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Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' of https://source.jalview.org/git...
[jalview.git]
/
src
/
jalview
/
schemes
/
2013-10-17
Jim Procter
JAL-1397 propagate any consensus/conservation coloursch...
tree
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commitdiff
2013-10-17
Jim Procter
JAL-1397 getters for originalColours flag
tree
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commitdiff
2013-10-15
Jim Procter
JAL-1159 Merging 2.8.1 patches and Anne Menards work...
tree
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commitdiff
2013-10-14
Jim Procter
Merge branch 'develop' into dev_from_2_8_1
tree
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commitdiff
2013-08-30
Daniel Barton
Colour be RNA helices bug fixed
tree
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commitdiff
2013-06-23
Jim Procter
Merge branch 'develop' into develop_m2_8_1_2
tree
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commitdiff
2013-06-23
Jim Procter
Merge commit '72c628b' into develop
tree
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commitdiff
2013-06-21
Jim Procter
JAL-1241 - generate colour for all annotation values...
tree
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commitdiff
2013-06-18
Jim Procter
Merge branch 'develop' into develop_m2_8_1_2
tree
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commitdiff
2013-06-17
Jim Procter
Merge branch 'JAL-1312_ambiguity_na' into develop
tree
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commitdiff
2013-06-17
Jim Procter
JAL-1027 fix errors in alternative codon table
tree
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commitdiff
2013-06-17
Jim Procter
JAL-1027 use alternative codon table in ResidueProperti...
tree
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commitdiff
2013-06-17
Jim Procter
JAL-529 - IUBMB nucleotide ambiguity codes and programm...
tree
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commitdiff
2012-12-07
jprocter
revised renderer and annotation model to support differ...
tree
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commitdiff
2012-12-07
jprocter
typing
tree
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commitdiff
2012-12-07
jprocter
remove mentions of non-functional RNAInteraction colour...
tree
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commitdiff
2012-11-15
jprocter
source formatting
tree
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commitdiff
2012-11-15
jprocter
Merge branch 'develop' into menard
tree
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commitdiff
2012-10-22
jprocter
Jalview 2.8 Source Header
tree
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commitdiff
2012-10-03
jprocter
formatting
tree
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commitdiff
2012-09-06
jprocter
JAL-1027 JAL-1167 documentation and patched DNA/RNA...
tree
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commitdiff
2012-09-06
jprocter
JAL-1167 method and simple tests for printing score...
tree
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commitdiff
2012-08-31
jprocter
Merge branch 'develop' into menard
tree
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commitdiff
2012-08-28
jprocter
JAL-1066 - per-sequence colouring with sequence associa...
tree
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commitdiff
2012-08-17
jprocter
Merge branch 'develop' into menard
tree
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commitdiff
2012-08-14
Anne Menard
last version stay many bugs ..
tree
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commitdiff
2012-08-01
jprocter
JAL-1066 patch regression ac33424148b2a4de29b3ca43f9411...
tree
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commitdiff
2012-07-16
Anne Menard
Last version
tree
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commitdiff
2012-07-16
Anne Menard
Merge branch 'develop' of https://source.jalview.org...
tree
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commitdiff
2012-07-10
Anne Menard
v2
tree
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commitdiff
2012-07-05
Anne Menard
Add support RNAML format
tree
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commitdiff
2012-06-29
jprocter
JAL-1065 JAL-1066 ensure non-residue based schemes...
tree
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commitdiff
2012-06-29
jprocter
JAL-1065 JAL-1066 allow different lookup tables for...
tree
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commitdiff
2012-06-15
jprocter
Merge branch 'JAL-1013_pca_rna_dna' into develop
tree
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commitdiff
2012-05-30
jprocter
JAL-1109 JAL-1065 resolve t-coffee score scheme by...
tree
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commitdiff
2012-05-30
jprocter
JAL-1114 - refactor methods handling Vectors and Hashta...
tree
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commitdiff
2012-05-23
jprocter
todo for JAL-1106
tree
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commitdiff
2012-05-23
jprocter
JAL-1066,JAL-1068,JAL-961 - use alignment annotation...
tree
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commitdiff
2012-05-22
jprocter
Merge remote-tracking branch 'origin/Tcoffee_JAL-1065...
tree
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commitdiff
2011-12-08
jprocter
(JAL-1013) gap character index for each sequence alphabet
tree
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commitdiff
2011-12-08
jprocter
JAL-1027 fixed up nucleotide subt matrix so it is symme...
tree
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commitdiff
2011-10-28
jprocter
(JAL-889) ensure latest version of RNA pairlist is...
tree
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commitdiff
2011-10-28
jprocter
refactor to use model API
tree
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commitdiff
2011-10-28
jprocter
(JAL-963) refactor RNA helix helper class to schemes
tree
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commitdiff
2011-10-10
jprocter
update author list in license for (JAL-826)
tree
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commitdiff
2011-10-04
jprocter
Merge remote-tracking branch 'remotes/origin/2_5_1_rna_...
tree
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commitdiff
2011-09-27
jprocter
apply version 2.7 copyright
tree
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commitdiff
2011-07-25
janengelhardt
Start merging of Laurens Code
tree
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commitdiff
2010-09-23
jprocter
apply jalview code style
tree
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commitdiff
2010-09-23
jprocter
Jalview 2.6 source licence
tree
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commitdiff
2010-08-04
jprocter
reorganised colourscheme enumeration to make it easier...
tree
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commitdiff
2010-05-14
jprocter
fix for JAL-533
tree
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commitdiff
2010-04-30
jprocter
jalview 2.5 release banner
tree
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commitdiff
2010-04-16
jprocter
default for colourBylabel is false
tree
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commitdiff
2010-04-14
jprocter
todo and disable selection sharing between views on...
tree
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commitdiff
2010-04-02
jprocter
javadoc
tree
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commitdiff
2010-04-02
jprocter
made threshold type enumaration into set of constants
tree
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commitdiff
2009-09-10
jprocter
fix null pointer exception when using blosum colourscheme
tree
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commitdiff
2009-08-21
jprocter
asparagine is polar but not charged
tree
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commitdiff
2009-07-24
jprocter
feature colour by label flag/style
tree
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commitdiff
2009-06-08
jprocter
apply gpl development license
tree
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commitdiff
2009-06-01
jprocter
added graduated colourscheme support for feature file
tree
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commitdiff
2009-03-17
jprocter
holds shading and range parameters rendering a feature...
tree
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commitdiff
2009-03-17
jprocter
fixes launchApp bug where user defined colourscheme...
tree
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commitdiff
2008-11-12
jprocter
gracefully translate ambigous nucleotides as 'X'
tree
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commitdiff
2008-11-04
jprocter
bugfix for transfer of user defined colourscheme from...
tree
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commitdiff
2008-09-04
jprocter
merge from 2_4_Release branch
tree
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commitdiff
2008-08-11
jprocter
Ensure 'None' translates into no colour scheme applied
tree
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commitdiff
2008-07-18
jprocter
User defined colourschemes are automatically generated...
tree
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commitdiff
2008-06-30
jprocter
included includeGaps flag in clustalW colour calculatio...
tree
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commitdiff
2008-02-24
jprocter
sequenceId is a string, not an integer - allows generat...
tree
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commitdiff
2007-08-08
jprocter
histidine should be midblue (noticed by Peter Knight...
tree
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commitdiff
2007-04-30
jprocter
dssp 7-state to three state lookup
tree
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commitdiff
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
tree
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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 []
tree
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commitdiff
2006-11-28
amwaterhouse
CurrentColour must not be accessed by multiple sequence...
tree
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commitdiff
2006-11-28
amwaterhouse
CurrentColour must not be accessed by multiple sequence...
tree
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commitdiff
2006-11-14
amwaterhouse
we already have c defined
tree
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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
tree
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commitdiff
2006-10-12
amwaterhouse
Null element checked
tree
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commitdiff
2006-10-10
amwaterhouse
Check on null consensus
tree
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commitdiff
2006-10-10
amwaterhouse
aaIndex replaces aaHash
tree
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commitdiff
2006-10-06
amwaterhouse
Set consensus as hashtble[]
tree
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commitdiff
2006-10-05
amwaterhouse
lower case available
tree
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commitdiff
2006-09-11
amwaterhouse
Comment out lower case colouring for bug fix release
tree
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commitdiff
2006-08-30
amwaterhouse
Gap added to aa3Hash
tree
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commitdiff
2006-08-30
amwaterhouse
User colours are case sensitive
tree
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commitdiff
2006-08-21
amwaterhouse
header updated
tree
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commitdiff
2006-06-14
amwaterhouse
parseAppletParameter
tree
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commitdiff
2006-06-09
amwaterhouse
createColourFromName
tree
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commitdiff
2006-04-07
amwaterhouse
Must check consensus length if autocalculate off
tree
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commitdiff
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