jalview.git
18 years agomoved modellerpir to io
jprocter [Mon, 10 Apr 2006 14:00:46 +0000 (14:00 +0000)]
moved modellerpir to io

18 years agodescribing the Modeller/PIR output.
jprocter [Mon, 10 Apr 2006 13:59:34 +0000 (13:59 +0000)]
describing the Modeller/PIR output.

18 years agoFixed table border and updated restrictions
jprocter [Mon, 10 Apr 2006 13:18:43 +0000 (13:18 +0000)]
Fixed table border and updated restrictions

18 years agoEditing tab
amwaterhouse [Mon, 10 Apr 2006 13:15:18 +0000 (13:15 +0000)]
Editing tab

18 years agoadded bit about modeller/pir
jprocter [Mon, 10 Apr 2006 13:10:43 +0000 (13:10 +0000)]
added bit about modeller/pir

18 years agoadded annotationColouring to whats new and updated IO and cursorMode
jprocter [Mon, 10 Apr 2006 13:06:40 +0000 (13:06 +0000)]
added annotationColouring to whats new and updated IO and cursorMode
(mac os and backspace==delete)

18 years agodel and backspace do the same thing
amwaterhouse [Mon, 10 Apr 2006 12:32:58 +0000 (12:32 +0000)]
del and backspace do the same thing

18 years agoRelease Date width
amwaterhouse [Mon, 10 Apr 2006 11:41:39 +0000 (11:41 +0000)]
Release Date width

18 years agoextended preamble and added new heading for user defined annotation
jprocter [Mon, 10 Apr 2006 11:34:16 +0000 (11:34 +0000)]
extended preamble and added new heading for user defined annotation
instructions.

18 years agotab name is editing
amwaterhouse [Mon, 10 Apr 2006 11:33:35 +0000 (11:33 +0000)]
tab name is editing

18 years agodoco
jprocter [Mon, 10 Apr 2006 11:31:10 +0000 (11:31 +0000)]
doco

18 years agodoco changes.
jprocter [Mon, 10 Apr 2006 11:27:04 +0000 (11:27 +0000)]
doco changes.

18 years agoadded 2.08 application version dialog box.
jprocter [Mon, 10 Apr 2006 11:21:47 +0000 (11:21 +0000)]
added 2.08 application version dialog box.

18 years agofeature settings dialog box for jalview 2.08 application
jprocter [Mon, 10 Apr 2006 11:19:45 +0000 (11:19 +0000)]
feature settings dialog box for jalview 2.08 application

18 years agoProtein desc bug fixed
amwaterhouse [Mon, 10 Apr 2006 11:11:17 +0000 (11:11 +0000)]
Protein desc bug fixed

18 years agodont need to set - to -
amwaterhouse [Mon, 10 Apr 2006 11:10:26 +0000 (11:10 +0000)]
dont need to set - to -

18 years agoFixed protein desc bug
amwaterhouse [Mon, 10 Apr 2006 11:10:06 +0000 (11:10 +0000)]
Fixed protein desc bug

18 years agodoco writing.
jprocter [Sun, 9 Apr 2006 18:02:49 +0000 (18:02 +0000)]
doco writing.

18 years agoTakes popup away from mouseevent, prevents immediate copy
amwaterhouse [Fri, 7 Apr 2006 14:15:40 +0000 (14:15 +0000)]
Takes popup away from mouseevent, prevents immediate copy

18 years agoNo need for vetoablechange
amwaterhouse [Fri, 7 Apr 2006 13:58:11 +0000 (13:58 +0000)]
No need for vetoablechange

18 years agoSet all gaps to - symbol
amwaterhouse [Fri, 7 Apr 2006 13:48:39 +0000 (13:48 +0000)]
Set all gaps to - symbol

18 years agopadGaps set in preferences
amwaterhouse [Fri, 7 Apr 2006 12:57:17 +0000 (12:57 +0000)]
padGaps set in preferences

18 years agoPadgaps pref set
amwaterhouse [Fri, 7 Apr 2006 12:52:54 +0000 (12:52 +0000)]
Padgaps pref set

18 years agoModellerOutput set in preferences
amwaterhouse [Fri, 7 Apr 2006 12:52:29 +0000 (12:52 +0000)]
ModellerOutput set in preferences

18 years agoAutocalculate consensus set in preferences
amwaterhouse [Fri, 7 Apr 2006 11:27:55 +0000 (11:27 +0000)]
Autocalculate consensus set in preferences

18 years agoScroll cursor wrapped alignment
amwaterhouse [Fri, 7 Apr 2006 11:27:19 +0000 (11:27 +0000)]
Scroll cursor wrapped alignment

18 years ago+1 error in group edit all sequences
amwaterhouse [Fri, 7 Apr 2006 10:05:51 +0000 (10:05 +0000)]
+1 error in group edit all sequences

18 years agoremove new line in alquality
amwaterhouse [Fri, 7 Apr 2006 09:36:36 +0000 (09:36 +0000)]
remove new line in alquality

18 years agoadded full keyset for cursorMode
jprocter [Fri, 7 Apr 2006 09:21:14 +0000 (09:21 +0000)]
added full keyset for cursorMode

18 years agoMust check consensus length if autocalculate off
amwaterhouse [Fri, 7 Apr 2006 08:23:34 +0000 (08:23 +0000)]
Must check consensus length if autocalculate off

18 years agoadded cursorMode feature page and rearranged keystrokes documentation.
jprocter [Thu, 6 Apr 2006 17:02:12 +0000 (17:02 +0000)]
added cursorMode feature page and rearranged keystrokes documentation.

18 years agoHide ref to HiddenRegion
amwaterhouse [Thu, 6 Apr 2006 11:11:34 +0000 (11:11 +0000)]
Hide ref to HiddenRegion

18 years agoremoved dross, added a safety check to buildextclients and added references to docs...
jprocter [Thu, 6 Apr 2006 09:41:17 +0000 (09:41 +0000)]
removed dross, added a safety check to buildextclients and added references to docs/building.html

18 years agoMust copy feature settings from one frame to another as they are not attached ot...
amwaterhouse [Thu, 6 Apr 2006 09:26:58 +0000 (09:26 +0000)]
Must copy feature settings from one frame to another as they are not attached ot the dataset

18 years agoMust copy feature settings from one frame to another as they are not attached ot...
amwaterhouse [Thu, 6 Apr 2006 09:24:42 +0000 (09:24 +0000)]
Must copy feature settings from one frame to another as they are not attached ot the dataset

18 years agoMaintain feature order
amwaterhouse [Wed, 5 Apr 2006 16:40:20 +0000 (16:40 +0000)]
Maintain feature order

18 years agoSave annotationColours
amwaterhouse [Wed, 5 Apr 2006 15:53:09 +0000 (15:53 +0000)]
Save annotationColours

18 years agoPublic get methods
amwaterhouse [Wed, 5 Apr 2006 15:52:56 +0000 (15:52 +0000)]
Public get methods

18 years agopublic get methods
amwaterhouse [Wed, 5 Apr 2006 15:52:35 +0000 (15:52 +0000)]
public get methods

18 years agoSave graph threshold and annotation colours
amwaterhouse [Wed, 5 Apr 2006 15:52:01 +0000 (15:52 +0000)]
Save graph threshold and annotation colours

18 years ago2.08 updates
amwaterhouse [Wed, 5 Apr 2006 12:30:26 +0000 (12:30 +0000)]
2.08 updates

18 years agoOrder of menuitems
amwaterhouse [Wed, 5 Apr 2006 11:41:34 +0000 (11:41 +0000)]
Order of menuitems

18 years agoTurn off validation for speed
amwaterhouse [Wed, 5 Apr 2006 11:41:06 +0000 (11:41 +0000)]
Turn off validation for speed

18 years agoNo need for minorSpacing
amwaterhouse [Wed, 5 Apr 2006 11:40:46 +0000 (11:40 +0000)]
No need for minorSpacing

18 years agoShift also for group editing
amwaterhouse [Wed, 5 Apr 2006 11:40:16 +0000 (11:40 +0000)]
Shift also for group editing

18 years agoPadgap history
amwaterhouse [Wed, 5 Apr 2006 11:39:42 +0000 (11:39 +0000)]
Padgap history

18 years agoNote on build target being usage
amwaterhouse [Wed, 5 Apr 2006 11:38:40 +0000 (11:38 +0000)]
Note on build target being usage

18 years agoDefault raget is :usage
amwaterhouse [Wed, 5 Apr 2006 11:37:35 +0000 (11:37 +0000)]
Default raget is :usage

18 years ago2.08 update
amwaterhouse [Wed, 5 Apr 2006 11:01:49 +0000 (11:01 +0000)]
2.08 update

18 years ago2.08 updates
amwaterhouse [Tue, 4 Apr 2006 17:18:54 +0000 (17:18 +0000)]
2.08 updates

18 years agoModified for 2.08
amwaterhouse [Tue, 4 Apr 2006 17:07:14 +0000 (17:07 +0000)]
Modified for 2.08

18 years agoNew files
amwaterhouse [Tue, 4 Apr 2006 17:06:01 +0000 (17:06 +0000)]
New files

18 years agoDraw threshold over graph
amwaterhouse [Tue, 4 Apr 2006 13:09:28 +0000 (13:09 +0000)]
Draw threshold over graph

18 years agoloadDataFile is public
amwaterhouse [Tue, 4 Apr 2006 12:53:36 +0000 (12:53 +0000)]
loadDataFile is public

18 years agoAdd annoations from the command line
amwaterhouse [Tue, 4 Apr 2006 12:53:14 +0000 (12:53 +0000)]
Add annoations from the command line

18 years agoOverview follows cursor movement
amwaterhouse [Tue, 4 Apr 2006 10:58:29 +0000 (10:58 +0000)]
Overview follows cursor movement

18 years agoSet keyboard numbers to null if esc pressed
amwaterhouse [Tue, 4 Apr 2006 10:50:04 +0000 (10:50 +0000)]
Set keyboard numbers to null if esc pressed

18 years agoKeyboard editing added to applet
amwaterhouse [Tue, 4 Apr 2006 10:47:57 +0000 (10:47 +0000)]
Keyboard editing added to applet

18 years agoset current tree once the tree is prepared
amwaterhouse [Tue, 4 Apr 2006 09:38:11 +0000 (09:38 +0000)]
set current tree once the tree is prepared

18 years agoJalview2XML does not use static load
amwaterhouse [Tue, 4 Apr 2006 09:37:38 +0000 (09:37 +0000)]
Jalview2XML does not use static load

18 years agoPad gaps removes excess gaps
amwaterhouse [Tue, 4 Apr 2006 09:37:12 +0000 (09:37 +0000)]
Pad gaps removes excess gaps

18 years agoSpecify com.stevesoft.pat.Regex
amwaterhouse [Tue, 4 Apr 2006 09:36:15 +0000 (09:36 +0000)]
Specify com.stevesoft.pat.Regex

18 years agoAutocalculate consensus
amwaterhouse [Tue, 4 Apr 2006 09:35:34 +0000 (09:35 +0000)]
Autocalculate consensus

18 years agoMore keys for editing
amwaterhouse [Tue, 4 Apr 2006 09:33:58 +0000 (09:33 +0000)]
More keys for editing

18 years agoGet hiddenBoundaryLeft and right
amwaterhouse [Tue, 4 Apr 2006 09:33:40 +0000 (09:33 +0000)]
Get hiddenBoundaryLeft and right

18 years agoJalview2XML does not use static load anymore
amwaterhouse [Tue, 4 Apr 2006 09:33:12 +0000 (09:33 +0000)]
Jalview2XML does not use static load anymore

18 years agoDisable hide regions
amwaterhouse [Tue, 4 Apr 2006 09:32:51 +0000 (09:32 +0000)]
Disable hide regions

18 years agoScrolls if dragged off the screen
amwaterhouse [Tue, 4 Apr 2006 09:32:28 +0000 (09:32 +0000)]
Scrolls if dragged off the screen

18 years agoKeyboard editing
amwaterhouse [Tue, 4 Apr 2006 09:31:52 +0000 (09:31 +0000)]
Keyboard editing

18 years agoCursor colour
amwaterhouse [Tue, 4 Apr 2006 09:31:35 +0000 (09:31 +0000)]
Cursor colour

18 years agoSet current tree when ready
amwaterhouse [Tue, 4 Apr 2006 09:31:17 +0000 (09:31 +0000)]
Set current tree when ready

18 years agoAllows loading of archive XML
amwaterhouse [Tue, 4 Apr 2006 09:31:05 +0000 (09:31 +0000)]
Allows loading of archive XML

18 years agoFor archive only
amwaterhouse [Tue, 4 Apr 2006 09:30:50 +0000 (09:30 +0000)]
For archive only

18 years agoUses descriptors
amwaterhouse [Tue, 4 Apr 2006 09:30:27 +0000 (09:30 +0000)]
Uses descriptors

18 years agoBinding with descriptors
amwaterhouse [Tue, 4 Apr 2006 09:29:54 +0000 (09:29 +0000)]
Binding with descriptors

18 years agoNamespace changes
amwaterhouse [Tue, 4 Apr 2006 09:28:59 +0000 (09:28 +0000)]
Namespace changes

18 years agoFeature settings Root_VamJalview_2_07b+
amwaterhouse [Fri, 24 Mar 2006 16:29:00 +0000 (16:29 +0000)]
Feature settings

18 years agoHas its own featureRenderer
amwaterhouse [Fri, 24 Mar 2006 16:28:29 +0000 (16:28 +0000)]
Has its own featureRenderer

18 years agoGroup colours not used
amwaterhouse [Fri, 24 Mar 2006 15:36:53 +0000 (15:36 +0000)]
Group colours not used

18 years agoAssociated Data menu item
amwaterhouse [Fri, 24 Mar 2006 15:36:33 +0000 (15:36 +0000)]
Associated Data menu item

18 years agoCursor added
amwaterhouse [Fri, 24 Mar 2006 15:36:04 +0000 (15:36 +0000)]
Cursor added

18 years agoTypo
amwaterhouse [Fri, 24 Mar 2006 15:35:44 +0000 (15:35 +0000)]
Typo

18 years agofr.transferSettings
amwaterhouse [Fri, 24 Mar 2006 15:35:31 +0000 (15:35 +0000)]
fr.transferSettings

18 years agoFeatureSettings bug fixed
amwaterhouse [Fri, 24 Mar 2006 15:35:10 +0000 (15:35 +0000)]
FeatureSettings bug fixed

18 years agoFeature added to group search results
amwaterhouse [Fri, 24 Mar 2006 15:34:48 +0000 (15:34 +0000)]
Feature added to group search results

18 years agoGroups compatibility
amwaterhouse [Fri, 24 Mar 2006 15:34:21 +0000 (15:34 +0000)]
Groups compatibility

18 years agoNo need to hava SSX as array
amwaterhouse [Fri, 24 Mar 2006 15:33:44 +0000 (15:33 +0000)]
No need to hava SSX as array

18 years agoCursoMode added
amwaterhouse [Fri, 24 Mar 2006 15:33:20 +0000 (15:33 +0000)]
CursoMode added

18 years agoLoad data file added
amwaterhouse [Fri, 24 Mar 2006 15:32:50 +0000 (15:32 +0000)]
Load data file added

18 years agoTrim line
amwaterhouse [Fri, 24 Mar 2006 15:32:22 +0000 (15:32 +0000)]
Trim line

18 years agoFeatures added to group Uniprot
amwaterhouse [Fri, 24 Mar 2006 15:32:08 +0000 (15:32 +0000)]
Features added to group Uniprot

18 years agoAdd check if sequence already exists
amwaterhouse [Fri, 24 Mar 2006 15:31:42 +0000 (15:31 +0000)]
Add check if sequence already exists

18 years agoFeaturesGroup added to constructor
amwaterhouse [Fri, 24 Mar 2006 15:31:11 +0000 (15:31 +0000)]
FeaturesGroup added to constructor

18 years ago1 too many
amwaterhouse [Fri, 24 Mar 2006 15:29:33 +0000 (15:29 +0000)]
1 too many

18 years agoFeatures added to group search results
amwaterhouse [Fri, 24 Mar 2006 15:28:54 +0000 (15:28 +0000)]
Features added to group search results

18 years ago-1 +1 check removed
amwaterhouse [Fri, 24 Mar 2006 15:28:30 +0000 (15:28 +0000)]
-1 +1 check removed

18 years ago1 too many in drawgraph
amwaterhouse [Fri, 24 Mar 2006 15:27:59 +0000 (15:27 +0000)]
1 too many in drawgraph

18 years agoAnnotation colour scheme added
amwaterhouse [Fri, 24 Mar 2006 15:27:21 +0000 (15:27 +0000)]
Annotation colour scheme added

18 years agoCalled from AnnotationColourChooser and Feature Settings
amwaterhouse [Fri, 24 Mar 2006 15:26:37 +0000 (15:26 +0000)]
Called from AnnotationColourChooser and Feature Settings

18 years agoAnnotation colours added to applet
amwaterhouse [Fri, 24 Mar 2006 15:25:59 +0000 (15:25 +0000)]
Annotation colours added to applet