11 Oct 2013 16:20:08 +0000 (17:20 +0100)]
JAL-1164 regression on JAL-1292 use bitset to mark graphGroup as rendered
Jim Procter [Fri, 11 Oct 2013 10:45:26 +0000 (11:45 +0100)]
JAL-1164 scope bySequence analysis methods to start/end of selected region or alignment region.
Jim Procter [Fri, 11 Oct 2013 10:44:19 +0000 (11:44 +0100)]
JAL-1114 javadoc
Jim Procter [Fri, 11 Oct 2013 10:44:03 +0000 (11:44 +0100)]
JAL-1114 promote start/end attributes to gettable fields of annotatable collections
Jim Procter [Fri, 11 Oct 2013 10:40:23 +0000 (11:40 +0100)]
JAL-1114 API javadoc
Jim Procter [Fri, 11 Oct 2013 09:58:00 +0000 (10:58 +0100)]
JAL-1164 only predict on currently selected sequences for perSequence
Jim Procter [Mon, 7 Oct 2013 16:02:45 +0000 (17:02 +0100)]
JAL-1385 expose core view model methods in interface
Jim Procter [Fri, 12 Jul 2013 15:58:47 +0000 (16:58 +0100)]
Merge branch 'JAL-1347' into Release_2_8_Branch
Jim Procter [Fri, 12 Jul 2013 15:58:22 +0000 (16:58 +0100)]
JAL-1347 RNA Structure consensus follows the alignment viewport consensus rendering settings in version 2.8.x
Jim Procter [Fri, 12 Jul 2013 15:57:45 +0000 (16:57 +0100)]
JAL-1347 flow control for display of profile data is upstream from this method
Jim Procter [Thu, 11 Jul 2013 12:57:40 +0000 (13:57 +0100)]
Merge branch 'JAL-1347' into Release_2_8_Branch
Jim Procter [Thu, 11 Jul 2013 12:57:03 +0000 (13:57 +0100)]
JAL-1347 identify and set rendering settings for consensus annotation rows
JAL-966 Note - should abstract this logic even further away in Jalview v3
Jim Procter [Thu, 11 Jul 2013 12:54:25 +0000 (13:54 +0100)]
JAL-1347 refactor logic for setting display flags for histogram and profile to main control loop
Jim Procter [Thu, 11 Jul 2013 12:53:27 +0000 (13:53 +0100)]
JAL-1347 make it efficient to call getConsensus to test identity of alignment annotation rows
Jim Procter [Mon, 8 Jul 2013 12:48:56 +0000 (13:48 +0100)]
Merge branch 'Release_2_8_1_Branch' into Release_2_8_Branch
Jim Procter [Mon, 8 Jul 2013 12:48:09 +0000 (13:48 +0100)]
make sure 'example alignment' can be found in documentation
Jim Procter [Sun, 7 Jul 2013 12:19:41 +0000 (13:19 +0100)]
Merge branch 'structures/JAL-1016' into Release_2_8_Branch
Jim Procter [Sun, 7 Jul 2013 12:08:52 +0000 (13:08 +0100)]
JAL-1345 - set nSeconds arg for chemapps.stolaf.edu/jmol/docs/#compare according to total number of superpositions
Jim Procter [Sun, 7 Jul 2013 11:44:25 +0000 (12:44 +0100)]
JAL-1016 Instruct user to report situations where the race condition still happens
Jim Procter [Sun, 7 Jul 2013 11:42:59 +0000 (12:42 +0100)]
JAL-1332 make SSM context discovery safer (particularly in plugin context)
Jim Procter [Sun, 7 Jul 2013 11:39:43 +0000 (12:39 +0100)]
JAL-583 refactor todo about separating code to construct Jmol superposition from the code that obtains the atom matching used to construct the expression
Jim Procter [Sun, 7 Jul 2013 11:39:23 +0000 (12:39 +0100)]
fix for JAL-1016 - wait around until we have a complete set of PDB filename mappings available in Jmol
Jim Procter [Sun, 7 Jul 2013 11:38:02 +0000 (12:38 +0100)]
JAL-1016 - do our assertions immediatly
Jim Procter [Sun, 23 Jun 2013 18:06:23 +0000 (19:06 +0100)]
Merge branch 'bug/JAL-1230' into Release_2_8_Branch
Jim Procter [Sun, 23 Jun 2013 18:05:42 +0000 (19:05 +0100)]
JAL-1230 update alignment state for annotation edits, and validate annotation panel height to ensure any autocalculated annotation is made visible
Jim Procter [Sun, 23 Jun 2013 18:03:53 +0000 (19:03 +0100)]
JAL-1230 proxy method for synchronising internal AlignmentI state in response to changes in alignment annotation
Jim Procter [Sun, 23 Jun 2013 18:02:20 +0000 (19:02 +0100)]
JAL-1230 simplify initialisation of consensus, conservation and structure consensus rows
Jim Procter [Sun, 23 Jun 2013 13:00:05 +0000 (14:00 +0100)]
Merge branch 'bug/JAL-1230' into Release_2_8_Branch
Jim Procter [Sun, 23 Jun 2013 12:58:40 +0000 (13:58 +0100)]
Merge commit '72c628b' into Release_2_8_Branch
Jim Procter [Sat, 22 Jun 2013 13:17:34 +0000 (14:17 +0100)]
Merge branch 'feature/JAL-1330' into Release_2_8_Branch
Jim Procter [Sat, 22 Jun 2013 13:17:14 +0000 (14:17 +0100)]
JAL-1330 pick primary seqeunce data source for authority rather than first node of sub tree
Jim Procter [Fri, 21 Jun 2013 16:20:03 +0000 (17:20 +0100)]
JAL-1230 comment unused code to avoid NPE
Jim Procter [Fri, 21 Jun 2013 14:09:01 +0000 (15:09 +0100)]
JAL-1327 TODO
Jim Procter [Fri, 21 Jun 2013 14:08:37 +0000 (15:08 +0100)]
JAL-1326 JAL-1327 update all graphline thresholds with flag for interactive or final adjustment event
Jim Procter [Fri, 21 Jun 2013 13:29:41 +0000 (14:29 +0100)]
JAL-1241 - generate colour for all annotation values within range
Jim Procter [Fri, 21 Jun 2013 13:12:49 +0000 (14:12 +0100)]
Merge branch 'JAL-1294_iupredexportimport' into Release_2_8_Branch
Jim Procter [Fri, 21 Jun 2013 12:59:53 +0000 (13:59 +0100)]
JAL-1325 formatting
Jim Procter [Fri, 21 Jun 2013 12:59:35 +0000 (13:59 +0100)]
JAL-1325 JAL-1294 resolve SEQUENCE_REF and GROUP_REF for GRAPHLINE statements
Jim Procter [Fri, 21 Jun 2013 12:58:42 +0000 (13:58 +0100)]
JAL-1294 JAL-1325 store graphline for individual annotation rows.
Jim Procter [Fri, 21 Jun 2013 11:20:11 +0000 (12:20 +0100)]
JAL-1294 JAL-1325 bugfix equals
Jim Procter [Fri, 21 Jun 2013 10:58:47 +0000 (11:58 +0100)]
JAL-1294 JAL-1325 test annotation threshold line equivalence
Jim Procter [Fri, 21 Jun 2013 10:36:17 +0000 (11:36 +0100)]
Merge branch 'JAL-1321_jws2_tooltips' into Release_2_8_Branch
Jim Procter [Fri, 21 Jun 2013 10:35:07 +0000 (11:35 +0100)]
JAL-1127 set option widgets to service defaults only when showing default settings
Jim Procter [Wed, 19 Jun 2013 16:41:27 +0000 (17:41 +0100)]
JAL-1240 avoid NPE when source has no proxy available
Jim Procter [Wed, 19 Jun 2013 16:00:37 +0000 (17:00 +0100)]
Merge branch 'JAL-1321_jws2_tooltips' into Release_2_8_Branch
Jim Procter [Tue, 18 Jun 2013 20:57:45 +0000 (21:57 +0100)]
JAL-1320 ascending alphabetical order
Jim Procter [Tue, 18 Jun 2013 20:57:02 +0000 (21:57 +0100)]
JAL-1320 preserve option/parameter order with LinkedHashMap
Jim Procter [Tue, 18 Jun 2013 20:38:16 +0000 (21:38 +0100)]
JAL-1320 sort options and parameters according to their name
Jim Procter [Tue, 18 Jun 2013 20:29:29 +0000 (21:29 +0100)]
typo
Jim Procter [Tue, 18 Jun 2013 20:28:57 +0000 (21:28 +0100)]
JAL-1321 don't show a tooltip for empty strings
Jim Procter [Mon, 17 Jun 2013 17:26:47 +0000 (18:26 +0100)]
Merge branch 'JAL-1319_jronn_npe' into Release_2_8_Branch
Jim Procter [Mon, 17 Jun 2013 17:25:54 +0000 (18:25 +0100)]
JAL-1319 (blacklist fix) check for presence of a score object before we start making annotation
Jim Procter [Mon, 17 Jun 2013 16:51:33 +0000 (17:51 +0100)]
Merge branch 'JAL-1312_ambiguity_na' into Release_2_8_Branch
Jim Procter [Mon, 17 Jun 2013 16:45:23 +0000 (17:45 +0100)]
JAL-1027 fix errors in alternative codon table
Jim Procter [Mon, 17 Jun 2013 16:45:03 +0000 (17:45 +0100)]
JAL-1027 check that ResidueProperties.codonHash2 is actually identical to the codon table used in previous versions
git://source.jalview.org / jalview.git / log