jalview.git
19 years agofix wrap alignment vscroll visible amount
amwaterhouse [Sat, 16 Apr 2005 15:37:07 +0000 (15:37 +0000)]
fix wrap alignment vscroll visible amount

19 years agocheck if colourscheme is null
amwaterhouse [Sat, 16 Apr 2005 15:36:30 +0000 (15:36 +0000)]
check if colourscheme is null

19 years agoAlignPanel RefreshPanels put into paintComponent
amwaterhouse [Sat, 16 Apr 2005 13:46:56 +0000 (13:46 +0000)]
AlignPanel RefreshPanels put into paintComponent

19 years agoclustalx exception in colourchange
amwaterhouse [Fri, 15 Apr 2005 15:16:54 +0000 (15:16 +0000)]
clustalx exception in colourchange

19 years agono longer used
amwaterhouse [Fri, 15 Apr 2005 15:09:18 +0000 (15:09 +0000)]
no longer used

19 years agoconsensus held in residueColour
amwaterhouse [Fri, 15 Apr 2005 15:06:50 +0000 (15:06 +0000)]
consensus held in residueColour

19 years agono need to send consensus
amwaterhouse [Fri, 15 Apr 2005 15:02:34 +0000 (15:02 +0000)]
no need to send consensus

19 years agotakes on methods previously in desktop
amwaterhouse [Fri, 15 Apr 2005 15:02:02 +0000 (15:02 +0000)]
takes on methods previously in desktop

19 years agono need to send consensus everytime
amwaterhouse [Fri, 15 Apr 2005 15:01:35 +0000 (15:01 +0000)]
no need to send consensus everytime

19 years agopid and conservation changes
amwaterhouse [Fri, 15 Apr 2005 15:00:57 +0000 (15:00 +0000)]
pid and conservation changes

19 years agoadjust annotation panel height when font changed
amwaterhouse [Fri, 15 Apr 2005 15:00:26 +0000 (15:00 +0000)]
adjust annotation panel height when font changed

19 years agopid and conservation slider moved to sliderPanel
amwaterhouse [Fri, 15 Apr 2005 14:59:46 +0000 (14:59 +0000)]
pid and conservation slider moved to sliderPanel

19 years agofontmetrics must be obtained after font change
amwaterhouse [Fri, 15 Apr 2005 14:59:24 +0000 (14:59 +0000)]
fontmetrics must be obtained after font change

19 years agodraw graph label lower down
amwaterhouse [Fri, 15 Apr 2005 14:58:34 +0000 (14:58 +0000)]
draw graph label lower down

19 years agopublic vconsensus available for PID and Blosum
amwaterhouse [Fri, 15 Apr 2005 14:58:13 +0000 (14:58 +0000)]
public vconsensus available for PID and Blosum

19 years agoPID and conservation colouring changes
amwaterhouse [Fri, 15 Apr 2005 14:57:25 +0000 (14:57 +0000)]
PID and conservation colouring changes

19 years agoconservation & consensus recalc if group changed
amwaterhouse [Fri, 15 Apr 2005 14:56:12 +0000 (14:56 +0000)]
conservation & consensus recalc if group changed

19 years agocomment out jnetpropb, h and c
amwaterhouse [Thu, 14 Apr 2005 16:56:24 +0000 (16:56 +0000)]
comment out jnetpropb, h and c

19 years agonot added to the palette layer
amwaterhouse [Thu, 14 Apr 2005 16:54:17 +0000 (16:54 +0000)]
not added to the palette layer

19 years agouse 3 as the threshold
amwaterhouse [Thu, 14 Apr 2005 16:53:51 +0000 (16:53 +0000)]
use 3 as the threshold

19 years agoif image is null, repaint
amwaterhouse [Thu, 14 Apr 2005 16:53:13 +0000 (16:53 +0000)]
if image is null, repaint

19 years agoblosum colour now displayed ok
amwaterhouse [Thu, 14 Apr 2005 16:52:43 +0000 (16:52 +0000)]
blosum colour now displayed ok

19 years agouse webservice info
amwaterhouse [Thu, 14 Apr 2005 15:05:08 +0000 (15:05 +0000)]
use webservice info

19 years agoupdate status bar with mouse over
amwaterhouse [Thu, 14 Apr 2005 15:04:45 +0000 (15:04 +0000)]
update status bar with mouse over

19 years agouse webservice info to display web service state
amwaterhouse [Thu, 14 Apr 2005 15:04:13 +0000 (15:04 +0000)]
use webservice info to display web service state

19 years agonew class
amwaterhouse [Thu, 14 Apr 2005 15:03:40 +0000 (15:03 +0000)]
new class

19 years agoconsistent percentage gaps filter for conservation calculation.
jprocter [Thu, 14 Apr 2005 14:43:25 +0000 (14:43 +0000)]
consistent percentage gaps filter for conservation calculation.

19 years agoadded quality calculation from Jalview118, and scale dependent
jprocter [Thu, 14 Apr 2005 09:14:19 +0000 (09:14 +0000)]
added quality calculation from Jalview118, and scale dependent
colouring of conservation and quality histograms.
Obvious for loop optimizations have also been applied.

19 years agoGap characters are now properly detected in the conservation and PID
jprocter [Wed, 13 Apr 2005 16:42:21 +0000 (16:42 +0000)]
Gap characters are now properly detected in the conservation and PID
calculation. They are always counted in the '-' element of the residue count hash.

19 years agoFixed so that all alternate residues are used to calculate blosum62
jprocter [Wed, 13 Apr 2005 16:40:53 +0000 (16:40 +0000)]
Fixed so that all alternate residues are used to calculate blosum62
conservation.

19 years agoAdded order-preservation for clustalW alignment. No support for
jprocter [Wed, 13 Apr 2005 16:39:13 +0000 (16:39 +0000)]
Added order-preservation for clustalW alignment. No support for
recovering order yet.

19 years agosortByTreeMenu added
amwaterhouse [Wed, 13 Apr 2005 16:37:15 +0000 (16:37 +0000)]
sortByTreeMenu added

19 years agouse AlignFrame.NEW_WINDOW_WIDTH
amwaterhouse [Wed, 13 Apr 2005 16:36:55 +0000 (16:36 +0000)]
use AlignFrame.NEW_WINDOW_WIDTH

19 years agogetTree method added
amwaterhouse [Wed, 13 Apr 2005 16:36:18 +0000 (16:36 +0000)]
getTree method added

19 years agoif not active tree, colour threshold grey
amwaterhouse [Wed, 13 Apr 2005 16:35:48 +0000 (16:35 +0000)]
if not active tree, colour threshold grey

19 years agouse NEW_WINDOW_WIDTH
amwaterhouse [Wed, 13 Apr 2005 16:35:22 +0000 (16:35 +0000)]
use NEW_WINDOW_WIDTH

19 years agoinvalidate alignPanel before changing size
amwaterhouse [Wed, 13 Apr 2005 16:34:48 +0000 (16:34 +0000)]
invalidate alignPanel before changing size

19 years agonew constructor for addtodesktop, sliders set to top layer
amwaterhouse [Wed, 13 Apr 2005 16:34:03 +0000 (16:34 +0000)]
new constructor for addtodesktop, sliders set to top layer

19 years agodraws last residue
amwaterhouse [Wed, 13 Apr 2005 16:33:26 +0000 (16:33 +0000)]
draws last residue

19 years agorepainting issues fixed
amwaterhouse [Wed, 13 Apr 2005 16:33:11 +0000 (16:33 +0000)]
repainting issues fixed

19 years agotreeMenuItem added, conservation sliders, finder top layer
amwaterhouse [Wed, 13 Apr 2005 16:32:55 +0000 (16:32 +0000)]
treeMenuItem added, conservation sliders, finder top layer

19 years agoadded the alignment quality calculation from the old jalview, and
jprocter [Mon, 11 Apr 2005 16:54:38 +0000 (16:54 +0000)]
added the alignment quality calculation from the old jalview, and
tried to debug conservation calculation based on existing alscript
code.

19 years agoConservation symbols : + = all props are conserved, * residues are
jprocter [Mon, 11 Apr 2005 16:46:14 +0000 (16:46 +0000)]
Conservation symbols : + = all props are conserved, * residues are
identical.

19 years agoFixed the job-failed message.
jprocter [Mon, 11 Apr 2005 16:45:36 +0000 (16:45 +0000)]
Fixed the job-failed message.

19 years agoNow tries to set viewing parameters for distances and bootstraps appropriately.
jprocter [Mon, 11 Apr 2005 16:39:33 +0000 (16:39 +0000)]
Now tries to set viewing parameters for distances and bootstraps appropriately.

19 years agoslight mods again.
jprocter [Fri, 8 Apr 2005 16:17:38 +0000 (16:17 +0000)]
slight mods again.

19 years agotry out spinning logo
amwaterhouse [Fri, 8 Apr 2005 16:15:29 +0000 (16:15 +0000)]
try out spinning logo

19 years agoreturn from painting if size is 0
amwaterhouse [Fri, 8 Apr 2005 16:15:06 +0000 (16:15 +0000)]
return from painting if size is 0

19 years agoPrinting wrapped alignment corrected
amwaterhouse [Fri, 8 Apr 2005 15:42:32 +0000 (15:42 +0000)]
Printing wrapped alignment corrected

19 years agoDisplay of wrapped search results corrected
amwaterhouse [Fri, 8 Apr 2005 15:35:27 +0000 (15:35 +0000)]
Display of wrapped search results corrected

19 years agoendREs -1
amwaterhouse [Fri, 8 Apr 2005 15:16:41 +0000 (15:16 +0000)]
endREs -1

19 years agoconservation changed to quality
amwaterhouse [Fri, 8 Apr 2005 15:16:10 +0000 (15:16 +0000)]
conservation changed to quality

19 years agoclear the last area in fast paint
amwaterhouse [Fri, 8 Apr 2005 15:04:23 +0000 (15:04 +0000)]
clear the last area in fast paint

19 years agoscale above, left right added
amwaterhouse [Fri, 8 Apr 2005 15:03:36 +0000 (15:03 +0000)]
scale above, left right added

19 years agobug adding null sequence to selection fixed
amwaterhouse [Fri, 8 Apr 2005 15:01:52 +0000 (15:01 +0000)]
bug adding null sequence to selection fixed

19 years agoreads fasta files from uniprot web page
amwaterhouse [Fri, 8 Apr 2005 15:01:16 +0000 (15:01 +0000)]
reads fasta files from uniprot web page

19 years agoscale above, left rigt added
amwaterhouse [Fri, 8 Apr 2005 15:00:52 +0000 (15:00 +0000)]
scale above, left rigt added

19 years agoWebStartLocation form.
jprocter [Fri, 8 Apr 2005 15:00:43 +0000 (15:00 +0000)]
WebStartLocation form.

19 years agotrival.
jprocter [Fri, 8 Apr 2005 14:54:24 +0000 (14:54 +0000)]
trival.

19 years agoFixed broken jnlp creation.
jprocter [Fri, 8 Apr 2005 14:51:09 +0000 (14:51 +0000)]
Fixed broken jnlp creation.

19 years agoremember: do not check in quick bug fixes that you didn't test.
jprocter [Fri, 8 Apr 2005 14:07:18 +0000 (14:07 +0000)]
remember: do not check in quick bug fixes that you didn't test.

19 years agorecent rebuild of the JPred client from WSDL2Java
jprocter [Fri, 8 Apr 2005 13:12:43 +0000 (13:12 +0000)]
recent rebuild of the JPred client from WSDL2Java

19 years agoAlignment quality with funky coloured histograms.
jprocter [Fri, 8 Apr 2005 12:47:56 +0000 (12:47 +0000)]
Alignment quality with funky coloured histograms.

19 years agoupdated build strategy and checking for portability.
jprocter [Fri, 8 Apr 2005 12:46:10 +0000 (12:46 +0000)]
updated build strategy and checking for portability.

19 years agono more group editor
amwaterhouse [Thu, 7 Apr 2005 17:00:14 +0000 (17:00 +0000)]
no more group editor

19 years agocheck annotation label widths as well as id widths
amwaterhouse [Thu, 7 Apr 2005 16:59:48 +0000 (16:59 +0000)]
check annotation label widths as well as id widths

19 years agocalls repaint, not just refreshpanels
amwaterhouse [Thu, 7 Apr 2005 16:59:13 +0000 (16:59 +0000)]
calls repaint, not just refreshpanels

19 years agofor now, draw selection box bottom -1
amwaterhouse [Thu, 7 Apr 2005 16:58:38 +0000 (16:58 +0000)]
for now, draw selection box bottom -1

19 years agoseals selection box if at bottom of alignment
amwaterhouse [Thu, 7 Apr 2005 16:57:57 +0000 (16:57 +0000)]
seals selection box if at bottom of alignment

19 years agodraws threshold position according to threshold, not mouse x
amwaterhouse [Thu, 7 Apr 2005 16:56:53 +0000 (16:56 +0000)]
draws threshold position according to threshold, not mouse x

19 years agono longer used
amwaterhouse [Thu, 7 Apr 2005 15:16:24 +0000 (15:16 +0000)]
no longer used

19 years agoRemove paintFlag ref
amwaterhouse [Thu, 7 Apr 2005 13:23:00 +0000 (13:23 +0000)]
Remove paintFlag ref

19 years agoGRPAH_HEIGHT variable
amwaterhouse [Thu, 7 Apr 2005 13:17:56 +0000 (13:17 +0000)]
GRPAH_HEIGHT variable

19 years agocheckfor gap characters
amwaterhouse [Thu, 7 Apr 2005 13:17:34 +0000 (13:17 +0000)]
checkfor gap characters

19 years agopaintFlag removed
amwaterhouse [Thu, 7 Apr 2005 11:35:02 +0000 (11:35 +0000)]
paintFlag removed

19 years agofastPaint flag added
amwaterhouse [Thu, 7 Apr 2005 11:34:45 +0000 (11:34 +0000)]
fastPaint flag added

19 years agoreomve call to repaint
amwaterhouse [Thu, 7 Apr 2005 10:42:44 +0000 (10:42 +0000)]
reomve call to repaint

19 years agofind top and bottom of group
amwaterhouse [Thu, 7 Apr 2005 10:42:03 +0000 (10:42 +0000)]
find top and bottom of group

19 years agoadd note about desktopManager
amwaterhouse [Thu, 7 Apr 2005 10:41:22 +0000 (10:41 +0000)]
add note about desktopManager

19 years agoadd fastPaint boolean
amwaterhouse [Thu, 7 Apr 2005 10:40:52 +0000 (10:40 +0000)]
add fastPaint boolean

19 years agoremove setdecorated line
amwaterhouse [Thu, 7 Apr 2005 10:40:30 +0000 (10:40 +0000)]
remove setdecorated line

19 years agoamino acid gifs
amwaterhouse [Thu, 7 Apr 2005 10:39:04 +0000 (10:39 +0000)]
amino acid gifs

19 years agodont draw first block if colour is null
amwaterhouse [Wed, 6 Apr 2005 17:14:39 +0000 (17:14 +0000)]
dont draw first block if colour is null

19 years agofill in the gaps
amwaterhouse [Wed, 6 Apr 2005 17:13:33 +0000 (17:13 +0000)]
fill in the gaps

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