no newline after licence comment
2 lines of code changed in:
added Release_2_4_branch
0 lines of code changed in:
fix vamas homedir link
1 lines of code changed in:
added keystore config properties
14 lines of code changed in:
update and test release build system
0 lines of code changed in:
2.4 release documentation update menus, service refs, new features and releases
574 lines of code changed in:
update Jpred3 service referenec
3 lines of code changed in:
allow '|' to be entered in URL text box and added regex extension form to instructions
12 lines of code changed in:
set title of viewer frame after file has been loaded (if possible) so Desktop window list entry is correct
7 lines of code changed in:
future bug fix todo
3 lines of code changed in:
new thread for initting of DBRefFetcher with latest SequenceFetcher
20 lines of code changed in:
uses shared singleton from jalview.gui.SequenceFetcher (consider revising so an instance of jalview.ws.SequenceFetcher is passed to constructor)
0 lines of code changed in:
added singleton access method to retrieve the latest shared instance of the jalview.ws.SequenceFetcher
43 lines of code changed in:
bugfix todo for the 'edit sequence' command
22 lines of code changed in:
tooltip for fetch db refs and more generic regex for 'Extract scores...'
5 lines of code changed in:
pdb xrefs added as dbrefs and as PDB file links
270 lines of code changed in:
ensure successive matches to a regex have distinct annotation name (indice suffix increases by one each time)
134 lines of code changed in:
Use 0f rather than NaN to specify non-valued annotation elements.
0 lines of code changed in:
tooltip displays formatted annotation row description including sequence reference name (if any)
22 lines of code changed in:
beginning of fix for embl/cds/highlighting IO in https://mantis.lifesci.dundee.ac.uk/view.php?id=36199
41 lines of code changed in:
fix for arrayoutofbounds bug when secondary structure element extends whole width of alignment (eg. PF00037 stockholm file)
11 lines of code changed in:
better check for molecule type when identifying internal sequence cross-references
0 lines of code changed in:
regex links for launching URL from single click on sequence ID
416 lines of code changed in:
update text and version checker
20 lines of code changed in:
dialog size on macs
2 lines of code changed in:
check for crossreferences every time the menus are updated
24 lines of code changed in:
catch invalid URL link exception properly
8 lines of code changed in:
increase height of dialog
2 lines of code changed in:
allow '|' in regex for URL links to be recovered from properties file properly
11 lines of code changed in:
safer copy constructor
4 lines of code changed in:
xrefs retrieved from Uniprot
13 lines of code changed in:
added castor back onto classpath
129 lines of code changed in:
check for null viewport on dataset recovery
5 lines of code changed in:
ensure input data can be recovered for tree and PCA even if alignment view was closed
515 lines of code changed in:
do not try to cancel jobs that cannot be cancelled
2 lines of code changed in:
ascii comment
42 lines of code changed in:
mac logo resourcelocation hack
4 lines of code changed in:
fix artefacts (again)
7 lines of code changed in:
corrected target name in documentation
1 lines of code changed in:
URL help update
29 lines of code changed in:
added nojmol parameter to disable check for jmol
374 lines of code changed in:
simpler regex-replace for path
5 lines of code changed in:
fixing paths
112 lines of code changed in:
regex blah
3 lines of code changed in:
trailing slash regexed out
1 lines of code changed in:
path fixing
1 lines of code changed in:
resources are relative to root of jalview install path
3 lines of code changed in:
update to InstallAnywhere 2008 VP1
11 lines of code changed in:
regular expression based URL link generation
233 lines of code changed in:
Ensure 'None' translates into no colour scheme applied
12 lines of code changed in:
Upgraded to IA Standard 2008 VP1
78 lines of code changed in:
Upgraded to InstallAnywhere 2008 Standard ValuePack 1
1 lines of code changed in:
migration to automated build test
21 lines of code changed in:
fix default build path
9 lines of code changed in:
exclude any InstallAnywhere build artefacts
8 lines of code changed in:
installanywhere to a destination location
2 lines of code changed in:
updating installAnywhere autobuild
464 lines of code changed in:
headless build of InstallAnywhere installer
39 lines of code changed in:
generation of additional URLs for DBRefs on a sequence that match the URL link name.
989 lines of code changed in:
extra checks for datasetsequence for when getDbRefs is called
2 lines of code changed in:
getDBRefs now always returns DBRefArray if it exists on this sequence or dataset sequence
8 lines of code changed in:
vamsas documentation
51 lines of code changed in:
new vamsas session does not open a dialog box
2 lines of code changed in:
web services and sequence fetcher added to contents
4 lines of code changed in:
added sequence fetcher and sequence features retrieval to web serviices index
70 lines of code changed in:
updated statement of limitations for interactive annotation editing with Jalview GUI
9 lines of code changed in:
new sequence fetcher documentation
34 lines of code changed in:
ensure das sequence sources are refreshed when das registry is changed
298 lines of code changed in:
showbutton default is true
2 lines of code changed in:
stackoverflow fix
0 lines of code changed in:
PFAM retrieval and new applet parameter
3 lines of code changed in:
pfam seed and full alignment retrieval and nicer ordering of sequence db sources in combobox
3 lines of code changed in:
added 'showbutton' applet parameter
16 lines of code changed in:
update to feature list (more to come here for 2.4 release)
55 lines of code changed in:
new SequenceFetcher gui and visual delay indication for initialisation and fetching
161 lines of code changed in:
updated jalview version of dasobert 1.53e client and added Das Sequence Source discovery to the sequence fetcher
1 lines of code changed in:
todo
3 lines of code changed in:
interface for windows that display progress bars
0 lines of code changed in: