Fix for feature name amended
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shift I to inverse sequence selection
1 lines of code changed in:
Append html
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Update features
195 lines of code changed in:
conservation lock
30 lines of code changed in:
deleteSequenceFeature
42 lines of code changed in:
Remove consensus annotation if out of memory
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updatingConsensus, updatingConservation is static - only one thread can run the calculation at once, otherwise we'll go out of memory
38 lines of code changed in:
PaintRefresher can calculate seqs added or removed
185 lines of code changed in:
Dont remove or add PaintRefresher registrations for explode, gather views
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-1 error
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Reset colour schemes and alignmentChanged moved to viewport
94 lines of code changed in:
If sequence is null, dont add it
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New padgaps works out number of gaps to insert, delete
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Rename old properties file before writing new
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Focus listener on Tabbed pane, gives keyboard focus back to alignFrame
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Only adds history item if size>0
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Returns number of columns deleted
38 lines of code changed in:
Remove system.out
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void changeCase(ActionEvent e
10 lines of code changed in:
set quality to null if removed
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showConservation, quality, identity not used
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Dont readd the undo
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check command.string[i] is not null
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Sequence length maybe less than end
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Error message changed
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Sequences may be hidden, not in this aligment
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Invert accelerators
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sequence may be null if hidden or deleted
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Set alignFrame of gathered panels to be the source AlignFrame
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remove gaps size range
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No need to reduce length if inserting more gaps at the end of a sequence
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Check if hiddenSequence has been deleted
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Known bugs fixed
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Dont scroll off width-1
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We can delete sequence 0
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Return if negative width, ie alignment deleted
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Check hiddenSequence before placing in tmp
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Get sequence in routine
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viewport.hasHiddenColumns updated after undo/redo performed
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EditCommand added to AlignFrame
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Adjusts columnSelection correctly
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Adjusts hiddenColumns correctly
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more accelerators
6 lines of code changed in:
Only send one call per sequence at the moment
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ShowConservation, quality, identity not used
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Must set alignIndex before delete takes place
17 lines of code changed in:
Use EditCommand.Cut
25 lines of code changed in:
HistoryItem replaced by CommandI
195 lines of code changed in:
EditCommand implemented
273 lines of code changed in:
must translate graphics back the same amountcvs diff SeqCanvas.java
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Change Case is undoable
57 lines of code changed in:
SequenceIndex might be beyond old height
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Must catch image outOfMemoryError
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changeCase, removeGaps moved to commands package
535 lines of code changed in:
maxIdLength redundant, deleteCols, trimLeft, removeGaps moved to Commands
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Uses RemoveGapsCommand
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Remove variables not used
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Remove unneccessary import
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Make everything final
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New accelerators
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Commented out for compilation
28 lines of code changed in:
setOrder is public
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Commands which can be done, or undone
815 lines of code changed in:
Its historycvs remove jalview/datamodel/HistoryItem.java
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fixes bug reported by Christopher Tan (help@jalview.org) - preservation of sequence description in aligned sequences.
226 lines of code changed in:
Wait for response from server before next sequence
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showqual, showcons never used
5 lines of code changed in:
remove html and body from tooltip
68 lines of code changed in:
new feature args
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Can set description for new features
48 lines of code changed in:
Faded anntotations when recalculating
67 lines of code changed in:
set conserve and quality null if outofmemory
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No longer a FeatureListener
4 lines of code changed in:
parseDescriptionHTML
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draw text after linkimage
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Remove system.out
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Gerneral XML parse error
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fixed array out of bounds exception in copy constructor
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showQuality may be updated during archive file load
7 lines of code changed in:
Convenient function findEndRes
32 lines of code changed in:
Add features from Popupmenu
142 lines of code changed in:
Overview may request index beyond alignment height
1 lines of code changed in:
Use i, not index if not representedSeqs
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If conservation is null, disable Blosum62 and conservation colouring
5 lines of code changed in:
Annotasiont[j] might be null
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Local adjustForhiddenSeqs routine
49 lines of code changed in:
RepresentGroup count items
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Null element checked
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HiddenSequences now array, not hashtable
108 lines of code changed in:
Comment out debug to compile applet
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fixes exception (array index out of bounds - due to off by one error) when applying conservation colouring to a group
540 lines of code changed in:
refined id matching to pick the closest match (by length) to the query and added '_' to the list of word separators
58 lines of code changed in:
debug message bugfix on duplicate tree leaf names.
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No need to find index when deleting
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Calculate alWidth earlier
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Remove growing hashtable
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Check on null consensus
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bugfix for dodgy trees which contain the same leafname more than once - so that all leaves in the tree are properly associated.
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Must repaint whole alignPanel
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MaxResidue must be at least 2
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Remove unneccessary separator
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Only getGroups once if groupEditingcvs update
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1.1 compatible
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Use AAFrequency final keys
5 lines of code changed in:
SetTooltip empty
4 lines of code changed in:
Optimized
78 lines of code changed in:
aaIndex replaces aaHash
11 lines of code changed in:
static final strings for consensus keys
26 lines of code changed in:
Consensus and conservation updated in threads
292 lines of code changed in:
aaIndex replaces aaHash
124 lines of code changed in:
fixed log4j complaints for vamsas logging (again)
3 lines of code changed in:
fixed log4j complaints for vamsas logging.
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excluded log4j properties.
0 lines of code changed in:
java 1.4 compliant classes.
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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.
5070 lines of code changed in:
set firstColumn property for an alignmentView object.
1072 lines of code changed in:
fixed getCompactAlignment method to return proper cigarArray and added 'firstColumn' parameter to AlignmentView object.
3 lines of code changed in:
Added filter so that input to a JPred job is *solely* the visible residues, and the profile and prediction are correctly mapped back to the original seuence.
256 lines of code changed in:
javadoc
9 lines of code changed in:
new getVisibleContigs method mirrors the getVisibleContigs method in AlignmentView
0 lines of code changed in:
javadoc
3 lines of code changed in:
AAFrequency optimized
142 lines of code changed in:
Set consensus as hashtble[]
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Multiple Views
1022 lines of code changed in:
BatchSize now 10
0 lines of code changed in:
OutOfMemoryError test
106 lines of code changed in:
TabbedPanes for views
37 lines of code changed in:
lower case available
7 lines of code changed in:
AlignFrame must take width and height
9 lines of code changed in:
Sequenceset may be empty, multiple views
0 lines of code changed in:
DEFAULT_WIDTH
25 lines of code changed in:
Viewname, sequencesetid, gatheredViews
3 lines of code changed in:
Sequences are optionalcvs diff vamsas.xsd
3 lines of code changed in:
Check annotation is editable
2 lines of code changed in:
Send DAS requests in batches of 20
0 lines of code changed in:
DB seqs may be lower or upper case
0 lines of code changed in:
BoldFont upperCase
28 lines of code changed in:
Remove empty() from feature ToolTip
6 lines of code changed in:
Check selection scroll beyond aligmnment height
6 lines of code changed in:
Check on vscrollMax values
9 lines of code changed in:
upperCaseBold
17 lines of code changed in:
TurnColour bug on popupmenu applet
1 lines of code changed in: