jalview.git
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

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