jalview.git
17 years agorunning jalview from the command line.
jprocter [Fri, 9 Feb 2007 18:02:17 +0000 (18:02 +0000)]
running jalview from the command line.

17 years agoadded command line help documentation and preferences help to
jprocter [Fri, 9 Feb 2007 18:00:40 +0000 (18:00 +0000)]
added command line help documentation and preferences help to
contents. Documented SHOW_OVERVIEW property in preferences.

17 years agoadded 'show overview' preference.
jprocter [Fri, 9 Feb 2007 17:50:33 +0000 (17:50 +0000)]
added 'show overview' preference.

17 years agofix on newquestionaire notification bug (again)
jprocter [Thu, 8 Feb 2007 15:30:44 +0000 (15:30 +0000)]
fix on newquestionaire notification bug (again)

17 years agoformatted
amwaterhouse [Wed, 7 Feb 2007 16:03:59 +0000 (16:03 +0000)]
formatted

17 years agorestore unformatted state
amwaterhouse [Wed, 7 Feb 2007 15:46:01 +0000 (15:46 +0000)]
restore unformatted state

17 years agoFormatting
amwaterhouse [Wed, 7 Feb 2007 15:11:09 +0000 (15:11 +0000)]
Formatting

17 years agoformatting
amwaterhouse [Wed, 7 Feb 2007 14:59:46 +0000 (14:59 +0000)]
formatting

17 years agoExtend annotation if too short
amwaterhouse [Wed, 7 Feb 2007 14:28:38 +0000 (14:28 +0000)]
Extend annotation if too short

17 years agoreload, just close this frame and open a new one
amwaterhouse [Wed, 7 Feb 2007 11:29:38 +0000 (11:29 +0000)]
reload, just close this frame and open a new one

17 years ago2.2.1 changes
amwaterhouse [Wed, 7 Feb 2007 10:38:54 +0000 (10:38 +0000)]
2.2.1 changes

17 years agoremoved
amwaterhouse [Wed, 7 Feb 2007 10:38:19 +0000 (10:38 +0000)]
removed

17 years agohardwired default user questionnaire url and by default will always check for a quest...
jprocter [Tue, 6 Feb 2007 17:29:00 +0000 (17:29 +0000)]
hardwired default user questionnaire url and by default will always check for a questionnaire when running with gui.

17 years agomore bugfixes.
jprocter [Tue, 6 Feb 2007 17:27:05 +0000 (17:27 +0000)]
more bugfixes.

17 years ago2.2.1 updates
amwaterhouse [Tue, 6 Feb 2007 17:20:10 +0000 (17:20 +0000)]
2.2.1 updates

17 years agoDont add null description to tooltip
amwaterhouse [Tue, 6 Feb 2007 15:52:17 +0000 (15:52 +0000)]
Dont add null description to tooltip

17 years agoApplet params cant read tab character
amwaterhouse [Tue, 6 Feb 2007 15:51:42 +0000 (15:51 +0000)]
Applet params cant read tab character

17 years agoAllow for frame insets
amwaterhouse [Tue, 6 Feb 2007 15:51:07 +0000 (15:51 +0000)]
Allow for frame insets

17 years agoFormat label
amwaterhouse [Tue, 6 Feb 2007 15:50:44 +0000 (15:50 +0000)]
Format label

17 years agodebug log message
jprocter [Tue, 6 Feb 2007 15:05:06 +0000 (15:05 +0000)]
debug log message

17 years agosimplified and refactored along with cgi-script.
jprocter [Mon, 5 Feb 2007 17:36:21 +0000 (17:36 +0000)]
simplified and refactored along with cgi-script.

17 years agoAlignment editing columns 0 and 1 fixed
amwaterhouse [Mon, 5 Feb 2007 16:11:52 +0000 (16:11 +0000)]
Alignment editing columns 0 and 1 fixed

17 years agocommand line hook for questionnaire url argument.
jprocter [Mon, 5 Feb 2007 14:46:57 +0000 (14:46 +0000)]
command line hook for questionnaire url argument.

17 years agokkv change
jprocter [Mon, 5 Feb 2007 14:44:38 +0000 (14:44 +0000)]
kkv change

17 years agoclient side machinery for user questionnaire responses
jprocter [Mon, 5 Feb 2007 14:44:17 +0000 (14:44 +0000)]
client side machinery for user questionnaire responses

17 years agoFixed bug in trim right annotation adjust
amwaterhouse [Mon, 5 Feb 2007 14:40:03 +0000 (14:40 +0000)]
Fixed bug in trim right annotation adjust

17 years agostop flickering annotationPanel
amwaterhouse [Mon, 5 Feb 2007 11:58:42 +0000 (11:58 +0000)]
stop flickering annotationPanel

17 years agoFixed bug in trim right annotation adjust
amwaterhouse [Mon, 5 Feb 2007 11:46:11 +0000 (11:46 +0000)]
Fixed bug in trim right annotation adjust

17 years agoimage is panel size
amwaterhouse [Mon, 5 Feb 2007 10:57:20 +0000 (10:57 +0000)]
image is panel size

17 years agoapplet can define groups as parameters
amwaterhouse [Mon, 5 Feb 2007 10:57:02 +0000 (10:57 +0000)]
applet can define groups as parameters

17 years agoDont add group if seqs not found
amwaterhouse [Fri, 2 Feb 2007 17:35:20 +0000 (17:35 +0000)]
Dont add group if seqs not found

17 years agogetWidth -1 for trim right
amwaterhouse [Fri, 2 Feb 2007 17:34:53 +0000 (17:34 +0000)]
getWidth -1 for trim right

17 years agocheck annotation size when cutting
amwaterhouse [Fri, 2 Feb 2007 17:34:11 +0000 (17:34 +0000)]
check annotation size when cutting

17 years agoannotation might have been deleted
amwaterhouse [Fri, 2 Feb 2007 17:17:39 +0000 (17:17 +0000)]
annotation might have been deleted

17 years agocatch control down before editing null pointer
amwaterhouse [Fri, 2 Feb 2007 17:17:10 +0000 (17:17 +0000)]
catch control down before editing null pointer

17 years ago22 = scrollbar and insets widthcvs diff gui/AlignmentPanel.java
amwaterhouse [Fri, 2 Feb 2007 11:44:09 +0000 (11:44 +0000)]
22 = scrollbar and insets widthcvs diff gui/AlignmentPanel.java

17 years agoMust allow for scollbar and frame insets when getting headless width
amwaterhouse [Fri, 2 Feb 2007 11:39:55 +0000 (11:39 +0000)]
Must allow for scollbar and frame insets when getting headless width

17 years agoLookandFeel must be set in headless state as window sizes will be affected
amwaterhouse [Fri, 2 Feb 2007 11:38:58 +0000 (11:38 +0000)]
LookandFeel must be set in headless state as window sizes will be affected

17 years agoremoved deprecated bits
amwaterhouse [Thu, 1 Feb 2007 18:35:20 +0000 (18:35 +0000)]
removed deprecated bits

17 years agofind colours uncommented
amwaterhouse [Thu, 1 Feb 2007 18:02:57 +0000 (18:02 +0000)]
find colours uncommented

17 years agosequence.getStart() in findTrueIndex
amwaterhouse [Thu, 1 Feb 2007 17:05:10 +0000 (17:05 +0000)]
sequence.getStart() in findTrueIndex

17 years agoget fontmetrics from pg
amwaterhouse [Thu, 1 Feb 2007 14:07:56 +0000 (14:07 +0000)]
get fontmetrics from pg

17 years agoDont add null tooltip
amwaterhouse [Thu, 1 Feb 2007 14:07:34 +0000 (14:07 +0000)]
Dont add null tooltip

17 years agoNew description
amwaterhouse [Thu, 1 Feb 2007 14:07:14 +0000 (14:07 +0000)]
New description

17 years agotooltips
amwaterhouse [Thu, 1 Feb 2007 12:49:24 +0000 (12:49 +0000)]
tooltips

17 years agoset description for groups
amwaterhouse [Thu, 1 Feb 2007 12:40:06 +0000 (12:40 +0000)]
set description for groups

17 years agoDoesnt move with mouse, friendlier for mac users
amwaterhouse [Thu, 1 Feb 2007 12:37:08 +0000 (12:37 +0000)]
Doesnt move with mouse, friendlier for mac users

17 years agoDont repaint tooltip
amwaterhouse [Thu, 1 Feb 2007 12:36:46 +0000 (12:36 +0000)]
Dont repaint tooltip

17 years agoOne class for edit name/description
amwaterhouse [Thu, 1 Feb 2007 12:36:22 +0000 (12:36 +0000)]
One class for edit name/description

17 years agoslightly larger window edit name/desc
amwaterhouse [Wed, 31 Jan 2007 16:39:00 +0000 (16:39 +0000)]
slightly larger window edit name/desc

17 years agoedit annotation name/description
amwaterhouse [Wed, 31 Jan 2007 16:38:44 +0000 (16:38 +0000)]
edit annotation name/description

17 years agoCan edit annotation name/description
amwaterhouse [Wed, 31 Jan 2007 16:23:19 +0000 (16:23 +0000)]
Can edit annotation name/description

17 years agoConsensus, conservation, quality labels may have changed
amwaterhouse [Wed, 31 Jan 2007 16:22:34 +0000 (16:22 +0000)]
Consensus, conservation, quality labels may have changed

17 years agoaligned not used
amwaterhouse [Wed, 31 Jan 2007 15:33:00 +0000 (15:33 +0000)]
aligned not used

17 years agoDont export annotations if not visible
amwaterhouse [Wed, 31 Jan 2007 15:29:13 +0000 (15:29 +0000)]
Dont export annotations if not visible

17 years agoUnique name for new group and treegroup
amwaterhouse [Wed, 31 Jan 2007 15:28:47 +0000 (15:28 +0000)]
Unique name for new group and treegroup

17 years agoAdjust features when cutting and pasting
amwaterhouse [Wed, 31 Jan 2007 14:47:57 +0000 (14:47 +0000)]
Adjust features when cutting and pasting

17 years agomake new dataset seq if residues deleted
amwaterhouse [Wed, 31 Jan 2007 14:47:35 +0000 (14:47 +0000)]
make new dataset seq if residues deleted

17 years agocopy feature: check for null values
amwaterhouse [Wed, 31 Jan 2007 14:46:57 +0000 (14:46 +0000)]
copy feature: check for null values

17 years agoaligned not used
amwaterhouse [Wed, 31 Jan 2007 14:44:28 +0000 (14:44 +0000)]
aligned not used

17 years agoCheck valid residues in ss
amwaterhouse [Tue, 30 Jan 2007 18:23:35 +0000 (18:23 +0000)]
Check valid residues in ss

17 years agoCheck seqs in group exist in this alignment
amwaterhouse [Tue, 30 Jan 2007 15:35:26 +0000 (15:35 +0000)]
Check seqs in group exist in this alignment

17 years agoAny character non aa or nucleotide is a space
amwaterhouse [Tue, 30 Jan 2007 15:35:01 +0000 (15:35 +0000)]
Any character non aa or nucleotide is a space

17 years agomoved painting routine
amwaterhouse [Tue, 30 Jan 2007 15:11:09 +0000 (15:11 +0000)]
moved painting routine

17 years agoconsensusColouring never used
amwaterhouse [Tue, 30 Jan 2007 13:40:16 +0000 (13:40 +0000)]
consensusColouring never used

17 years agoDraw helices correctly
amwaterhouse [Tue, 30 Jan 2007 13:39:53 +0000 (13:39 +0000)]
Draw helices correctly

17 years agoUse util toHexString
amwaterhouse [Tue, 30 Jan 2007 12:53:04 +0000 (12:53 +0000)]
Use util toHexString

17 years agoOutput groups in annotation file
amwaterhouse [Tue, 30 Jan 2007 12:52:50 +0000 (12:52 +0000)]
Output groups in annotation file

17 years agoDont clear graphics g before drawing the image
amwaterhouse [Mon, 29 Jan 2007 17:42:02 +0000 (17:42 +0000)]
Dont clear graphics g before drawing the image

17 years agoImage for labels, stops flickering
amwaterhouse [Mon, 29 Jan 2007 17:41:31 +0000 (17:41 +0000)]
Image for labels, stops flickering

17 years agoNew view copies annotations across
amwaterhouse [Mon, 29 Jan 2007 17:41:12 +0000 (17:41 +0000)]
New view copies annotations across

17 years agoTooltips for group names, descriptions
amwaterhouse [Mon, 29 Jan 2007 17:40:50 +0000 (17:40 +0000)]
Tooltips for group names, descriptions

17 years agoDescription added
amwaterhouse [Mon, 29 Jan 2007 17:40:30 +0000 (17:40 +0000)]
Description added

17 years agoSequenceGroup parsing added to annotation file
amwaterhouse [Mon, 29 Jan 2007 17:39:59 +0000 (17:39 +0000)]
SequenceGroup parsing added to annotation file

17 years agoID_ITALICS option in preferences
amwaterhouse [Mon, 29 Jan 2007 11:33:02 +0000 (11:33 +0000)]
ID_ITALICS option in preferences

17 years agoscaleAbove, left and right set when tab selection changes
amwaterhouse [Mon, 29 Jan 2007 11:31:52 +0000 (11:31 +0000)]
scaleAbove, left and right set when tab selection changes

17 years agoMarios annotation bug fixed
amwaterhouse [Mon, 29 Jan 2007 11:31:23 +0000 (11:31 +0000)]
Marios annotation bug fixed

17 years agoAnnotationId is hashcode of object
amwaterhouse [Fri, 26 Jan 2007 17:31:51 +0000 (17:31 +0000)]
AnnotationId is hashcode of object

17 years agoOnly set the sequence oncecvs diff datamodel/Alignment.java
amwaterhouse [Fri, 26 Jan 2007 17:30:49 +0000 (17:30 +0000)]
Only set the sequence oncecvs diff datamodel/Alignment.java

17 years agoAdjusts annotations for sequence edits
amwaterhouse [Fri, 26 Jan 2007 17:30:23 +0000 (17:30 +0000)]
Adjusts annotations for sequence edits

17 years agoIf its null, set tip empty
amwaterhouse [Fri, 26 Jan 2007 17:30:07 +0000 (17:30 +0000)]
If its null, set tip empty

17 years agopreliminary documentation for DNA->protein codon features and EMBL coding region...
jprocter [Fri, 26 Jan 2007 10:24:08 +0000 (10:24 +0000)]
preliminary documentation for DNA->protein codon features and EMBL coding region parsing

17 years agoadded doc for PDBResNum features
jprocter [Fri, 26 Jan 2007 10:23:23 +0000 (10:23 +0000)]
added doc for PDBResNum features

17 years agoCommand takes alignment, not gapChar
amwaterhouse [Thu, 25 Jan 2007 18:47:18 +0000 (18:47 +0000)]
Command takes alignment, not gapChar

17 years agoAnnotations move when full alignment edited
amwaterhouse [Thu, 25 Jan 2007 18:46:31 +0000 (18:46 +0000)]
Annotations move when full alignment edited

17 years agoAnnotation adjustment moved to EditCommand
amwaterhouse [Thu, 25 Jan 2007 18:45:46 +0000 (18:45 +0000)]
Annotation adjustment moved to EditCommand

17 years agoRemove unneccessary lines
amwaterhouse [Thu, 25 Jan 2007 18:45:14 +0000 (18:45 +0000)]
Remove unneccessary lines

17 years agoAlignmentAnnotations require id
amwaterhouse [Thu, 25 Jan 2007 18:44:47 +0000 (18:44 +0000)]
AlignmentAnnotations require id

17 years agoAllow for hidden columns
amwaterhouse [Thu, 25 Jan 2007 16:03:20 +0000 (16:03 +0000)]
Allow for hidden columns

17 years agoOnly output visible annotations
amwaterhouse [Thu, 25 Jan 2007 16:02:36 +0000 (16:02 +0000)]
Only output visible annotations

17 years agoload/get Annotation
amwaterhouse [Thu, 25 Jan 2007 16:02:21 +0000 (16:02 +0000)]
load/get Annotation

17 years agoRemove unnecessary line
amwaterhouse [Thu, 25 Jan 2007 16:01:59 +0000 (16:01 +0000)]
Remove unnecessary line

17 years agoOutput annotations
amwaterhouse [Thu, 25 Jan 2007 16:00:41 +0000 (16:00 +0000)]
Output annotations

17 years ago1.1 enabled
amwaterhouse [Thu, 25 Jan 2007 16:00:21 +0000 (16:00 +0000)]
1.1 enabled

17 years agoreinstating class implementation.
jprocter [Thu, 25 Jan 2007 15:38:27 +0000 (15:38 +0000)]
reinstating class implementation.

17 years agochecks for irreflexive mapping in main tester
jprocter [Thu, 25 Jan 2007 15:36:51 +0000 (15:36 +0000)]
checks for irreflexive mapping in main tester

17 years agoConservation etc have autoCalculated flag set true
amwaterhouse [Wed, 24 Jan 2007 17:30:49 +0000 (17:30 +0000)]
Conservation etc have autoCalculated flag set true

17 years agoAdjustAnnotations needs position, number and insert
amwaterhouse [Wed, 24 Jan 2007 17:30:12 +0000 (17:30 +0000)]
AdjustAnnotations needs position, number and insert

17 years agoThis constructor is never called
amwaterhouse [Wed, 24 Jan 2007 17:29:38 +0000 (17:29 +0000)]
This constructor is never called

17 years agoFeatures output for javascript
amwaterhouse [Wed, 24 Jan 2007 17:29:20 +0000 (17:29 +0000)]
Features output for javascript