jalview.git
18 years agoChanges case to end of alignment
amwaterhouse [Wed, 10 May 2006 12:55:17 +0000 (12:55 +0000)]
Changes case to end of alignment

18 years agoremove import
amwaterhouse [Wed, 10 May 2006 12:54:52 +0000 (12:54 +0000)]
remove import

18 years agoSave seqref with annotations
amwaterhouse [Wed, 10 May 2006 12:52:11 +0000 (12:52 +0000)]
Save seqref with annotations

18 years agospelling err
amwaterhouse [Tue, 2 May 2006 16:44:32 +0000 (16:44 +0000)]
spelling err

18 years ago2.08.1
amwaterhouse [Tue, 2 May 2006 12:24:48 +0000 (12:24 +0000)]
2.08.1

18 years agoMake nullFrame only once
amwaterhouse [Tue, 2 May 2006 12:23:48 +0000 (12:23 +0000)]
Make nullFrame only once

18 years agoRemove unnecessary panel, also nullFrame created only once
amwaterhouse [Tue, 2 May 2006 12:23:28 +0000 (12:23 +0000)]
Remove unnecessary panel, also nullFrame created only once

18 years agoMiddle mouse to compress alignment
amwaterhouse [Tue, 2 May 2006 12:23:01 +0000 (12:23 +0000)]
Middle mouse to compress alignment

18 years agoCheck that fontsize > 0
amwaterhouse [Tue, 2 May 2006 12:22:20 +0000 (12:22 +0000)]
Check that fontsize > 0

18 years agoToggle Case added
amwaterhouse [Tue, 2 May 2006 12:21:57 +0000 (12:21 +0000)]
Toggle Case added

18 years agoToggle case added to popup menu
amwaterhouse [Tue, 2 May 2006 09:28:24 +0000 (09:28 +0000)]
Toggle case added to popup menu

18 years agoRemove edit menu if no group defined
amwaterhouse [Mon, 1 May 2006 14:29:21 +0000 (14:29 +0000)]
Remove edit menu if no group defined

18 years agoMaintain original transparency setting
amwaterhouse [Mon, 1 May 2006 14:28:51 +0000 (14:28 +0000)]
Maintain original transparency setting

18 years agoChange name to editMenu
amwaterhouse [Mon, 1 May 2006 14:28:32 +0000 (14:28 +0000)]
Change name to editMenu

18 years agoIf Mac, use the fillRoundRect method
amwaterhouse [Mon, 1 May 2006 13:24:10 +0000 (13:24 +0000)]
If Mac, use the fillRoundRect method

18 years agoForces init of alignPanel if annotations added
amwaterhouse [Mon, 1 May 2006 13:23:46 +0000 (13:23 +0000)]
Forces init of alignPanel if annotations added

18 years agoFixes redraw top of group bug
amwaterhouse [Mon, 1 May 2006 13:22:58 +0000 (13:22 +0000)]
Fixes redraw top of group bug

18 years agoIf no group, hide menu
amwaterhouse [Mon, 1 May 2006 13:22:38 +0000 (13:22 +0000)]
If no group, hide menu

18 years agoIf mac, use the fillRoundRect
amwaterhouse [Mon, 1 May 2006 13:22:22 +0000 (13:22 +0000)]
If mac, use the fillRoundRect

18 years agojava 1.1 compatibility
amwaterhouse [Mon, 1 May 2006 13:22:02 +0000 (13:22 +0000)]
java 1.1 compatibility

18 years agoHelix sizes
amwaterhouse [Fri, 28 Apr 2006 17:07:13 +0000 (17:07 +0000)]
Helix sizes

18 years agoMake sure end is less than sequence width
amwaterhouse [Fri, 28 Apr 2006 16:38:33 +0000 (16:38 +0000)]
Make sure end is less than sequence width

18 years agoGroup width -1
amwaterhouse [Fri, 28 Apr 2006 16:38:10 +0000 (16:38 +0000)]
Group width -1

18 years agoWatch for exceeding width limit
amwaterhouse [Fri, 28 Apr 2006 16:37:58 +0000 (16:37 +0000)]
Watch for exceeding width limit

18 years agoIf autoCalculate selected, recalculate immediately
amwaterhouse [Fri, 28 Apr 2006 13:47:24 +0000 (13:47 +0000)]
If autoCalculate selected, recalculate immediately

18 years agoBack to gray line
amwaterhouse [Fri, 28 Apr 2006 13:45:40 +0000 (13:45 +0000)]
Back to gray line

18 years agoBack to gray line
amwaterhouse [Fri, 28 Apr 2006 13:42:04 +0000 (13:42 +0000)]
Back to gray line

18 years agovalidCharWidth moved to viewport
amwaterhouse [Fri, 28 Apr 2006 13:38:39 +0000 (13:38 +0000)]
validCharWidth moved to viewport

18 years agoAnnoying little line at end of wrapped alignment
amwaterhouse [Fri, 28 Apr 2006 13:26:22 +0000 (13:26 +0000)]
Annoying little line at end of wrapped alignment

18 years agovalidCharWidth checks
amwaterhouse [Fri, 28 Apr 2006 12:35:12 +0000 (12:35 +0000)]
validCharWidth checks

18 years agoEdit menu added
amwaterhouse [Fri, 28 Apr 2006 12:34:28 +0000 (12:34 +0000)]
Edit menu added

18 years agoAdd to palette layer
amwaterhouse [Fri, 28 Apr 2006 12:34:18 +0000 (12:34 +0000)]
Add to palette layer

18 years agoHelix glyphs fixed
amwaterhouse [Fri, 28 Apr 2006 12:34:06 +0000 (12:34 +0000)]
Helix glyphs fixed

18 years agoCase sensitive
amwaterhouse [Fri, 28 Apr 2006 12:33:44 +0000 (12:33 +0000)]
Case sensitive

18 years agochangeCase
amwaterhouse [Fri, 28 Apr 2006 12:33:24 +0000 (12:33 +0000)]
changeCase

18 years agoHelix glyphs drawn correctly
amwaterhouse [Fri, 28 Apr 2006 12:32:58 +0000 (12:32 +0000)]
Helix glyphs drawn correctly

18 years agoDont select groups on ids
amwaterhouse [Fri, 28 Apr 2006 12:32:36 +0000 (12:32 +0000)]
Dont select groups on ids

18 years agoCase shifter
amwaterhouse [Fri, 28 Apr 2006 12:32:12 +0000 (12:32 +0000)]
Case shifter

18 years agoAlignment compression on middle mouse button
amwaterhouse [Fri, 21 Apr 2006 11:19:13 +0000 (11:19 +0000)]
Alignment compression on middle mouse button

18 years agoModified sequence selection
amwaterhouse [Fri, 21 Apr 2006 10:41:29 +0000 (10:41 +0000)]
Modified sequence selection

18 years agoMultiple views, alignpanels not being used
amwaterhouse [Wed, 19 Apr 2006 15:58:15 +0000 (15:58 +0000)]
Multiple views, alignpanels not being used

18 years agoAlignment might not have any annotations
amwaterhouse [Wed, 19 Apr 2006 14:32:11 +0000 (14:32 +0000)]
Alignment might not have any annotations

18 years ago-1 from east scale, wrapped alignment
amwaterhouse [Tue, 18 Apr 2006 13:17:20 +0000 (13:17 +0000)]
-1 from east scale, wrapped alignment

18 years agoshowInternalMessage jdk1.5 bug
amwaterhouse [Thu, 13 Apr 2006 13:28:42 +0000 (13:28 +0000)]
showInternalMessage jdk1.5 bug

18 years agoadd back in again
amwaterhouse [Mon, 10 Apr 2006 15:54:47 +0000 (15:54 +0000)]
add back in again

18 years agoold image
amwaterhouse [Mon, 10 Apr 2006 15:30:41 +0000 (15:30 +0000)]
old image

18 years agoold images
amwaterhouse [Mon, 10 Apr 2006 15:29:56 +0000 (15:29 +0000)]
old images

18 years agoNew images
amwaterhouse [Mon, 10 Apr 2006 15:27:02 +0000 (15:27 +0000)]
New images

18 years ago2.08, not 2.07
amwaterhouse [Mon, 10 Apr 2006 15:16:46 +0000 (15:16 +0000)]
2.08, not 2.07

18 years agoTo export page
amwaterhouse [Mon, 10 Apr 2006 14:53:10 +0000 (14:53 +0000)]
To export page

18 years agoLinks
amwaterhouse [Mon, 10 Apr 2006 14:52:56 +0000 (14:52 +0000)]
Links

18 years agoload features/annotations typo.
jprocter [Mon, 10 Apr 2006 14:36:49 +0000 (14:36 +0000)]
load features/annotations typo.

18 years agoadded note about cursor mode disabling the popup menu.
jprocter [Mon, 10 Apr 2006 14:32:54 +0000 (14:32 +0000)]
added note about cursor mode disabling the popup menu.

18 years agotypo and explanation for ignore gaps in consensus
jprocter [Mon, 10 Apr 2006 14:31:18 +0000 (14:31 +0000)]
typo and explanation for ignore gaps in consensus

18 years agoreworded pad gaps
jprocter [Mon, 10 Apr 2006 14:29:02 +0000 (14:29 +0000)]
reworded pad gaps

18 years agoreworded pad gaps.
jprocter [Mon, 10 Apr 2006 14:28:53 +0000 (14:28 +0000)]
reworded pad gaps.

18 years ago2.08 update
amwaterhouse [Mon, 10 Apr 2006 14:17:47 +0000 (14:17 +0000)]
2.08 update

18 years agoput modellerpir in correct place!
jprocter [Mon, 10 Apr 2006 14:17:16 +0000 (14:17 +0000)]
put modellerpir in correct place!

18 years agoupdated menus and rearranged seqfeatures (again)
jprocter [Mon, 10 Apr 2006 14:16:55 +0000 (14:16 +0000)]
updated menus and rearranged seqfeatures (again)

18 years agoDisplays error line on error
amwaterhouse [Mon, 10 Apr 2006 14:15:00 +0000 (14:15 +0000)]
Displays error line on error

18 years agofix links to complex html (that don't display) by quoting them
jprocter [Mon, 10 Apr 2006 14:14:58 +0000 (14:14 +0000)]
fix links to complex html (that don't display) by quoting them
verbatim.

18 years agoJust removing new line character
amwaterhouse [Mon, 10 Apr 2006 14:14:18 +0000 (14:14 +0000)]
Just removing new line character

18 years agomoved Modeller/PIR description to its own home.
jprocter [Mon, 10 Apr 2006 14:01:04 +0000 (14:01 +0000)]
moved Modeller/PIR description to its own home.

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