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Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into...
[jalview.git]
/
src
/
jalview
/
schemes
/
2007-04-27
amwaterhouse
Annotation gradient will use direct colours if no graph...
tree
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commitdiff
2007-04-27
amwaterhouse
Allow threshold to be min/max
tree
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commitdiff
2007-04-11
jprocter
fixed base lookup bug in dna pairwise alignment and...
tree
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commitdiff
2007-03-19
jprocter
note about selenocystine.
tree
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commitdiff
2007-02-27
amwaterhouse
check conservation length
tree
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commitdiff
2007-02-07
amwaterhouse
Formatting
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commitdiff
2007-01-30
amwaterhouse
Any character non aa or nucleotide is a space
tree
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commitdiff
2007-01-30
amwaterhouse
consensusColouring never used
tree
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commitdiff
2006-12-06
jprocter
general pairwise substitution score models for pairwise...
tree
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commitdiff
2006-12-05
amwaterhouse
Sequence is char []
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commitdiff
2006-11-28
amwaterhouse
CurrentColour must not be accessed by multiple sequence...
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commitdiff
2006-11-28
amwaterhouse
CurrentColour must not be accessed by multiple sequence...
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commitdiff
2006-11-14
amwaterhouse
we already have c defined
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commitdiff
2006-11-13
amwaterhouse
Enable lower case colours
tree
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commitdiff
2006-11-09
amwaterhouse
Check conensus is not null
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commitdiff
2006-10-12
amwaterhouse
Null element checked
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commitdiff
2006-10-10
amwaterhouse
Check on null consensus
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commitdiff
2006-10-10
amwaterhouse
aaIndex replaces aaHash
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commitdiff
2006-10-06
amwaterhouse
Set consensus as hashtble[]
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commitdiff
2006-10-05
amwaterhouse
lower case available
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commitdiff
2006-09-11
amwaterhouse
Comment out lower case colouring for bug fix release
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commitdiff
2006-08-30
amwaterhouse
Gap added to aa3Hash
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commitdiff
2006-08-30
amwaterhouse
User colours are case sensitive
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commitdiff
2006-08-21
amwaterhouse
header updated
tree
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commitdiff
2006-06-14
amwaterhouse
parseAppletParameter
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commitdiff
2006-06-09
amwaterhouse
createColourFromName
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commitdiff
2006-04-07
amwaterhouse
Must check consensus length if autocalculate off
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commitdiff
2006-04-05
amwaterhouse
public get methods
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commitdiff
2006-03-24
amwaterhouse
Group colours not used
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commitdiff
2006-03-16
amwaterhouse
Out of bounds check
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commitdiff
2006-02-16
amwaterhouse
Dont colour gaps
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commitdiff
2006-02-16
amwaterhouse
Use original colour scheme as base for annotation colouring
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commitdiff
2006-02-15
amwaterhouse
Threshold is a single element
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commitdiff
2006-02-09
amwaterhouse
If conservation is zero, colour is white
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commitdiff
2006-02-08
amwaterhouse
Colour above or below threshold
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commitdiff
2006-02-03
amwaterhouse
Conservation colouring does what it should always have...
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commitdiff
2006-02-03
amwaterhouse
Make java 1.1 compatible
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commitdiff
2006-01-30
amwaterhouse
Get min and max colour added
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commitdiff
2006-01-30
amwaterhouse
New files
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commitdiff
2005-12-06
amwaterhouse
after merge
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commitdiff
2005-11-18
jprocter
added 3 letter IUB codes for ambiguous residues/bases
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commitdiff
2005-10-07
amwaterhouse
comma separated rgb values
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commitdiff
2005-09-22
amwaterhouse
Add nucleotide names
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commitdiff
2005-09-15
amwaterhouse
Add Uracil as X unknown
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commitdiff
2005-09-08
amwaterhouse
If vconsensus is null, return
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commitdiff
2005-09-08
amwaterhouse
Add lowercase nucleotides to nucleotideHash
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commitdiff
2005-08-30
amwaterhouse
Make 24 colours to be sure
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commitdiff
2005-08-29
amwaterhouse
Default user colour is 23 white colours
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commitdiff
2005-08-22
amwaterhouse
finalize all these hashtables
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commitdiff
2005-08-22
amwaterhouse
Conservation colour scheme is no more
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commitdiff
2005-08-18
amwaterhouse
Character methods don't exist in java 1.1
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commitdiff
2005-08-18
amwaterhouse
Proceed with upperCase residue
Release_2_03
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commitdiff
2005-08-18
amwaterhouse
Use aa index for aboveThreshold as well as colour index
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commitdiff
2005-08-17
amwaterhouse
Scheme name added
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commitdiff
2005-08-15
amwaterhouse
Remove null check
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commitdiff
2005-08-15
amwaterhouse
super.setconsensus
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commitdiff
2005-08-15
amwaterhouse
Percentage precalculated in aafrequency
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commitdiff
2005-08-15
amwaterhouse
Add taylor to default colour check
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commitdiff
2005-08-15
amwaterhouse
Hashtable now in array, not vector
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commitdiff
2005-06-30
amwaterhouse
Formatting changes
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commitdiff
2005-06-13
amwaterhouse
Get colourScheme with seqs and width
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commitdiff
2005-06-08
amwaterhouse
Formatted source
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commitdiff
2005-06-08
amwaterhouse
GPL license added
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commitdiff
2005-05-25
amwaterhouse
reset colours added
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commitdiff
2005-05-25
amwaterhouse
all can threshold
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commitdiff
2005-05-25
jprocter
tidied up system.out messages and moved many to stderr.
tree
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commitdiff
2005-05-19
amwaterhouse
returns name if given colourscheme
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commitdiff
2005-05-03
amwaterhouse
1.1 compatible, formatting changes
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commitdiff
2005-04-29
amwaterhouse
just tidying up unused imports
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commitdiff
2005-04-28
amwaterhouse
no longer used
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commitdiff
2005-04-28
amwaterhouse
must set consensus in child colourscheme
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commitdiff
2005-04-28
amwaterhouse
Updated for use by preferences panel
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commitdiff
2005-04-15
amwaterhouse
no longer used
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commitdiff
2005-04-15
amwaterhouse
consensus held in residueColour
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commitdiff
2005-04-14
amwaterhouse
blosum colour now displayed ok
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commitdiff
2005-04-13
jprocter
Fixed so that all alternate residues are used to calcul...
tree
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commitdiff
2005-04-11
jprocter
Conservation symbols : + = all props are conserved...
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commitdiff
2005-03-23
amwaterhouse
no longer used
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commitdiff
2005-03-23
amwaterhouse
secondarycolour not used
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commitdiff
2005-03-08
amwaterhouse
add lower case residue props
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commitdiff
2005-03-08
amwaterhouse
if resIndex > 19 return color.white
tree
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commitdiff
2005-02-23
jprocter
bug fix for unaligned sequence sets and clustal colours...
tree
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commitdiff
2005-02-10
amwaterhouse
check that we're not off the end of a sequence
tree
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commitdiff
2005-02-01
amwaterhouse
No need for drawableSequence
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commitdiff
2005-02-01
amwaterhouse
Clustal colours now work
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commitdiff
2005-01-24
amwaterhouse
returns color.white if the underlying colourscheme...
tree
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commitdiff
2005-01-21
amwaterhouse
remove a few imports
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commitdiff
2005-01-21
amwaterhouse
Nucleotide colours added
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commitdiff
2005-01-21
amwaterhouse
New colourScheme
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commitdiff
2005-01-17
amwaterhouse
ClustalX added to ColourProperties
tree
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commitdiff
2005-01-14
amwaterhouse
Return color.white if a gap char is detected
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commitdiff
2004-12-15
amwaterhouse
colours are right, but not the conservation bit!!
tree
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commitdiff
2004-12-15
amwaterhouse
no need to send sequence to determine residue colour
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commitdiff
2004-12-15
amwaterhouse
Added for the moment, only used by ClustalxColourScheme
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commitdiff
2004-12-15
amwaterhouse
No need to sened sequence to determine residue colour
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commitdiff
2004-12-15
amwaterhouse
isGap method implemented in utils, and optimized
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commitdiff
2004-12-15
amwaterhouse
isGap method implemented in utils
tree
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commitdiff
2004-12-14
amwaterhouse
PID Colour scheme now operational!
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commitdiff
2004-12-14
amwaterhouse
Getcolours is not needed ????
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commitdiff
2004-12-10
amwaterhouse
No longer exclusive to SequenceGroups
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commitdiff
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