jalview.git
18 years agoTooltips for features, links for features added
amwaterhouse [Wed, 7 Jun 2006 12:52:43 +0000 (12:52 +0000)]
Tooltips for features, links for features added

18 years agoNEW FILES
amwaterhouse [Wed, 7 Jun 2006 12:51:47 +0000 (12:51 +0000)]
NEW FILES

18 years agobroken link typo. (SEVENtwentyfour alert)
jprocter [Wed, 7 Jun 2006 10:20:18 +0000 (10:20 +0000)]
broken link typo. (SEVENtwentyfour alert)

18 years agoadded future method comment
jprocter [Thu, 18 May 2006 09:22:26 +0000 (09:22 +0000)]
added future method comment

18 years agoadded the jnetfile parameter to specify a JNet concise file to be
jprocter [Wed, 17 May 2006 16:54:44 +0000 (16:54 +0000)]
added the jnetfile parameter to specify a JNet concise file to be
parsed to add jnet predictions to the first sequence in the alignment

18 years agoadded unofficial support for concise output parsing from the JNet server to extract...
jprocter [Wed, 17 May 2006 16:52:58 +0000 (16:52 +0000)]
added unofficial support for concise output parsing from the JNet server to extract the sequence profile.

18 years agorefactored code for creating JNet annotations
jprocter [Wed, 17 May 2006 16:51:29 +0000 (16:51 +0000)]
refactored code for creating JNet annotations

18 years agoRefactored code for creating annotation objects from a jnetfile object.
jprocter [Wed, 17 May 2006 16:48:49 +0000 (16:48 +0000)]
Refactored code for creating annotation objects from a jnetfile object.

18 years agoRestrict annotation panel to 50% window on load
amwaterhouse [Wed, 17 May 2006 16:24:32 +0000 (16:24 +0000)]
Restrict annotation panel to 50% window on load

18 years agographColour, graphGroup, more relaxed annotation requirements
amwaterhouse [Tue, 16 May 2006 13:06:01 +0000 (13:06 +0000)]
graphColour, graphGroup, more relaxed annotation requirements

18 years agoSave annotation colours, hideConsevation etc, graphGroups
amwaterhouse [Tue, 16 May 2006 13:04:56 +0000 (13:04 +0000)]
Save annotation colours, hideConsevation etc, graphGroups

18 years agoSwitch off dashedline after drawing groups
amwaterhouse [Tue, 16 May 2006 12:01:13 +0000 (12:01 +0000)]
Switch off dashedline after drawing groups

18 years agoRemove unwanted line
amwaterhouse [Tue, 16 May 2006 11:09:02 +0000 (11:09 +0000)]
Remove unwanted line

18 years agoAllow for scroller position
amwaterhouse [Tue, 16 May 2006 11:08:34 +0000 (11:08 +0000)]
Allow for scroller position

18 years agoRemove system.out
amwaterhouse [Tue, 16 May 2006 10:24:02 +0000 (10:24 +0000)]
Remove system.out

18 years agoRearrange annotations
amwaterhouse [Tue, 16 May 2006 10:23:48 +0000 (10:23 +0000)]
Rearrange annotations

18 years agoadded popup warning when proxy settings must be configured.
jprocter [Tue, 16 May 2006 09:32:56 +0000 (09:32 +0000)]
added popup warning when proxy settings must be configured.

18 years agoMonospaced font not allowed if charWidth stretched
amwaterhouse [Mon, 15 May 2006 14:52:51 +0000 (14:52 +0000)]
Monospaced font not allowed if charWidth stretched

18 years agoBrackets around orgin calculation
amwaterhouse [Mon, 15 May 2006 14:52:26 +0000 (14:52 +0000)]
Brackets around orgin calculation

18 years agoAll or nothing drawing display char
amwaterhouse [Mon, 15 May 2006 14:09:34 +0000 (14:09 +0000)]
All or nothing drawing display char

18 years agoEPS font width is a double, check this for monospacedFont
amwaterhouse [Mon, 15 May 2006 13:28:35 +0000 (13:28 +0000)]
EPS font width is a double, check this for monospacedFont

18 years agoIf headless, get the width of Jalview wrapped window correct
amwaterhouse [Mon, 15 May 2006 13:28:07 +0000 (13:28 +0000)]
If headless, get the width of Jalview wrapped window correct

18 years agorearranged discoverer to dynamically update on demand
jprocter [Fri, 12 May 2006 16:00:21 +0000 (16:00 +0000)]
rearranged discoverer to dynamically update on demand

18 years agoreturns to zero degrees when stopped
amwaterhouse [Fri, 12 May 2006 10:55:27 +0000 (10:55 +0000)]
returns to zero degrees when stopped

18 years agopass viewport to fileloader, as we need to firepropertychange once sequences are...
amwaterhouse [Fri, 12 May 2006 08:47:16 +0000 (08:47 +0000)]
pass viewport to fileloader, as we need to firepropertychange once sequences are added

18 years agoSlight mod url chooser for Mac users
amwaterhouse [Thu, 11 May 2006 15:07:21 +0000 (15:07 +0000)]
Slight mod url chooser for Mac users

18 years agoRemove commented line
amwaterhouse [Thu, 11 May 2006 14:54:59 +0000 (14:54 +0000)]
Remove commented line

18 years agoSlightly smaller recent panel
amwaterhouse [Thu, 11 May 2006 14:54:42 +0000 (14:54 +0000)]
Slightly smaller recent panel

18 years agoMaintain numbering if remove left is undone
amwaterhouse [Thu, 11 May 2006 14:06:16 +0000 (14:06 +0000)]
Maintain numbering if remove left is undone

18 years agoTypo
amwaterhouse [Thu, 11 May 2006 13:54:27 +0000 (13:54 +0000)]
Typo

18 years agoInvert selection
amwaterhouse [Thu, 11 May 2006 13:54:10 +0000 (13:54 +0000)]
Invert selection

18 years agoRecently loaded files, urls, append sequences to Alignment
amwaterhouse [Thu, 11 May 2006 13:53:49 +0000 (13:53 +0000)]
Recently loaded files, urls, append sequences to Alignment

18 years agosequenceRef added to annotation
amwaterhouse [Wed, 10 May 2006 14:06:51 +0000 (14:06 +0000)]
sequenceRef added to annotation

18 years agoCorrection for sequences with start not equal to 1
amwaterhouse [Wed, 10 May 2006 13:30:10 +0000 (13:30 +0000)]
Correction for sequences with start not equal to 1

18 years agoCopy and paste of annotations with seqrefs
amwaterhouse [Wed, 10 May 2006 12:59:19 +0000 (12:59 +0000)]
Copy and paste of annotations with seqrefs

18 years agoimplements ClipboardOwner
amwaterhouse [Wed, 10 May 2006 12:58:44 +0000 (12:58 +0000)]
implements ClipboardOwner

18 years agosaves and loads annotations with seqrefs
amwaterhouse [Wed, 10 May 2006 12:57:56 +0000 (12:57 +0000)]
saves and loads annotations with seqrefs

18 years agoDraw an offscreen Image
amwaterhouse [Wed, 10 May 2006 12:57:39 +0000 (12:57 +0000)]
Draw an offscreen Image

18 years agoAnnotations must createSequenceMapping if seqRef not null
amwaterhouse [Wed, 10 May 2006 12:57:21 +0000 (12:57 +0000)]
Annotations must createSequenceMapping if seqRef not null

18 years agoCreate sequence mapping for annotations
amwaterhouse [Wed, 10 May 2006 12:56:30 +0000 (12:56 +0000)]
Create sequence mapping for annotations

18 years agoaddAnnotation with seqRef
amwaterhouse [Wed, 10 May 2006 12:56:02 +0000 (12:56 +0000)]
addAnnotation with seqRef

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)