jalview.git
17 years agofr==null check.
jprocter [Mon, 2 Apr 2007 13:11:13 +0000 (13:11 +0000)]
fr==null check.

17 years agofeature group state and type order preference storage/retrieval.
jprocter [Mon, 2 Apr 2007 13:10:05 +0000 (13:10 +0000)]
feature group state and type order preference storage/retrieval.

17 years agofeaturesAdded call for transferred PDB features
jprocter [Mon, 2 Apr 2007 13:09:32 +0000 (13:09 +0000)]
featuresAdded call for transferred PDB features

17 years agofeaturesAdded() method, state change support between feature setting box and featureR...
jprocter [Mon, 2 Apr 2007 13:08:20 +0000 (13:08 +0000)]
featuresAdded() method, state change support between feature setting box and featureRenderer, feature ordering conserved between group selections, new features appear on top of old, and 'optimise' feature ordering button added.

17 years agoadded feature type order preference attribute and visible feature group state element
jprocter [Mon, 2 Apr 2007 13:05:09 +0000 (13:05 +0000)]
added feature type order preference attribute and visible feature group state element

17 years agoNew seq feature name not added here
amwaterhouse [Mon, 2 Apr 2007 12:52:40 +0000 (12:52 +0000)]
New seq feature name not added here

17 years agogetAllFeaturesAtRes replace by findFeaturesAtRes
amwaterhouse [Mon, 2 Apr 2007 12:51:14 +0000 (12:51 +0000)]
getAllFeaturesAtRes replace by findFeaturesAtRes

17 years agoaddElement
amwaterhouse [Mon, 2 Apr 2007 12:50:07 +0000 (12:50 +0000)]
addElement

17 years agodestroy destroyed
amwaterhouse [Mon, 2 Apr 2007 12:38:13 +0000 (12:38 +0000)]
destroy destroyed

17 years agodestroy destroyed
amwaterhouse [Mon, 2 Apr 2007 12:29:21 +0000 (12:29 +0000)]
destroy destroyed

17 years agoDestroy alignment moved to finalize
amwaterhouse [Mon, 2 Apr 2007 12:28:28 +0000 (12:28 +0000)]
Destroy alignment moved to finalize

17 years agoChain might be null
amwaterhouse [Mon, 2 Apr 2007 11:21:35 +0000 (11:21 +0000)]
Chain might be null

17 years agoDestroy Alignment when closing frame
amwaterhouse [Mon, 2 Apr 2007 11:21:13 +0000 (11:21 +0000)]
Destroy Alignment when closing frame

17 years agoDestroy aligment method added
amwaterhouse [Mon, 2 Apr 2007 11:17:25 +0000 (11:17 +0000)]
Destroy aligment method added

17 years agoMust allow for scrollbar height
amwaterhouse [Mon, 2 Apr 2007 11:16:53 +0000 (11:16 +0000)]
Must allow for scrollbar height

17 years agoPick atom highlighted
amwaterhouse [Tue, 27 Mar 2007 09:14:02 +0000 (09:14 +0000)]
Pick atom highlighted

17 years agoUpdated PDB loading params
amwaterhouse [Tue, 27 Mar 2007 09:02:34 +0000 (09:02 +0000)]
Updated PDB loading params

17 years agoJmol calls user colours
amwaterhouse [Mon, 26 Mar 2007 17:29:37 +0000 (17:29 +0000)]
Jmol calls user colours

17 years agoJalview colour schemes added
amwaterhouse [Mon, 26 Mar 2007 17:28:56 +0000 (17:28 +0000)]
Jalview colour schemes added

17 years agoAdd seq mapping for multiple seq 2 pdbs
amwaterhouse [Mon, 26 Mar 2007 17:25:41 +0000 (17:25 +0000)]
Add seq mapping for multiple seq 2 pdbs

17 years agoMenu changes
amwaterhouse [Mon, 26 Mar 2007 17:25:14 +0000 (17:25 +0000)]
Menu changes

17 years agofix single sequence features added rendering bug.
jprocter [Mon, 26 Mar 2007 14:31:39 +0000 (14:31 +0000)]
fix single sequence features added rendering bug.

17 years agoPDB residue numberings transfered and alignment view refreshed to update featureRenderer.
jprocter [Mon, 26 Mar 2007 14:19:52 +0000 (14:19 +0000)]
PDB residue numberings transfered and alignment view refreshed to update featureRenderer.

17 years agogrammar.
jprocter [Mon, 26 Mar 2007 14:15:54 +0000 (14:15 +0000)]
grammar.

17 years agoupdates to console
amwaterhouse [Fri, 23 Mar 2007 17:26:20 +0000 (17:26 +0000)]
updates to console

17 years agoslide is transparent to hidden columns
amwaterhouse [Fri, 23 Mar 2007 17:25:58 +0000 (17:25 +0000)]
slide is transparent to hidden columns

17 years agogeneralised feature attribute parsing slightly (no embl specs to work from yet)
jprocter [Fri, 23 Mar 2007 16:36:02 +0000 (16:36 +0000)]
generalised feature attribute parsing slightly (no embl specs to work from yet)

17 years agobugfix for 1.1 conversion.
jprocter [Fri, 23 Mar 2007 15:41:11 +0000 (15:41 +0000)]
bugfix for 1.1 conversion.

17 years agoreenable canceldas after a cancel and subsequence fetch
jprocter [Fri, 23 Mar 2007 15:40:38 +0000 (15:40 +0000)]
reenable canceldas after a cancel and subsequence fetch

17 years agolastSeq==null to force refresh of sequencefeature array reference
jprocter [Fri, 23 Mar 2007 15:39:20 +0000 (15:39 +0000)]
lastSeq==null to force refresh of sequencefeature array reference

17 years agoremoved Iterator usage.
jprocter [Fri, 23 Mar 2007 15:38:21 +0000 (15:38 +0000)]
removed Iterator usage.

17 years agorun and halt buttons must have listeners added
amwaterhouse [Fri, 23 Mar 2007 11:45:08 +0000 (11:45 +0000)]
run and halt buttons must have listeners added

17 years agoloadingFromArchive flag added
amwaterhouse [Fri, 23 Mar 2007 10:47:10 +0000 (10:47 +0000)]
loadingFromArchive flag added

17 years agorun halt hidden, help moved to menu item for stupid mac users
amwaterhouse [Fri, 23 Mar 2007 10:46:47 +0000 (10:46 +0000)]
run halt hidden, help moved to menu item for stupid mac users

17 years agosave structures
amwaterhouse [Thu, 22 Mar 2007 18:33:37 +0000 (18:33 +0000)]
save structures

17 years agoCommented out userDefColours for compilation. Class now redundant anyway
amwaterhouse [Thu, 22 Mar 2007 18:33:02 +0000 (18:33 +0000)]
Commented out userDefColours for compilation. Class now redundant anyway

17 years agoNow a JPanel, plus some modifications
amwaterhouse [Thu, 22 Mar 2007 18:32:12 +0000 (18:32 +0000)]
Now a JPanel, plus some modifications

17 years agoCheck exploded pos is not the same as current frame
amwaterhouse [Thu, 22 Mar 2007 18:31:45 +0000 (18:31 +0000)]
Check exploded pos is not the same as current frame

17 years agoSet gatherViewsHere false when making a new tab
amwaterhouse [Thu, 22 Mar 2007 18:31:14 +0000 (18:31 +0000)]
Set gatherViewsHere false when making a new tab

17 years agoSaves structures
amwaterhouse [Thu, 22 Mar 2007 18:30:40 +0000 (18:30 +0000)]
Saves structures

17 years agoJalview colours added to Jmol
amwaterhouse [Thu, 22 Mar 2007 18:30:27 +0000 (18:30 +0000)]
Jalview colours added to Jmol

17 years agoSaves Jmol status
amwaterhouse [Thu, 22 Mar 2007 18:29:49 +0000 (18:29 +0000)]
Saves Jmol status

17 years agoDAS features mapped to local reference frame
jprocter [Mon, 19 Mar 2007 15:48:12 +0000 (15:48 +0000)]
DAS features mapped to local reference frame

17 years agotranslate aligned cDNA to aligned peptide
jprocter [Mon, 19 Mar 2007 15:41:54 +0000 (15:41 +0000)]
translate aligned cDNA to aligned peptide

17 years agoretrieve and parse EMBL records to view exons.
jprocter [Mon, 19 Mar 2007 15:40:42 +0000 (15:40 +0000)]
retrieve and parse EMBL records to view exons.

17 years agoconvenience method to get visible selected region.
jprocter [Mon, 19 Mar 2007 14:36:47 +0000 (14:36 +0000)]
convenience method to get visible selected region.

17 years agonull exception when annotation created with no description.
jprocter [Mon, 19 Mar 2007 14:05:37 +0000 (14:05 +0000)]
null exception when annotation created with no description.

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