jalview.git
19 years agoformatAdapter.formats, remove redundant code
amwaterhouse [Tue, 3 May 2005 12:46:13 +0000 (12:46 +0000)]
formatAdapter.formats, remove redundant code

19 years ago1.1 compatible, formatting changes
amwaterhouse [Tue, 3 May 2005 12:43:54 +0000 (12:43 +0000)]
1.1 compatible, formatting changes

19 years agoFormatAdapter readFile
amwaterhouse [Tue, 3 May 2005 12:42:25 +0000 (12:42 +0000)]
FormatAdapter readFile

19 years ago1.1 compatible
amwaterhouse [Tue, 3 May 2005 12:41:39 +0000 (12:41 +0000)]
1.1 compatible

19 years agofindKmers and fetchSequenceFeatures removed
amwaterhouse [Tue, 3 May 2005 12:39:06 +0000 (12:39 +0000)]
findKmers and fetchSequenceFeatures removed

19 years agoRemoved as obfuscation of classes wiill change class names
amwaterhouse [Tue, 3 May 2005 12:38:04 +0000 (12:38 +0000)]
Removed as obfuscation of classes wiill change class names

19 years agoselects default colour
amwaterhouse [Fri, 29 Apr 2005 15:27:31 +0000 (15:27 +0000)]
selects default colour

19 years agojust tidying up unused imports
amwaterhouse [Fri, 29 Apr 2005 15:26:51 +0000 (15:26 +0000)]
just tidying up unused imports

19 years agostopped duplicate jars appearing in jalview.jar
jprocter [Fri, 29 Apr 2005 14:50:01 +0000 (14:50 +0000)]
stopped duplicate jars appearing in jalview.jar
beginning of 'automatic ws client' generation.

19 years agoREad in defaultColour
amwaterhouse [Fri, 29 Apr 2005 11:05:11 +0000 (11:05 +0000)]
REad in defaultColour

19 years agopreferences held statically
amwaterhouse [Fri, 29 Apr 2005 10:42:48 +0000 (10:42 +0000)]
preferences held statically

19 years agopreferences moved to desktop
amwaterhouse [Fri, 29 Apr 2005 10:41:47 +0000 (10:41 +0000)]
preferences moved to desktop

19 years agoread in preferences at start up
amwaterhouse [Fri, 29 Apr 2005 10:40:43 +0000 (10:40 +0000)]
read in preferences at start up

19 years agoAdded MuscleWS back in
jprocter [Thu, 28 Apr 2005 16:15:18 +0000 (16:15 +0000)]
Added MuscleWS back in

19 years agoFirst try with MuscleWS and vamsas.simple.objects
jprocter [Thu, 28 Apr 2005 15:50:11 +0000 (15:50 +0000)]
First try with MuscleWS and vamsas.simple.objects

19 years agoFirst try with MuscleWS
jprocter [Thu, 28 Apr 2005 15:46:32 +0000 (15:46 +0000)]
First try with MuscleWS

19 years agono longer used
amwaterhouse [Thu, 28 Apr 2005 15:44:35 +0000 (15:44 +0000)]
no longer used

19 years agoLabel changes as AF recommended
amwaterhouse [Thu, 28 Apr 2005 15:42:34 +0000 (15:42 +0000)]
Label changes as AF recommended

19 years agomust set consensus in child colourscheme
amwaterhouse [Thu, 28 Apr 2005 15:41:58 +0000 (15:41 +0000)]
must set consensus in child colourscheme

19 years agoUpdated for use by preferences panel
amwaterhouse [Thu, 28 Apr 2005 15:41:34 +0000 (15:41 +0000)]
Updated for use by preferences panel

19 years agoGUI changes
amwaterhouse [Thu, 28 Apr 2005 15:35:30 +0000 (15:35 +0000)]
GUI changes

19 years agoPreferences panel added
amwaterhouse [Thu, 28 Apr 2005 15:33:56 +0000 (15:33 +0000)]
Preferences panel added

19 years agoViewport now looks at preferences when loading up
amwaterhouse [Thu, 28 Apr 2005 15:33:12 +0000 (15:33 +0000)]
Viewport now looks at preferences when loading up

19 years agoSet fullscreen if in preferences
amwaterhouse [Thu, 28 Apr 2005 15:32:28 +0000 (15:32 +0000)]
Set fullscreen if in preferences

19 years agocan search ids
amwaterhouse [Thu, 28 Apr 2005 15:31:43 +0000 (15:31 +0000)]
can search ids

19 years agoset as default added
amwaterhouse [Thu, 28 Apr 2005 15:31:28 +0000 (15:31 +0000)]
set as default added

19 years agosearch ids added
amwaterhouse [Thu, 28 Apr 2005 15:31:09 +0000 (15:31 +0000)]
search ids added

19 years agoMenu names changed
amwaterhouse [Thu, 28 Apr 2005 15:30:28 +0000 (15:30 +0000)]
Menu names changed

19 years agoJInternalFrame is within class. Method to load default added
amwaterhouse [Thu, 28 Apr 2005 15:29:54 +0000 (15:29 +0000)]
JInternalFrame is within class. Method to load default added

19 years agoPreferences panel added
amwaterhouse [Thu, 28 Apr 2005 15:28:28 +0000 (15:28 +0000)]
Preferences panel added

19 years agoset gap char modified
amwaterhouse [Thu, 28 Apr 2005 15:27:57 +0000 (15:27 +0000)]
set gap char modified

19 years agoadded MuscleWS and did a bit more standardisation of WS threads.
jprocter [Thu, 28 Apr 2005 14:28:43 +0000 (14:28 +0000)]
added MuscleWS and did a bit more standardisation of WS threads.

19 years agoif applet, load properties in void init
amwaterhouse [Mon, 25 Apr 2005 16:50:52 +0000 (16:50 +0000)]
if applet, load properties in void init

19 years ago+1 in fastpaint sends coloured text outofbounds
amwaterhouse [Mon, 25 Apr 2005 16:50:27 +0000 (16:50 +0000)]
+1 in fastpaint sends coloured text outofbounds

19 years agodont update overview every repaint
amwaterhouse [Mon, 25 Apr 2005 08:58:03 +0000 (08:58 +0000)]
dont update overview every repaint

19 years agoLoading alignment threaded
amwaterhouse [Mon, 25 Apr 2005 08:52:13 +0000 (08:52 +0000)]
Loading alignment threaded

19 years agoSyncronize drawPanel, as overviewpanel is threaded
amwaterhouse [Mon, 25 Apr 2005 08:51:33 +0000 (08:51 +0000)]
Syncronize drawPanel, as overviewpanel is threaded

19 years agoOverviewpanel allows for large alignments
amwaterhouse [Mon, 25 Apr 2005 08:50:50 +0000 (08:50 +0000)]
Overviewpanel allows for large alignments

19 years agoadd consslider to palette layer
amwaterhouse [Thu, 21 Apr 2005 17:24:58 +0000 (17:24 +0000)]
add consslider to palette layer

19 years agoAllow for clipped region when printing
amwaterhouse [Thu, 21 Apr 2005 17:23:30 +0000 (17:23 +0000)]
Allow for clipped region when printing

19 years agoTick 5 and 10 marks
amwaterhouse [Thu, 21 Apr 2005 17:23:03 +0000 (17:23 +0000)]
Tick 5 and 10 marks

19 years agoPrinting changes
amwaterhouse [Thu, 21 Apr 2005 17:22:27 +0000 (17:22 +0000)]
Printing changes

19 years agoupdate conSlider when colour changes
amwaterhouse [Thu, 21 Apr 2005 17:21:59 +0000 (17:21 +0000)]
update conSlider when colour changes

19 years agoAllow for -open arg
amwaterhouse [Thu, 21 Apr 2005 17:21:20 +0000 (17:21 +0000)]
Allow for -open arg

19 years agono need to keep setting selected, its on the palette layer
amwaterhouse [Tue, 19 Apr 2005 16:18:04 +0000 (16:18 +0000)]
no need to keep setting selected, its on the palette layer

19 years agoadd splash to palette layer
amwaterhouse [Tue, 19 Apr 2005 16:17:37 +0000 (16:17 +0000)]
add splash to palette layer

19 years agoPrinting of trees corrected. Antialiasing on
amwaterhouse [Tue, 19 Apr 2005 12:15:13 +0000 (12:15 +0000)]
Printing of trees corrected. Antialiasing on

19 years agopainting syncronized, spin increments in units, not loops of the thread
amwaterhouse [Mon, 18 Apr 2005 16:05:30 +0000 (16:05 +0000)]
painting syncronized, spin increments in units, not loops of the thread

19 years agowrap alignment box paints correctly
amwaterhouse [Mon, 18 Apr 2005 16:04:37 +0000 (16:04 +0000)]
wrap alignment box paints correctly

19 years agoblosum62 must have its on consensus
amwaterhouse [Mon, 18 Apr 2005 16:03:51 +0000 (16:03 +0000)]
blosum62 must have its on consensus

19 years agosetendres -1
amwaterhouse [Mon, 18 Apr 2005 16:03:24 +0000 (16:03 +0000)]
setendres -1

19 years agoposition of bioinformatics
amwaterhouse [Mon, 18 Apr 2005 16:02:56 +0000 (16:02 +0000)]
position of bioinformatics

19 years agoset PNG antialiasing on
amwaterhouse [Mon, 18 Apr 2005 16:02:27 +0000 (16:02 +0000)]
set PNG antialiasing on

19 years agoshow sliders when first selecting conservation,PID
amwaterhouse [Mon, 18 Apr 2005 16:01:42 +0000 (16:01 +0000)]
show sliders when first selecting conservation,PID

19 years agodont drag beyond end of alignment
amwaterhouse [Mon, 18 Apr 2005 08:08:05 +0000 (08:08 +0000)]
dont drag beyond end of alignment

19 years agoselected group draws last residue
amwaterhouse [Mon, 18 Apr 2005 08:07:27 +0000 (08:07 +0000)]
selected group draws last residue

19 years agorepaint removed
amwaterhouse [Mon, 18 Apr 2005 08:05:41 +0000 (08:05 +0000)]
repaint removed

19 years agofastPaint modified incase scroll is more than page size
amwaterhouse [Mon, 18 Apr 2005 08:04:44 +0000 (08:04 +0000)]
fastPaint modified incase scroll is more than page size

19 years agocalls fontChanged
amwaterhouse [Mon, 18 Apr 2005 08:03:56 +0000 (08:03 +0000)]
calls fontChanged

19 years agofontChanged method added, componentListener removed
amwaterhouse [Mon, 18 Apr 2005 08:03:41 +0000 (08:03 +0000)]
fontChanged method added, componentListener removed

19 years agomake sure we draw last line of wrapped alignment
amwaterhouse [Sat, 16 Apr 2005 15:40:32 +0000 (15:40 +0000)]
make sure we draw last line of wrapped alignment

19 years agoallow for final line of alignment
amwaterhouse [Sat, 16 Apr 2005 15:38:16 +0000 (15:38 +0000)]
allow for final line of alignment

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