Jim Procter [Wed, 29 Jan 2014 09:21:01 +0000 (09:21 +0000)]
JAL-970 JAL-1400 fixed layout
Jim Procter [Tue, 28 Jan 2014 21:23:28 +0000 (21:23 +0000)]
JAL-957 reinstate the PDBfile parameter
Jim Procter [Tue, 28 Jan 2014 16:00:09 +0000 (16:00 +0000)]
JAL-1400 sign the jnlp for arbitrary memory
Jim Procter [Tue, 28 Jan 2014 14:59:25 +0000 (14:59 +0000)]
JAL-957 JAL-1400 only sign specific jar artefacts for applet publishing
Jim Procter [Tue, 28 Jan 2014 14:36:02 +0000 (14:36 +0000)]
JAL-957 neater boilerplate link to signed/unsigned examples and shortcuts for downloading applet jars
Jim Procter [Tue, 28 Jan 2014 14:35:36 +0000 (14:35 +0000)]
JAL-957 shorten title for linked applets example
Jim Procter [Tue, 28 Jan 2014 14:35:20 +0000 (14:35 +0000)]
JAL-957 removed cruft on appletParameters page
Jim Procter [Tue, 28 Jan 2014 13:52:28 +0000 (13:52 +0000)]
JAL-957 make a copy of the applet/Jmol applet jars for the unsigned example pages
Jim Procter [Tue, 28 Jan 2014 12:08:51 +0000 (12:08 +0000)]
Merge branch 'JAL-1400_sandboxapp' into JAL-957_jbake
Jim Procter [Tue, 28 Jan 2014 11:41:12 +0000 (11:41 +0000)]
JAL-957 permissions property for example pages (jbake generated)
Jim Procter [Tue, 28 Jan 2014 11:39:53 +0000 (11:39 +0000)]
JAL-957 unsigned applet demo pages created with jbake
Jim Procter [Tue, 28 Jan 2014 11:36:42 +0000 (11:36 +0000)]
JAL-957 tidier source and ensure permissions is explicitly set for signed example
Jim Procter [Tue, 28 Jan 2014 11:25:13 +0000 (11:25 +0000)]
JAL-957 new jbake-generated example pages
Jim Procter [Tue, 28 Jan 2014 11:24:26 +0000 (11:24 +0000)]
JAL-957 instructions on runnning Jbake to regenerate JalviewLite example pages
Jim Procter [Tue, 28 Jan 2014 11:15:33 +0000 (11:15 +0000)]
JAL-957 standardise formatting for example preamble
Jim Procter [Tue, 28 Jan 2014 11:14:51 +0000 (11:14 +0000)]
JAL-957 standard link to signed/unsigned demo pages clearly shown at top of page
Jim Procter [Tue, 28 Jan 2014 11:14:04 +0000 (11:14 +0000)]
JAL-957 tidy jbake directory
jprocter [Tue, 21 Jan 2014 15:07:34 +0000 (15:07 +0000)]
JAL-957 JAL-1400 unsigned applet examples
jprocter [Tue, 21 Jan 2014 15:06:01 +0000 (15:06 +0000)]
JAL-957 JAL-1400 use signed/unsigned applet as needed
jprocter [Tue, 21 Jan 2014 15:05:35 +0000 (15:05 +0000)]
JAL-957 JAL-1400 JAL-1407 signed and unsigned jalviewApplet example links.
jprocter [Tue, 21 Jan 2014 15:04:50 +0000 (15:04 +0000)]
JAL-957 tidy up formatting
jprocter [Tue, 21 Jan 2014 12:00:54 +0000 (12:00 +0000)]
JAL-957 javascript api documentation page
jprocter [Tue, 21 Jan 2014 11:59:04 +0000 (11:59 +0000)]
JAL-957 macro-ise the sidebar generation loop and add mechanism for linking to signed/unsigned version of the applet example pages
jprocter [Tue, 21 Jan 2014 11:57:57 +0000 (11:57 +0000)]
JAL-957 only include content body for 'normal' pages - workaround an apparent FreeMarker bug causing metadata to be included in content body
jprocter [Tue, 21 Jan 2014 11:57:04 +0000 (11:57 +0000)]
JAL-957 fix layout of pages
jprocter [Sat, 18 Jan 2014 19:08:45 +0000 (19:08 +0000)]
formatting
jprocter [Sat, 18 Jan 2014 19:07:34 +0000 (19:07 +0000)]
JAL-1400 numeric version numbers only for minimum jre compatibility
jprocter [Fri, 17 Jan 2014 16:39:16 +0000 (16:39 +0000)]
JAL-1400 still fixing JmolApplet manifest issue
jprocter [Fri, 17 Jan 2014 16:27:25 +0000 (16:27 +0000)]
JAL-1400 tweaking to ensure JmolApplet build correctly
jprocter [Fri, 17 Jan 2014 15:58:37 +0000 (15:58 +0000)]
formatting
jprocter [Fri, 17 Jan 2014 15:55:53 +0000 (15:55 +0000)]
JAL-1400 default JalviewLite build is signed applet with sandbox permissions
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
git://source.jalview.org / jalview.git / log