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JAL-4059 fix that boolean for non-value query string args
[jalview.git]
/
src
/
jalview
/
analysis
/
Conservation.java
2023-08-10
Ben Soares
JAL-629 Change all stdout and stderr output to use...
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commitdiff
2022-03-08
Jim Procter
JAL-3438 spotless for 2.11.2.0
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diff to current
2021-09-21
Ben Soares
JAL-3691 automatic insertion of Locale.ROOT to toUpperC...
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diff to current
2019-07-16
gmungoc
JAL-3210 Merge branch 'develop' into trialMerge
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diff to current
2019-03-20
Ben Soares
JAL-3130 Lots of deprecation fixes. See utils/deprecat...
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diff to current
2018-10-17
Jim Procter
Merge branch 'feature/JAL-3063JAXB' into Jalview-BH...
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diff to current
2018-09-06
Jim Procter
JAL-3105 reallocate quality and consensus annotation...
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2018-06-21
gmungoc
JAL-3032 round Quality score for tooltip (as it becomes...
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diff to current
2017-10-03
gmungoc
JAL-2738 copy to spikes/mungo
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2017-08-21
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
features/JAL-2446NCList
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diff to current
2017-08-16
Jim Procter
JAL-2418 source formatting
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2017-06-14
gmungoc
JAL-2598 Sequence.getSequence return a copy of the...
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diff to current
2017-06-09
gmungoc
JAL-2446 merged to spike branch
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2017-03-29
gmungoc
JAL-2416 JAL-728 reduced dependency on Blosum62 impleme...
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2017-03-28
gmungoc
JAL-2416 JAL-2403 remove unused '*' row/column from...
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diff to current
2017-03-27
gmungoc
JAL-2416 score matrix gap symbol (if any) dynamically...
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diff to current
2017-02-21
gmungoc
JAL-2416 quality calculation now only depends on loaded...
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diff to current
2017-02-18
gmungoc
JAL-2416 better encapsulated 'constants' for BLOSUM62...
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2017-02-17
gmungoc
JAL-2416 BLOSUM62 removed from ResidueProperties
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diff to current
2017-02-13
gmungoc
JAL-1632 JAL-2416 load score matrices from file, as...
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diff to current
2017-01-04
gmungoc
JAL-2371 CollectionColourScheme wraps ColourSchemeI
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diff to current
2016-12-16
gmungoc
JAL-1705 JAL-98 use SortedMap as more accurate type...
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diff to current
2016-11-02
gmungoc
JAL-98 JAL-1854 encapsulate 'magic number' threshold...
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diff to current
2016-11-02
gmungoc
JAL-98 Profile and ResidueCount moved from analysis...
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diff to current
2016-11-02
gmungoc
JAL-98 wording "negatively conserved" now "absence...
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diff to current
2016-11-01
gmungoc
Conservation now using ResidueCount; tests added
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diff to current
2016-10-25
Jim Procter
JAL-2089 patch broken merge to master for Release 2...
releases/Release_2_10_0_Branch
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2016-10-06
gmungoc
Merge branch 'develop' into bug/JAL-98consensusMemory
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2016-10-06
Jim Procter
JAL-2089 Merge branch releases/Release_2_10_Branch...
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diff to current
2016-10-05
Jim Procter
JAL-2189 source formatting
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commitdiff
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diff to current
2016-09-26
gmungoc
JAL-98 bug fix, string optimisation, sorted AA properties
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diff to current
2016-09-23
gmungoc
JAL-98 use SparseIntArray (wip)
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diff to current
2016-09-22
gmungoc
JAL-1421 use declared type of ResidueProperties.propHash
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diff to current
2016-09-22
gmungoc
JAL-1421 typed ResidueProperties.propHash; JAL-2176...
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diff to current
2016-09-20
gmungoc
JAL-1306 calculate Quality also when Conservation not...
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2016-07-18
Jim Procter
JAL-2145 improvement: ensure conservation calculation...
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diff to current
2016-05-26
gmungoc
JAL-1797 non-case-sensitive counting of residues /...
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2015-10-16
Jim Procter
JAL-1925 update source version in license
Release_2_9_0b2
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commitdiff
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2015-10-08
Jim Procter
JAL-1894 update year/version in copyright
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commitdiff
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diff to current
2015-09-10
Jim Procter
JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
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diff to current
2015-09-10
Jim Procter
JAL-1645 source formatting and organise imports
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diff to current
2015-08-10
Jim Procter
JAL-736 relocate group associated conservation symbols...
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2015-08-10
Jim Procter
JAL-736 source formatting
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2015-03-06
Jim Procter
JAL-1683 replace year/version strings with tokens in...
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diff to current
2015-03-06
Jim Procter
Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...
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2014-12-15
Jim Procter
JAL-1620 version bump and release notes
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diff to current
2014-06-13
Jim Procter
Merge branch 'Release_2_8_2_Branch' into JAL-1483_featu...
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diff to current
2014-06-06
Jim Procter
JAL-1517 fix copyright for 2.8.2
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diff to current
2014-06-05
Jim Procter
JAL-1517 update copyright to version 2.8.2
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2014-05-22
Jim Procter
JAL-1503 update version in GPL header
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2014-04-21
Jim Procter
JAL-736 hack to show the conserved property values...
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commitdiff
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2014-01-29
Jim Procter
JAL-1432 updated copyright notices
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commitdiff
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diff to current
2012-10-22
jprocter
Jalview 2.8 Source Header
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2012-10-03
jprocter
formatting
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diff to current
2011-10-21
jprocter
static convenience methods for constructing and calcula...
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diff to current
2011-10-21
jprocter
use List rather than Vector
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diff to current
2011-10-10
jprocter
update author list in license for (JAL-826)
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diff to current
2011-10-04
jprocter
Merge remote-tracking branch 'remotes/origin/2_5_1_rna_...
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diff to current
2011-09-27
jprocter
apply version 2.7 copyright
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commitdiff
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diff to current
2011-07-29
janengelhardt
JAL-885; Implementation of StructureFrequency.java...
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commitdiff
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diff to current
2011-02-18
jprocter
fix for occasional race conditions
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commitdiff
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diff to current
2010-09-23
jprocter
Jalview 2.6 source licence
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2010-04-30
jprocter
jalview 2.5 release banner
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2009-08-21
jprocter
1.1 compatibility
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commitdiff
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diff to current
2009-08-21
jprocter
start/stop for per-group consensus calculation
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2009-07-24
jprocter
complete alignment annotation row procedure
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diff to current
2009-06-08
jprocter
apply gpl development license
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diff to current
2008-09-04
jprocter
merge from 2_4_Release branch
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2008-04-10
jprocter
quick fix for conservation calculation when residue...
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diff to current
2007-02-07
amwaterhouse
Formatting
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diff to current
2007-01-30
amwaterhouse
Any character non aa or nucleotide is a space
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2006-12-14
amwaterhouse
one less cast
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2006-12-05
amwaterhouse
sequence is char []
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2006-11-07
amwaterhouse
warning note added to consequence
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2006-11-06
amwaterhouse
If start is not zero, we need to put -- at the start
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diff to current
2006-10-26
amwaterhouse
Error message changed
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diff to current
2006-10-11
jprocter
fixes exception (array index out of bounds - due to...
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2006-10-10
amwaterhouse
Optimized
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2006-08-21
amwaterhouse
header updated
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diff to current
2006-04-10
amwaterhouse
dont need to set - to -
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2006-04-07
amwaterhouse
Set all gaps to - symbol
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2005-08-18
amwaterhouse
Character methods don't exist in java 1.1
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2005-08-18
jprocter
various case sensitivity bugs fixed in residue comparis...
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commitdiff
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diff to current
2005-08-15
amwaterhouse
Declare variables outside loops
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commitdiff
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diff to current
2005-06-30
amwaterhouse
Formatting changes
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2005-06-08
amwaterhouse
Formatted source
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commitdiff
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diff to current
2005-06-08
amwaterhouse
GPL license added
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2005-05-25
jprocter
tidied up system.out messages and moved many to stderr.
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2005-05-03
amwaterhouse
1.1 compatible
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diff to current
2005-04-11
jprocter
added the alignment quality calculation from the old...
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diff to current
2005-04-08
jprocter
remember: do not check in quick bug fixes that you...
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diff to current
2005-04-08
jprocter
Alignment quality with funky coloured histograms.
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diff to current
2005-03-23
amwaterhouse
drawableSequence removed
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diff to current
2004-12-15
amwaterhouse
isGap method added to utils
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commitdiff
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2004-12-14
amwaterhouse
Hastable is not used anywhere
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commitdiff
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diff to current
2004-12-14
amwaterhouse
Hashtable size must allow for total-start
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diff to current
2004-11-16
amwaterhouse
Removed spaces
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diff to current
2004-11-02
amwaterhouse
Jalview Imported Sources
start
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diff to current