jalview.git
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

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

19 years agoview full id name optional
amwaterhouse [Thu, 17 Mar 2005 10:38:00 +0000 (10:38 +0000)]
view full id name optional

19 years agouses jalviewfilechooser
amwaterhouse [Wed, 16 Mar 2005 14:53:03 +0000 (14:53 +0000)]
uses jalviewfilechooser

19 years agosmaller splashscreen
amwaterhouse [Wed, 16 Mar 2005 14:52:21 +0000 (14:52 +0000)]
smaller splashscreen

19 years agoscale bug fixed
amwaterhouse [Wed, 16 Mar 2005 14:52:01 +0000 (14:52 +0000)]
scale bug fixed

19 years agoselection area search bugs fixed
amwaterhouse [Wed, 16 Mar 2005 14:51:41 +0000 (14:51 +0000)]
selection area search bugs fixed

19 years agoNew class, allows sorting
amwaterhouse [Wed, 16 Mar 2005 14:49:17 +0000 (14:49 +0000)]
New class, allows sorting

19 years agoSaves screen size on exit
amwaterhouse [Tue, 15 Mar 2005 17:10:46 +0000 (17:10 +0000)]
Saves screen size on exit

19 years agosetbackground white
amwaterhouse [Tue, 15 Mar 2005 16:34:06 +0000 (16:34 +0000)]
setbackground white

19 years agoinitial label width bug might be fixed at last
amwaterhouse [Tue, 15 Mar 2005 16:33:36 +0000 (16:33 +0000)]
initial label width bug might be fixed at last

19 years agostick with cross platform look and feel!!!
amwaterhouse [Tue, 15 Mar 2005 16:33:03 +0000 (16:33 +0000)]
stick with cross platform look and feel!!!

19 years agoset groups visible(false)
amwaterhouse [Tue, 15 Mar 2005 16:13:12 +0000 (16:13 +0000)]
set groups visible(false)

19 years agonew hscrollfillpanel
amwaterhouse [Tue, 15 Mar 2005 16:12:42 +0000 (16:12 +0000)]
new hscrollfillpanel

19 years agouse the fileview
amwaterhouse [Tue, 15 Mar 2005 16:12:00 +0000 (16:12 +0000)]
use the fileview

19 years agonew class
amwaterhouse [Tue, 15 Mar 2005 16:08:15 +0000 (16:08 +0000)]
new class

19 years agotry system look and feel for a change
amwaterhouse [Tue, 15 Mar 2005 16:07:24 +0000 (16:07 +0000)]
try system look and feel for a change

19 years agoselection removed, now SelectionGroup does same job as id select and residue select
amwaterhouse [Tue, 15 Mar 2005 16:06:54 +0000 (16:06 +0000)]
selection removed, now SelectionGroup does same job as id select and residue select

19 years agonew file image
amwaterhouse [Tue, 15 Mar 2005 16:05:35 +0000 (16:05 +0000)]
new file image

19 years agofonts added to properties
amwaterhouse [Thu, 10 Mar 2005 10:13:48 +0000 (10:13 +0000)]
fonts added to properties

19 years agoactionlisteners added
amwaterhouse [Thu, 10 Mar 2005 10:13:18 +0000 (10:13 +0000)]
actionlisteners added

19 years agosearch and font frames are now internalframes
amwaterhouse [Thu, 10 Mar 2005 10:12:48 +0000 (10:12 +0000)]
search and font frames are now internalframes

19 years agoresized scale panel
amwaterhouse [Thu, 10 Mar 2005 10:12:16 +0000 (10:12 +0000)]
resized scale panel

19 years agofonts changed as selection made
amwaterhouse [Thu, 10 Mar 2005 10:12:01 +0000 (10:12 +0000)]
fonts changed as selection made

19 years agoScale canvas not needed
amwaterhouse [Thu, 10 Mar 2005 10:11:42 +0000 (10:11 +0000)]
Scale canvas not needed

19 years agoclear selection once group defined
amwaterhouse [Wed, 9 Mar 2005 18:40:15 +0000 (18:40 +0000)]
clear selection once group defined

19 years agoclear selection
amwaterhouse [Wed, 9 Mar 2005 18:39:45 +0000 (18:39 +0000)]
clear selection

19 years agodelete chars added
amwaterhouse [Wed, 9 Mar 2005 18:38:50 +0000 (18:38 +0000)]
delete chars added

19 years agoclear selection with escape key
amwaterhouse [Wed, 9 Mar 2005 18:37:50 +0000 (18:37 +0000)]
clear selection with escape key

19 years agofont chooser added
amwaterhouse [Wed, 9 Mar 2005 18:37:09 +0000 (18:37 +0000)]
font chooser added

19 years agoallows deletion of chars, font chooser added
amwaterhouse [Wed, 9 Mar 2005 18:36:17 +0000 (18:36 +0000)]
allows deletion of chars, font chooser added

19 years agoallows deletion of chars
amwaterhouse [Wed, 9 Mar 2005 18:35:46 +0000 (18:35 +0000)]
allows deletion of chars

19 years agodont perform blast search at present
amwaterhouse [Wed, 9 Mar 2005 18:35:03 +0000 (18:35 +0000)]
dont perform blast search at present

19 years agoadd lower case residue props
amwaterhouse [Tue, 8 Mar 2005 18:12:13 +0000 (18:12 +0000)]
add lower case residue props

19 years agofixed interface for PID method.
jprocter [Tue, 8 Mar 2005 16:45:22 +0000 (16:45 +0000)]
fixed interface for PID method.

19 years agofixed so that alignment percentage ID is used for distance calculation
jprocter [Tue, 8 Mar 2005 16:44:11 +0000 (16:44 +0000)]
fixed so that alignment percentage ID is used for distance calculation

19 years agofixed signing bug (also updated to latest javahelp library)
jprocter [Tue, 8 Mar 2005 16:43:05 +0000 (16:43 +0000)]
fixed signing bug (also updated to latest javahelp library)

19 years agomore precise methods information in help description.
jprocter [Tue, 8 Mar 2005 16:42:01 +0000 (16:42 +0000)]
more precise methods information in help description.

19 years agofixed some of the jar/wsdl deployment problems.
jprocter [Tue, 8 Mar 2005 16:40:45 +0000 (16:40 +0000)]
fixed some of the jar/wsdl deployment problems.

19 years agoremoved conservation calculation from calculations.
jprocter [Tue, 8 Mar 2005 16:40:11 +0000 (16:40 +0000)]
removed conservation calculation from calculations.

19 years agoTree fits to window by default
amwaterhouse [Tue, 8 Mar 2005 16:36:48 +0000 (16:36 +0000)]
Tree fits to window by default

19 years agogetCharwidth directly
amwaterhouse [Tue, 8 Mar 2005 14:49:41 +0000 (14:49 +0000)]
getCharwidth directly

19 years agoDont set paintFlags
amwaterhouse [Tue, 8 Mar 2005 14:41:51 +0000 (14:41 +0000)]
Dont set paintFlags

19 years agodont set seqPanel paint flag
amwaterhouse [Tue, 8 Mar 2005 14:35:26 +0000 (14:35 +0000)]
dont set seqPanel paint flag

19 years agoonly set graphics black once at beginning of text
amwaterhouse [Tue, 8 Mar 2005 14:34:10 +0000 (14:34 +0000)]
only set graphics black once at beginning of text

19 years agodont color gaps in sequence features
amwaterhouse [Tue, 8 Mar 2005 14:32:21 +0000 (14:32 +0000)]
dont color gaps in sequence features

19 years agoif resIndex > 19 return color.white
amwaterhouse [Tue, 8 Mar 2005 14:31:40 +0000 (14:31 +0000)]
if resIndex > 19 return color.white

19 years agoObsolete. Explanation within the conservation colourscheme entry.
jprocter [Tue, 1 Mar 2005 16:51:50 +0000 (16:51 +0000)]
Obsolete. Explanation within the conservation colourscheme entry.

19 years agoadded uniquify sequence id assertion.
jprocter [Mon, 28 Feb 2005 10:47:32 +0000 (10:47 +0000)]
added uniquify sequence id assertion.

19 years agopartial implementation of JNet server prediction.
jprocter [Mon, 28 Feb 2005 10:45:52 +0000 (10:45 +0000)]
partial implementation of JNet server prediction.

19 years agofirst stab at a JPredClient.
jprocter [Mon, 28 Feb 2005 10:43:43 +0000 (10:43 +0000)]
first stab at a JPredClient.

19 years agobasic jpred concise prediction reader.
jprocter [Wed, 23 Feb 2005 15:57:04 +0000 (15:57 +0000)]
basic jpred concise prediction reader.

19 years agonew resources location.
jprocter [Wed, 23 Feb 2005 15:53:19 +0000 (15:53 +0000)]
new resources location.

19 years agorearranged project structure
jprocter [Wed, 23 Feb 2005 15:51:59 +0000 (15:51 +0000)]
rearranged project structure

19 years agomaking Jemboss client more configurable.
jprocter [Wed, 23 Feb 2005 15:51:44 +0000 (15:51 +0000)]
making Jemboss client more configurable.