Jim Procter [Tue, 25 Feb 2014 16:49:39 +0000 (16:49 +0000)]
Merge branch 'JAL-1454_patch' into Release_2_8_1_Branch
Jim Procter [Tue, 25 Feb 2014 16:48:58 +0000 (16:48 +0000)]
JAL-1355 typo in key
Jim Procter [Tue, 25 Feb 2014 16:44:48 +0000 (16:44 +0000)]
Merge branch 'JAL-1454_patch' into Release_2_8_1_Branch
Jim Procter [Tue, 25 Feb 2014 16:44:29 +0000 (16:44 +0000)]
JAL-1454 catch exceptions during calculation and report any warnings in the PCA 'Output values...' dump.
Jim Procter [Tue, 25 Feb 2014 16:43:08 +0000 (16:43 +0000)]
JAL-1454 increase max for tqli iterations and throw exception rather than call System.exit()
Jim Procter [Fri, 21 Feb 2014 16:28:13 +0000 (16:28 +0000)]
Merge branch 'JAL-1364_patch' into Release_2_8_1_Branch
Jim Procter [Fri, 21 Feb 2014 16:27:50 +0000 (16:27 +0000)]
patch for JAL-1449 - continuance of JAL-1364 - check bounds of gapMap - not the VIENNA results
Jim Procter [Fri, 21 Feb 2014 15:07:45 +0000 (15:07 +0000)]
Merge branch 'pathc_JAL-1354' into Release_2_8_1_Branch
Jim Procter [Fri, 21 Feb 2014 15:06:23 +0000 (15:06 +0000)]
JAL-1448 reinstate non-locale sensitive code for reading/writing last read date from RSS and Jalview preferences
Jim Procter [Fri, 21 Feb 2014 14:44:48 +0000 (14:44 +0000)]
JAL-1354 typo
Jim Procter [Fri, 21 Feb 2014 14:44:35 +0000 (14:44 +0000)]
JAL-1354 use real var-args method signature to avoid ambiguity
Jim Procter [Fri, 21 Feb 2014 14:43:02 +0000 (14:43 +0000)]
JAL-1354 quoted format strings are not substituted
Jim Procter [Thu, 20 Feb 2014 15:27:30 +0000 (15:27 +0000)]
Merge branch 'JAL-1447' into Release_2_8_1_Branch
Jim Procter [Thu, 20 Feb 2014 15:18:28 +0000 (15:18 +0000)]
JAL-1447 patch to correctly recognise FASTA files containing '*'
Jim Procter [Thu, 20 Feb 2014 15:17:36 +0000 (15:17 +0000)]
test and data for JAL-1447
Jim Procter [Thu, 20 Feb 2014 15:15:40 +0000 (15:15 +0000)]
JAL-1447 - more flexible testing for file format Identity detection
Jim Procter [Tue, 18 Feb 2014 16:32:05 +0000 (16:32 +0000)]
Merge branch 'JAL-1445' into Release_2_8_1_Branch
Jim Procter [Tue, 18 Feb 2014 16:30:34 +0000 (16:30 +0000)]
clear out 2.8.0b1 what's new and add JAL-1445 to list of new features
Jim Procter [Tue, 18 Feb 2014 16:29:35 +0000 (16:29 +0000)]
JAL-1445 basic help docs for feature
Jim Procter [Tue, 18 Feb 2014 16:29:11 +0000 (16:29 +0000)]
JAL-1445 JAL-1354 english strings for select by feature
Jim Procter [Tue, 18 Feb 2014 09:41:56 +0000 (09:41 +0000)]
JAL-1445 (shift+) double click on feature type in desktop feature settings to select columns (not) containing features
Jim Procter [Tue, 18 Feb 2014 09:25:31 +0000 (09:25 +0000)]
JAL-1446 use popup event trigger instead of right-click event
Jim Procter [Mon, 17 Feb 2014 18:13:01 +0000 (18:13 +0000)]
JAL-1445 added menu items to select containing/non-containing features in FeatureSettings popup menu
Jim Procter [Mon, 17 Feb 2014 18:12:12 +0000 (18:12 +0000)]
JAL-1445 ported routine for selecting containing/non-containing columns from groovy example
Jim Procter [Mon, 17 Feb 2014 18:11:35 +0000 (18:11 +0000)]
JAL-1445 expose columnSelection setter.
Jim Procter [Mon, 17 Feb 2014 18:07:16 +0000 (18:07 +0000)]
JAL-535 interface for GUI state update methods that the AlignViewController can call
Jim Procter [Mon, 17 Feb 2014 16:29:17 +0000 (16:29 +0000)]
JAL-1445 groovy script demonstrating how to select columns according to a particular feature type
Jim Procter [Mon, 3 Feb 2014 17:50:44 +0000 (17:50 +0000)]
Merge branch 'try_r20b1_merge' into Release_2_8_1_Branch
Jim Procter [Mon, 3 Feb 2014 17:46:31 +0000 (17:46 +0000)]
Merge branch 'Release_2_8_1_Branch_i18n' into try_r20b1_merge
Conflicts:
src/jalview/gui/AlignFrame.java
src/jalview/gui/AppJmol.java
src/jalview/gui/PopupMenu.java
src/jalview/gui/UserDefinedColours.java
JAL-1354 merge in with some exceptions for non i18n bare strings and fix compilation errors from missing import of MessageManager
Jim Procter [Mon, 3 Feb 2014 17:20:12 +0000 (17:20 +0000)]
JAL-1358 JWS-69 add Daniel to the list of Jalview Authors
Jim Procter [Mon, 3 Feb 2014 17:17:52 +0000 (17:17 +0000)]
Merge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge
updating 2.8.1 with source formatting, branding, and new examples build mechanism
Conflicts:
build.xml
examples/linkedapplets_ng.html
help/helpTOC.xml
src/jalview/appletgui/AlignFrame.java
src/jalview/schemabinding/version2/AnnotationColours.java
src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
Jim Procter [Mon, 3 Feb 2014 16:49:32 +0000 (16:49 +0000)]
Merge branch 'JAL-957_jbake' into r281_JAL-957
Conflicts:
build.xml
examples/linkedapplets_ng.html
Jalview build Manager [Fri, 31 Jan 2014 08:48:49 +0000 (08:48 +0000)]
JAL-1432 ensure unsigned jmol jar is actually written
Jim Procter [Thu, 30 Jan 2014 15:48:13 +0000 (15:48 +0000)]
JAL-1432 'whats new' and release history
Jim Procter [Wed, 29 Jan 2014 21:20:21 +0000 (21:20 +0000)]
JAL-957 reinstate jnetfile parameter
Jim Procter [Wed, 29 Jan 2014 21:05:34 +0000 (21:05 +0000)]
JAL-1432 patch broken comments in css
Jim Procter [Wed, 29 Jan 2014 17:04:40 +0000 (17:04 +0000)]
JAL-1432 natasha's name on applet author list
Jim Procter [Wed, 29 Jan 2014 15:56:11 +0000 (15:56 +0000)]
JAL-1432 updated copyright notices
Jim Procter [Wed, 29 Jan 2014 14:11:30 +0000 (14:11 +0000)]
JAL-1432 AUTHORS file and updated authors properties for the about dialog.
Jim Procter [Wed, 29 Jan 2014 13:40:01 +0000 (13:40 +0000)]
JAL-1432 update dependency and licensing info
Jim Procter [Wed, 29 Jan 2014 13:39:31 +0000 (13:39 +0000)]
JAL-1432 bump version
Jim Procter [Wed, 29 Jan 2014 13:26:54 +0000 (13:26 +0000)]
Merge branch 'JAL-957_jbake' into Release_2_8_Branch
Jim Procter [Wed, 29 Jan 2014 09:21:31 +0000 (09:21 +0000)]
JAL-1400 added explanation about signed/unsigned applet compatibility with older java versions.
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 21:23:53 +0000 (21:23 +0000)]
Merge branch 'JAL-957_jbake' into Release_2_8_Branch
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 16:00:35 +0000 (16:00 +0000)]
Merge branch 'JAL-957_jbake' into Release_2_8_Branch
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 14:59:40 +0000 (14:59 +0000)]
Merge branch 'JAL-957_jbake' into Release_2_8_Branch
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 14:37:11 +0000 (14:37 +0000)]
Merge branch 'JAL-957_jbake' into Release_2_8_Branch
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 13:52:55 +0000 (13:52 +0000)]
Merge branch 'JAL-957_jbake' into Release_2_8_Branch
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 11:46:01 +0000 (11:46 +0000)]
Merge branch 'JAL-957_jbake' into Release_2_8_Branch
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
Jim Procter [Mon, 27 Jan 2014 13:53:40 +0000 (13:53 +0000)]
Merge branch 'JAL-1430_mfa_ext' into Release_2_8_Branch
Jim Procter [Mon, 27 Jan 2014 13:36:18 +0000 (13:36 +0000)]
JAL-1430 mfa added as a known extension for FASTA files
jprocter [Tue, 21 Jan 2014 16:14:13 +0000 (16:14 +0000)]
Merge branch 'JAL-1400_sandboxapp' into Release_2_8_Branch
working examples for signed sandboxed applet
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 16:39:47 +0000 (16:39 +0000)]
Merge branch 'JAL-1400_sandboxapp' into Release_2_8_Branch
jprocter [Fri, 17 Jan 2014 16:39:16 +0000 (16:39 +0000)]
JAL-1400 still fixing JmolApplet manifest issue
jprocter [Fri, 17 Jan 2014 16:28:37 +0000 (16:28 +0000)]
Merge branch 'JAL-1400_sandboxapp' into Release_2_8_Branch
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 15:59:50 +0000 (15:59 +0000)]
Merge branch 'JAL-1400_sandboxapp' into Release_2_8_Branch
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 14:20:35 +0000 (14:20 +0000)]
Merge branch 'JAL-1422_srs_r281' into Release_2_8_1_Branch
Jim Procter [Mon, 13 Jan 2014 14:13:29 +0000 (14:13 +0000)]
Merge branch 'Release_2_8_1_Branch' into Release_2_8_1_Branch_i18n
Jim Procter [Mon, 13 Jan 2014 14:09:34 +0000 (14:09 +0000)]
Merge branch 'JAL-1422_srs' into JAL-1422_srs_r281
Conflicts:
examples/linkedapplets_ng.html
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 14:02:48 +0000 (14:02 +0000)]
Merge branch 'fix_JAL-1423' into Release_2_8_1_Branch
git://source.jalview.org / jalview.git / log