jalview.git
10 years agoJAL-1239 cancelled flag should be checked and counted
Jim Procter [Tue, 13 May 2014 14:13:17 +0000 (15:13 +0100)]
JAL-1239 cancelled flag should be checked and counted

10 years agoJAL-1239 make doubly sure sub job status is set to complete/cancelled
Jim Procter [Tue, 13 May 2014 14:12:30 +0000 (15:12 +0100)]
JAL-1239 make doubly sure sub job status is set to complete/cancelled

10 years agoMerge branch 'JAL-1397' into Release_2_8_1_Branch
Jim Procter [Mon, 12 May 2014 15:05:53 +0000 (16:05 +0100)]
Merge branch 'JAL-1397' into Release_2_8_1_Branch

10 years agoJAL-1397 catch other random version strings
Jim Procter [Mon, 12 May 2014 14:05:11 +0000 (15:05 +0100)]
JAL-1397 catch other random version strings

10 years agopatch for regression introduced JAL-1397
Jim Procter [Mon, 12 May 2014 14:04:54 +0000 (15:04 +0100)]
patch for regression introduced JAL-1397

10 years agoMerge branch 'JAL-1397' into Release_2_8_1_Branch
Jim Procter [Fri, 2 May 2014 09:44:22 +0000 (10:44 +0100)]
Merge branch 'JAL-1397' into Release_2_8_1_Branch

10 years agoJAL-1397 JAL-1066 JAL-1233 refactored annotation colours XML parsing code and support...
Jim Procter [Fri, 2 May 2014 09:43:26 +0000 (10:43 +0100)]
JAL-1397 JAL-1066 JAL-1233 refactored annotation colours XML parsing code and support per group annotation colours

10 years agoJAL-1369 JAL-1397 version check to support correct interpretation for older projects...
Jim Procter [Fri, 2 May 2014 09:41:03 +0000 (10:41 +0100)]
JAL-1369 JAL-1397 version check to support correct interpretation for older projects where data semantics have changed

10 years agoformatting
Jim Procter [Fri, 2 May 2014 09:35:12 +0000 (10:35 +0100)]
formatting

10 years agoJAL-1233 JAL-1066 fix for JAL-1397 test: allow per group colour by annotation to...
Jim Procter [Fri, 2 May 2014 09:27:38 +0000 (10:27 +0100)]
JAL-1233 JAL-1066 fix for JAL-1397 test: allow per group colour by annotation to be stored/recovered in Jalview projects (version compatibility will be 2.8.1 and after)

10 years agoJAL-1397 (probably buggy) test for recovery of background and per group alignment...
Jim Procter [Thu, 1 May 2014 16:05:20 +0000 (17:05 +0100)]
JAL-1397 (probably buggy) test for recovery of background and per group alignment annotation shading

10 years agoremove todo
Jim Procter [Thu, 1 May 2014 14:42:07 +0000 (15:42 +0100)]
remove todo

10 years agoJAL-1492 formatting and squash NPEs
Jim Procter [Thu, 1 May 2014 14:41:20 +0000 (15:41 +0100)]
JAL-1492 formatting and squash NPEs

10 years agoJAL-1092 TODO - allow Jalview/JalviewLite to generate its own user defined colour...
Jim Procter [Thu, 1 May 2014 14:40:20 +0000 (15:40 +0100)]
JAL-1092 TODO - allow Jalview/JalviewLite to generate its own user defined colour scheme parameter strings

10 years agoJAL-1492 JAL-1397 make AnnotatedCollectionI context aware so groups can be coloured...
Jim Procter [Thu, 1 May 2014 14:38:57 +0000 (15:38 +0100)]
JAL-1492 JAL-1397 make AnnotatedCollectionI context aware so groups can be coloured based on annotation on their parent alignments.

10 years agoJAL-1492 JAL-1397 JAL-643 JAL-969 pull up global and group colourscheme logic and...
Jim Procter [Thu, 1 May 2014 14:33:59 +0000 (15:33 +0100)]
JAL-1492 JAL-1397 JAL-643 JAL-969 pull up global and group colourscheme logic and regularise interface

10 years agoJAL-1492 JAL-1397 JAL-643 JAL-969 factory method to clone and apply colour scheme...
Jim Procter [Thu, 1 May 2014 14:29:31 +0000 (15:29 +0100)]
JAL-1492 JAL-1397 JAL-643 JAL-969 factory method to clone and apply colour scheme to another alignment/group

10 years agoJAL-1492 JAL-1397 JAL-643 JAL-969 modifiable flag on colourscheme indicating conserva...
Jim Procter [Thu, 1 May 2014 14:26:07 +0000 (15:26 +0100)]
JAL-1492 JAL-1397 JAL-643 JAL-969 modifiable flag on colourscheme indicating conservation shading should be applied

10 years agojavadoc
Jim Procter [Thu, 1 May 2014 14:24:08 +0000 (15:24 +0100)]
javadoc

10 years agoproperly quit so JUnit marks tests as successful
Jim Procter [Thu, 1 May 2014 14:14:08 +0000 (15:14 +0100)]
properly quit so JUnit marks tests as successful

10 years agoJAL-1497 check to see if tree structure is ready for display, and show a 'tree loadin...
Jim Procter [Thu, 1 May 2014 14:12:07 +0000 (15:12 +0100)]
JAL-1497 check to see if tree structure is ready for display, and show a 'tree loading' message if it isn't.

10 years agofix for JAL-1495 - initialise menu entry from current state of apply to all groups...
Jim Procter [Thu, 1 May 2014 14:06:29 +0000 (15:06 +0100)]
fix for JAL-1495 - initialise menu entry from current state of apply to all groups flag !

10 years agofix for JAL-1494 tweaked logic to fix NPEs and modify settings for both background...
Jim Procter [Thu, 1 May 2014 14:03:33 +0000 (15:03 +0100)]
fix for JAL-1494 tweaked logic to fix NPEs and modify settings for both background and all defined groups

10 years agoJAL-969 remove unnecessary overrides
Jim Procter [Thu, 1 May 2014 13:57:30 +0000 (14:57 +0100)]
JAL-969 remove unnecessary overrides

10 years agoJAL-961 configure conservation worker from alignment viewport
Jim Procter [Thu, 1 May 2014 13:33:44 +0000 (14:33 +0100)]
JAL-961 configure conservation worker from alignment viewport

10 years agoJAL-961 store result of conservation analysis worker on the alignment viewport
Jim Procter [Thu, 1 May 2014 13:32:45 +0000 (14:32 +0100)]
JAL-961 store result of conservation analysis worker on the alignment viewport

10 years agomake sure valid value for non-gapped calculation with zero symbol data
Jim Procter [Thu, 1 May 2014 13:24:07 +0000 (14:24 +0100)]
make sure valid value for non-gapped calculation with zero symbol data

10 years agoJAL-643 - abstracted colourscheme components to allow consensus/colouring to be propa...
Jim Procter [Thu, 17 Oct 2013 12:44:25 +0000 (13:44 +0100)]
JAL-643 - abstracted colourscheme components to allow consensus/colouring to be propagated from background to a group

10 years agoMerge branch 'JAL-1340_redundancy' into Release_2_8_1_Branch
Jim Procter [Tue, 29 Apr 2014 12:25:35 +0000 (13:25 +0100)]
Merge branch 'JAL-1340_redundancy' into Release_2_8_1_Branch

10 years agoJAL-1340 mark redundant sequences as soon as redundancy calculation has finished
Jim Procter [Mon, 28 Apr 2014 12:32:52 +0000 (13:32 +0100)]
JAL-1340 mark redundant sequences as soon as redundancy calculation has finished

10 years agoJAL-1340 simpler and more efficient interactive highlighting of redundant sequences
Jim Procter [Mon, 28 Apr 2014 12:31:59 +0000 (13:31 +0100)]
JAL-1340 simpler and more efficient interactive highlighting of redundant sequences

10 years agoJAL-1340 ensure slider value wide enough to see three figures
Jim Procter [Mon, 28 Apr 2014 12:28:17 +0000 (13:28 +0100)]
JAL-1340 ensure slider value wide enough to see three figures

10 years agoMerge branch 'JAL-1322' into Release_2_8_1_Branch
Jim Procter [Sun, 27 Apr 2014 22:15:11 +0000 (23:15 +0100)]
Merge branch 'JAL-1322' into Release_2_8_1_Branch

10 years agoJAL-1322 avoid rounding error causing non functional slider and allow slider to reach...
Jim Procter [Sun, 27 Apr 2014 22:14:24 +0000 (23:14 +0100)]
JAL-1322 avoid rounding error causing non functional slider and allow slider to reach maximum value for parameter

10 years agoJAL-1322 allow slider to reach maximum value for parameter
Jim Procter [Sun, 27 Apr 2014 22:13:58 +0000 (23:13 +0100)]
JAL-1322 allow slider to reach maximum value for parameter

10 years agoJAL-1322 only update slider when return is pressed
Jim Procter [Sun, 27 Apr 2014 22:12:56 +0000 (23:12 +0100)]
JAL-1322 only update slider when return is pressed

10 years agoMerge branch 'JAL-952_rnahelix' into Release_2_8_1_Branch
Jim Procter [Sun, 27 Apr 2014 20:41:36 +0000 (21:41 +0100)]
Merge branch 'JAL-952_rnahelix' into Release_2_8_1_Branch

10 years agoMerge branch 'JAL-1164_regression' into Release_2_8_1_Branch
Jim Procter [Sun, 27 Apr 2014 20:41:29 +0000 (21:41 +0100)]
Merge branch 'JAL-1164_regression' into Release_2_8_1_Branch

10 years agoworkaround for JAL-1319 - catch unexpected NPE thrown by JABA client method
Jim Procter [Sun, 27 Apr 2014 17:44:12 +0000 (18:44 +0100)]
workaround for JAL-1319 - catch unexpected NPE thrown by JABA client method

10 years agoJAL-1164 (regression) reinstate 'apply disorder prediction to selection' functionalit...
Jim Procter [Sun, 27 Apr 2014 17:38:13 +0000 (18:38 +0100)]
JAL-1164 (regression) reinstate 'apply disorder prediction to selection' functionality in 2.8.1+ lost during JabaCalcWorker refactoring

10 years agoJAL-952 JAL-1268 document TCoffee and RNA helices colourschemes in applet properties
Jim Procter [Sun, 27 Apr 2014 15:59:31 +0000 (16:59 +0100)]
JAL-952 JAL-1268 document TCoffee and RNA helices colourschemes in applet properties

10 years agoJAL-952 JAL-1268 document RNA Helices and T-Coffee Scores as valid colour scheme...
Jim Procter [Sun, 27 Apr 2014 15:22:18 +0000 (16:22 +0100)]
JAL-952 JAL-1268 document RNA Helices and T-Coffee Scores as valid colour scheme names for applet parameters

10 years agoJAL-952 JAL-1268 add RNA Helices and T-Coffee to list of available colour schemes...
Jim Procter [Sun, 27 Apr 2014 15:17:11 +0000 (16:17 +0100)]
JAL-952 JAL-1268 add RNA Helices and T-Coffee to list of available colour schemes in jalview preferences

10 years agoJAL-952 resolve colour scheme as 'RNA Helices'
Jim Procter [Sun, 27 Apr 2014 15:16:41 +0000 (16:16 +0100)]
JAL-952 resolve colour scheme as 'RNA Helices'

10 years agoJAL-952 refactor code to select annotation for colouring the alignment
Jim Procter [Sun, 27 Apr 2014 15:12:42 +0000 (16:12 +0100)]
JAL-952 refactor code to select annotation for colouring the alignment

10 years agotest for JAL-952
Jim Procter [Sun, 27 Apr 2014 15:06:09 +0000 (16:06 +0100)]
test for JAL-952

10 years agoMerge branch 'JAL-1177_prop_rnasecstr' into Release_2_8_1_Branch
Jim Procter [Fri, 25 Apr 2014 16:11:28 +0000 (17:11 +0100)]
Merge branch 'JAL-1177_prop_rnasecstr' into Release_2_8_1_Branch

10 years agofix for JAL-1268
Jim Procter [Fri, 25 Apr 2014 16:10:10 +0000 (17:10 +0100)]
fix for JAL-1268

10 years agotest for JAL-1268
Jim Procter [Fri, 25 Apr 2014 16:09:55 +0000 (17:09 +0100)]
test for JAL-1268

10 years agoJAL-1177 additional saveState calls to write a dataset only jalview xml document
Jim Procter [Fri, 25 Apr 2014 13:27:23 +0000 (14:27 +0100)]
JAL-1177 additional saveState calls to write a dataset only jalview xml document

10 years agoJAL-1177 patches to loader to cope with dataset only jalview xml documents
Jim Procter [Fri, 25 Apr 2014 13:26:04 +0000 (14:26 +0100)]
JAL-1177 patches to loader to cope with dataset only jalview xml documents

10 years agoJAL-1177 new flag to write a dataset only jalview XML document
Jim Procter [Fri, 25 Apr 2014 13:24:56 +0000 (14:24 +0100)]
JAL-1177 new flag to write a dataset only jalview XML document

10 years agoJAL-1177 allow jalview alignments to be saved that have no alignment views, to suppor...
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

10 years agoJAL-1177 propagate sequence associated annotation to dataset sequence
Jim Procter [Fri, 25 Apr 2014 12:51:34 +0000 (13:51 +0100)]
JAL-1177 propagate sequence associated annotation to dataset sequence

10 years agoJAL-1177 refactored command line test harness
Jim Procter [Fri, 25 Apr 2014 12:50:47 +0000 (13:50 +0100)]
JAL-1177 refactored command line test harness

10 years agotest for JAL-1177 store and recover RNA secondary structure for a stockholm file...
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

10 years agoJAL-1232 fix - ensure display all columns flag is set if an RNA helix is created...
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.

10 years agoMerge branch 'JAL-1486_hiddenStartEnd' into Release_2_8_1_Branch
Jim Procter [Wed, 23 Apr 2014 16:15:57 +0000 (17:15 +0100)]
Merge branch 'JAL-1486_hiddenStartEnd' into Release_2_8_1_Branch

10 years agoJAL-1486 todo for 2.8.2 release
Jim Procter [Wed, 23 Apr 2014 16:15:04 +0000 (17:15 +0100)]
JAL-1486 todo for 2.8.2 release

10 years agoMerge branch 'jims_marckhacks' into Release_2_8_1_Branch
Jim Procter [Wed, 23 Apr 2014 15:37:13 +0000 (16:37 +0100)]
Merge branch 'jims_marckhacks' into Release_2_8_1_Branch

10 years agoJAL-1458 updated logo for installer
Jim Procter [Mon, 21 Apr 2014 21:25:17 +0000 (22:25 +0100)]
JAL-1458 updated logo for installer

10 years agoJAL-1383 scrubbed envision GUI and documentation
Jim Procter [Mon, 21 Apr 2014 20:21:36 +0000 (21:21 +0100)]
JAL-1383 scrubbed envision GUI and documentation

10 years agoJAL-1355 keys for colours
Jim Procter [Mon, 21 Apr 2014 17:39:55 +0000 (18:39 +0100)]
JAL-1355 keys for colours

10 years agofix for JAL-1438
Jim Procter [Mon, 21 Apr 2014 17:13:56 +0000 (18:13 +0100)]
fix for JAL-1438

10 years agoMerge branch 'jims_marckhacks' into Release_2_8_1_Branch
Jim Procter [Mon, 21 Apr 2014 16:32:38 +0000 (17:32 +0100)]
Merge branch 'jims_marckhacks' into Release_2_8_1_Branch

10 years agoJAL-1473 define defaults for DNA/Protein PCA calculation
Jim Procter [Mon, 21 Apr 2014 16:27:19 +0000 (17:27 +0100)]
JAL-1473 define defaults for DNA/Protein PCA calculation

10 years agoJAL-1485 JAL-1483 show i18n key for different available score models, and limit to...
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

10 years agoJAL-1473 JAL-1355 i18n for score model submenu
Jim Procter [Mon, 21 Apr 2014 16:24:56 +0000 (17:24 +0100)]
JAL-1473 JAL-1355 i18n for score model submenu

10 years agoJAL-1485 JAL-1473 use compound i18n messages to construct title of tree using transla...
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

10 years agoJAL-1485
Jim Procter [Mon, 21 Apr 2014 16:21:23 +0000 (17:21 +0100)]
JAL-1485

10 years agoJAL-1484 always update the dataset sequence if 'trimDatasetSeqs' option is not set.
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.

10 years agoJAL-1466 don't include empty columns if no upstream sequence data available for align...
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

10 years agoJAL-1355 JAL-1466 i18n for flanking sequence menu entry and tooltip messages
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

10 years agoMerge branch 'jims_marckhacks' into Release_2_8_1_Branch
Jim Procter [Mon, 21 Apr 2014 13:24:56 +0000 (14:24 +0100)]
Merge branch 'jims_marckhacks' into Release_2_8_1_Branch

10 years agoJAL-741 (poss related JAL-971) - fix NPE raised when attempting to sort alignment...
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

10 years agoJAL-1476 JAL-1016 avoid NPE messiness if structures fail to align for some reason
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

10 years agodon't unhook existing group associated annotation JAL-1480
Jim Procter [Sat, 19 Apr 2014 12:46:03 +0000 (13:46 +0100)]
don't unhook existing group associated annotation JAL-1480

10 years agofix for JAL-1478
Jim Procter [Fri, 18 Apr 2014 15:22:38 +0000 (16:22 +0100)]
fix for JAL-1478

10 years agoJAL-1478 test to demonstrate bug
Jim Procter [Fri, 18 Apr 2014 15:18:36 +0000 (16:18 +0100)]
JAL-1478 test to demonstrate bug

10 years agoJAL-1477 tooltip
Jim Procter [Fri, 18 Apr 2014 14:17:42 +0000 (15:17 +0100)]
JAL-1477 tooltip

10 years agoJAL-1476 - don't send broken commands to Jmol when no columns exist to superimpose...
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

10 years agoJAL-1477 first implementation of 'View all representative structures' option.
Jim Procter [Fri, 18 Apr 2014 09:50:15 +0000 (10:50 +0100)]
JAL-1477 first implementation of 'View all representative structures' option.

10 years agoJAL-1466 import full length sequence to dataset sequence or trim it to local sequence...
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

10 years agoJAL-1466 flag and jalview_properties setting to control retrieval of full 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

10 years agoJAL-1466 improved test and patched off by one that deleted one dataset residue from...
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

10 years agoJAL-1466 new calculation menu option to recover the full width sequences either side...
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.

10 years agotidy imports
Jim Procter [Tue, 15 Apr 2014 17:47:56 +0000 (18:47 +0100)]
tidy imports

10 years agopatch v2 for JAL-1474 add the newly recovered dataset sequence to the dataset current...
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

10 years agopatch v1 for JAL-1474 - make sure we actually set the dataset sequence's string
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

10 years agoJAL-1474 note about buggy 'merge sequence' operation pointing to relevant issue
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

10 years agoJAL-1473 tree calcs performed with ScoreModelI instances
Jim Procter [Tue, 15 Apr 2014 17:11:07 +0000 (18:11 +0100)]
JAL-1473 tree calcs performed with ScoreModelI instances

10 years agodon't finness the alignment annotation modification methods by modifying the vector...
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!

10 years agopatch for JAL-1465 - set min/max thresholds for each disorder annotation row
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

10 years agoJAL-1473 menu entries for different score models available for NJ/UPGMA tree building...
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!)

10 years agoJAL-1473 provide Amino acid physicochemical conservation based score matrices
Jim Procter [Tue, 15 Apr 2014 15:16:26 +0000 (16:16 +0100)]
JAL-1473 provide Amino acid physicochemical conservation based score matrices

10 years agoJAL-1473 show available score matrices for use in PCA calculation
Jim Procter [Tue, 15 Apr 2014 15:15:36 +0000 (16:15 +0100)]
JAL-1473 show available score matrices for use in PCA calculation

10 years agoJAL-1473 refactor score matrices and tree score calculations to interface/api and...
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

10 years agoJAL-1355 missing message
Jim Procter [Tue, 15 Apr 2014 14:40:35 +0000 (15:40 +0100)]
JAL-1355 missing message

10 years agofix for JAL-1464 avoid NPE with per-sequence annotation with no positional elements...
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)

10 years agoMerge branch 'r281_JAL-1211' into Release_2_8_1_Branch
Jim Procter [Sat, 5 Apr 2014 12:23:27 +0000 (13:23 +0100)]
Merge branch 'r281_JAL-1211' into Release_2_8_1_Branch