jalview.git
18 years agoReturns number of columns deleted
amwaterhouse [Thu, 26 Oct 2006 13:09:20 +0000 (13:09 +0000)]
Returns number of columns deleted

18 years agoRemove system.out
amwaterhouse [Thu, 26 Oct 2006 13:08:46 +0000 (13:08 +0000)]
Remove system.out

18 years agovoid changeCase(ActionEvent e
amwaterhouse [Thu, 26 Oct 2006 12:19:46 +0000 (12:19 +0000)]
void changeCase(ActionEvent e

18 years agoset quality to null if removed
amwaterhouse [Thu, 26 Oct 2006 12:19:16 +0000 (12:19 +0000)]
set quality to null if removed

18 years agoshowConservation, quality, identity not used
amwaterhouse [Thu, 26 Oct 2006 12:18:52 +0000 (12:18 +0000)]
showConservation, quality, identity not used

18 years agoDont readd the undo
amwaterhouse [Thu, 26 Oct 2006 12:18:13 +0000 (12:18 +0000)]
Dont readd the undo

18 years agocheck command.string[i] is not null
amwaterhouse [Thu, 26 Oct 2006 12:17:51 +0000 (12:17 +0000)]
check command.string[i] is not null

18 years agoSequence length maybe less than end
amwaterhouse [Thu, 26 Oct 2006 12:17:13 +0000 (12:17 +0000)]
Sequence length maybe less than end

18 years agoError message changed
amwaterhouse [Thu, 26 Oct 2006 12:11:20 +0000 (12:11 +0000)]
Error message changed

18 years agoSequences may be hidden, not in this aligment
amwaterhouse [Thu, 26 Oct 2006 10:19:14 +0000 (10:19 +0000)]
Sequences may be hidden, not in this aligment

18 years agoInvert accelerators
amwaterhouse [Thu, 26 Oct 2006 09:42:04 +0000 (09:42 +0000)]
Invert accelerators

18 years agosequence may be null if hidden or deleted
amwaterhouse [Thu, 26 Oct 2006 09:41:36 +0000 (09:41 +0000)]
sequence may be null if hidden or deleted

18 years agoSet alignFrame of gathered panels to be the source AlignFrame
amwaterhouse [Thu, 26 Oct 2006 09:41:12 +0000 (09:41 +0000)]
Set alignFrame of gathered panels to be the source AlignFrame

18 years agoremove gaps size range
amwaterhouse [Thu, 26 Oct 2006 09:40:35 +0000 (09:40 +0000)]
remove gaps size range

18 years agoNo need to reduce length if inserting more gaps at the end of a sequence
amwaterhouse [Thu, 26 Oct 2006 09:39:54 +0000 (09:39 +0000)]
No need to reduce length if inserting more gaps at the end of a sequence

18 years agoCheck if hiddenSequence has been deleted
amwaterhouse [Thu, 26 Oct 2006 09:39:01 +0000 (09:39 +0000)]
Check if hiddenSequence has been deleted

18 years agoKnown bugs fixed
amwaterhouse [Thu, 26 Oct 2006 09:37:58 +0000 (09:37 +0000)]
Known bugs fixed

18 years agoDont scroll off width-1
amwaterhouse [Thu, 26 Oct 2006 09:37:18 +0000 (09:37 +0000)]
Dont scroll off width-1

18 years agoWe can delete sequence 0
amwaterhouse [Wed, 25 Oct 2006 14:58:18 +0000 (14:58 +0000)]
We can delete sequence 0

18 years agoReturn if negative width, ie alignment deleted
amwaterhouse [Wed, 25 Oct 2006 14:57:37 +0000 (14:57 +0000)]
Return if negative width, ie alignment deleted

18 years agoCheck hiddenSequence before placing in tmp
amwaterhouse [Wed, 25 Oct 2006 14:57:02 +0000 (14:57 +0000)]
Check hiddenSequence before placing in tmp

18 years agoGet sequence in routine
amwaterhouse [Wed, 25 Oct 2006 14:46:20 +0000 (14:46 +0000)]
Get sequence in routine

18 years agoviewport.hasHiddenColumns updated after undo/redo performed
amwaterhouse [Wed, 25 Oct 2006 14:03:43 +0000 (14:03 +0000)]
viewport.hasHiddenColumns updated after undo/redo performed

18 years agoEditCommand added to AlignFrame
amwaterhouse [Wed, 25 Oct 2006 14:02:07 +0000 (14:02 +0000)]
EditCommand added to AlignFrame

18 years agoAdjusts columnSelection correctly
amwaterhouse [Wed, 25 Oct 2006 14:00:35 +0000 (14:00 +0000)]
Adjusts columnSelection correctly

18 years agoAdjusts hiddenColumns correctly
amwaterhouse [Wed, 25 Oct 2006 13:59:54 +0000 (13:59 +0000)]
Adjusts hiddenColumns correctly

18 years agomore accelerators
amwaterhouse [Wed, 25 Oct 2006 13:58:30 +0000 (13:58 +0000)]
more accelerators

18 years agoOnly send one call per sequence at the moment
amwaterhouse [Tue, 24 Oct 2006 12:36:20 +0000 (12:36 +0000)]
Only send one call per sequence at the moment

18 years agoShowConservation, quality, identity not used
amwaterhouse [Tue, 24 Oct 2006 12:22:43 +0000 (12:22 +0000)]
ShowConservation, quality, identity not used

18 years agoMust set alignIndex before delete takes place
amwaterhouse [Tue, 24 Oct 2006 12:05:01 +0000 (12:05 +0000)]
Must set alignIndex before delete takes place

18 years agoUse EditCommand.Cut
amwaterhouse [Tue, 24 Oct 2006 11:36:59 +0000 (11:36 +0000)]
Use EditCommand.Cut

18 years agoHistoryItem replaced by CommandI
amwaterhouse [Tue, 24 Oct 2006 11:24:39 +0000 (11:24 +0000)]
HistoryItem replaced by CommandI

18 years agoEditCommand implemented
amwaterhouse [Tue, 24 Oct 2006 11:24:20 +0000 (11:24 +0000)]
EditCommand implemented

18 years agomust translate graphics back the same amountcvs diff SeqCanvas.java
amwaterhouse [Tue, 24 Oct 2006 11:24:04 +0000 (11:24 +0000)]
must translate graphics back the same amountcvs diff SeqCanvas.java

18 years agoChange Case is undoable
amwaterhouse [Tue, 24 Oct 2006 11:23:29 +0000 (11:23 +0000)]
Change Case is undoable

18 years agoSequenceIndex might be beyond old height
amwaterhouse [Tue, 24 Oct 2006 11:23:03 +0000 (11:23 +0000)]
SequenceIndex might be beyond old height

18 years agoMust catch image outOfMemoryError
amwaterhouse [Tue, 24 Oct 2006 11:22:29 +0000 (11:22 +0000)]
Must catch image outOfMemoryError

18 years agochangeCase, removeGaps moved to commands package
amwaterhouse [Tue, 24 Oct 2006 11:21:25 +0000 (11:21 +0000)]
changeCase, removeGaps moved to commands package

18 years agomaxIdLength redundant, deleteCols, trimLeft, removeGaps moved to Commands
amwaterhouse [Tue, 24 Oct 2006 11:20:33 +0000 (11:20 +0000)]
maxIdLength redundant, deleteCols, trimLeft, removeGaps moved to Commands

18 years agoUses RemoveGapsCommand
amwaterhouse [Tue, 24 Oct 2006 11:19:30 +0000 (11:19 +0000)]
Uses RemoveGapsCommand

18 years agoRemove variables not used
amwaterhouse [Tue, 24 Oct 2006 11:19:12 +0000 (11:19 +0000)]
Remove variables not used

18 years agoRemove unneccessary import
amwaterhouse [Tue, 24 Oct 2006 11:18:13 +0000 (11:18 +0000)]
Remove unneccessary import

18 years agoMake everything final
amwaterhouse [Tue, 24 Oct 2006 11:17:51 +0000 (11:17 +0000)]
Make everything final

18 years agoNew accelerators
amwaterhouse [Tue, 24 Oct 2006 11:17:16 +0000 (11:17 +0000)]
New accelerators

18 years agoCommented out for compilation
amwaterhouse [Tue, 24 Oct 2006 11:16:53 +0000 (11:16 +0000)]
Commented out for compilation

18 years agosetOrder is public
amwaterhouse [Tue, 24 Oct 2006 11:12:54 +0000 (11:12 +0000)]
setOrder is public

18 years agoCommands which can be done, or undone
amwaterhouse [Tue, 24 Oct 2006 11:12:13 +0000 (11:12 +0000)]
Commands which can be done, or undone

18 years agoIts historycvs remove jalview/datamodel/HistoryItem.java
amwaterhouse [Tue, 24 Oct 2006 11:09:09 +0000 (11:09 +0000)]
Its historycvs remove jalview/datamodel/HistoryItem.java

18 years agofixes bug reported by Christopher Tan (help@jalview.org) - preservation of sequence...
jprocter [Tue, 24 Oct 2006 08:11:22 +0000 (08:11 +0000)]
fixes bug reported by Christopher Tan (help@jalview.org) - preservation of sequence description in aligned sequences.

18 years agoWait for response from server before next sequence
amwaterhouse [Wed, 18 Oct 2006 13:10:10 +0000 (13:10 +0000)]
Wait for response from server before next sequence

18 years agoshowqual, showcons never used
amwaterhouse [Wed, 18 Oct 2006 13:06:55 +0000 (13:06 +0000)]
showqual, showcons never used

18 years agoremove html and body from tooltip
amwaterhouse [Wed, 18 Oct 2006 13:05:05 +0000 (13:05 +0000)]
remove html and body from tooltip

18 years agonew feature args
amwaterhouse [Wed, 18 Oct 2006 13:04:40 +0000 (13:04 +0000)]
new feature args

18 years agoCan set description for new features
amwaterhouse [Wed, 18 Oct 2006 13:03:22 +0000 (13:03 +0000)]
Can set description for new features

18 years agoFaded anntotations when recalculating
amwaterhouse [Wed, 18 Oct 2006 13:02:58 +0000 (13:02 +0000)]
Faded anntotations when recalculating

18 years agoset conserve and quality null if outofmemory
amwaterhouse [Wed, 18 Oct 2006 13:02:17 +0000 (13:02 +0000)]
set conserve and quality null if outofmemory

18 years agoNo longer a FeatureListener
amwaterhouse [Wed, 18 Oct 2006 13:01:16 +0000 (13:01 +0000)]
No longer a FeatureListener

18 years agoparseDescriptionHTML
amwaterhouse [Wed, 18 Oct 2006 13:00:26 +0000 (13:00 +0000)]
parseDescriptionHTML

18 years agodraw text after linkimage
amwaterhouse [Wed, 18 Oct 2006 13:00:02 +0000 (13:00 +0000)]
draw text after linkimage

18 years agoRemove system.out
amwaterhouse [Wed, 18 Oct 2006 12:59:39 +0000 (12:59 +0000)]
Remove system.out

18 years agoGerneral XML parse error
amwaterhouse [Wed, 18 Oct 2006 12:58:00 +0000 (12:58 +0000)]
Gerneral XML parse error

18 years agofixed array out of bounds exception in copy constructor
jprocter [Sun, 15 Oct 2006 12:44:45 +0000 (12:44 +0000)]
fixed array out of bounds exception in copy constructor

18 years agoshowQuality may be updated during archive file load
amwaterhouse [Thu, 12 Oct 2006 17:15:45 +0000 (17:15 +0000)]
showQuality may be updated during archive file load

18 years agoConvenient function findEndRes
amwaterhouse [Thu, 12 Oct 2006 16:14:23 +0000 (16:14 +0000)]
Convenient function findEndRes

18 years agoAdd features from Popupmenu
amwaterhouse [Thu, 12 Oct 2006 16:14:02 +0000 (16:14 +0000)]
Add features from Popupmenu

18 years agoOverview may request index beyond alignment height
amwaterhouse [Thu, 12 Oct 2006 14:13:22 +0000 (14:13 +0000)]
Overview may request index beyond alignment height

18 years agoUse i, not index if not representedSeqs
amwaterhouse [Thu, 12 Oct 2006 13:35:17 +0000 (13:35 +0000)]
Use i, not index if not representedSeqs

18 years agoIf conservation is null, disable Blosum62 and conservation colouring
amwaterhouse [Thu, 12 Oct 2006 13:23:21 +0000 (13:23 +0000)]
If conservation is null, disable Blosum62 and conservation colouring

18 years agoAnnotasiont[j] might be null
amwaterhouse [Thu, 12 Oct 2006 13:22:03 +0000 (13:22 +0000)]
Annotasiont[j] might be null

18 years agoLocal adjustForhiddenSeqs routine
amwaterhouse [Thu, 12 Oct 2006 13:21:41 +0000 (13:21 +0000)]
Local adjustForhiddenSeqs routine

18 years agoRepresentGroup count items
amwaterhouse [Thu, 12 Oct 2006 13:21:09 +0000 (13:21 +0000)]
RepresentGroup count items

18 years agoNull element checked
amwaterhouse [Thu, 12 Oct 2006 13:18:56 +0000 (13:18 +0000)]
Null element checked

18 years agoHiddenSequences now array, not hashtable
amwaterhouse [Thu, 12 Oct 2006 13:18:40 +0000 (13:18 +0000)]
HiddenSequences now array, not hashtable

18 years agoComment out debug to compile applet
amwaterhouse [Thu, 12 Oct 2006 13:18:02 +0000 (13:18 +0000)]
Comment out debug to compile applet

18 years agofixes exception (array index out of bounds - due to off by one error) when applying...
jprocter [Wed, 11 Oct 2006 09:53:46 +0000 (09:53 +0000)]
fixes exception (array index out of bounds - due to off by one error) when applying conservation colouring to a group

18 years agorefined id matching to pick the closest match (by length) to the query and added...
jprocter [Tue, 10 Oct 2006 16:01:58 +0000 (16:01 +0000)]
refined id matching to pick the closest match (by length) to the query and added '_' to the list of word separators

18 years agodebug message bugfix on duplicate tree leaf names.
jprocter [Tue, 10 Oct 2006 15:31:41 +0000 (15:31 +0000)]
debug message bugfix on duplicate tree leaf names.

18 years agoNo need to find index when deleting
amwaterhouse [Tue, 10 Oct 2006 14:11:53 +0000 (14:11 +0000)]
No need to find index when deleting

18 years agoCalculate alWidth earlier
amwaterhouse [Tue, 10 Oct 2006 14:10:35 +0000 (14:10 +0000)]
Calculate alWidth earlier

18 years agoRemove growing hashtable
amwaterhouse [Tue, 10 Oct 2006 14:09:24 +0000 (14:09 +0000)]
Remove growing hashtable

18 years agoCheck on null consensus
amwaterhouse [Tue, 10 Oct 2006 14:08:47 +0000 (14:08 +0000)]
Check on null consensus

18 years agobugfix for dodgy trees which contain the same leafname more than once - so that all...
jprocter [Tue, 10 Oct 2006 14:07:12 +0000 (14:07 +0000)]
bugfix for dodgy trees which contain the same leafname more than once - so that all leaves in the tree are properly associated.

18 years agoMust repaint whole alignPanel
amwaterhouse [Tue, 10 Oct 2006 13:37:23 +0000 (13:37 +0000)]
Must repaint whole alignPanel

18 years agoMaxResidue must be at least 2
amwaterhouse [Tue, 10 Oct 2006 13:36:58 +0000 (13:36 +0000)]
MaxResidue must be at least 2

18 years agoRemove unneccessary separator
amwaterhouse [Tue, 10 Oct 2006 11:19:08 +0000 (11:19 +0000)]
Remove unneccessary separator

18 years agoOnly getGroups once if groupEditingcvs update
amwaterhouse [Tue, 10 Oct 2006 11:15:58 +0000 (11:15 +0000)]
Only getGroups once if groupEditingcvs update

18 years ago1.1 compatible
amwaterhouse [Tue, 10 Oct 2006 10:44:03 +0000 (10:44 +0000)]
1.1 compatible

18 years agoUse AAFrequency final keys
amwaterhouse [Tue, 10 Oct 2006 10:43:52 +0000 (10:43 +0000)]
Use AAFrequency final keys

18 years agoSetTooltip empty
amwaterhouse [Tue, 10 Oct 2006 10:29:03 +0000 (10:29 +0000)]
SetTooltip empty

18 years agoOptimized
amwaterhouse [Tue, 10 Oct 2006 10:28:31 +0000 (10:28 +0000)]
Optimized

18 years agoaaIndex replaces aaHash
amwaterhouse [Tue, 10 Oct 2006 10:28:05 +0000 (10:28 +0000)]
aaIndex replaces aaHash

18 years agostatic final strings for consensus keys
amwaterhouse [Tue, 10 Oct 2006 10:27:36 +0000 (10:27 +0000)]
static final strings for consensus keys

18 years agoConsensus and conservation updated in threads
amwaterhouse [Tue, 10 Oct 2006 10:26:58 +0000 (10:26 +0000)]
Consensus and conservation updated in threads

18 years agofixed log4j complaints for vamsas logging (again)
jprocter [Mon, 9 Oct 2006 17:15:57 +0000 (17:15 +0000)]
fixed log4j complaints for vamsas logging (again)

18 years agofixed log4j complaints for vamsas logging.
jprocter [Mon, 9 Oct 2006 17:13:05 +0000 (17:13 +0000)]
fixed log4j complaints for vamsas logging.

18 years agoexcluded log4j properties.
jprocter [Mon, 9 Oct 2006 17:02:33 +0000 (17:02 +0000)]
excluded log4j properties.

18 years agojava 1.4 compliant classes.
jprocter [Mon, 9 Oct 2006 16:45:45 +0000 (16:45 +0000)]
java 1.4 compliant classes.

18 years agoimported Vamsas bindings and alpha vamsas client code from VamJalview cvs branch...
jprocter [Mon, 9 Oct 2006 16:13:13 +0000 (16:13 +0000)]
imported Vamsas bindings and alpha vamsas client code from VamJalview cvs branch. Compilation requires vamsas-client.jar but Jalview can be distributed without the vamsas-client.jar.

18 years agoset firstColumn property for an alignmentView object.
jprocter [Mon, 9 Oct 2006 16:10:39 +0000 (16:10 +0000)]
set firstColumn property for an alignmentView object.

18 years agofixed getCompactAlignment method to return proper cigarArray and added 'firstColumn...
jprocter [Mon, 9 Oct 2006 16:07:31 +0000 (16:07 +0000)]
fixed getCompactAlignment method to return proper cigarArray and added 'firstColumn' parameter to AlignmentView object.