jalview.git
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

19 years agodrag and drop files into jalview
amwaterhouse [Tue, 22 Mar 2005 12:18:16 +0000 (12:18 +0000)]
drag and drop files into jalview

19 years agoadd swing runnable to refresh panel on startup
amwaterhouse [Tue, 22 Mar 2005 12:17:56 +0000 (12:17 +0000)]
add swing runnable to refresh panel on startup