jalview.git
17 years agoNew method for mapping from common database sources to canonical jalview name. Added...
jprocter [Mon, 19 Mar 2007 14:02:46 +0000 (14:02 +0000)]
New method for mapping from common database sources to canonical jalview name. Added EMBL to list of mappings between internal DBRefSources and das coordinate system.

17 years agonote about selenocystine.
jprocter [Mon, 19 Mar 2007 13:59:52 +0000 (13:59 +0000)]
note about selenocystine.

17 years agodisambiguate jalview.datamodel.Mapping from castor's Mapping object.
jprocter [Mon, 19 Mar 2007 13:47:34 +0000 (13:47 +0000)]
disambiguate jalview.datamodel.Mapping from castor's Mapping object.

17 years agoinitial support for EMBL file parsing.
jprocter [Mon, 19 Mar 2007 13:44:18 +0000 (13:44 +0000)]
initial support for EMBL file parsing.

17 years agoequals operation used for canonicalisation of DBRefList (rather than explict 'equals...
jprocter [Mon, 19 Mar 2007 13:43:23 +0000 (13:43 +0000)]
equals operation used for canonicalisation of DBRefList (rather than explict 'equals' on attributes)

17 years agomapping implemented by MapList added to DBRefEntry.
jprocter [Mon, 19 Mar 2007 13:42:40 +0000 (13:42 +0000)]
mapping implemented by MapList added to DBRefEntry.

17 years agojavadoc typo
jprocter [Mon, 19 Mar 2007 13:38:44 +0000 (13:38 +0000)]
javadoc typo

17 years agocopy constructor
jprocter [Mon, 19 Mar 2007 13:37:57 +0000 (13:37 +0000)]
copy constructor

17 years agoUncomment graphics 2d bit
amwaterhouse [Tue, 27 Feb 2007 13:43:24 +0000 (13:43 +0000)]
Uncomment graphics 2d bit

17 years agoLaunch applet jmol
amwaterhouse [Tue, 27 Feb 2007 13:39:49 +0000 (13:39 +0000)]
Launch applet jmol

17 years agoUse paintAlignment
amwaterhouse [Tue, 27 Feb 2007 13:39:19 +0000 (13:39 +0000)]
Use paintAlignment

17 years agocheck conservation length
amwaterhouse [Tue, 27 Feb 2007 13:38:40 +0000 (13:38 +0000)]
check conservation length

17 years agoStructure listener
amwaterhouse [Tue, 27 Feb 2007 13:38:21 +0000 (13:38 +0000)]
Structure listener

17 years agoremove p+3 < query.length
amwaterhouse [Tue, 27 Feb 2007 13:37:31 +0000 (13:37 +0000)]
remove p+3 < query.length

17 years agoNo longer use ref to seqcanvas for painting
amwaterhouse [Tue, 27 Feb 2007 13:36:10 +0000 (13:36 +0000)]
No longer use ref to seqcanvas for painting

17 years agoblank space for chain name if empty
amwaterhouse [Tue, 27 Feb 2007 13:30:37 +0000 (13:30 +0000)]
blank space for chain name if empty

17 years agokeep record of atomIndeX
amwaterhouse [Tue, 27 Feb 2007 13:28:47 +0000 (13:28 +0000)]
keep record of atomIndeX

17 years agojmol added
amwaterhouse [Tue, 27 Feb 2007 13:27:58 +0000 (13:27 +0000)]
jmol added

17 years agojmol
amwaterhouse [Tue, 27 Feb 2007 13:26:32 +0000 (13:26 +0000)]
jmol

17 years agoversion 3.7
amwaterhouse [Mon, 12 Feb 2007 14:48:20 +0000 (14:48 +0000)]
version 3.7

17 years agodate added
amwaterhouse [Mon, 12 Feb 2007 12:43:52 +0000 (12:43 +0000)]
date added

17 years ago>0 rather than -1 check
amwaterhouse [Mon, 12 Feb 2007 12:10:30 +0000 (12:10 +0000)]
>0 rather than -1 check

17 years agotranfer pdbresno features to dataset sequence.
jprocter [Mon, 12 Feb 2007 10:05:31 +0000 (10:05 +0000)]
tranfer pdbresno features to dataset sequence.

17 years agoReload jar files
amwaterhouse [Mon, 12 Feb 2007 09:44:15 +0000 (09:44 +0000)]
Reload jar files

17 years agoHashtable for previously loaded pdb files
amwaterhouse [Mon, 12 Feb 2007 09:44:01 +0000 (09:44 +0000)]
Hashtable for previously loaded pdb files

17 years agoMake checkbox bigger for text on mac
amwaterhouse [Mon, 12 Feb 2007 09:43:40 +0000 (09:43 +0000)]
Make checkbox bigger for text on mac

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