jalview.git
16 years agomerge from 2_4_Release branch
jprocter [Thu, 4 Sep 2008 13:34:15 +0000 (13:34 +0000)]
merge from 2_4_Release branch

16 years agono newline after licence comment
jprocter [Wed, 27 Aug 2008 13:52:51 +0000 (13:52 +0000)]
no newline after licence comment

16 years agoadded Release_2_4_branch
jprocter [Wed, 27 Aug 2008 12:27:29 +0000 (12:27 +0000)]
added Release_2_4_branch

16 years agofix vamas homedir link
jprocter [Wed, 27 Aug 2008 12:11:58 +0000 (12:11 +0000)]
fix vamas homedir link

16 years agoadded keystore config properties
jprocter [Wed, 27 Aug 2008 12:11:41 +0000 (12:11 +0000)]
added keystore config properties

16 years agoupdate and test release build system Release_2_4
jprocter [Tue, 26 Aug 2008 17:09:08 +0000 (17:09 +0000)]
update and test release build system

16 years ago2.4 release documentation update menus, service refs, new features and releases
jprocter [Tue, 26 Aug 2008 15:54:16 +0000 (15:54 +0000)]
2.4 release documentation update menus, service refs, new features and releases

16 years agoupdate Jpred3 service referenec
jprocter [Tue, 26 Aug 2008 15:53:42 +0000 (15:53 +0000)]
update Jpred3 service referenec

16 years agoallow '|' to be entered in URL text box and added regex extension form to instructions
jprocter [Tue, 26 Aug 2008 11:19:07 +0000 (11:19 +0000)]
allow '|' to be entered in URL text box and added regex extension form to instructions

16 years agoset title of viewer frame after file has been loaded (if possible) so Desktop window...
jprocter [Tue, 26 Aug 2008 10:48:24 +0000 (10:48 +0000)]
set title of viewer frame after file has been loaded (if possible) so Desktop window list entry is correct

16 years agofuture bug fix todo
jprocter [Tue, 26 Aug 2008 10:47:54 +0000 (10:47 +0000)]
future bug fix todo

16 years agonew thread for initting of DBRefFetcher with latest SequenceFetcher
jprocter [Tue, 26 Aug 2008 10:10:18 +0000 (10:10 +0000)]
new thread for initting of DBRefFetcher with latest SequenceFetcher

16 years agouses shared singleton from jalview.gui.SequenceFetcher (consider revising so an insta...
jprocter [Tue, 26 Aug 2008 10:09:55 +0000 (10:09 +0000)]
uses shared singleton from jalview.gui.SequenceFetcher (consider revising so an instance of jalview.ws.SequenceFetcher is passed to constructor)

16 years agoadded singleton access method to retrieve the latest shared instance of the jalview...
jprocter [Tue, 26 Aug 2008 10:07:03 +0000 (10:07 +0000)]
added singleton access method to retrieve the latest shared instance of the jalview.ws.SequenceFetcher

16 years agobugfix todo for the 'edit sequence' command
jprocter [Tue, 26 Aug 2008 09:38:43 +0000 (09:38 +0000)]
bugfix todo for the 'edit sequence' command

16 years agotooltip for fetch db refs and more generic regex for 'Extract scores...'
jprocter [Tue, 26 Aug 2008 09:14:11 +0000 (09:14 +0000)]
tooltip for fetch db refs and more generic regex for 'Extract scores...'

16 years agopdb xrefs added as dbrefs and as PDB file links
jprocter [Tue, 26 Aug 2008 09:10:53 +0000 (09:10 +0000)]
pdb xrefs added as dbrefs and as PDB file links

16 years agoensure successive matches to a regex have distinct annotation name (indice suffix...
jprocter [Tue, 26 Aug 2008 08:59:10 +0000 (08:59 +0000)]
ensure successive matches to a regex have distinct annotation name (indice suffix increases by one each time)

16 years agoUse 0f rather than NaN to specify non-valued annotation elements.
jprocter [Wed, 20 Aug 2008 15:54:22 +0000 (15:54 +0000)]
Use 0f rather than NaN to specify non-valued annotation elements.

16 years agotooltip displays formatted annotation row description including sequence reference...
jprocter [Wed, 20 Aug 2008 15:53:34 +0000 (15:53 +0000)]
tooltip displays formatted annotation row description including sequence reference name (if any)

16 years agobeginning of fix for embl/cds/highlighting IO in https://mantis.lifesci.dundee.ac...
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

16 years agofix for arrayoutofbounds bug when secondary structure element extends whole width...
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)

16 years agobetter check for molecule type when identifying internal sequence cross-references
jprocter [Tue, 19 Aug 2008 09:38:38 +0000 (09:38 +0000)]
better check for molecule type when identifying internal sequence cross-references

16 years agoregex links for launching URL from single click on sequence ID
jprocter [Tue, 19 Aug 2008 09:37:52 +0000 (09:37 +0000)]
regex links for launching URL from single click on sequence ID

16 years agoupdate text and version checker
jprocter [Fri, 15 Aug 2008 11:37:29 +0000 (11:37 +0000)]
update text and version checker

16 years agodialog size on macs
jprocter [Fri, 15 Aug 2008 10:34:52 +0000 (10:34 +0000)]
dialog size on macs

16 years agocheck for crossreferences every time the menus are updated
jprocter [Fri, 15 Aug 2008 10:02:43 +0000 (10:02 +0000)]
check for crossreferences every time the menus are updated

16 years agocatch invalid URL link exception properly
jprocter [Fri, 15 Aug 2008 10:02:16 +0000 (10:02 +0000)]
catch invalid URL link exception properly

16 years agoincrease height of dialog
jprocter [Fri, 15 Aug 2008 10:02:01 +0000 (10:02 +0000)]
increase height of dialog

16 years agoallow '|' in regex for URL links to be recovered from properties file properly
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

16 years agosafer copy constructor
jprocter [Fri, 15 Aug 2008 10:01:05 +0000 (10:01 +0000)]
safer copy constructor

16 years agoxrefs retrieved from Uniprot
jprocter [Fri, 15 Aug 2008 10:00:51 +0000 (10:00 +0000)]
xrefs retrieved from Uniprot

16 years agoadded castor back onto classpath
jprocter [Fri, 15 Aug 2008 09:59:33 +0000 (09:59 +0000)]
added castor back onto classpath

16 years agocheck for null viewport on dataset recovery
jprocter [Wed, 13 Aug 2008 13:47:10 +0000 (13:47 +0000)]
check for null viewport on dataset recovery

16 years agoensure input data can be recovered for tree and PCA even if alignment view was closed
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

16 years agodo not try to cancel jobs that cannot be cancelled
jprocter [Wed, 13 Aug 2008 10:42:21 +0000 (10:42 +0000)]
do not try to cancel jobs that cannot be cancelled

16 years agoascii comment
jprocter [Tue, 12 Aug 2008 21:12:11 +0000 (21:12 +0000)]
ascii comment

16 years agomac logo resourcelocation hack
jprocter [Tue, 12 Aug 2008 21:11:47 +0000 (21:11 +0000)]
mac logo resourcelocation hack

16 years agofix artefacts (again)
jprocter [Tue, 12 Aug 2008 14:41:50 +0000 (14:41 +0000)]
fix artefacts (again)

16 years agocorrected target name in documentation
jprocter [Tue, 12 Aug 2008 14:19:40 +0000 (14:19 +0000)]
corrected target name in documentation

16 years agoURL help update
jprocter [Tue, 12 Aug 2008 14:19:03 +0000 (14:19 +0000)]
URL help update

16 years agoadded nojmol parameter to disable check for jmol
jprocter [Tue, 12 Aug 2008 14:18:45 +0000 (14:18 +0000)]
added nojmol parameter to disable check for jmol

16 years agosimpler regex-replace for path
jprocter [Tue, 12 Aug 2008 13:38:42 +0000 (13:38 +0000)]
simpler regex-replace for path

16 years agofixing paths
jprocter [Tue, 12 Aug 2008 12:23:29 +0000 (12:23 +0000)]
fixing paths

16 years agoregex blah
jprocter [Tue, 12 Aug 2008 11:15:42 +0000 (11:15 +0000)]
regex blah

16 years agotrailing slash regexed out
jprocter [Tue, 12 Aug 2008 10:44:53 +0000 (10:44 +0000)]
trailing slash regexed out

16 years agopath fixing
jprocter [Tue, 12 Aug 2008 10:34:04 +0000 (10:34 +0000)]
path fixing

16 years agoresources are relative to root of jalview install path
jprocter [Tue, 12 Aug 2008 10:26:02 +0000 (10:26 +0000)]
resources are relative to root of jalview install path

16 years agoupdate to InstallAnywhere 2008 VP1
jprocter [Tue, 12 Aug 2008 07:40:21 +0000 (07:40 +0000)]
update to InstallAnywhere 2008 VP1

16 years agoregular expression based URL link generation
jprocter [Mon, 11 Aug 2008 14:56:31 +0000 (14:56 +0000)]
regular expression based URL link generation

16 years agoEnsure 'None' translates into no colour scheme applied
jprocter [Mon, 11 Aug 2008 14:55:49 +0000 (14:55 +0000)]
Ensure 'None' translates into no colour scheme applied

16 years agoUpgraded to IA Standard 2008 VP1
jprocter [Mon, 11 Aug 2008 12:30:53 +0000 (12:30 +0000)]
Upgraded to IA Standard 2008 VP1

16 years agoUpgraded to InstallAnywhere 2008 Standard ValuePack 1
jprocter [Mon, 11 Aug 2008 12:30:31 +0000 (12:30 +0000)]
Upgraded to InstallAnywhere 2008 Standard ValuePack 1

16 years agomigration to automated build test
jprocter [Sun, 10 Aug 2008 11:16:03 +0000 (11:16 +0000)]
migration to automated build test

16 years agofix default build path
jprocter [Sat, 9 Aug 2008 15:41:07 +0000 (15:41 +0000)]
fix default build path

16 years agoexclude any InstallAnywhere build artefacts
jprocter [Sat, 9 Aug 2008 15:02:35 +0000 (15:02 +0000)]
exclude any InstallAnywhere build artefacts

16 years agoinstallanywhere to a destination location
jprocter [Sat, 9 Aug 2008 14:27:17 +0000 (14:27 +0000)]
installanywhere to a destination location

16 years agoupdating installAnywhere autobuild
jprocter [Thu, 7 Aug 2008 17:10:02 +0000 (17:10 +0000)]
updating installAnywhere autobuild

16 years agoheadless build of InstallAnywhere installer
jprocter [Thu, 7 Aug 2008 16:42:34 +0000 (16:42 +0000)]
headless build of InstallAnywhere installer

16 years agogeneration of additional URLs for DBRefs on a sequence that match the URL link name.
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.

16 years agoextra checks for datasetsequence for when getDbRefs is called
jprocter [Wed, 6 Aug 2008 12:16:06 +0000 (12:16 +0000)]
extra checks for datasetsequence for when getDbRefs is called

16 years agogetDBRefs now always returns DBRefArray if it exists on this sequence or dataset...
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

16 years agovamsas documentation
jprocter [Tue, 5 Aug 2008 16:52:03 +0000 (16:52 +0000)]
vamsas documentation

16 years agonew vamsas session does not open a dialog box
jprocter [Tue, 5 Aug 2008 16:51:39 +0000 (16:51 +0000)]
new vamsas session does not open a dialog box

16 years agoweb services and sequence fetcher added to contents
jprocter [Tue, 5 Aug 2008 15:33:19 +0000 (15:33 +0000)]
web services and sequence fetcher added to contents

16 years agoadded sequence fetcher and sequence features retrieval to web serviices index
jprocter [Tue, 5 Aug 2008 15:33:03 +0000 (15:33 +0000)]
added sequence fetcher and sequence features retrieval to web serviices index

16 years agoupdated statement of limitations for interactive annotation editing with Jalview GUI
jprocter [Tue, 5 Aug 2008 15:32:38 +0000 (15:32 +0000)]
updated statement of limitations for interactive annotation editing with Jalview GUI

16 years agonew sequence fetcher documentation
jprocter [Tue, 5 Aug 2008 15:32:09 +0000 (15:32 +0000)]
new sequence fetcher documentation

16 years agoensure das sequence sources are refreshed when das registry is changed
jprocter [Tue, 5 Aug 2008 14:51:23 +0000 (14:51 +0000)]
ensure das sequence sources are refreshed when das registry is changed

16 years agoshowbutton default is true
jprocter [Tue, 5 Aug 2008 12:35:45 +0000 (12:35 +0000)]
showbutton default is true

16 years agostackoverflow fix
jprocter [Mon, 4 Aug 2008 16:52:00 +0000 (16:52 +0000)]
stackoverflow fix

16 years agoPFAM retrieval and new applet parameter
jprocter [Mon, 4 Aug 2008 14:19:28 +0000 (14:19 +0000)]
PFAM retrieval and new applet parameter

16 years agopfam seed and full alignment retrieval and nicer ordering of sequence db sources...
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

16 years agoadded 'showbutton' applet parameter
jprocter [Mon, 4 Aug 2008 11:08:03 +0000 (11:08 +0000)]
added 'showbutton' applet parameter

16 years agoupdate to feature list (more to come here for 2.4 release)
jprocter [Fri, 1 Aug 2008 13:22:21 +0000 (13:22 +0000)]
update to feature list (more to come here for 2.4 release)

16 years agonew SequenceFetcher gui and visual delay indication for initialisation and fetching
jprocter [Fri, 1 Aug 2008 13:19:48 +0000 (13:19 +0000)]
new SequenceFetcher gui and visual delay indication for initialisation and fetching

16 years agoupdated jalview version of dasobert 1.53e client and added Das Sequence Source discov...
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

16 years agotodo
jprocter [Fri, 1 Aug 2008 13:17:21 +0000 (13:17 +0000)]
todo

16 years agointerface for windows that display progress bars
jprocter [Fri, 1 Aug 2008 13:16:39 +0000 (13:16 +0000)]
interface for windows that display progress bars

16 years agouse canonical DbSource name in GUI box, and ensure only one instance of DbSourceProxy...
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

16 years agorefactored method for registering instance of a dbSource with the SequenceFetcher...
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

16 years agoquick fix for the new uniprot name schema - description line for retrieved uniprot...
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.

16 years agoadded specific retrieval arguments to SequneceFetcher's main method.
jprocter [Thu, 31 Jul 2008 10:09:55 +0000 (10:09 +0000)]
added specific retrieval arguments to SequneceFetcher's main method.

16 years agoresolve 1:many mappings for sequence associated annotation to all alignment sequence...
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

16 years agoresolve 1:many mappings from feature sequence ID to 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

16 years agoallow findSeq to begin *after* a given sequence in the alignment
jprocter [Fri, 18 Jul 2008 15:03:36 +0000 (15:03 +0000)]
allow findSeq to begin *after* a given sequence in the alignment

16 years agoSequence label colour stored for each sequence group
jprocter [Fri, 18 Jul 2008 13:31:02 +0000 (13:31 +0000)]
Sequence label colour stored for each sequence group

16 years agocomment
jprocter [Fri, 18 Jul 2008 13:27:57 +0000 (13:27 +0000)]
comment

16 years agoannotation file format updated to take idColour and specify single colour groups...
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

16 years agoSequence label colour stored for each sequence group
jprocter [Fri, 18 Jul 2008 12:31:53 +0000 (12:31 +0000)]
Sequence label colour stored for each sequence group

16 years agoUser defined colourschemes are automatically generated from colour names or RGB colou...
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

16 years agoprevent exception when no default timeout is specified
jprocter [Fri, 18 Jul 2008 12:29:54 +0000 (12:29 +0000)]
prevent exception when no default timeout is specified

16 years agoensure annotationElements in non-graphical annotation objects do not automatically...
jprocter [Fri, 11 Jul 2008 15:07:03 +0000 (15:07 +0000)]
ensure annotationElements in non-graphical annotation objects do not automatically get values

16 years agojavadoc and constraint to ensure annotation labels are not wider than alignment frame
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

16 years agojava 1.1 compatibility
jprocter [Mon, 30 Jun 2008 09:50:27 +0000 (09:50 +0000)]
java 1.1 compatibility

16 years agotiming of 'on load' output before any gui thread operations
jprocter [Mon, 30 Jun 2008 09:50:13 +0000 (09:50 +0000)]
timing of 'on load' output before any gui thread operations

16 years agosafer retrieval of groovy scripts from URLs
jprocter [Mon, 30 Jun 2008 09:49:44 +0000 (09:49 +0000)]
safer retrieval of groovy scripts from URLs

16 years agoincluded includeGaps flag in clustalW colour calculation - behaviour for includeGaps...
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.

16 years agoadded URLEncoder.encode to properly escape CGI encoded arguments so they are safely...
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.

16 years agolocal sequence properties are preserved in SeqCigar representation of sequence using...
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.