jalview.git
19 years agosetDesktopManager(new)
amwaterhouse [Wed, 6 Apr 2005 17:12:58 +0000 (17:12 +0000)]
setDesktopManager(new)

19 years agopaint is now in drawComponent
amwaterhouse [Wed, 6 Apr 2005 17:12:15 +0000 (17:12 +0000)]
paint is now in drawComponent

19 years agoshowAnnotation added
amwaterhouse [Wed, 6 Apr 2005 17:11:39 +0000 (17:11 +0000)]
showAnnotation added

19 years agoannoation in print version
amwaterhouse [Wed, 6 Apr 2005 17:11:08 +0000 (17:11 +0000)]
annoation in print version

19 years agoDONT SHOW ANNOTATIONS IF WRAPPED
amwaterhouse [Wed, 6 Apr 2005 17:10:14 +0000 (17:10 +0000)]
DONT SHOW ANNOTATIONS IF WRAPPED

19 years agonext version of Jpred functionality using new client code.
jprocter [Wed, 6 Apr 2005 16:20:55 +0000 (16:20 +0000)]
next version of Jpred functionality using new client code.

19 years agoNew method for helping to quickly map different aligned versions of a
jprocter [Wed, 6 Apr 2005 16:05:43 +0000 (16:05 +0000)]
New method for helping to quickly map different aligned versions of a
sequence.

19 years agoNew client code for JPred service includes return of msa and
jprocter [Wed, 6 Apr 2005 16:03:52 +0000 (16:03 +0000)]
New client code for JPred service includes return of msa and
Jprediction, and better job status information
(vamsas.dataTypes.Result).

19 years agomosueOver graph gives int, not float
amwaterhouse [Wed, 6 Apr 2005 11:39:34 +0000 (11:39 +0000)]
mosueOver graph gives int, not float

19 years agoFast paint method implemented
amwaterhouse [Wed, 6 Apr 2005 11:38:59 +0000 (11:38 +0000)]
Fast paint method implemented

19 years agoAlignment Annotation added
amwaterhouse [Fri, 1 Apr 2005 16:46:10 +0000 (16:46 +0000)]
Alignment Annotation added

19 years agoignore jnetconf
amwaterhouse [Fri, 1 Apr 2005 16:45:29 +0000 (16:45 +0000)]
ignore jnetconf

19 years agoparses jpredfile into new alignment annotation
amwaterhouse [Fri, 1 Apr 2005 16:44:57 +0000 (16:44 +0000)]
parses jpredfile into new alignment annotation

19 years agoupdate conservation and consensus
amwaterhouse [Fri, 1 Apr 2005 16:44:16 +0000 (16:44 +0000)]
update conservation and consensus

19 years agoanti_aliasing on
amwaterhouse [Fri, 1 Apr 2005 16:43:42 +0000 (16:43 +0000)]
anti_aliasing on

19 years agoUses conservation graph
amwaterhouse [Fri, 1 Apr 2005 16:42:42 +0000 (16:42 +0000)]
Uses conservation graph

19 years agotesting Graphics2D
amwaterhouse [Fri, 1 Apr 2005 16:42:25 +0000 (16:42 +0000)]
testing Graphics2D

19 years agosetMaximizable(false)
amwaterhouse [Fri, 1 Apr 2005 16:41:50 +0000 (16:41 +0000)]
setMaximizable(false)

19 years agoBuild date determination
amwaterhouse [Fri, 1 Apr 2005 16:38:04 +0000 (16:38 +0000)]
Build date determination

19 years agodoh - stupid jim.
jprocter [Thu, 31 Mar 2005 17:34:34 +0000 (17:34 +0000)]
doh - stupid jim.

19 years agoutility classes used in build.xml, and a dodgy perl script for
jprocter [Thu, 31 Mar 2005 10:01:04 +0000 (10:01 +0000)]
utility classes used in build.xml, and a dodgy perl script for
removing the signatures from jars.

19 years agoJavaC target set to 1.4 for proper compilation of 1.5 code.
jprocter [Thu, 31 Mar 2005 09:56:11 +0000 (09:56 +0000)]
JavaC target set to 1.4 for proper compilation of 1.5 code.

19 years agoAdded a flag to control if the "/<seq_start>-<seq_end>" field of
jprocter [Thu, 31 Mar 2005 09:54:19 +0000 (09:54 +0000)]
Added a flag to control if the "/<seq_start>-<seq_end>" field of
SequenceI.Name is included in fastA format files. This is used in the
Jemboss client.

19 years agoadded a an axis log4j appender property to the jalview.Cache.
jprocter [Thu, 31 Mar 2005 09:52:29 +0000 (09:52 +0000)]
added a an axis log4j appender property to the jalview.Cache.

19 years agonew libraries for soap bits.
jprocter [Wed, 30 Mar 2005 17:19:16 +0000 (17:19 +0000)]
new libraries for soap bits.

19 years agofixed the log4j messages.
jprocter [Wed, 30 Mar 2005 17:15:20 +0000 (17:15 +0000)]
fixed the log4j messages.

19 years agocleaned up some comments and exception messages.
jprocter [Wed, 30 Mar 2005 14:02:39 +0000 (14:02 +0000)]
cleaned up some comments and exception messages.

19 years agoUpdated version of axis to fix the j1.5 webstart problems.
jprocter [Wed, 30 Mar 2005 13:54:29 +0000 (13:54 +0000)]
Updated version of axis to fix the j1.5 webstart problems.

19 years agoFixed a sensible default leaf distance (for files where only a few, or no distances...
jprocter [Wed, 30 Mar 2005 13:49:20 +0000 (13:49 +0000)]
Fixed a sensible default leaf distance (for files where only a few, or no distances are specified).

19 years agofix printing error
amwaterhouse [Thu, 24 Mar 2005 08:52:23 +0000 (08:52 +0000)]
fix printing error

19 years agonew seq selection -1
amwaterhouse [Wed, 23 Mar 2005 16:28:12 +0000 (16:28 +0000)]
new seq selection -1

19 years agoadjustForRemoveLeft / Right added
amwaterhouse [Wed, 23 Mar 2005 16:27:38 +0000 (16:27 +0000)]
adjustForRemoveLeft / Right added

19 years agoworks even if col is 1 residue
amwaterhouse [Wed, 23 Mar 2005 15:39:17 +0000 (15:39 +0000)]
works even if col is 1 residue

19 years agoreads MSF files even if PILEUP is missing
amwaterhouse [Wed, 23 Mar 2005 15:38:53 +0000 (15:38 +0000)]
reads MSF files even if PILEUP is missing

19 years agodrawableSequence removed
amwaterhouse [Wed, 23 Mar 2005 15:38:14 +0000 (15:38 +0000)]
drawableSequence removed

19 years agono longer used
amwaterhouse [Wed, 23 Mar 2005 15:37:11 +0000 (15:37 +0000)]
no longer used

19 years agosecondarycolour not used
amwaterhouse [Wed, 23 Mar 2005 15:36:10 +0000 (15:36 +0000)]
secondarycolour not used

19 years agoadd .fasta to save dialog
amwaterhouse [Wed, 23 Mar 2005 11:57:37 +0000 (11:57 +0000)]
add .fasta to save dialog

19 years agocorrect wrap alignment scrollbar size
amwaterhouse [Wed, 23 Mar 2005 11:57:06 +0000 (11:57 +0000)]
correct wrap alignment scrollbar size

19 years agoresetSeqLimits altered
amwaterhouse [Wed, 23 Mar 2005 11:56:15 +0000 (11:56 +0000)]
resetSeqLimits altered

19 years agooverride showSaveDialog to prompt user if file exists
amwaterhouse [Wed, 23 Mar 2005 11:55:39 +0000 (11:55 +0000)]
override showSaveDialog to prompt user if file exists

19 years agoput bioinformatics into message
amwaterhouse [Tue, 22 Mar 2005 12:18:44 +0000 (12:18 +0000)]
put bioinformatics into message

19 years agodrag and drop files into jalview
amwaterhouse [Tue, 22 Mar 2005 12:18:16 +0000 (12:18 +0000)]
drag and drop files into jalview

19 years agoadd swing runnable to refresh panel on startup
amwaterhouse [Tue, 22 Mar 2005 12:17:56 +0000 (12:17 +0000)]
add swing runnable to refresh panel on startup

19 years agoread start end if available
amwaterhouse [Tue, 22 Mar 2005 12:17:29 +0000 (12:17 +0000)]
read start end if available

19 years agoaltered layout
amwaterhouse [Mon, 21 Mar 2005 18:50:05 +0000 (18:50 +0000)]
altered layout

19 years agoalter vgap
amwaterhouse [Mon, 21 Mar 2005 18:49:29 +0000 (18:49 +0000)]
alter vgap

19 years agoidentifies more varied blc files
amwaterhouse [Mon, 21 Mar 2005 18:48:58 +0000 (18:48 +0000)]
identifies more varied blc files

19 years agoblc file reader modified
amwaterhouse [Mon, 21 Mar 2005 18:48:39 +0000 (18:48 +0000)]
blc file reader modified

19 years agoadd setValue method
amwaterhouse [Mon, 21 Mar 2005 18:48:20 +0000 (18:48 +0000)]
add setValue method

19 years agofix select group bug
amwaterhouse [Mon, 21 Mar 2005 18:47:48 +0000 (18:47 +0000)]
fix select group bug

19 years agonew method for outlining groups
amwaterhouse [Mon, 21 Mar 2005 18:47:17 +0000 (18:47 +0000)]
new method for outlining groups

19 years agoadd outline colour
amwaterhouse [Mon, 21 Mar 2005 18:46:44 +0000 (18:46 +0000)]
add outline colour

19 years agoprevent idpanel being to narrow
amwaterhouse [Mon, 21 Mar 2005 18:46:25 +0000 (18:46 +0000)]
prevent idpanel being to narrow

19 years agomaintain slider values when click on a group
amwaterhouse [Mon, 21 Mar 2005 18:45:56 +0000 (18:45 +0000)]
maintain slider values when click on a group

19 years agohide idwidthadjuster if wrapped
amwaterhouse [Mon, 21 Mar 2005 18:45:18 +0000 (18:45 +0000)]
hide idwidthadjuster if wrapped

19 years agoadd coloursChanging boolean
amwaterhouse [Mon, 21 Mar 2005 18:44:46 +0000 (18:44 +0000)]
add coloursChanging boolean

19 years agogroup has outline colour
amwaterhouse [Mon, 21 Mar 2005 18:42:46 +0000 (18:42 +0000)]
group has outline colour

19 years agouse system l&f
amwaterhouse [Mon, 21 Mar 2005 18:42:23 +0000 (18:42 +0000)]
use system l&f

19 years agoCreated by jalview
amwaterhouse [Mon, 21 Mar 2005 09:55:42 +0000 (09:55 +0000)]
Created by jalview

19 years agocorrect eps png bug missing last 2 lines
amwaterhouse [Mon, 21 Mar 2005 09:55:17 +0000 (09:55 +0000)]
correct eps png bug missing last 2 lines

19 years agodarkened image
amwaterhouse [Mon, 21 Mar 2005 09:54:50 +0000 (09:54 +0000)]
darkened image

19 years agoeps and png output
amwaterhouse [Fri, 18 Mar 2005 18:28:17 +0000 (18:28 +0000)]
eps and png output

19 years agoremove jpg output
amwaterhouse [Fri, 18 Mar 2005 18:27:37 +0000 (18:27 +0000)]
remove jpg output

19 years agosave eps and png
amwaterhouse [Fri, 18 Mar 2005 18:26:21 +0000 (18:26 +0000)]
save eps and png

19 years agodelete postscript output!!
amwaterhouse [Fri, 18 Mar 2005 18:25:36 +0000 (18:25 +0000)]
delete postscript output!!

19 years agorough JPredService client copied from WebServices project.
jprocter [Fri, 18 Mar 2005 17:42:35 +0000 (17:42 +0000)]
rough JPredService client copied from WebServices project.

19 years agonull point bug fixed
amwaterhouse [Fri, 18 Mar 2005 17:34:56 +0000 (17:34 +0000)]
null point bug fixed

19 years agovarious loadTree bits for loading and saving trees.
jprocter [Fri, 18 Mar 2005 17:23:36 +0000 (17:23 +0000)]
various loadTree bits for loading and saving trees.

19 years agomerged Loadtree and EPSfile and changed crlf.
jprocter [Fri, 18 Mar 2005 17:08:17 +0000 (17:08 +0000)]
merged Loadtree and EPSfile and changed crlf.

19 years agoSave tree.
jprocter [Fri, 18 Mar 2005 16:56:38 +0000 (16:56 +0000)]
Save tree.

19 years agoLoad and Save trees.
jprocter [Fri, 18 Mar 2005 16:56:21 +0000 (16:56 +0000)]
Load and Save trees.

19 years agoTree io modifications, including support for polytomous trees by the
jprocter [Fri, 18 Mar 2005 16:54:55 +0000 (16:54 +0000)]
Tree io modifications, including support for polytomous trees by the
generation of dummy nodes.

19 years agoNew constructors for turning NewickFile objects into renderable trees
jprocter [Fri, 18 Mar 2005 16:53:46 +0000 (16:53 +0000)]
New constructors for turning NewickFile objects into renderable trees
mapped onto the current set of sequences by matching leafnames to
sequence names (where one string must contain the other, rather than
direct equivalence).

19 years agoadd all suffixes to file open
amwaterhouse [Fri, 18 Mar 2005 16:53:17 +0000 (16:53 +0000)]
add all suffixes to file open

19 years agopng and eps
amwaterhouse [Fri, 18 Mar 2005 16:22:50 +0000 (16:22 +0000)]
png and eps

19 years agoupdated with all schemes in 1 table
amwaterhouse [Fri, 18 Mar 2005 16:22:26 +0000 (16:22 +0000)]
updated with all schemes in 1 table

19 years agodont' use index at the moment
amwaterhouse [Fri, 18 Mar 2005 16:21:57 +0000 (16:21 +0000)]
dont' use index at the moment

19 years agoeps output facility
amwaterhouse [Fri, 18 Mar 2005 16:14:47 +0000 (16:14 +0000)]
eps output facility

19 years ago filefilter added
amwaterhouse [Fri, 18 Mar 2005 16:12:45 +0000 (16:12 +0000)]
 filefilter added

19 years agomake eps, png files, filefilter added
amwaterhouse [Fri, 18 Mar 2005 16:11:37 +0000 (16:11 +0000)]
make eps, png files, filefilter added

19 years agoremove unused constants
amwaterhouse [Fri, 18 Mar 2005 16:10:04 +0000 (16:10 +0000)]
remove unused constants

19 years agouse new file filter
amwaterhouse [Fri, 18 Mar 2005 16:09:26 +0000 (16:09 +0000)]
use new file filter

19 years agoalign suffix updated
amwaterhouse [Fri, 18 Mar 2005 16:09:12 +0000 (16:09 +0000)]
align suffix updated

19 years agoacknowledge source and modify to take filter
amwaterhouse [Fri, 18 Mar 2005 16:08:32 +0000 (16:08 +0000)]
acknowledge source and modify to take filter

19 years agonew class
amwaterhouse [Fri, 18 Mar 2005 16:08:11 +0000 (16:08 +0000)]
new class

19 years agopng and eps output added
amwaterhouse [Fri, 18 Mar 2005 16:07:43 +0000 (16:07 +0000)]
png and eps output added

19 years agohide image with mouse released
amwaterhouse [Thu, 17 Mar 2005 17:02:20 +0000 (17:02 +0000)]
hide image with mouse released

19 years agoadd a border
amwaterhouse [Thu, 17 Mar 2005 17:02:01 +0000 (17:02 +0000)]
add a border

19 years agorelocation of images
amwaterhouse [Thu, 17 Mar 2005 16:36:23 +0000 (16:36 +0000)]
relocation of images

19 years agomoved to resources
amwaterhouse [Thu, 17 Mar 2005 16:33:10 +0000 (16:33 +0000)]
moved to resources

19 years agoNewick/New Hampshire tree format parser and generator.
jprocter [Thu, 17 Mar 2005 16:13:18 +0000 (16:13 +0000)]
Newick/New Hampshire tree format parser and generator.

19 years agoversion and last modified added
amwaterhouse [Thu, 17 Mar 2005 15:08:48 +0000 (15:08 +0000)]
version and last modified added

19 years agochecks for last update
amwaterhouse [Thu, 17 Mar 2005 15:08:07 +0000 (15:08 +0000)]
checks for last update

19 years agonew image
amwaterhouse [Thu, 17 Mar 2005 10:41:46 +0000 (10:41 +0000)]
new image

19 years agoidspacefillerpanel has borderlayout
amwaterhouse [Thu, 17 Mar 2005 10:41:12 +0000 (10:41 +0000)]
idspacefillerpanel has borderlayout

19 years agofullid is optional
amwaterhouse [Thu, 17 Mar 2005 10:40:36 +0000 (10:40 +0000)]
fullid is optional

19 years agotakes into account fullid display
amwaterhouse [Thu, 17 Mar 2005 10:40:18 +0000 (10:40 +0000)]
takes into account fullid display

19 years agonew class
amwaterhouse [Thu, 17 Mar 2005 10:39:36 +0000 (10:39 +0000)]
new class

19 years agoidwidth is calculated in alignpanel, not idcanvas
amwaterhouse [Thu, 17 Mar 2005 10:38:59 +0000 (10:38 +0000)]
idwidth is calculated in alignpanel, not idcanvas