jprocter [Wed, 20 Aug 2008 15:53:34 +0000 (15:53 +0000)]
tooltip displays formatted annotation row description including sequence reference name (if any)
jprocter [Tue, 19 Aug 2008 13:36:34 +0000 (13:36 +0000)]
beginning of fix for embl/cds/highlighting IO in https://mantis.lifesci.dundee.ac.uk/view.php?id=36199
jprocter [Tue, 19 Aug 2008 13:34:10 +0000 (13:34 +0000)]
fix for arrayoutofbounds bug when secondary structure element extends whole width of alignment (eg. PF00037 stockholm file)
jprocter [Tue, 19 Aug 2008 09:38:38 +0000 (09:38 +0000)]
better check for molecule type when identifying internal sequence cross-references
jprocter [Tue, 19 Aug 2008 09:37:52 +0000 (09:37 +0000)]
regex links for launching URL from single click on sequence ID
jprocter [Fri, 15 Aug 2008 11:37:29 +0000 (11:37 +0000)]
update text and version checker
jprocter [Fri, 15 Aug 2008 10:34:52 +0000 (10:34 +0000)]
dialog size on macs
jprocter [Fri, 15 Aug 2008 10:02:43 +0000 (10:02 +0000)]
check for crossreferences every time the menus are updated
jprocter [Fri, 15 Aug 2008 10:02:16 +0000 (10:02 +0000)]
catch invalid URL link exception properly
jprocter [Fri, 15 Aug 2008 10:02:01 +0000 (10:02 +0000)]
increase height of dialog
jprocter [Fri, 15 Aug 2008 10:01:47 +0000 (10:01 +0000)]
allow '|' in regex for URL links to be recovered from properties file properly
jprocter [Fri, 15 Aug 2008 10:01:05 +0000 (10:01 +0000)]
safer copy constructor
jprocter [Fri, 15 Aug 2008 10:00:51 +0000 (10:00 +0000)]
xrefs retrieved from Uniprot
jprocter [Fri, 15 Aug 2008 09:59:33 +0000 (09:59 +0000)]
added castor back onto classpath
jprocter [Wed, 13 Aug 2008 13:47:10 +0000 (13:47 +0000)]
check for null viewport on dataset recovery
jprocter [Wed, 13 Aug 2008 13:31:06 +0000 (13:31 +0000)]
ensure input data can be recovered for tree and PCA even if alignment view was closed
jprocter [Wed, 13 Aug 2008 10:42:21 +0000 (10:42 +0000)]
do not try to cancel jobs that cannot be cancelled
jprocter [Tue, 12 Aug 2008 21:12:11 +0000 (21:12 +0000)]
ascii comment
jprocter [Tue, 12 Aug 2008 21:11:47 +0000 (21:11 +0000)]
mac logo resourcelocation hack
jprocter [Tue, 12 Aug 2008 14:41:50 +0000 (14:41 +0000)]
fix artefacts (again)
jprocter [Tue, 12 Aug 2008 14:19:40 +0000 (14:19 +0000)]
corrected target name in documentation
jprocter [Tue, 12 Aug 2008 14:19:03 +0000 (14:19 +0000)]
URL help update
jprocter [Tue, 12 Aug 2008 14:18:45 +0000 (14:18 +0000)]
added nojmol parameter to disable check for jmol
jprocter [Tue, 12 Aug 2008 13:38:42 +0000 (13:38 +0000)]
simpler regex-replace for path
jprocter [Tue, 12 Aug 2008 12:23:29 +0000 (12:23 +0000)]
fixing paths
jprocter [Tue, 12 Aug 2008 11:15:42 +0000 (11:15 +0000)]
regex blah
jprocter [Tue, 12 Aug 2008 10:44:53 +0000 (10:44 +0000)]
trailing slash regexed out
jprocter [Tue, 12 Aug 2008 10:34:04 +0000 (10:34 +0000)]
path fixing
jprocter [Tue, 12 Aug 2008 10:26:02 +0000 (10:26 +0000)]
resources are relative to root of jalview install path
jprocter [Tue, 12 Aug 2008 07:40:21 +0000 (07:40 +0000)]
update to InstallAnywhere 2008 VP1
jprocter [Mon, 11 Aug 2008 14:56:31 +0000 (14:56 +0000)]
regular expression based URL link generation
jprocter [Mon, 11 Aug 2008 14:55:49 +0000 (14:55 +0000)]
Ensure 'None' translates into no colour scheme applied
jprocter [Mon, 11 Aug 2008 12:30:53 +0000 (12:30 +0000)]
Upgraded to IA Standard 2008 VP1
jprocter [Mon, 11 Aug 2008 12:30:31 +0000 (12:30 +0000)]
Upgraded to InstallAnywhere 2008 Standard ValuePack 1
jprocter [Sun, 10 Aug 2008 11:16:03 +0000 (11:16 +0000)]
migration to automated build test
jprocter [Sat, 9 Aug 2008 15:41:07 +0000 (15:41 +0000)]
fix default build path
jprocter [Sat, 9 Aug 2008 15:02:35 +0000 (15:02 +0000)]
exclude any InstallAnywhere build artefacts
jprocter [Sat, 9 Aug 2008 14:27:17 +0000 (14:27 +0000)]
installanywhere to a destination location
jprocter [Thu, 7 Aug 2008 17:10:02 +0000 (17:10 +0000)]
updating installAnywhere autobuild
jprocter [Thu, 7 Aug 2008 16:42:34 +0000 (16:42 +0000)]
headless build of InstallAnywhere installer
jprocter [Wed, 6 Aug 2008 12:16:51 +0000 (12:16 +0000)]
generation of additional URLs for DBRefs on a sequence that match the URL link name.
jprocter [Wed, 6 Aug 2008 12:16:06 +0000 (12:16 +0000)]
extra checks for datasetsequence for when getDbRefs is called
jprocter [Wed, 6 Aug 2008 12:14:06 +0000 (12:14 +0000)]
getDBRefs now always returns DBRefArray if it exists on this sequence or dataset sequence
jprocter [Tue, 5 Aug 2008 16:52:03 +0000 (16:52 +0000)]
vamsas documentation
jprocter [Tue, 5 Aug 2008 16:51:39 +0000 (16:51 +0000)]
new vamsas session does not open a dialog box
jprocter [Tue, 5 Aug 2008 15:33:19 +0000 (15:33 +0000)]
web services and sequence fetcher added to contents
jprocter [Tue, 5 Aug 2008 15:33:03 +0000 (15:33 +0000)]
added sequence fetcher and sequence features retrieval to web serviices index
jprocter [Tue, 5 Aug 2008 15:32:38 +0000 (15:32 +0000)]
updated statement of limitations for interactive annotation editing with Jalview GUI
jprocter [Tue, 5 Aug 2008 15:32:09 +0000 (15:32 +0000)]
new sequence fetcher documentation
jprocter [Tue, 5 Aug 2008 14:51:23 +0000 (14:51 +0000)]
ensure das sequence sources are refreshed when das registry is changed
jprocter [Tue, 5 Aug 2008 12:35:45 +0000 (12:35 +0000)]
showbutton default is true
jprocter [Mon, 4 Aug 2008 16:52:00 +0000 (16:52 +0000)]
stackoverflow fix
jprocter [Mon, 4 Aug 2008 14:19:28 +0000 (14:19 +0000)]
PFAM retrieval and new applet parameter
jprocter [Mon, 4 Aug 2008 14:16:18 +0000 (14:16 +0000)]
pfam seed and full alignment retrieval and nicer ordering of sequence db sources in combobox
jprocter [Mon, 4 Aug 2008 11:08:03 +0000 (11:08 +0000)]
added 'showbutton' applet parameter
jprocter [Fri, 1 Aug 2008 13:22:21 +0000 (13:22 +0000)]
update to feature list (more to come here for 2.4 release)
jprocter [Fri, 1 Aug 2008 13:19:48 +0000 (13:19 +0000)]
new SequenceFetcher gui and visual delay indication for initialisation and fetching
jprocter [Fri, 1 Aug 2008 13:19:10 +0000 (13:19 +0000)]
updated jalview version of dasobert 1.53e client and added Das Sequence Source discovery to the sequence fetcher
jprocter [Fri, 1 Aug 2008 13:17:21 +0000 (13:17 +0000)]
todo
jprocter [Fri, 1 Aug 2008 13:16:39 +0000 (13:16 +0000)]
interface for windows that display progress bars
jprocter [Thu, 31 Jul 2008 11:00:21 +0000 (11:00 +0000)]
use canonical DbSource name in GUI box, and ensure only one instance of DbSourceProxy is presented for each canonical name
jprocter [Thu, 31 Jul 2008 10:15:50 +0000 (10:15 +0000)]
refactored method for registering instance of a dbSource with the SequenceFetcher from the factory method for creating a dbSource instance
jprocter [Thu, 31 Jul 2008 10:11:57 +0000 (10:11 +0000)]
quick fix for the new uniprot name schema - description line for retrieved uniprot sequences gets the first recommendedName.fullName string found in the entry.
jprocter [Thu, 31 Jul 2008 10:09:55 +0000 (10:09 +0000)]
added specific retrieval arguments to SequneceFetcher's main method.
jprocter [Fri, 18 Jul 2008 15:10:29 +0000 (15:10 +0000)]
resolve 1:many mappings for sequence associated annotation to all alignment sequence(s) with same ID
jprocter [Fri, 18 Jul 2008 15:05:30 +0000 (15:05 +0000)]
resolve 1:many mappings from feature sequence ID to alignment sequence(s) with same ID
jprocter [Fri, 18 Jul 2008 15:03:36 +0000 (15:03 +0000)]
allow findSeq to begin *after* a given sequence in the alignment
jprocter [Fri, 18 Jul 2008 13:31:02 +0000 (13:31 +0000)]
Sequence label colour stored for each sequence group
jprocter [Fri, 18 Jul 2008 13:27:57 +0000 (13:27 +0000)]
comment
jprocter [Fri, 18 Jul 2008 12:32:02 +0000 (12:32 +0000)]
annotation file format updated to take idColour and specify single colour groups with rgb triplets and names
jprocter [Fri, 18 Jul 2008 12:31:53 +0000 (12:31 +0000)]
Sequence label colour stored for each sequence group
jprocter [Fri, 18 Jul 2008 12:30:57 +0000 (12:30 +0000)]
User defined colourschemes are automatically generated from colour names or RGB colour triplets
jprocter [Fri, 18 Jul 2008 12:29:54 +0000 (12:29 +0000)]
prevent exception when no default timeout is specified
jprocter [Fri, 11 Jul 2008 15:07:03 +0000 (15:07 +0000)]
ensure annotationElements in non-graphical annotation objects do not automatically get values
jprocter [Mon, 30 Jun 2008 10:49:49 +0000 (10:49 +0000)]
javadoc and constraint to ensure annotation labels are not wider than alignment frame
jprocter [Mon, 30 Jun 2008 09:50:27 +0000 (09:50 +0000)]
java 1.1 compatibility
jprocter [Mon, 30 Jun 2008 09:50:13 +0000 (09:50 +0000)]
timing of 'on load' output before any gui thread operations
jprocter [Mon, 30 Jun 2008 09:49:44 +0000 (09:49 +0000)]
safer retrieval of groovy scripts from URLs
jprocter [Mon, 30 Jun 2008 09:48:06 +0000 (09:48 +0000)]
included includeGaps flag in clustalW colour calculation - behaviour for includeGaps=false is not verified to match ClustalX as yet.
jprocter [Thu, 26 Jun 2008 17:13:17 +0000 (17:13 +0000)]
added URLEncoder.encode to properly escape CGI encoded arguments so they are safely transmitted to the launchApp servlet.
jprocter [Mon, 23 Jun 2008 07:45:38 +0000 (07:45 +0000)]
local sequence properties are preserved in SeqCigar representation of sequence using SeqHash/SeqUnhash in jalview.analysis.SeqsetUtils. Ensures input data and alignment results from webservice have same visible names as original sequences input.
jprocter [Mon, 26 May 2008 10:24:08 +0000 (10:24 +0000)]
Uniprot is not actually a multi-acc capable source any more. see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=32464
jprocter [Mon, 26 May 2008 10:23:30 +0000 (10:23 +0000)]
bugfix so MULTI_ACC capable sources value property is actually used by DBRefFetcher
jprocter [Mon, 26 May 2008 09:55:37 +0000 (09:55 +0000)]
minor bugfix for case when PDB sequence strings are not parsed and added new javascript API methods for getting selected sequences (https://mantis.lifesci.dundee.ac.uk/view.php?id=32977)
jprocter [Mon, 12 May 2008 07:56:53 +0000 (07:56 +0000)]
fixed Jalview project archive bug where alignment view is not written to Jar that was introduced through refactoring JarEntry output code.
jprocter [Fri, 2 May 2008 13:04:01 +0000 (13:04 +0000)]
bugfix to avoid null pointer exceptions being raised for groups with no colourscheme set.
jprocter [Thu, 1 May 2008 09:22:43 +0000 (09:22 +0000)]
fix for unicode char labels causing arrayOutOfBoundsException bug spotted by cameron weadicks
jprocter [Tue, 29 Apr 2008 10:53:40 +0000 (10:53 +0000)]
comments and version wget ping timeout fix for when www connection is unavailable due to proxy taking too long to respond
jprocter [Tue, 29 Apr 2008 10:51:04 +0000 (10:51 +0000)]
added SeqSearch service interface. Documented and refactored web service client (tbc - more refactors to come).
jprocter [Tue, 29 Apr 2008 10:15:04 +0000 (10:15 +0000)]
trial fix for parsing NHX style trees to extract the bootstrap values
jprocter [Fri, 25 Apr 2008 13:18:48 +0000 (13:18 +0000)]
potential fix for hang on opening of application window when run in a proxied network environment (splashscreen constructor blocks whilst jalview.jnlp is fetched)
jprocter [Tue, 22 Apr 2008 10:14:34 +0000 (10:14 +0000)]
typo on Jalview help url
jprocter [Mon, 21 Apr 2008 17:34:41 +0000 (17:34 +0000)]
documented and refactored to facilitate headless feature file generation
jprocter [Mon, 21 Apr 2008 17:27:54 +0000 (17:27 +0000)]
added centre column labels menu entry to format menu
jprocter [Mon, 21 Apr 2008 17:27:08 +0000 (17:27 +0000)]
added centre annotation labels menu entry (and commented out SeqSearch web service handler builder code)
jprocter [Mon, 21 Apr 2008 17:19:03 +0000 (17:19 +0000)]
centrecolumnlabels format menu item and parameter added to applet
jprocter [Mon, 21 Apr 2008 17:18:05 +0000 (17:18 +0000)]
castor debug option cleared
jprocter [Thu, 17 Apr 2008 16:37:47 +0000 (16:37 +0000)]
bugfix for refactoring (webservice windows wouldn't open!!)
jprocter [Thu, 17 Apr 2008 15:47:56 +0000 (15:47 +0000)]
javadoc and refactor of setWebService method to allow headless client operation
jprocter [Thu, 17 Apr 2008 15:06:43 +0000 (15:06 +0000)]
todo for refactoring webservice GUI creation mechanism