jalview.git
18 years agojavadoc
jprocter [Sun, 20 Aug 2006 12:00:35 +0000 (12:00 +0000)]
javadoc

18 years agoCheck colourScheme is not null - jalview prior 2.5 incompatibility
amwaterhouse [Fri, 18 Aug 2006 16:54:54 +0000 (16:54 +0000)]
Check colourScheme is not null - jalview prior 2.5 incompatibility

18 years agodont remove all representative seqs on delete groups
amwaterhouse [Fri, 18 Aug 2006 14:02:52 +0000 (14:02 +0000)]
dont remove all representative seqs on delete groups

18 years agoremove all representative seqs on delete groups
amwaterhouse [Fri, 18 Aug 2006 13:57:14 +0000 (13:57 +0000)]
remove all representative seqs on delete groups

18 years agotreeFile = treeFile
amwaterhouse [Fri, 18 Aug 2006 09:23:25 +0000 (09:23 +0000)]
treeFile = treeFile

18 years agoOnly discover DAS sources if panel shown
amwaterhouse [Fri, 18 Aug 2006 08:53:07 +0000 (08:53 +0000)]
Only discover DAS sources if panel shown

18 years agoonly set new layout if 2 buttons visible
amwaterhouse [Fri, 18 Aug 2006 08:52:28 +0000 (08:52 +0000)]
only set new layout if 2 buttons visible

18 years agoJalview features format adds links as hrefs
amwaterhouse [Fri, 18 Aug 2006 08:51:58 +0000 (08:51 +0000)]
Jalview features format adds links as hrefs

18 years agoH key updates
amwaterhouse [Thu, 17 Aug 2006 14:06:02 +0000 (14:06 +0000)]
H key updates

18 years agoOptionPane invokeLater
amwaterhouse [Thu, 17 Aug 2006 13:51:56 +0000 (13:51 +0000)]
OptionPane invokeLater

18 years agoIf no annotation exists
amwaterhouse [Thu, 17 Aug 2006 13:41:37 +0000 (13:41 +0000)]
If no annotation exists

18 years agoSet bg white
amwaterhouse [Thu, 17 Aug 2006 13:41:10 +0000 (13:41 +0000)]
Set bg white

18 years agoHold onto selected region when hiding all columns only
amwaterhouse [Thu, 17 Aug 2006 13:40:57 +0000 (13:40 +0000)]
Hold onto selected region when hiding all columns only

18 years agomoved visible sub-alignment extraction and update from MsaWSThread to
jprocter [Thu, 17 Aug 2006 13:33:59 +0000 (13:33 +0000)]
moved visible sub-alignment extraction and update from MsaWSThread to
an AlignmentView method, refactored JPredClient to new abstraction and
added flags for canMergeResults and openResultsImmediatly to web
service gui.

18 years agojavadoc
jprocter [Thu, 17 Aug 2006 13:31:23 +0000 (13:31 +0000)]
javadoc

18 years agoMonospace check
amwaterhouse [Thu, 17 Aug 2006 12:34:07 +0000 (12:34 +0000)]
Monospace check

18 years ago1 more pixel allowed between chars and graph
amwaterhouse [Thu, 17 Aug 2006 12:33:55 +0000 (12:33 +0000)]
1 more pixel allowed between chars and graph

18 years agoKeys update
amwaterhouse [Thu, 17 Aug 2006 10:14:00 +0000 (10:14 +0000)]
Keys update

18 years agocontrol and shift
amwaterhouse [Thu, 17 Aug 2006 10:11:48 +0000 (10:11 +0000)]
control and shift

18 years agoDont set group null hideCOls
amwaterhouse [Thu, 17 Aug 2006 10:08:46 +0000 (10:08 +0000)]
Dont set group null hideCOls

18 years agoOptionPanes invokeLater
amwaterhouse [Thu, 17 Aug 2006 10:08:18 +0000 (10:08 +0000)]
OptionPanes invokeLater

18 years agoControl and alt for toggle hide
amwaterhouse [Thu, 17 Aug 2006 10:08:02 +0000 (10:08 +0000)]
Control and alt for toggle hide

18 years agoFire alignment changed if seqs hidden / revealed
amwaterhouse [Wed, 16 Aug 2006 08:05:35 +0000 (08:05 +0000)]
Fire alignment changed if seqs hidden / revealed

18 years agoCorrect title for sequence parameter applets
amwaterhouse [Tue, 15 Aug 2006 12:47:04 +0000 (12:47 +0000)]
Correct title for sequence parameter applets

18 years agoSequences can be added as parameter
amwaterhouse [Tue, 15 Aug 2006 12:36:11 +0000 (12:36 +0000)]
Sequences can be added as parameter

18 years agoH key added
amwaterhouse [Tue, 15 Aug 2006 11:14:25 +0000 (11:14 +0000)]
H key added

18 years agomake annotation label font size follow alignment font size.
jprocter [Tue, 15 Aug 2006 11:10:03 +0000 (11:10 +0000)]
make annotation label font size follow alignment font size.

18 years agofirst stage of adapting JNet client to hidden regions and new WSClient
jprocter [Tue, 15 Aug 2006 10:59:31 +0000 (10:59 +0000)]
first stage of adapting JNet client to hidden regions and new WSClient
structure.

18 years agofixed alignment ordering name.
jprocter [Tue, 15 Aug 2006 10:57:59 +0000 (10:57 +0000)]
fixed alignment ordering name.

18 years agoensure that close widget is available for jobs that cannot be
jprocter [Tue, 15 Aug 2006 10:57:32 +0000 (10:57 +0000)]
ensure that close widget is available for jobs that cannot be
cancelled.

18 years agoAcknowledgement
amwaterhouse [Tue, 15 Aug 2006 10:35:37 +0000 (10:35 +0000)]
Acknowledgement

18 years agoSetselectiongroup null on hide
amwaterhouse [Tue, 15 Aug 2006 10:35:09 +0000 (10:35 +0000)]
Setselectiongroup null on hide

18 years agoH key to hide / reveal
amwaterhouse [Tue, 15 Aug 2006 10:34:56 +0000 (10:34 +0000)]
H key to hide / reveal

18 years agoAdd key listener to scalePanel and annotationPanel
amwaterhouse [Tue, 15 Aug 2006 10:34:29 +0000 (10:34 +0000)]
Add key listener to scalePanel and annotationPanel

18 years agoSelect revealed seqs
amwaterhouse [Tue, 15 Aug 2006 10:34:11 +0000 (10:34 +0000)]
Select revealed seqs

18 years agoWRITEABLE_FORMATS and READABLE_FORMATS string []
amwaterhouse [Tue, 15 Aug 2006 10:02:12 +0000 (10:02 +0000)]
WRITEABLE_FORMATS and READABLE_FORMATS string []

18 years agoMove features to dataset
amwaterhouse [Tue, 15 Aug 2006 09:59:24 +0000 (09:59 +0000)]
Move features to dataset

18 years agoStockholm parser added
amwaterhouse [Mon, 14 Aug 2006 16:10:00 +0000 (16:10 +0000)]
Stockholm parser added

18 years agoStockholm parser
amwaterhouse [Mon, 14 Aug 2006 16:09:17 +0000 (16:09 +0000)]
Stockholm parser

18 years agorefactored to create generic polling thread and subjobs
jprocter [Mon, 14 Aug 2006 15:23:07 +0000 (15:23 +0000)]
refactored to create generic polling thread and subjobs

18 years ago2.1 updates
amwaterhouse [Mon, 14 Aug 2006 15:22:36 +0000 (15:22 +0000)]
2.1 updates

18 years agofunction to indicate job has finished but no results are available.
jprocter [Mon, 14 Aug 2006 15:22:16 +0000 (15:22 +0000)]
function to indicate job has finished but no results are available.

18 years agoNew file
amwaterhouse [Mon, 14 Aug 2006 15:20:50 +0000 (15:20 +0000)]
New file

18 years agonew feature added
amwaterhouse [Mon, 14 Aug 2006 15:11:33 +0000 (15:11 +0000)]
new feature added

18 years agoStop loading must be before JOptionPane, 1.5 bug
amwaterhouse [Mon, 14 Aug 2006 15:11:12 +0000 (15:11 +0000)]
Stop loading must be before JOptionPane, 1.5 bug

18 years agoNo need to check selection group size
amwaterhouse [Mon, 14 Aug 2006 15:10:32 +0000 (15:10 +0000)]
No need to check selection group size

18 years agofindSequenceMatch returns multiple sequences
amwaterhouse [Mon, 14 Aug 2006 15:10:09 +0000 (15:10 +0000)]
findSequenceMatch returns multiple sequences

18 years agoDo a loop for multiple seq matches
amwaterhouse [Mon, 14 Aug 2006 15:09:43 +0000 (15:09 +0000)]
Do a loop for multiple seq matches

18 years agoCorrect test string
amwaterhouse [Mon, 14 Aug 2006 15:09:23 +0000 (15:09 +0000)]
Correct test string

18 years agomultiple subjobs can be cancelled and gui only allows results when a
jprocter [Mon, 14 Aug 2006 12:52:03 +0000 (12:52 +0000)]
multiple subjobs can be cancelled and gui only allows results when a
subjob actually completes.

18 years agofixed off by one bug in end sequence from getSubSequence and added new
jprocter [Mon, 14 Aug 2006 12:50:35 +0000 (12:50 +0000)]
fixed off by one bug in end sequence from getSubSequence and added new
subSequence method (not properly tested yet).

18 years agofindingFeatures flag set
amwaterhouse [Mon, 14 Aug 2006 12:30:58 +0000 (12:30 +0000)]
findingFeatures flag set

18 years ago2.1 updates
amwaterhouse [Mon, 14 Aug 2006 11:08:54 +0000 (11:08 +0000)]
2.1 updates

18 years ago2.1 updates
amwaterhouse [Mon, 14 Aug 2006 10:18:22 +0000 (10:18 +0000)]
2.1 updates

18 years ago2.1 new files
amwaterhouse [Mon, 14 Aug 2006 10:17:04 +0000 (10:17 +0000)]
2.1 new files

18 years agoReplaced image
amwaterhouse [Mon, 14 Aug 2006 10:16:13 +0000 (10:16 +0000)]
Replaced image

18 years agoMerged with edit
amwaterhouse [Mon, 14 Aug 2006 10:15:55 +0000 (10:15 +0000)]
Merged with edit

18 years agoend<start for empty sequences in Sequence[] from SeqCigar[]
jprocter [Mon, 14 Aug 2006 09:51:25 +0000 (09:51 +0000)]
end<start for empty sequences in Sequence[] from SeqCigar[]

18 years agoelementAt instead of get for 1.1 compatibility
amwaterhouse [Mon, 14 Aug 2006 09:02:12 +0000 (09:02 +0000)]
elementAt instead of get for 1.1 compatibility

18 years agofixing residue clip bug in MsaWSThread and adding minimum sequence length constraints.
jprocter [Mon, 14 Aug 2006 08:46:44 +0000 (08:46 +0000)]
fixing residue clip bug in MsaWSThread and adding minimum sequence length constraints.

18 years agofixed end-residue bug and subjob panel names bug
jprocter [Sun, 13 Aug 2006 13:58:29 +0000 (13:58 +0000)]
fixed end-residue bug and subjob panel names bug

18 years agomultiple web service jobs from visible blocks of an alignment.
jprocter [Fri, 11 Aug 2006 17:30:22 +0000 (17:30 +0000)]
multiple web service jobs from visible blocks of an alignment.

18 years agoUpdate overview on conservation/pid slider mouseRelease
amwaterhouse [Fri, 11 Aug 2006 16:34:23 +0000 (16:34 +0000)]
Update overview on conservation/pid slider mouseRelease

18 years agoalignpanel.repaint
amwaterhouse [Fri, 11 Aug 2006 16:09:44 +0000 (16:09 +0000)]
alignpanel.repaint

18 years agoAdd links menu if no sequence is selected
amwaterhouse [Fri, 11 Aug 2006 16:06:11 +0000 (16:06 +0000)]
Add links menu if no sequence is selected

18 years agopopup must be added to panel before showing
amwaterhouse [Fri, 11 Aug 2006 16:05:40 +0000 (16:05 +0000)]
popup must be added to panel before showing

18 years agoparam tree replaces treeFile
amwaterhouse [Fri, 11 Aug 2006 14:32:44 +0000 (14:32 +0000)]
param tree replaces treeFile

18 years ago2.1 updates
amwaterhouse [Fri, 11 Aug 2006 14:20:29 +0000 (14:20 +0000)]
2.1 updates

18 years ago2.1 updates
amwaterhouse [Fri, 11 Aug 2006 14:20:28 +0000 (14:20 +0000)]
2.1 updates

18 years ago2.1 updates
amwaterhouse [Fri, 11 Aug 2006 14:20:27 +0000 (14:20 +0000)]
2.1 updates

18 years ago2.1 updates
amwaterhouse [Fri, 11 Aug 2006 14:20:26 +0000 (14:20 +0000)]
2.1 updates

18 years ago2.1 updates
amwaterhouse [Fri, 11 Aug 2006 14:20:25 +0000 (14:20 +0000)]
2.1 updates

18 years ago2.1 updates
amwaterhouse [Fri, 11 Aug 2006 14:20:24 +0000 (14:20 +0000)]
2.1 updates

18 years ago2.1 updates
amwaterhouse [Fri, 11 Aug 2006 14:20:23 +0000 (14:20 +0000)]
2.1 updates

18 years ago2.1 updates
amwaterhouse [Fri, 11 Aug 2006 14:20:22 +0000 (14:20 +0000)]
2.1 updates

18 years ago2.1 updates
amwaterhouse [Fri, 11 Aug 2006 14:20:21 +0000 (14:20 +0000)]
2.1 updates

18 years agonew files
amwaterhouse [Fri, 11 Aug 2006 14:19:46 +0000 (14:19 +0000)]
new files

18 years agodud file
amwaterhouse [Fri, 11 Aug 2006 14:18:35 +0000 (14:18 +0000)]
dud file

18 years agoDesktop is null if -noDisplay is set
amwaterhouse [Fri, 11 Aug 2006 08:39:21 +0000 (08:39 +0000)]
Desktop is null if -noDisplay is set

18 years agoMake a new FeatureRenderer
amwaterhouse [Fri, 11 Aug 2006 08:22:57 +0000 (08:22 +0000)]
Make a new FeatureRenderer

18 years agoAlignPanel.repaint
amwaterhouse [Fri, 11 Aug 2006 08:22:44 +0000 (08:22 +0000)]
AlignPanel.repaint

18 years agoPrintstacktrace
amwaterhouse [Fri, 11 Aug 2006 08:22:17 +0000 (08:22 +0000)]
Printstacktrace

18 years agoinFile might be null if PDB was pasted
amwaterhouse [Fri, 11 Aug 2006 08:21:39 +0000 (08:21 +0000)]
inFile might be null if PDB was pasted

18 years agoSmoother drawing
amwaterhouse [Thu, 10 Aug 2006 14:57:52 +0000 (14:57 +0000)]
Smoother drawing

18 years agoCheck selection size before making tree
amwaterhouse [Thu, 10 Aug 2006 14:57:40 +0000 (14:57 +0000)]
Check selection size before making tree

18 years agogroup.getSize should be ab.alignment.getGroups
amwaterhouse [Thu, 10 Aug 2006 14:57:13 +0000 (14:57 +0000)]
group.getSize should be ab.alignment.getGroups

18 years agoCheck alAndColSel are not null
amwaterhouse [Thu, 10 Aug 2006 14:56:21 +0000 (14:56 +0000)]
Check alAndColSel are not null

18 years agoControl and shift for col selection
amwaterhouse [Thu, 10 Aug 2006 13:40:59 +0000 (13:40 +0000)]
Control and shift for col selection

18 years agoReset button added
amwaterhouse [Thu, 10 Aug 2006 13:18:12 +0000 (13:18 +0000)]
Reset button added

18 years agoRight mouse works with cursor mode
amwaterhouse [Thu, 10 Aug 2006 13:17:54 +0000 (13:17 +0000)]
Right mouse works with cursor mode

18 years agoOnly add 1 feature settings table
amwaterhouse [Thu, 10 Aug 2006 13:17:29 +0000 (13:17 +0000)]
Only add 1 feature settings table

18 years agoComment out start and end refs
amwaterhouse [Thu, 10 Aug 2006 12:58:00 +0000 (12:58 +0000)]
Comment out start and end refs

18 years ago1.1 compatible
amwaterhouse [Thu, 10 Aug 2006 09:50:14 +0000 (09:50 +0000)]
1.1 compatible

18 years agofile: is a URL
amwaterhouse [Thu, 10 Aug 2006 09:48:51 +0000 (09:48 +0000)]
file: is a URL

18 years agoInvert column selection
amwaterhouse [Thu, 10 Aug 2006 09:48:32 +0000 (09:48 +0000)]
Invert column selection

18 years agonew SequenceI method for making a sub sequence from a range on the
jprocter [Wed, 9 Aug 2006 16:21:36 +0000 (16:21 +0000)]
new SequenceI method for making a sub sequence from a range on the
current sequence.

18 years agoalignment from seqCigars will correctly mark deleted residues as
jprocter [Wed, 9 Aug 2006 16:20:41 +0000 (16:20 +0000)]
alignment from seqCigars will correctly mark deleted residues as
isolated insertions.

18 years agorefactored hidden regions methods and made an AlignmentView preserve
jprocter [Wed, 9 Aug 2006 16:19:24 +0000 (16:19 +0000)]
refactored hidden regions methods and made an AlignmentView preserve
the alignment in hidden regions.

18 years agofixed multiple shifts bug.
jprocter [Wed, 9 Aug 2006 16:12:58 +0000 (16:12 +0000)]
fixed multiple shifts bug.

18 years agoMust save all the feature settings
amwaterhouse [Wed, 9 Aug 2006 15:56:48 +0000 (15:56 +0000)]
Must save all the feature settings