jprocter [Wed, 14 Sep 2011 10:47:02 +0000 (11:47 +0100)]
fix for JAL-930
jprocter [Wed, 14 Sep 2011 10:41:31 +0000 (11:41 +0100)]
JAL-766 JAL-733 - new alignment->jmol associations are automatically used to colour structure
jprocter [Mon, 12 Sep 2011 15:55:50 +0000 (16:55 +0100)]
JAL-927 ensure api method calls that affect GUI state or spawn javascript callbacks are executed on the AWT worker thread
jprocter [Mon, 5 Sep 2011 13:47:44 +0000 (14:47 +0100)]
note about ensuring callers of loadAlignment(..) save the new alignment
windows reference so they can use it in other calls to the API.
jprocter [Mon, 5 Sep 2011 09:46:46 +0000 (10:46 +0100)]
removed old VARNA library
jprocter [Tue, 30 Aug 2011 15:22:54 +0000 (16:22 +0100)]
patch for JAL-731
jprocter [Tue, 30 Aug 2011 15:12:04 +0000 (16:12 +0100)]
patch for JAL-729 - NPE avoided and cut and paste import pane is opened
jprocter [Tue, 30 Aug 2011 14:41:19 +0000 (15:41 +0100)]
JAL-915 - ensured that exceptions are not raised in applet or application, and that sequence ID popup menu includes the 'reveal all' item to show all sequences again.
jprocter [Tue, 30 Aug 2011 13:27:27 +0000 (14:27 +0100)]
fix for JAL-917 - ensure all sequence strings are made uppercase before alignment
jprocter [Tue, 30 Aug 2011 13:18:16 +0000 (14:18 +0100)]
fix for JAL-917 - ensure all sequence strings are made uppercase before alignment
jprocter [Tue, 30 Aug 2011 13:03:11 +0000 (14:03 +0100)]
JAL-715 - conditional to hide the RSBS service editing pane until system fully implemented
jprocter [Tue, 30 Aug 2011 13:02:46 +0000 (14:02 +0100)]
JAL-715 rsbs service editing
jprocter [Tue, 30 Aug 2011 13:01:45 +0000 (14:01 +0100)]
JAL-715 JalviewDialog for RSBS service editing pane
jprocter [Tue, 30 Aug 2011 12:58:50 +0000 (13:58 +0100)]
JAL-715 store/reset .jalview_properties setting for RSBS service list
jprocter [Tue, 30 Aug 2011 10:28:27 +0000 (11:28 +0100)]
JAL-715 serialise and deserialise multiple rest client strings as a jalview property
jprocter [Tue, 30 Aug 2011 10:27:00 +0000 (11:27 +0100)]
JAL-715 - notify user of parsing problems for results from a service's URL
jprocter [Tue, 30 Aug 2011 10:23:58 +0000 (11:23 +0100)]
retrieve URL for datasource of packed set
jprocter [Tue, 30 Aug 2011 10:22:31 +0000 (11:22 +0100)]
ensure parsing errors and 'lack of data' errors are passed back as exceptions
jprocter [Tue, 30 Aug 2011 10:21:28 +0000 (11:21 +0100)]
JAL-715 need to URLencode constant values when serializing them to ensure URL string is valid
jprocter [Mon, 29 Aug 2011 15:54:25 +0000 (16:54 +0100)]
JAL-715 - grammar for warning message.
jprocter [Mon, 29 Aug 2011 15:29:28 +0000 (16:29 +0100)]
added notes on third party library licencing and updated netbeans builder library deps
jprocter [Mon, 29 Aug 2011 14:44:06 +0000 (15:44 +0100)]
JAL-919, JAL-715 - prototype service editing dialog using jalview parameter model to configure service definition and associated bug fixes to jalview.ws.rest package
jprocter [Mon, 29 Aug 2011 14:41:22 +0000 (15:41 +0100)]
JAL-633, JAL-591 - refactored ArgumentI.getValue from jabaws .getDefaultValue
Introduced 'compact' parameter display mode and more refactoring
jprocter [Mon, 29 Aug 2011 14:35:56 +0000 (15:35 +0100)]
refactored popup dialog boilerplate code to own class
jprocter [Mon, 29 Aug 2011 12:49:17 +0000 (13:49 +0100)]
JAL-633 simple concrete parameter and option objects for use within Jalview
jprocter [Mon, 29 Aug 2011 12:48:41 +0000 (13:48 +0100)]
JAL-633, JAL-591 - refactored ArgumentI.getValue from jabaws .getDefaultValue
janengelhardt [Sun, 28 Aug 2011 04:32:18 +0000 (06:32 +0200)]
Including of VARNAv-3.9;
Change-Id: Ib55f047ae763999c7db2b601105b6655132ee171
jprocter [Thu, 25 Aug 2011 13:02:33 +0000 (14:02 +0100)]
constructor only needs GUI container interface
jprocter [Thu, 25 Aug 2011 12:58:16 +0000 (13:58 +0100)]
JAL-591 - refactored web service parameter dialog to allow options and parameters to be used in other dialog boxes
jprocter [Thu, 25 Aug 2011 09:52:05 +0000 (10:52 +0100)]
JAL-715 - better validation logic
jprocter [Thu, 25 Aug 2011 09:51:24 +0000 (10:51 +0100)]
debug dialog
jprocter [Thu, 25 Aug 2011 09:24:27 +0000 (10:24 +0100)]
JAL-715 - prevent empty elements being generated
jprocter [Wed, 24 Aug 2011 14:43:08 +0000 (15:43 +0100)]
JAL-715 dialog for interactively editing a new or existing rest service
jprocter [Wed, 24 Aug 2011 14:42:01 +0000 (15:42 +0100)]
new Swing and SWT capable form layout manager - miglayout
jprocter [Wed, 24 Aug 2011 14:38:33 +0000 (15:38 +0100)]
JAL-715 bugfixes and refactor of parsing code for use in service designer GUI
jprocter [Wed, 24 Aug 2011 14:37:04 +0000 (15:37 +0100)]
refactor labelled button creator to JvSwingUtils
jprocter [Tue, 23 Aug 2011 12:30:22 +0000 (13:30 +0100)]
JAL-715 - simple tests and functions for IO of service as '|' string
jprocter [Tue, 23 Aug 2011 12:28:20 +0000 (13:28 +0100)]
JAL-715 - allow rest service attributes to be exported and imported as a | separated string
janengelhardt [Sun, 21 Aug 2011 23:25:34 +0000 (01:25 +0200)]
JAL-913; Extending documentation; VARNA help;
Change-Id: If1deae2cf040ac9a28ab770019a0e3040f74daeb
janengelhardt [Fri, 19 Aug 2011 11:43:28 +0000 (13:43 +0200)]
JAL-913; Documentation of RNA Structure Conservation
Change-Id: I695f08d01e4feba87b5c5f15981896f7ee484dd4
jprocter [Fri, 19 Aug 2011 10:06:22 +0000 (11:06 +0100)]
JAL-908 JAL-912 JAL-516 documented annotation HTML description line and general tidyup of group associated annotation documentation for 2.7 update.
jprocter [Fri, 19 Aug 2011 10:05:09 +0000 (11:05 +0100)]
JAL-908,JAL-701 - patch applet to strip HTML tags from HTML annotation description
jprocter [Fri, 19 Aug 2011 10:03:02 +0000 (11:03 +0100)]
JAL-908 JAL-701 refactored HTML escape/unescape code for sequence feature descriptions
jprocter [Thu, 18 Aug 2011 13:02:28 +0000 (14:02 +0100)]
testdata for JAL-701 and JAL-908
jprocter [Thu, 18 Aug 2011 11:20:41 +0000 (12:20 +0100)]
remove debug message
jprocter [Thu, 18 Aug 2011 11:02:45 +0000 (12:02 +0100)]
fix for JAL-701 - ensure '<' appears in tooltip in application and allow html tags (JAL-908)
jprocter [Thu, 18 Aug 2011 11:02:09 +0000 (12:02 +0100)]
minor efficiency refactor
jprocter [Thu, 18 Aug 2011 10:52:10 +0000 (11:52 +0100)]
JAL-907 testdata for JAL-701
jprocter [Thu, 18 Aug 2011 10:45:56 +0000 (11:45 +0100)]
JAL-907 - test data directory readme
jprocter [Wed, 17 Aug 2011 15:10:26 +0000 (16:10 +0100)]
JAL-853 use service action attribute to index services in webservices menu and hardwire jaba services to populate Alignment service menu
jprocter [Wed, 17 Aug 2011 13:44:30 +0000 (14:44 +0100)]
remove any trailing '/' from the URL before validation and acceptance
jprocter [Wed, 17 Aug 2011 13:43:49 +0000 (14:43 +0100)]
avoid NPE race condition when several threads waiting on a sequence fetcher discovery thread
jprocter [Wed, 17 Aug 2011 12:04:37 +0000 (13:04 +0100)]
fix for JAL-888
jprocter [Wed, 17 Aug 2011 11:15:36 +0000 (12:15 +0100)]
fix for JAL-888
jprocter [Wed, 17 Aug 2011 10:57:54 +0000 (11:57 +0100)]
JAL-898 - ensure we only remove a clargs progress bar if we added it
jprocter [Wed, 17 Aug 2011 10:35:00 +0000 (11:35 +0100)]
JAL-813 fix - check whether conservation is applied to colourscheme before we set conservation object (and so enable conservation)
jprocter [Wed, 17 Aug 2011 09:20:15 +0000 (10:20 +0100)]
JAL-867 - rejigged layout to a single splitpane wide enough for longest combobox (paramset name or option) and removed dead code
janengelhardt [Tue, 16 Aug 2011 11:45:46 +0000 (13:45 +0200)]
JAL-842; Text element containing the structure is not visible anymore
in VARNA;
Change-Id: I589055fe74542eae28bc7a5ff47180eaee83c5a3
janengelhardt [Mon, 15 Aug 2011 23:15:03 +0000 (01:15 +0200)]
JAL-891; Tooltips for Structure logos implemented;
Change-Id: I8601aa5b9b9c50e9c1a7b8f6f39dd6f6e358cf6a
janengelhardt [Mon, 15 Aug 2011 23:13:38 +0000 (01:13 +0200)]
JAL-878; Structures associated to a sequence are available via
Popupmenu;
Change-Id: I20050a77bf494782893d6383f3d2e901cae7d3f1
jprocter [Mon, 15 Aug 2011 14:22:46 +0000 (15:22 +0100)]
JAL-750 automaticScrolling is true by default
jprocter [Mon, 15 Aug 2011 14:21:56 +0000 (15:21 +0100)]
JAL-750 - automaticScrolling=true by default. Refactored to use getDefaultParameter for parsing boolean applet parameters
jprocter [Mon, 15 Aug 2011 13:55:34 +0000 (14:55 +0100)]
JAL-747 - warning dialog if Jalview can't resolve filename for a structure in a Jmol view.
jprocter [Mon, 15 Aug 2011 13:28:38 +0000 (14:28 +0100)]
JAL-904 added scrollToRow and scrollToColumn methods to javascript API and reintroduced getSequenceSetId to retrieve the unique ID for an alignment.
janengelhardt [Mon, 15 Aug 2011 09:15:30 +0000 (11:15 +0200)]
JAL-891; Labeling of structure conservation is improved a bit.
Brackets instead of 'H'.
Change-Id: I220e86f21e2ff539ab5828bba4c0d07d76777422
janengelhardt [Mon, 15 Aug 2011 09:02:14 +0000 (11:02 +0200)]
JAL-891; Sorting of Structure logo implemented; bug that caused
exception after editing a structure solved (sequences have different
lengths after editing);
Change-Id: If2cb0ea0c683dc99a5df7002a4f9907283ce27cb
jprocter [Thu, 11 Aug 2011 08:13:33 +0000 (09:13 +0100)]
avoid NPE for null annotation element columns JAL-896
janengelhardt [Thu, 11 Aug 2011 00:07:08 +0000 (02:07 +0200)]
JAL-885; hasRNAStructure method was introduced to AlignmentI and
Alignment; determines if Alignment contains an RNA structure;
Structure conservation row is just added if yes;
Change-Id: I6fa20f14e54cd656c65f82bc6b68f84d1d6f2c64
janengelhardt [Wed, 10 Aug 2011 23:42:18 +0000 (01:42 +0200)]
JAL-885; Structure conservation row is just added if alignment
isNucleotide(); StructureFrequency.java cleaned;
Change-Id: Ic86908cbea0791e7174b440cc4c7e7b12b978927
janengelhardt [Tue, 9 Aug 2011 23:01:22 +0000 (01:01 +0200)]
JAL-891; base-pair logos can now be activated for structure
conservation row;
Change-Id: Ib3450f328f901eaf12ea094c9c914322f8398a88
janengelhardt [Mon, 8 Aug 2011 21:32:30 +0000 (23:32 +0200)]
JAL-891; structure logo is adapted to two char's; Missing: calculate
bp frequencies and include them in the draw-part;
Change-Id: Ie43edd7a074f6b219c808fa2519d2b88659f30e5
janengelhardt [Mon, 8 Aug 2011 10:04:57 +0000 (12:04 +0200)]
JAL-891; sequence logos are available on structure conservation row
now; has to be adopted to base pair interaction;
Change-Id: I86cf329d794d6ff78cb4bb4c5248cadcc34b2681
jprocter [Fri, 5 Aug 2011 15:52:30 +0000 (16:52 +0100)]
example script that will submit a muscle jabaws job using the currently loaded alignment (JAL-894)
jprocter [Fri, 5 Aug 2011 15:49:55 +0000 (16:49 +0100)]
fetch groovy script from URL (JAL-899) and show progress bar when handling CLI commands (JAL-898)
jprocter [Fri, 5 Aug 2011 15:47:56 +0000 (16:47 +0100)]
allow several progress bars on the desktop window (JAL-898)
jprocter [Thu, 4 Aug 2011 18:01:18 +0000 (19:01 +0100)]
JAL-896 - patch to ensure arrows in different directions are visually
distinct. Raises new bug - JAL-897 - test with RF00011 to demonstrate
problem.
jprocter [Thu, 4 Aug 2011 16:16:33 +0000 (17:16 +0100)]
JAL-883 - refactored and debugged arrow, stem and helix rendering code
jprocter [Wed, 3 Aug 2011 13:44:43 +0000 (14:44 +0100)]
Merge branch 'master' of https://source.jalview.org/git/jalview
jprocter [Wed, 3 Aug 2011 13:37:41 +0000 (14:37 +0100)]
refactored resolvetocodebase code and reused for resource location as well as showURL completion (JAL-786, JAL-787 and JAL-359)
jprocter [Wed, 3 Aug 2011 13:37:41 +0000 (14:37 +0100)]
refactored resolvetocodebase code and reused for resource location as well as showURL completion (JAL-786 and JAL-359)
jprocter [Wed, 3 Aug 2011 13:00:12 +0000 (14:00 +0100)]
fix NPE when applets stop. seems to make the simple applet alignment+structure example work again (JAL-592 ?)
janengelhardt [Wed, 3 Aug 2011 12:30:54 +0000 (14:30 +0200)]
JAL-885; Multi-helix bug is solved; One should think about a more
efficient solution; either by creating a Hashtable of pairs in
StructureFrequency or directly in a RNA class;
Change-Id: I7bd21eb4d952f22579c786f3d78395949fa046d0
jprocter [Wed, 3 Aug 2011 11:33:21 +0000 (12:33 +0100)]
refactor schema to group swing window geometry attributes
janengelhardt [Sun, 31 Jul 2011 22:42:25 +0000 (00:42 +0200)]
JAL-885; StructureConservation row is displayed at the bottom of the
AlignmentPanel; StructureFrequency class was introduced and is called
by thread in AlignViewport that is called by AlignFrame; everything is
according to Conservation-Row
Change-Id: I3753bbb5678147cbc0c9d1d6bc1a4886b0551a59
janengelhardt [Fri, 29 Jul 2011 12:38:27 +0000 (14:38 +0200)]
JAL-885; Implementation of StructureFrequency.java and according
methods in AlignViewport.java; completeConsensus is still missing;
Change-Id: I3678fc75af84aa5a8974faed6b76f47c76a74638
jprocter [Thu, 28 Jul 2011 10:30:55 +0000 (11:30 +0100)]
refer to local default setting for proxy when connecting to
www.jalview.org (JAL-864)
jprocter [Thu, 28 Jul 2011 10:03:33 +0000 (11:03 +0100)]
added 'since 2.x notes to parameters'. User configurable help URL for
JalviewLite (JAL-864). resolvetocodebase parameter introduced to
allow pre-2.7 style codebase+relative URL resolution (JAL-359, JAL-786)
jprocter [Tue, 26 Jul 2011 11:52:08 +0000 (12:52 +0100)]
example alignment for JAL-862 - removed signal peptides
jprocter [Mon, 25 Jul 2011 16:05:57 +0000 (17:05 +0100)]
use proper encoding for storing colour as user preference (JAL-234)
janengelhardt [Mon, 25 Jul 2011 12:46:35 +0000 (14:46 +0200)]
some print statements to test things
Change-Id: I0730499d395e8f84b9cfd9ec2aaaa7283fc4b1fa
janengelhardt [Mon, 25 Jul 2011 10:58:33 +0000 (12:58 +0200)]
JAL-882; VARNA crashed when non-standard gaps where in structure; the
are now replaced with standard gaps before commiting to VARNA in
AppVarna.java
Change-Id: I36b523fb7f1063dc2fa5924cb4569f15e0067df2
janengelhardt [Fri, 22 Jul 2011 11:11:03 +0000 (13:11 +0200)]
JAL-878; Additional structures with a 'GR' tag in StockholmFiles are
associated their specific sequence.
Change-Id: I26913db05bef3983b63397304c97351f5361d61d
janengelhardt [Wed, 20 Jul 2011 14:09:34 +0000 (16:09 +0200)]
JAL-842; toy example to insert nucleotides in sequences in the
AlignmentPanel;
Change-Id: I9901d08b1f06861c4d9b7795a4a935ac040d7b2b
janengelhardt [Wed, 20 Jul 2011 12:30:09 +0000 (14:30 +0200)]
JAL-842; Implement transmitting of Jalview Sequence highlights to
Varna
Change-Id: I8e1fbc375cdcec6cf36a46cdac56800740c42180
janengelhardt [Mon, 18 Jul 2011 00:54:33 +0000 (02:54 +0200)]
JAL-842: some bugfixes;
Change-Id: Ia349eeb750da7b51673a76be805737e4356524e7
janengelhardt [Tue, 12 Jul 2011 08:28:19 +0000 (10:28 +0200)]
JAL-842; Added the TextField to edit structure in VARNA
Change-Id: I93a90da2468c4c6b69570aac9741b286300b6430
janengelhardt [Mon, 11 Jul 2011 01:20:30 +0000 (03:20 +0200)]
JAL-842; trimming single structures for single sequences added;
Change-Id: I041c71aafd0081875b948b9978c2411154033408
janengelhardt [Fri, 1 Jul 2011 14:57:01 +0000 (16:57 +0200)]
JAL-842; Give Varna frames name for window organizer; always display
the consensus structure and the 'trimmed' structure for a sequence;
Change-Id: If4e9b054455de3c0f43967e27fb399df4c23b751
janengelhardt [Thu, 30 Jun 2011 14:54:40 +0000 (16:54 +0200)]
Varna external frame bug solved
Change-Id: Ie60149059d664fb63d6bd99d748c1f34c1b01703
janengelhardt [Thu, 30 Jun 2011 10:07:42 +0000 (12:07 +0200)]
Reorganize the class structure, unfortunately breaks the VARNA-Frame
Change-Id: Ia3dde7af1beb73e9261e49e81afe3e8594c945bb