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JAL-4059 fix that boolean for non-value query string args
[jalview.git]
/
src
/
jalview
/
analysis
/
AAFrequency.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
2019-07-16
gmungoc
JAL-3210 Merge branch 'develop' into trialMerge
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diff to current
2019-06-18
gmungoc
JAL-3313 don't double count mapped codons
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diff to current
2019-04-18
hansonr
explicit Hashtable objects
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diff to current
2019-02-27
gmungoc
JAL-3202 discard zero percentages in extracted profile
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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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commitdiff
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diff to current
2017-08-16
Jim Procter
JAL-2418 source formatting
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commitdiff
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diff to current
2017-06-14
gmungoc
JAL-2598 Sequence.getSequence return a copy of the...
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2017-06-09
gmungoc
JAL-2446 merged to spike branch
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commitdiff
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2017-05-03
Jim Procter
JAL-1933 show occupancy in tooltip for row
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commitdiff
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diff to current
2017-04-27
Jim Procter
JAL-1933 shade occupancy from light grey to black for...
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commitdiff
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diff to current
2017-04-27
Jim Procter
JAL-1933 don’t show symbol counts under histogram ...
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commitdiff
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diff to current
2017-03-16
Jim Procter
JAL-1933 refactor parameter for code clarity
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diff to current
2016-12-04
Jim Procter
JAL-1933 show occupancy count as a tooltip
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commitdiff
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diff to current
2016-12-04
Jim Procter
JAL-1933 switch from gap count to occupancy
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commitdiff
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diff to current
2016-12-02
gmungoc
JAL-1933 gap value as description; minor formatting
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diff to current
2016-12-01
Jim Procter
JAL-1933 update the bounds for the Gap annotation row...
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commitdiff
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diff to current
2016-12-01
Jim Procter
JAL-1933 basic hack to get gap counts shown as an annot...
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commitdiff
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diff to current
2016-11-17
gmungoc
JAL-98 ProfilesI container for profiles for columns
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commitdiff
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diff to current
2016-11-02
gmungoc
JAL-98 ProfileI interface for Profile
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commitdiff
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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
2016-10-25
gmungoc
JAL-98 minor fixes to / tests for annotation derivation
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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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diff to current
2016-10-25
gmungoc
JAL-98 javadoc / comments updated
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2016-10-24
gmungoc
JAL-98 fixme comment removed - nothing to do
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diff to current
2016-10-06
Jim Procter
JAL-2089 Merge branch releases/Release_2_10_Branch...
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commitdiff
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diff to current
2016-10-03
gmungoc
JAL-98 use Profile to store consensus, ResidueCount...
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diff to current
2016-09-26
gmungoc
JAL-98 don't include gaps in maxResidue!
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commitdiff
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diff to current
2016-09-23
gmungoc
JAL-98 performance tweaks to use of SparseIntArray
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commitdiff
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diff to current
2016-09-23
gmungoc
JAL-98 first working version
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commitdiff
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diff to current
2016-09-23
gmungoc
JAL-98 use SparseIntArray (wip)
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commitdiff
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diff to current
2016-07-20
gmungoc
JAL-2023 JAL-1681 fixed bug in computing '+' for co...
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commitdiff
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diff to current
2015-12-22
gmungoc
JAL-653 AlignedCodonFrame internal refactor, merge...
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commitdiff
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diff to current
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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diff to current
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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commitdiff
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diff to current
2015-09-10
Jim Procter
JAL-1645 source formatting and organise imports
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commitdiff
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diff to current
2015-07-08
gmungoc
JAL-1759 merge from develop
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commitdiff
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diff to current
2015-07-01
gmungoc
JAL-1681 more condensed tooltip where codons share...
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commitdiff
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diff to current
2015-05-29
Jim Procter
JAL-1755 fix for NPE when setting up temporary variables
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commitdiff
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diff to current
2015-03-26
gmungoc
Merge develop to Release_2_8_3_Branch
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commitdiff
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diff to current
2015-03-06
Jim Procter
JAL-1683 replace year/version strings with tokens in...
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commitdiff
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diff to current
2014-12-15
Jim Procter
JAL-1620 version bump and release notes
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commitdiff
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diff to current
2014-06-06
Jim Procter
JAL-1517 source formatting
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commitdiff
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diff to current
2014-06-06
Jim Procter
JAL-1517 fix copyright for 2.8.2
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commitdiff
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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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commitdiff
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diff to current
2014-05-22
Jim Procter
JAL-1503 update version in GPL header
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commitdiff
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diff to current
2014-05-01
Jim Procter
make sure valid value for non-gapped calculation with...
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commitdiff
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diff to current
2014-02-03
Jim Procter
Merge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge
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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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2013-10-16
Jim Procter
JAL-1395 do not calculate non-gap consensus when no...
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commitdiff
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diff to current
2013-09-03
Jim Procter
JAL-1373 tweak precision calculation so alignments...
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commitdiff
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diff to current
2013-09-03
Jim Procter
JAL-920 compute a consensus for single sequence
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commitdiff
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2013-09-02
Jim Procter
JAL-1373 generate percentages with appropriate precision
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commitdiff
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diff to current
2013-09-02
Jim Procter
JAL-1373 pass size of sequence set to consensus renderi...
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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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commitdiff
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diff to current
2012-10-03
jprocter
formatting
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commitdiff
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diff to current
2012-06-07
jprocter
JAL-967, JAL-1114, JAL-1115 - modified render and calcu...
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commitdiff
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diff to current
2012-05-31
jprocter
formatting
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diff to current
2012-05-30
jprocter
JAL-1114 - refactor methods handling Vectors and Hashta...
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commitdiff
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diff to current
2011-10-11
jprocter
normalised logo rendering (JAL-958)
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commitdiff
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diff to current
2011-10-10
jprocter
update author list in license for (JAL-826)
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commitdiff
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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
2011-07-31
janengelhardt
JAL-885; StructureConservation row is displayed at...
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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
2010-09-23
jprocter
NPE race condition alert - see JAL-661
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commitdiff
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diff to current
2010-09-23
jprocter
apply jalview code style
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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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commitdiff
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diff to current
2010-09-02
jprocter
fix occasional arrayIndexOutOfBounds when sequences...
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commitdiff
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diff to current
2010-06-29
jprocter
patch for npe that occurs for importing Jalview project...
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commitdiff
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diff to current
2010-04-30
jprocter
jalview 2.5 release banner
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commitdiff
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diff to current
2009-08-21
jprocter
store symbol profile and extract it for display
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commitdiff
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diff to current
2009-07-24
jprocter
complete alignment annotation row procedure
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commitdiff
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diff to current
2009-06-08
jprocter
apply gpl development license
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commitdiff
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diff to current
2008-09-04
jprocter
merge from 2_4_Release branch
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commitdiff
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diff to current
2007-02-07
amwaterhouse
Formatting
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commitdiff
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diff to current
2007-01-30
amwaterhouse
Any character non aa or nucleotide is a space
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commitdiff
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2006-12-05
amwaterhouse
sequence is char []
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commitdiff
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diff to current
2006-11-28
amwaterhouse
off by one group consensus calculation
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commitdiff
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diff to current
2006-11-15
amwaterhouse
Check if groupWidth is greater than sequence width
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commitdiff
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diff to current
2006-10-10
amwaterhouse
MaxResidue must be at least 2
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commitdiff
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diff to current
2006-10-10
amwaterhouse
static final strings for consensus keys
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commitdiff
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diff to current
2006-10-06
amwaterhouse
AAFrequency optimized
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commitdiff
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diff to current
2006-08-21
amwaterhouse
header updated
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commitdiff
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diff to current
2005-09-30
amwaterhouse
Remove redundancy in Eclipse
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commitdiff
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diff to current
2005-08-23
amwaterhouse
Finalize calculate method
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commitdiff
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diff to current
2005-08-18
amwaterhouse
Character methods don't exist in java 1.1
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commitdiff
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diff to current
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
Calculate gap and nogap ratio here
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commitdiff
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diff to current
2005-06-30
amwaterhouse
Formatting changes
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commitdiff
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diff to current
2005-06-10
amwaterhouse
Remove imports
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commitdiff
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diff to current
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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commitdiff
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diff to current
2005-04-13
jprocter
Gap characters are now properly detected in the conserv...
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commitdiff
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diff to current
2005-04-07
amwaterhouse
checkfor gap characters
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commitdiff
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diff to current
2004-11-02
amwaterhouse
Jalview Imported Sources
start
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commitdiff
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diff to current