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[jalview.git] / src / jalview / schemes / ResidueProperties.java

2021-09-21	Ben Soares	JAL-3691 automatic insertion of Locale.ROOT to toUpperC...	blob \| commitdiff
2019-04-04	gmungoc	JAL-3220 j2sIgnore on main methods on test / utility...	blob \| commitdiff \| diff to current
2019-03-05	gmungoc	Merge remote-tracking branch 'origin/features/JAL-2620a...	blob \| commitdiff \| diff to current
2019-02-25	gmungoc	JAL-3200 fast lookup of DSSP3 notation	blob \| commitdiff \| diff to current
2018-03-16	gmungoc	JAL-2620 alternative genetic code translation tables	blob \| commitdiff \| diff to current
2018-01-30	gmungoc	JAL-1793 update spike build to latest incl stop and...	blob \| commitdiff \| diff to current
2018-01-30	gmungoc	JAL-2898 show 'stop_gained' variants on peptide sequences	blob \| commitdiff \| diff to current
2017-10-03	gmungoc	JAL-2738 copy to spikes/mungo	blob \| commitdiff \| diff to current
2017-08-16	Jim Procter	JAL-2418 source formatting	blob \| commitdiff \| diff to current
2017-06-09	gmungoc	JAL-2446 merged to spike branch	blob \| commitdiff \| diff to current
2017-02-17	gmungoc	JAL-2416 BLOSUM62 removed from ResidueProperties	blob \| commitdiff \| diff to current
2017-02-17	gmungoc	JAL-2416 removed DNA and PAM250 matrices from ResiduePr...	blob \| commitdiff \| diff to current
2017-02-17	gmungoc	JAL-2416 scoreMatrices removed from ResidueProperties	blob \| commitdiff \| diff to current
2017-02-13	gmungoc	JAL-1632 JAL-2416 load score matrices from file, as...	blob \| commitdiff \| diff to current
2017-02-13	gmungoc	JAL-1632 first cut of Tree chooser dialog and ScoreMode...	blob \| commitdiff \| diff to current
2017-02-09	gmungoc	Merge branch 'develop' into features/JAL-2379pcaMemory features/JAL-2379pcaMemory	blob \| commitdiff \| diff to current
2017-02-07	gmungoc	JAL-2398 corrected entry for C->R in Blosum62 matrix	blob \| commitdiff \| diff to current
2017-01-31	gmungoc	JAL-2385 more tests/bug fixes mostly for gui.SliderPane...	blob \| commitdiff \| diff to current
2016-11-08	gmungoc	JAL-2301 made T hydrophobic as per the cited conservati...	blob \| commitdiff \| diff to current
2016-11-01	gmungoc	JAL-98 use Integer constants; tests added for propHash...	blob \| commitdiff \| diff to current
2016-10-25	Jim Procter	JAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch	blob \| commitdiff \| diff to current
2016-10-06	Jim Procter	JAL-2089 Merge branch releases/Release_2_10_Branch...	blob \| commitdiff \| diff to current
2016-10-05	Jim Procter	JAL-2189 source formatting	blob \| commitdiff \| diff to current
2016-09-22	gmungoc	JAL-1421 typed ResidueProperties.propHash; JAL-2176...	blob \| commitdiff \| diff to current
2016-08-12	gmungoc	JAL-1841 bug fixes / code tidy for rna SS rendering...	blob \| commitdiff \| diff to current
2016-02-01	gmungoc	Merge branch 'develop' into features/JAL-653_JAL-1766_h...	blob \| commitdiff \| diff to current
2016-01-21	tcofoegbu	JAL-1479 JAL-1979 updated the modified-aminoacid triple...	blob \| commitdiff \| diff to current
2015-12-22	gmungoc	JAL-1421 parameterised map constructor used	blob \| commitdiff \| diff to current
2015-10-16	Jim Procter	JAL-1925 update source version in license Release_2_9_0b2	blob \| commitdiff \| diff to current
2015-10-08	Jim Procter	JAL-1894 update year/version in copyright	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 source formatting and organise imports	blob \| commitdiff \| diff to current
2015-09-07	gmungoc	JAL-1636 translate stop codon as '', mouseover as...	blob \| commitdiff \| diff to current
2015-09-03	gmungoc	JAL-1828 lookup table to convert MSE to MET when parsin...	blob \| commitdiff \| diff to current
2015-05-20	gmungoc	JAL-1741 nucleotide-aware colour schemes applied to...	blob \| commitdiff \| diff to current
2015-03-26	gmungoc	Merge develop to Release_2_8_3_Branch	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	JAL-1683 replace year/version strings with tokens in...	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...	blob \| commitdiff \| diff to current
2015-01-07	Jim Procter	JAL-1483 register feature similarity model	blob \| commitdiff \| diff to current
2014-12-22	Jim Procter	Merge: 497958b 68dcaa7	blob \| commitdiff \| diff to current
2014-12-15	Jim Procter	JAL-1620 version bump and release notes	blob \| commitdiff \| diff to current
2014-11-23	Jim Procter	JAL-1569 test for open/close RNA parenthesis character	blob \| commitdiff \| diff to current
2014-11-23	Jim Procter	JAL-1569 formatting	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 source formatting	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 fix copyright for 2.8.2	blob \| commitdiff \| diff to current
2014-06-05	Jim Procter	JAL-1517 update copyright to version 2.8.2	blob \| commitdiff \| diff to current
2014-06-05	Jim Procter	Merge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch	blob \| commitdiff \| diff to current
2014-06-03	Jim Procter	JAL-1512 comment out for 2.8.1 release	blob \| commitdiff \| diff to current
2014-06-03	Jim Procter	JAL-1512 fix calculation once again and include score...	blob \| commitdiff \| diff to current
2014-06-02	Jim Procter	JAL-1512 rejig buggy conservation-basesd score matrix...	blob \| commitdiff \| diff to current
2014-05-22	Jim Procter	JAL-1503 update version in GPL header	blob \| commitdiff \| diff to current
2014-04-21	Jim Procter	Merge branch 'jims_marckhacks' into develop	blob \| commitdiff \| diff to current
2014-04-21	Jim Procter	JAL-1473 provide Amino acid physicochemical conservatio...	blob \| commitdiff \| diff to current
2014-04-21	Jim Procter	JAL-1473 refactor score matrices and tree score calcula...	blob \| commitdiff \| diff to current
2014-02-18	Jim Procter	Merge branch 'JAL-1445' into develop	blob \| commitdiff \| diff to current
2014-01-29	Jim Procter	JAL-1432 updated copyright notices	blob \| commitdiff \| diff to current
2013-06-18	Jim Procter	Merge branch 'develop' into develop_m2_8_1_2	blob \| commitdiff \| diff to current
2013-06-17	Jim Procter	Merge branch 'JAL-1312_ambiguity_na' into develop	blob \| commitdiff \| diff to current
2013-06-17	Jim Procter	JAL-1027 fix errors in alternative codon table	blob \| commitdiff \| diff to current
2013-06-17	Jim Procter	JAL-1027 use alternative codon table in ResidueProperti...	blob \| commitdiff \| diff to current
2013-06-17	Jim Procter	JAL-529 - IUBMB nucleotide ambiguity codes and programm...	blob \| commitdiff \| diff to current
2012-12-07	jprocter	revised renderer and annotation model to support differ...	blob \| commitdiff \| diff to current
2012-12-07	jprocter	typing	blob \| commitdiff \| diff to current
2012-11-15	jprocter	Merge branch 'develop' into menard	blob \| commitdiff \| diff to current
2012-10-22	jprocter	Jalview 2.8 Source Header	blob \| commitdiff \| diff to current
2012-10-03	jprocter	formatting	blob \| commitdiff \| diff to current
2012-09-06	jprocter	JAL-1027 JAL-1167 documentation and patched DNA/RNA...	blob \| commitdiff \| diff to current
2012-08-14	Anne Menard	last version stay many bugs ..	blob \| commitdiff \| diff to current
2012-07-05	Anne Menard	Add support RNAML format	blob \| commitdiff \| diff to current
2012-06-15	jprocter	Merge branch 'JAL-1013_pca_rna_dna' into develop	blob \| commitdiff \| diff to current
2011-12-08	jprocter	(JAL-1013) gap character index for each sequence alphabet	blob \| commitdiff \| diff to current
2011-12-08	jprocter	JAL-1027 fixed up nucleotide subt matrix so it is symme...	blob \| commitdiff \| diff to current
2011-10-10	jprocter	update author list in license for (JAL-826)	blob \| commitdiff \| diff to current
2011-10-04	jprocter	Merge remote-tracking branch 'remotes/origin/2_5_1_rna_...	blob \| commitdiff \| diff to current
2011-09-27	jprocter	apply version 2.7 copyright	blob \| commitdiff \| diff to current
2011-07-25	janengelhardt	Start merging of Laurens Code	blob \| commitdiff \| diff to current
2010-09-23	jprocter	apply jalview code style	blob \| commitdiff \| diff to current
2010-09-23	jprocter	Jalview 2.6 source licence	blob \| commitdiff \| diff to current
2010-04-30	jprocter	jalview 2.5 release banner	blob \| commitdiff \| diff to current
2010-04-14	jprocter	todo and disable selection sharing between views on...	blob \| commitdiff \| diff to current
2009-08-21	jprocter	asparagine is polar but not charged	blob \| commitdiff \| diff to current
2009-06-08	jprocter	apply gpl development license	blob \| commitdiff \| diff to current
2008-11-12	jprocter	gracefully translate ambigous nucleotides as 'X'	blob \| commitdiff \| diff to current
2008-09-04	jprocter	merge from 2_4_Release branch	blob \| commitdiff \| diff to current
2008-02-24	jprocter	sequenceId is a string, not an integer - allows generat...	blob \| commitdiff \| diff to current
2007-08-08	jprocter	histidine should be midblue (noticed by Peter Knight...	blob \| commitdiff \| diff to current
2007-04-30	jprocter	dssp 7-state to three state lookup	blob \| commitdiff \| diff to current
2007-04-11	jprocter	fixed base lookup bug in dna pairwise alignment and...	blob \| commitdiff \| diff to current
2007-03-19	jprocter	note about selenocystine.	blob \| commitdiff \| diff to current
2007-02-07	amwaterhouse	Formatting	blob \| commitdiff \| diff to current
2007-01-30	amwaterhouse	Any character non aa or nucleotide is a space	blob \| commitdiff \| diff to current
2006-12-06	jprocter	general pairwise substitution score models for pairwise...	blob \| commitdiff \| diff to current
2006-12-05	amwaterhouse	Sequence is char []	blob \| commitdiff \| diff to current
2006-10-10	amwaterhouse	aaIndex replaces aaHash	blob \| commitdiff \| diff to current
2006-08-30	amwaterhouse	Gap added to aa3Hash	blob \| commitdiff \| diff to current
2006-08-21	amwaterhouse	header updated	blob \| commitdiff \| diff to current
2006-03-24	amwaterhouse	Group colours not used	blob \| commitdiff \| diff to current
2005-12-06	amwaterhouse	after merge	blob \| commitdiff \| diff to current
2005-11-18	jprocter	added 3 letter IUB codes for ambiguous residues/bases	blob \| commitdiff \| diff to current
2005-09-22	amwaterhouse	Add nucleotide names	blob \| commitdiff \| diff to current
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