selects default colour
40 lines of code changed in:
just tidying up unused imports
29 lines of code changed in:
stopped duplicate jars appearing in jalview.jar
beginning of 'automatic ws client' generation.
43 lines of code changed in:
REad in defaultColour
5 lines of code changed in:
preferences held statically
124 lines of code changed in:
preferences moved to desktop
1241 lines of code changed in:
read in preferences at start up
2 lines of code changed in:
Added MuscleWS back in
13 lines of code changed in:
First try with MuscleWS and vamsas.simple.objects
1356 lines of code changed in:
First try with MuscleWS
734 lines of code changed in:
no longer used
0 lines of code changed in:
Label changes as AF recommended
119 lines of code changed in:
must set consensus in child colourscheme
88 lines of code changed in:
Updated for use by preferences panel
77 lines of code changed in:
GUI changes
598 lines of code changed in:
Preferences panel added
13 lines of code changed in:
Viewport now looks at preferences when loading up
66 lines of code changed in:
Set fullscreen if in preferences
13 lines of code changed in:
can search ids
17 lines of code changed in:
set as default added
20 lines of code changed in:
search ids added
36 lines of code changed in:
Menu names changed
31 lines of code changed in:
JInternalFrame is within class. Method to load default added
43 lines of code changed in:
Preferences panel added
113 lines of code changed in:
set gap char modified
2 lines of code changed in:
added MuscleWS and did a bit more standardisation of WS threads.
62 lines of code changed in:
if applet, load properties in void init
1 lines of code changed in:
+1 in fastpaint sends coloured text outofbounds
1 lines of code changed in:
dont update overview every repaint
0 lines of code changed in:
Loading alignment threaded
33 lines of code changed in:
Syncronize drawPanel, as overviewpanel is threaded
1 lines of code changed in:
Overviewpanel allows for large alignments
155 lines of code changed in:
add consslider to palette layer
3 lines of code changed in:
Allow for clipped region when printing
15 lines of code changed in:
Tick 5 and 10 marks
29 lines of code changed in:
Printing changes
161 lines of code changed in:
update conSlider when colour changes
2 lines of code changed in:
Allow for -open arg
7 lines of code changed in:
no need to keep setting selected, its on the palette layer
1 lines of code changed in:
add splash to palette layer
3 lines of code changed in:
Printing of trees corrected. Antialiasing on
49 lines of code changed in:
painting syncronized, spin increments in units, not loops of the thread
9 lines of code changed in:
wrap alignment box paints correctly
15 lines of code changed in:
blosum62 must have its on consensus
8 lines of code changed in:
setendres -1
1 lines of code changed in:
position of bioinformatics
3 lines of code changed in:
set PNG antialiasing on
10 lines of code changed in:
show sliders when first selecting conservation,PID
3 lines of code changed in:
dont drag beyond end of alignment
2 lines of code changed in:
selected group draws last residue
1 lines of code changed in:
repaint removed
0 lines of code changed in:
fastPaint modified incase scroll is more than page size
12 lines of code changed in:
calls fontChanged
1 lines of code changed in:
fontChanged method added, componentListener removed
20 lines of code changed in:
make sure we draw last line of wrapped alignment
1 lines of code changed in:
allow for final line of alignment
1 lines of code changed in:
fix wrap alignment vscroll visible amount
1 lines of code changed in:
check if colourscheme is null
3 lines of code changed in:
AlignPanel RefreshPanels put into paintComponent
78 lines of code changed in:
clustalx exception in colourchange
14 lines of code changed in:
no longer used
0 lines of code changed in:
consensus held in residueColour
50 lines of code changed in:
no need to send consensus
1 lines of code changed in:
takes on methods previously in desktop
107 lines of code changed in:
no need to send consensus everytime
1 lines of code changed in:
pid and conservation changes
28 lines of code changed in:
adjust annotation panel height when font changed
1 lines of code changed in:
pid and conservation slider moved to sliderPanel
0 lines of code changed in:
fontmetrics must be obtained after font change
3 lines of code changed in:
draw graph label lower down
7 lines of code changed in:
public vconsensus available for PID and Blosum
17 lines of code changed in:
PID and conservation colouring changes
87 lines of code changed in:
conservation & consensus recalc if group changed
24 lines of code changed in:
comment out jnetpropb, h and c
3 lines of code changed in:
not added to the palette layer
0 lines of code changed in:
use 3 as the threshold
3 lines of code changed in:
if image is null, repaint
1 lines of code changed in:
blosum colour now displayed ok
9 lines of code changed in:
use webservice info
29 lines of code changed in:
update status bar with mouse over
7 lines of code changed in:
use webservice info to display web service state
38 lines of code changed in:
new class
222 lines of code changed in:
consistent percentage gaps filter for conservation calculation.
11 lines of code changed in:
added quality calculation from Jalview118, and scale dependent
colouring of conservation and quality histograms.
Obvious for loop optimizations have also been applied.
48 lines of code changed in:
Gap characters are now properly detected in the conservation and PID
calculation. They are always counted in the '-' element of the residue count hash.
27 lines of code changed in:
Fixed so that all alternate residues are used to calculate blosum62
conservation.
24 lines of code changed in:
Added order-preservation for clustalW alignment. No support for
recovering order yet.
11 lines of code changed in:
sortByTreeMenu added
35 lines of code changed in:
use AlignFrame.NEW_WINDOW_WIDTH
1 lines of code changed in:
getTree method added
4 lines of code changed in:
if not active tree, colour threshold grey
6 lines of code changed in:
use NEW_WINDOW_WIDTH
3 lines of code changed in:
invalidate alignPanel before changing size
1 lines of code changed in:
new constructor for addtodesktop, sliders set to top layer
19 lines of code changed in:
draws last residue
6 lines of code changed in:
repainting issues fixed
2 lines of code changed in:
treeMenuItem added, conservation sliders, finder top layer
77 lines of code changed in:
added the alignment quality calculation from the old jalview, and
tried to debug conservation calculation based on existing alscript
code.
47 lines of code changed in:
Conservation symbols : + = all props are conserved, * residues are
identical.
2 lines of code changed in:
Fixed the job-failed message.
3 lines of code changed in:
Now tries to set viewing parameters for distances and bootstraps appropriately.
2 lines of code changed in:
slight mods again.
1 lines of code changed in:
try out spinning logo
27 lines of code changed in:
return from painting if size is 0
2 lines of code changed in:
Printing wrapped alignment corrected
6 lines of code changed in:
Display of wrapped search results corrected
4 lines of code changed in:
endREs -1
3 lines of code changed in:
conservation changed to quality
2 lines of code changed in:
clear the last area in fast paint
6 lines of code changed in:
scale above, left right added
201 lines of code changed in:
bug adding null sequence to selection fixed
5 lines of code changed in:
reads fasta files from uniprot web page
6 lines of code changed in:
scale above, left rigt added
54 lines of code changed in:
WebStartLocation form.
1 lines of code changed in:
trival.
1 lines of code changed in:
Fixed broken jnlp creation.
8 lines of code changed in:
remember: do not check in quick bug fixes that you didn't test.
5 lines of code changed in:
recent rebuild of the JPred client from WSDL2Java
24 lines of code changed in:
Alignment quality with funky coloured histograms.
206 lines of code changed in:
updated build strategy and checking for portability.
194 lines of code changed in:
no more group editor
5 lines of code changed in:
check annotation label widths as well as id widths
14 lines of code changed in:
calls repaint, not just refreshpanels
1 lines of code changed in:
for now, draw selection box bottom -1
20 lines of code changed in:
seals selection box if at bottom of alignment
1 lines of code changed in:
draws threshold position according to threshold, not mouse x
8 lines of code changed in:
no more group editor
0 lines of code changed in:
no longer used
0 lines of code changed in:
Remove paintFlag ref
0 lines of code changed in:
GRPAH_HEIGHT variable
6 lines of code changed in:
checkfor gap characters
7 lines of code changed in:
paintFlag removed
0 lines of code changed in:
fastPaint flag added
43 lines of code changed in:
reomve call to repaint
0 lines of code changed in:
find top and bottom of group
32 lines of code changed in:
add note about desktopManager
6 lines of code changed in:
add fastPaint boolean
24 lines of code changed in:
remove setdecorated line
0 lines of code changed in:
amino acid gifs
171 lines of code changed in:
dont draw first block if colour is null
8 lines of code changed in:
fill in the gaps
30 lines of code changed in:
setDesktopManager(new)
2 lines of code changed in:
paint is now in drawComponent
5 lines of code changed in:
showAnnotation added
12 lines of code changed in:
annoation in print version
32 lines of code changed in:
DONT SHOW ANNOTATIONS IF WRAPPED
13 lines of code changed in:
next version of Jpred functionality using new client code.
190 lines of code changed in:
New method for helping to quickly map different aligned versions of a
sequence.
17 lines of code changed in:
New client code for JPred service includes return of msa and
Jprediction, and better job status information
(vamsas.dataTypes.Result).
909 lines of code changed in:
mosueOver graph gives int, not float
1 lines of code changed in:
Fast paint method implemented
196 lines of code changed in:
Alignment Annotation added
46 lines of code changed in:
ignore jnetconf
4 lines of code changed in:
parses jpredfile into new alignment annotation
88 lines of code changed in:
update conservation and consensus
6 lines of code changed in:
anti_aliasing on
20 lines of code changed in:
Uses conservation graph
3 lines of code changed in:
testing Graphics2D
3 lines of code changed in:
setMaximizable(false)
3 lines of code changed in:
Alignment Annotation added
230 lines of code changed in:
Build date determination
11 lines of code changed in:
Alignment Annotation added
819 lines of code changed in: