git://source.jalview.org
/
jalview.git
/ history
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
first ⋅ prev ⋅ next
Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git]
/
src
/
jalview
/
datamodel
/ AlignedCodonFrame.java
2023-11-03
James Procter
JAL-4090 JAL-1551 spotlessApply
commit
|
commitdiff
2023-08-10
Ben Soares
JAL-629 Change all stdout and stderr output to use...
commit
|
commitdiff
2022-03-08
Jim Procter
JAL-3438 spotless for 2.11.2.0
commit
|
commitdiff
2022-02-04
Jim Procter
Merge branch 'bug/JAL-3806_mappingCoversSequence_for211...
bug/JAL-3806_without_shared_DS_for_2_11_2
commit
|
commitdiff
2022-02-04
Jim Procter
JAL-3806 require mapping extent covers both sequence...
commit
|
commitdiff
2022-01-26
gmungoc
JAL-3806 (2.11.2 version) more lax allowance (3 positio...
commit
|
commitdiff
2021-03-04
Jim Procter
Revert "Merge branch 'bug/JAL-3806_mappingCoversSequenc...
commit
|
commitdiff
2021-01-28
gmungoc
JAL-3806 more lax allowance (3 positions) for stop...
commit
|
commitdiff
2020-10-22
gmungoc
JAL-3763 Javadoc, check for null, additional tests
commit
|
commitdiff
2020-10-22
gmungoc
JAL-3763 test coverage for AlignedCodonFrame.markMapped...
commit
|
commitdiff
2020-10-22
gmungoc
JAL-3763 failsafe check for null
commit
|
commitdiff
2020-10-22
gmungoc
JAL-3763 refactored getCoveringMapping for virtual...
commit
|
commitdiff
2020-10-22
gmungoc
JAL-3700 additions and corrections to unit tests
commit
|
commitdiff
2020-10-22
gmungoc
JAL-3763 Javadoc, check for null, additional tests
task/JAL-3763_newDatasetForCds
commit
|
commitdiff
2020-10-22
gmungoc
JAL-3763 test coverage for AlignedCodonFrame.markMapped...
commit
|
commitdiff
2020-10-15
gmungoc
JAL-3763 unused method removed
commit
|
commitdiff
2020-10-08
gmungoc
JAL-3763 failsafe check for null
commit
|
commitdiff
2020-10-08
gmungoc
JAL-3763 refactored getCoveringMapping for virtual...
commit
|
commitdiff
2020-09-23
Jim Procter
JAL-3748 not testing for sequence’s containment in...
bug/JAL-3700_JAL-3748_reconstructCDSafterProteinMSA_for2_11_1_2
commit
|
commitdiff
2020-09-23
Jim Procter
JAL-3748 fix compilation error
commit
|
commitdiff
2020-09-23
Jim Procter
JAL-3748 allow AlignedCodonFrame.covers to optionally...
commit
|
commitdiff
2020-09-17
gmungoc
JAL-3700 additions and corrections to unit tests
bug/JAL-3700_mapSequenceSelection
commit
|
commitdiff
2020-09-16
Jim Procter
JAL-3748 make findAlignedSequence require mapped from...
commit
|
commitdiff
2020-09-16
Jim Procter
JAL-3748 pass a list to findAlignedSequence to return...
commit
|
commitdiff
2020-09-16
Jim Procter
JAL-3700 JAL-3748 use AlignedCodonFrame.covers(seq...
commit
|
commitdiff
2020-09-16
Jim Procter
JAL-3700 JAL-3748 AlignedCodonFrame.covers(seq,true...
commit
|
commitdiff
2020-09-16
gmungoc
JAL-3700 fix for propagation of sort commands
commit
|
commitdiff
2020-09-16
gmungoc
JAL-3700 check for 'covering' mapping when matching...
commit
|
commitdiff
2020-08-05
gmungoc
JAL-3700 fix for propagation of sort commands
commit
|
commitdiff
2020-08-03
gmungoc
JAL-3700 check for 'covering' mapping when matching...
commit
|
commitdiff
2019-06-11
gmungoc
JAL-3187 CDS has same dataset sequence as transcript
commit
|
commitdiff
2019-01-21
gmungoc
JAL-3187 (hacked up) show complement features on struct...
commit
|
commitdiff
2017-10-03
gmungoc
JAL-2738 copy to spikes/mungo
commit
|
commitdiff
2017-08-21
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
features/JAL-2446NCList
commit
|
commitdiff
2017-08-16
Jim Procter
JAL-2418 source formatting
commit
|
commitdiff
2017-06-14
gmungoc
JAL-2598 Sequence.getSequence return a copy of the...
commit
|
commitdiff
2016-10-28
Jim Procter
JAL-966 JAL-1738 JAL-345 interfaces for SearchResults...
commit
|
commitdiff
2016-10-25
Jim Procter
JAL-2089 patch broken merge to master for Release 2...
releases/Release_2_10_0_Branch
commit
|
commitdiff
2016-10-06
Jim Procter
JAL-2089 Merge branch releases/Release_2_10_Branch...
commit
|
commitdiff
2016-10-05
Jim Procter
JAL-2189 source formatting
commit
|
commitdiff
2016-07-06
gmungoc
JAL-2110 ensuring mapped dbrefs between protein and cds
commit
|
commitdiff
2016-07-04
gmungoc
JAL-2110 defensive check in code
commit
|
commitdiff
2016-07-01
gmungoc
JAL-2110 bug fixing and tidying for get cross-refs
commit
|
commitdiff
2016-06-16
Jim Procter
JAL-2110 equals and hashcode should check fromSeq
commit
|
commitdiff
2016-06-16
Jim Procter
JAL-2110 typo caused infinite loop
commit
|
commitdiff
2016-06-14
gmungoc
JAL-1686 JAL-2110 equals and/or hashCode method added
commit
|
commitdiff
2016-04-01
gmungoc
JAL-1705 ensure the right mapping is used to align...
commit
|
commitdiff
2016-04-01
gmungoc
JAL-1705 reworked AlignmentUtils.makeCdsAlignment and...
commit
|
commitdiff
2016-03-28
gmungoc
JAL-1705 Javadoc / debug output tweaks
commit
|
commitdiff
2016-02-19
gmungoc
JAL-1705 handle case of sequence with no dataset sequence
commit
|
commitdiff
2016-01-21
gmungoc
JAL-1705 isEmpty() and (debug) toString() methods added
commit
|
commitdiff
2015-12-22
gmungoc
JAL-653 AlignedCodonFrame internal refactor, merge...
commit
|
commitdiff
2015-11-30
gmungoc
JAL-653 (experimental) methods to resolve dummy to...
commit
|
commitdiff
2015-10-16
Jim Procter
JAL-1925 update source version in license
Release_2_9_0b2
commit
|
commitdiff
2015-10-08
Jim Procter
JAL-1894 update year/version in copyright
commit
|
commitdiff
2015-09-22
Jim Procter
Merge branch 'develop' into Release_2_9_0b1_Branch
commit
|
commitdiff
2015-09-14
gmungoc
JAL-1880 handle sequence offsets properly when mapping...
commit
|
commitdiff
2015-09-10
Jim Procter
JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
commit
|
commitdiff
2015-09-10
Jim Procter
JAL-1645 source formatting and organise imports
commit
|
commitdiff
2015-06-05
Jim Procter
JAL-1551 formatting
commit
|
commitdiff
2015-04-14
gmungoc
JAL-1693 generate multiple exon sequences for 1-many...
commit
|
commitdiff
2015-03-26
gmungoc
Merge develop to Release_2_8_3_Branch
commit
|
commitdiff
2015-03-06
Jim Procter
JAL-1683 replace year/version strings with tokens in...
commit
|
commitdiff
2014-12-15
Jim Procter
JAL-1620 version bump and release notes
commit
|
commitdiff
2014-06-06
Jim Procter
JAL-1517 source formatting
commit
|
commitdiff
2014-06-06
Jim Procter
JAL-1517 fix copyright for 2.8.2
commit
|
commitdiff
2014-06-05
Jim Procter
JAL-1517 update copyright to version 2.8.2
commit
|
commitdiff
2014-05-22
Jim Procter
JAL-1503 update version in GPL header
commit
|
commitdiff
2014-01-29
Jim Procter
JAL-1432 updated copyright notices
commit
|
commitdiff
2013-06-17
Jim Procter
JAL-1312 patch for regression noticed after patch to...
commit
|
commitdiff
2012-10-22
jprocter
Jalview 2.8 Source Header
commit
|
commitdiff
2011-10-10
jprocter
update author list in license for (JAL-826)
commit
|
commitdiff
2011-09-27
jprocter
apply version 2.7 copyright
commit
|
commitdiff
2010-09-23
jprocter
Jalview 2.6 source licence
commit
|
commitdiff
2010-04-30
jprocter
jalview 2.5 release banner
commit
|
commitdiff
2009-06-08
jprocter
apply gpl development license
commit
|
commitdiff
2008-09-04
jprocter
merge from 2_4_Release branch
commit
|
commitdiff
2007-12-21
jprocter
temporary bugfix ?
commit
|
commitdiff
2007-07-13
jprocter
mapping bug fixes
commit
|
commitdiff
2007-06-17
jprocter
AlignedCodonFrame holds mapping information between...
commit
|
commitdiff