jprocter [Fri, 21 Jan 2011 17:03:40 +0000 (17:03 +0000)]
ensure source is rarely null
jprocter [Fri, 21 Jan 2011 17:03:10 +0000 (17:03 +0000)]
extended mouseover message with absolute sequence position info JAL-433
jprocter [Tue, 18 Jan 2011 17:46:08 +0000 (17:46 +0000)]
patch for JAL-695 - need to test if this is observed in applet
jprocter [Tue, 18 Jan 2011 17:43:16 +0000 (17:43 +0000)]
patch for JAL-695
jprocter [Tue, 18 Jan 2011 17:41:48 +0000 (17:41 +0000)]
javadoc
jprocter [Tue, 18 Jan 2011 17:40:53 +0000 (17:40 +0000)]
javadoc
jprocter [Tue, 18 Jan 2011 17:40:16 +0000 (17:40 +0000)]
avoid creating lots of identical search results. patch for JAL-751
jprocter [Tue, 18 Jan 2011 10:42:20 +0000 (10:42 +0000)]
removed securityException caused by accessing class directly from sun. package
jprocter [Tue, 18 Jan 2011 10:33:11 +0000 (10:33 +0000)]
refactored VamsasListener to allow the source of the event to be passed to handlers
jprocter [Mon, 17 Jan 2011 15:54:27 +0000 (15:54 +0000)]
additional test - koders.com/java/fid4C9593FE80CE8AA81158AF712B50C7A689488FD8.aspx c.f. JAL-749
jprocter [Mon, 17 Jan 2011 15:36:06 +0000 (15:36 +0000)]
warn user that no JS callbacks will work by default, and show stacktrace if debug is enabled JAL-749
jprocter [Mon, 17 Jan 2011 15:11:46 +0000 (15:11 +0000)]
need to own lock to notify
jprocter [Mon, 17 Jan 2011 14:48:52 +0000 (14:48 +0000)]
need to own lock to notify
jprocter [Mon, 17 Jan 2011 14:32:45 +0000 (14:32 +0000)]
avoid 1.5 specific methods
jprocter [Mon, 17 Jan 2011 14:28:35 +0000 (14:28 +0000)]
revised default separator string expression to avoid utf8 warnings. Regularised new api methods (select, selectIn(alignFrame..), ). improved separatorList routines and added onInit javascript callback.
jprocter [Mon, 17 Jan 2011 14:27:06 +0000 (14:27 +0000)]
allow debug messages to be output before jscallback execution
jprocter [Mon, 17 Jan 2011 13:59:00 +0000 (13:59 +0000)]
refactored javascript callback to parent class.
jprocter [Mon, 17 Jan 2011 13:57:51 +0000 (13:57 +0000)]
eliminate utf8 compilation errors
jprocter [Mon, 17 Jan 2011 13:56:09 +0000 (13:56 +0000)]
use local reference for current target frame as set by JAL-451
jprocter [Mon, 17 Jan 2011 13:51:25 +0000 (13:51 +0000)]
JAL-750 and JAL-451
jprocter [Thu, 13 Jan 2011 11:03:47 +0000 (11:03 +0000)]
output jsexception message
jprocter [Wed, 12 Jan 2011 23:01:10 +0000 (23:01 +0000)]
handlers with no specified alignframe broadcast events from all applet's alignFrames
jprocter [Wed, 12 Jan 2011 22:14:57 +0000 (22:14 +0000)]
application compilation time dependency plugin.jar needed for jalview.javascript interfaces
jprocter [Wed, 12 Jan 2011 22:01:29 +0000 (22:01 +0000)]
updated jar dependencies
jprocter [Wed, 12 Jan 2011 18:41:02 +0000 (18:41 +0000)]
1.1 compat
jprocter [Wed, 12 Jan 2011 17:05:05 +0000 (17:05 +0000)]
javascript callback for selection, mousover, and functions for selection and highlighting JAL-469 JAL-433 JAL-744
jprocter [Wed, 12 Jan 2011 17:02:47 +0000 (17:02 +0000)]
selection should be sent after refresh happens
jprocter [Wed, 12 Jan 2011 16:59:19 +0000 (16:59 +0000)]
javadoc
jprocter [Wed, 12 Jan 2011 16:59:00 +0000 (16:59 +0000)]
java side javascript callback enactors JAL-469
jprocter [Wed, 12 Jan 2011 16:57:50 +0000 (16:57 +0000)]
updated dependencies for project
jprocter [Wed, 12 Jan 2011 16:57:24 +0000 (16:57 +0000)]
jalviewLite now needs plugin.jar from jre so it can access JSObject class for javascript/java callbacks JAL-469
jprocter [Mon, 10 Jan 2011 17:00:30 +0000 (17:00 +0000)]
patch for JAL-740
jprocter [Fri, 7 Jan 2011 13:17:22 +0000 (13:17 +0000)]
refactored dropFile allowing known information to be passed in if available
jprocter [Fri, 7 Jan 2011 13:16:49 +0000 (13:16 +0000)]
bulk associate pdb files dropped on to alignment : JAL-732
jprocter [Fri, 7 Jan 2011 13:16:24 +0000 (13:16 +0000)]
refactored guts of pdb file association code
jprocter [Fri, 7 Jan 2011 13:11:36 +0000 (13:11 +0000)]
check for all http protocols
jprocter [Fri, 7 Jan 2011 13:10:41 +0000 (13:10 +0000)]
refactored to use SequenceI
jprocter [Thu, 6 Jan 2011 15:53:25 +0000 (15:53 +0000)]
JAL-730
jprocter [Wed, 5 Jan 2011 16:06:36 +0000 (16:06 +0000)]
more robust calculation of partition from possibly overlapping groups, and check to ensure minimum group size is honoured
jprocter [Wed, 5 Jan 2011 16:06:03 +0000 (16:06 +0000)]
inline submission of alignment with correct crlf
jprocter [Wed, 5 Jan 2011 16:05:47 +0000 (16:05 +0000)]
ensure group props are recalculated before alignment displayed
jprocter [Wed, 5 Jan 2011 16:05:15 +0000 (16:05 +0000)]
revised shmr service
jprocter [Wed, 5 Jan 2011 16:04:56 +0000 (16:04 +0000)]
todo and ensure old annotation/groups are removed before new ones loaded back
jprocter [Wed, 5 Jan 2011 16:04:17 +0000 (16:04 +0000)]
todo
jprocter [Wed, 5 Jan 2011 16:03:33 +0000 (16:03 +0000)]
exception reporting for bad URLs
jprocter [Wed, 5 Jan 2011 15:52:16 +0000 (15:52 +0000)]
JAL-727
jprocter [Wed, 5 Jan 2011 15:37:11 +0000 (15:37 +0000)]
JAL-727
jprocter [Wed, 5 Jan 2011 15:36:30 +0000 (15:36 +0000)]
propagated groups trimmed to correct region on viscontig
jprocter [Wed, 5 Jan 2011 15:36:05 +0000 (15:36 +0000)]
graphThreshold not being copied by constructor
jprocter [Fri, 17 Dec 2010 16:54:42 +0000 (16:54 +0000)]
first publicly accessible test of JAL-724
jprocter [Fri, 17 Dec 2010 16:53:32 +0000 (16:53 +0000)]
JAL-715 and JAL-724
jprocter [Fri, 17 Dec 2010 16:53:13 +0000 (16:53 +0000)]
JAL-715
jprocter [Fri, 17 Dec 2010 16:48:26 +0000 (16:48 +0000)]
refined modification test
jprocter [Fri, 17 Dec 2010 16:47:51 +0000 (16:47 +0000)]
refactored gap insert/visible view modification code from JPredThread
jprocter [Fri, 17 Dec 2010 16:47:26 +0000 (16:47 +0000)]
adjust start and end of intersecting group relative to selected region
jprocter [Fri, 17 Dec 2010 14:24:26 +0000 (14:24 +0000)]
1.1 compat
jprocter [Fri, 17 Dec 2010 13:56:04 +0000 (13:56 +0000)]
1.1 compat
jprocter [Fri, 17 Dec 2010 13:17:29 +0000 (13:17 +0000)]
refactored gap insert/visible view modification code from JPredThread
jprocter [Fri, 17 Dec 2010 13:17:03 +0000 (13:17 +0000)]
javadoc
jprocter [Wed, 15 Dec 2010 14:54:18 +0000 (14:54 +0000)]
incremental refinement of results parsing
jprocter [Wed, 15 Dec 2010 14:53:25 +0000 (14:53 +0000)]
allow client to check if the original alignment data was annotated by results from service
jprocter [Wed, 15 Dec 2010 14:51:23 +0000 (14:51 +0000)]
javadoc
jprocter [Wed, 15 Dec 2010 14:51:08 +0000 (14:51 +0000)]
update modification state flag according to parsing activity
jprocter [Wed, 15 Dec 2010 14:50:40 +0000 (14:50 +0000)]
getters and modification state flag
jprocter [Wed, 15 Dec 2010 14:49:47 +0000 (14:49 +0000)]
more accurate determination of annotation modification
jprocter [Wed, 15 Dec 2010 09:51:00 +0000 (09:51 +0000)]
refactored key calc for hash to separate function
jprocter [Tue, 14 Dec 2010 18:10:14 +0000 (18:10 +0000)]
1.1 compat
jprocter [Tue, 14 Dec 2010 18:08:06 +0000 (18:08 +0000)]
1.1 compat
jprocter [Tue, 14 Dec 2010 18:02:26 +0000 (18:02 +0000)]
more fixes and extension to allow return data types to be specified JAL-715
jprocter [Tue, 14 Dec 2010 18:01:39 +0000 (18:01 +0000)]
render of html job logs and link opening JAL-720
jprocter [Tue, 14 Dec 2010 18:01:00 +0000 (18:01 +0000)]
more efficient set/append
jprocter [Tue, 14 Dec 2010 17:59:54 +0000 (17:59 +0000)]
method to recover sources from packed stream
jprocter [Tue, 14 Dec 2010 17:57:48 +0000 (17:57 +0000)]
always provide reference to hashtable so feature settings can be stored
jprocter [Tue, 14 Dec 2010 17:56:25 +0000 (17:56 +0000)]
JAL-725 - show progress when opening URL in browser
jprocter [Tue, 14 Dec 2010 16:43:57 +0000 (16:43 +0000)]
JAL-724
jprocter [Tue, 14 Dec 2010 10:40:00 +0000 (10:40 +0000)]
refactored and patched for JAL-721
new view creation functions for JAL-715
jprocter [Tue, 14 Dec 2010 10:39:18 +0000 (10:39 +0000)]
refactored and patched for JAL-721
jprocter [Fri, 10 Dec 2010 11:51:16 +0000 (11:51 +0000)]
mime types and handler
jprocter [Fri, 10 Dec 2010 11:44:31 +0000 (11:44 +0000)]
additional dependencies for httpcleint
jprocter [Fri, 10 Dec 2010 11:34:43 +0000 (11:34 +0000)]
javadoc
jprocter [Fri, 10 Dec 2010 11:32:51 +0000 (11:32 +0000)]
remove implicit non-1.1 compatible call
jprocter [Thu, 9 Dec 2010 17:34:45 +0000 (17:34 +0000)]
fix case when groups overlap - ensure groups are non-empty and always add up to length of alignment
jprocter [Thu, 9 Dec 2010 17:34:15 +0000 (17:34 +0000)]
java 1.1 patches
jprocter [Thu, 9 Dec 2010 16:35:01 +0000 (16:35 +0000)]
java 1.1 patches
jprocter [Thu, 9 Dec 2010 16:29:03 +0000 (16:29 +0000)]
dependency for Rest client framework (JAL-715)
jprocter [Thu, 9 Dec 2010 16:27:59 +0000 (16:27 +0000)]
initial implementation of Rest client framework (JAL-715)
jprocter [Thu, 9 Dec 2010 16:02:26 +0000 (16:02 +0000)]
dataIn.ready() is not a test of data source validity!
jprocter [Thu, 9 Dec 2010 16:00:41 +0000 (16:00 +0000)]
initial list of mime-type bindings to jalview data-file classes for JAL-719
jprocter [Thu, 9 Dec 2010 15:59:29 +0000 (15:59 +0000)]
initial implementation for JAL-718
jprocter [Thu, 9 Dec 2010 15:33:08 +0000 (15:33 +0000)]
refactored and added methods for getting richer AlignmentView object (JAL-716)
jprocter [Thu, 9 Dec 2010 15:32:14 +0000 (15:32 +0000)]
new methods and test code for JAL-716
jprocter [Thu, 9 Dec 2010 15:31:33 +0000 (15:31 +0000)]
new constructor and refactored methods for intersecting selection with alignment when constructing CigarArray (JAL-716)
jprocter [Thu, 9 Dec 2010 15:29:48 +0000 (15:29 +0000)]
new methods for testing for/storing selection/group membership re JAL-716
jprocter [Thu, 9 Dec 2010 15:28:45 +0000 (15:28 +0000)]
javadoc and additional convenience method for JAL-716
jprocter [Thu, 2 Dec 2010 16:15:57 +0000 (16:15 +0000)]
refactored visible contig/gap map array intersection code to alignmentView
jprocter [Mon, 15 Nov 2010 11:00:40 +0000 (11:00 +0000)]
2.6.1 update
jprocter [Sun, 14 Nov 2010 22:38:38 +0000 (22:38 +0000)]
refactored to decouple dependencies due to FileParse's derived classes
jprocter [Sun, 14 Nov 2010 14:58:59 +0000 (14:58 +0000)]
refactored protocol check to jalview.io.FileParse
jprocter [Sun, 14 Nov 2010 14:58:04 +0000 (14:58 +0000)]
import annotation file from datasource
jprocter [Sun, 14 Nov 2010 14:56:35 +0000 (14:56 +0000)]
refactored protocol parser and allow human readable datasource name to be modified