Jim Procter [Fri, 25 Apr 2014 13:20:42 +0000 (14:20 +0100)]
JAL-1177 allow jalview alignments to be saved that have no alignment views, to support storage of parent datasets
Jim Procter [Fri, 25 Apr 2014 12:51:34 +0000 (13:51 +0100)]
JAL-1177 propagate sequence associated annotation to dataset sequence
Jim Procter [Fri, 25 Apr 2014 12:50:47 +0000 (13:50 +0100)]
JAL-1177 refactored command line test harness
Jim Procter [Fri, 25 Apr 2014 12:49:44 +0000 (13:49 +0100)]
test for JAL-1177 store and recover RNA secondary structure for a stockholm file with sequence associated RNA structure
Jim Procter [Thu, 24 Apr 2014 16:39:58 +0000 (17:39 +0100)]
JAL-1232 fix - ensure display all columns flag is set if an RNA helix is created on an annotation row.
Jim Procter [Wed, 23 Apr 2014 16:15:57 +0000 (17:15 +0100)]
Merge branch 'JAL-1486_hiddenStartEnd' into Release_2_8_1_Branch
Jim Procter [Wed, 23 Apr 2014 16:15:04 +0000 (17:15 +0100)]
JAL-1486 todo for 2.8.2 release
Jim Procter [Wed, 23 Apr 2014 15:37:13 +0000 (16:37 +0100)]
Merge branch 'jims_marckhacks' into Release_2_8_1_Branch
Jim Procter [Mon, 21 Apr 2014 21:25:17 +0000 (22:25 +0100)]
JAL-1458 updated logo for installer
Jim Procter [Mon, 21 Apr 2014 20:21:36 +0000 (21:21 +0100)]
JAL-1383 scrubbed envision GUI and documentation
Jim Procter [Mon, 21 Apr 2014 17:39:55 +0000 (18:39 +0100)]
JAL-1355 keys for colours
Jim Procter [Mon, 21 Apr 2014 17:13:56 +0000 (18:13 +0100)]
fix for JAL-1438
Jim Procter [Mon, 21 Apr 2014 16:32:38 +0000 (17:32 +0100)]
Merge branch 'jims_marckhacks' into Release_2_8_1_Branch
Jim Procter [Mon, 21 Apr 2014 16:27:19 +0000 (17:27 +0100)]
JAL-1473 define defaults for DNA/Protein PCA calculation
Jim Procter [Mon, 21 Apr 2014 16:26:52 +0000 (17:26 +0100)]
JAL-1485 JAL-1483 show i18n key for different available score models, and limit to those applicable for a protein / DNA
Jim Procter [Mon, 21 Apr 2014 16:24:56 +0000 (17:24 +0100)]
JAL-1473 JAL-1355 i18n for score model submenu
Jim Procter [Mon, 21 Apr 2014 16:23:57 +0000 (17:23 +0100)]
JAL-1485 JAL-1473 use compound i18n messages to construct title of tree using translations of score model and calculation method
Jim Procter [Mon, 21 Apr 2014 16:21:23 +0000 (17:21 +0100)]
JAL-1485
Jim Procter [Mon, 21 Apr 2014 15:06:30 +0000 (16:06 +0100)]
JAL-1484 always update the dataset sequence if 'trimDatasetSeqs' option is not set.
Jim Procter [Mon, 21 Apr 2014 15:02:03 +0000 (16:02 +0100)]
JAL-1466 don't include empty columns if no upstream sequence data available for aligned subsequences
Jim Procter [Mon, 21 Apr 2014 15:00:45 +0000 (16:00 +0100)]
JAL-1355 JAL-1466 i18n for flanking sequence menu entry and tooltip messages
Jim Procter [Mon, 21 Apr 2014 13:24:56 +0000 (14:24 +0100)]
Merge branch 'jims_marckhacks' into Release_2_8_1_Branch
Jim Procter [Sat, 19 Apr 2014 12:56:18 +0000 (13:56 +0100)]
JAL-741 (poss related JAL-971) - fix NPE raised when attempting to sort alignment by feature when lots of groups displayed
Jim Procter [Sat, 19 Apr 2014 12:53:11 +0000 (13:53 +0100)]
JAL-1476 JAL-1016 avoid NPE messiness if structures fail to align for some reason
Jim Procter [Sat, 19 Apr 2014 12:46:03 +0000 (13:46 +0100)]
don't unhook existing group associated annotation JAL-1480
Jim Procter [Fri, 18 Apr 2014 15:22:38 +0000 (16:22 +0100)]
fix for JAL-1478
Jim Procter [Fri, 18 Apr 2014 15:18:36 +0000 (16:18 +0100)]
JAL-1478 test to demonstrate bug
Jim Procter [Fri, 18 Apr 2014 14:17:42 +0000 (15:17 +0100)]
JAL-1477 tooltip
Jim Procter [Fri, 18 Apr 2014 09:56:53 +0000 (10:56 +0100)]
JAL-1476 - don't send broken commands to Jmol when no columns exist to superimpose structures
Jim Procter [Fri, 18 Apr 2014 09:50:15 +0000 (10:50 +0100)]
JAL-1477 first implementation of 'View all representative structures' option.
Jim Procter [Fri, 18 Apr 2014 09:14:54 +0000 (10:14 +0100)]
JAL-1466 import full length sequence to dataset sequence or trim it to local sequence's length
Jim Procter [Fri, 18 Apr 2014 09:12:40 +0000 (10:12 +0100)]
JAL-1466 flag and jalview_properties setting to control retrieval of full length dataset sequence
Jim Procter [Fri, 18 Apr 2014 09:08:57 +0000 (10:08 +0100)]
JAL-1466 improved test and patched off by one that deleted one dataset residue from flanking alignment
Jim Procter [Tue, 15 Apr 2014 17:50:12 +0000 (18:50 +0100)]
JAL-1466 new calculation menu option to recover the full width sequences either side of the current alignment and append them.
Jim Procter [Tue, 15 Apr 2014 17:47:56 +0000 (18:47 +0100)]
tidy imports
Jim Procter [Tue, 15 Apr 2014 17:43:34 +0000 (18:43 +0100)]
patch v2 for JAL-1474 add the newly recovered dataset sequence to the dataset currently being build/operated on if it isn't already present
Jim Procter [Tue, 15 Apr 2014 17:42:48 +0000 (18:42 +0100)]
patch v1 for JAL-1474 - make sure we actually set the dataset sequence's string
Jim Procter [Tue, 15 Apr 2014 17:41:57 +0000 (18:41 +0100)]
JAL-1474 note about buggy 'merge sequence' operation pointing to relevant issue
Jim Procter [Tue, 15 Apr 2014 17:11:07 +0000 (18:11 +0100)]
JAL-1473 tree calcs performed with ScoreModelI instances
Jim Procter [Tue, 15 Apr 2014 15:23:35 +0000 (16:23 +0100)]
don't finness the alignment annotation modification methods by modifying the vector directly!
Jim Procter [Tue, 15 Apr 2014 15:21:02 +0000 (16:21 +0100)]
patch for JAL-1465 - set min/max thresholds for each disorder annotation row
Jim Procter [Tue, 15 Apr 2014 15:19:50 +0000 (16:19 +0100)]
JAL-1473 menu entries for different score models available for NJ/UPGMA tree building (note - this will not scale well!)
Jim Procter [Tue, 15 Apr 2014 15:16:26 +0000 (16:16 +0100)]
JAL-1473 provide Amino acid physicochemical conservation based score matrices
Jim Procter [Tue, 15 Apr 2014 15:15:36 +0000 (16:15 +0100)]
JAL-1473 show available score matrices for use in PCA calculation
Jim Procter [Tue, 15 Apr 2014 15:09:20 +0000 (16:09 +0100)]
JAL-1473 refactor score matrices and tree score calculations to interface/api and base implementations
Jim Procter [Tue, 15 Apr 2014 14:40:35 +0000 (15:40 +0100)]
JAL-1355 missing message
Jim Procter [Sun, 6 Apr 2014 11:29:11 +0000 (12:29 +0100)]
fix for JAL-1464 avoid NPE with per-sequence annotation with no positional elements as generated by 'extract scores' (related to JAL-1066)
Jim Procter [Sat, 5 Apr 2014 12:23:27 +0000 (13:23 +0100)]
Merge branch 'r281_JAL-1211' into Release_2_8_1_Branch
Jim Procter [Fri, 4 Apr 2014 15:38:24 +0000 (16:38 +0100)]
JAL-1211 - set annotation panel height according to the amount of annotation present on the alignment and the relative size of the alignment.
Jim Procter [Fri, 4 Apr 2014 15:18:24 +0000 (16:18 +0100)]
JAL-1211 - pick up site-defined defined window geometry before we calculate layout
Jim Procter [Fri, 4 Apr 2014 15:16:58 +0000 (16:16 +0100)]
fix for JAL-1461 - check that filetype setting in browser is non-null
Jim Procter [Fri, 4 Apr 2014 13:36:57 +0000 (14:36 +0100)]
Merge branch 'Release_2_8_1_Branch_i18n' into Release_2_8_1_Branch
Jim Procter [Fri, 4 Apr 2014 13:35:53 +0000 (14:35 +0100)]
JAL-1335 typo and 'edit' action
Jim Procter [Wed, 26 Feb 2014 17:23:03 +0000 (17:23 +0000)]
Merge branch 'JAL-1226' into Release_2_8_1_Branch_i18n
Jim Procter [Wed, 26 Feb 2014 17:22:58 +0000 (17:22 +0000)]
Merge branch 'JAL-1226' into Release_2_8_1_Branch
Jim Procter [Wed, 26 Feb 2014 17:22:38 +0000 (17:22 +0000)]
fix for JAL-1226
Jim Procter [Wed, 26 Feb 2014 16:21:03 +0000 (16:21 +0000)]
Merge branch 'JAL-686' into Release_2_8_1_Branch_i18n
Jim Procter [Wed, 26 Feb 2014 16:20:43 +0000 (16:20 +0000)]
Merge branch 'JAL-686' into Release_2_8_1_Branch
Jim Procter [Wed, 26 Feb 2014 16:19:34 +0000 (16:19 +0000)]
JAL-1457 refactoring to explore why '-' appear in annotation rows (see AlignmentAnnotation.padGaps)
Jim Procter [Wed, 26 Feb 2014 16:14:31 +0000 (16:14 +0000)]
fix for JAL-686 - don't trim spaces before creating annotation
Jim Procter [Tue, 25 Feb 2014 16:50:29 +0000 (16:50 +0000)]
Merge branch 'Release_2_8_1_Branch' into Release_2_8_1_Branch_i18n
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 15:08:38 +0000 (15:08 +0000)]
Merge branch 'Release_2_8_1_Branch' into Release_2_8_1_Branch_i18n
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
git://source.jalview.org / jalview.git / log