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JAL-4059 fix that boolean for non-value query string args
[jalview.git]
/
src
/
jalview
/
analysis
/
AlignmentUtils.java
2023-11-03
James Procter
JAL-4090 JAL-1551 spotlessApply
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2023-08-10
Ben Soares
JAL-629 Change all stdout and stderr output to use...
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2023-06-22
James Procter
JAL-4213 - document the addReferenceAnnotations method...
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diff to current
2023-05-22
James Procter
JAL-1551 spotless
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diff to current
2023-05-19
James Procter
JAL-1551 spotlessApply
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commitdiff
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diff to current
2023-05-19
James Procter
JAL-1551 spotlessApply
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diff to current
2023-05-15
James Procter
JAL-4182 patch - map selection group onto sequence...
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2023-05-13
James Procter
JAL-2349 JAL-3855 helper method to make it easy to...
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diff to current
2023-03-15
James Procter
JAL-4091 JAL-629 ‘Add Reference Annotations’ takes...
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diff to current
2022-12-05
Ben Soares
JAL-629 implementation of --tempfac options
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diff to current
2022-10-17
Jim Procter
JAL-2349 JAL-3855 Integrate pAE retrieval in StructureF...
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diff to current
2022-03-08
Jim Procter
JAL-3438 spotless for 2.11.2.0
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diff to current
2022-02-11
Jim Procter
JAL-3949 - refactor logging from jalview.bin.Cache...
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diff to current
2022-02-11
Ben Soares
JAL-3949 Complete new abstracted logging framework...
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2022-01-26
Jim Procter
Merge branch 'task/JAL-3763_newDatasetForCds' into...
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2021-09-21
Ben Soares
JAL-3691 automatic insertion of Locale.ROOT to toUpperC...
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2020-10-27
Jim Procter
JAL-3700 JAL-3748 JAL-3763 don’t add stop codon via...
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2020-10-22
gmungoc
JAL-3763 always make a new dataset sequence for CDS...
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diff to current
2020-10-08
gmungoc
JAL-3763 always make a new dataset sequence for CDS...
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2020-09-16
Jim Procter
JAL-3748 pass a list to findAlignedSequence to return...
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2020-03-30
gmungoc
Merge branch 'develop' into Jalview-JS/develop
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2020-02-18
Mungo Carstairs
JAL-3536 JAL-3187 don't create duplicate CDS-to-protein...
bug/JAL-3536getCrossrefTwice
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2020-01-28
gmungoc
JAL-3187 one more obsolete method removed
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2019-10-08
gmungoc
Merge branch 'develop' into Jalview-JS/develop
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2019-08-22
gmungoc
JAL-3187 one more obsolete method removed
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2019-08-09
gmungoc
JAL-3187 removal of variant feature (non-virtual) trans...
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2019-07-16
gmungoc
JAL-3210 Merge branch 'develop' into trialMerge
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2019-06-17
gmungoc
JAL-3187 update alignAs code and unit tests for 'shared...
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2019-06-11
gmungoc
JAL-3187 CDS has same dataset sequence as transcript
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2019-06-07
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
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2019-06-07
gmungoc
JAL-2738 use GeneLocus extends DBRefEntry to hold chrom...
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2019-02-20
gmungoc
Merge branch 'feature/JAL-3143ensemblJSON' into feature...
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2019-02-19
gmungoc
JAL-3187 hacks to get peptide variant in to Jmol hover...
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2019-01-29
gmungoc
Merge branch 'feature/JAL-3143ensemblJSON' into trialMerge
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2019-01-26
hansonr
Jalview.isJS() --> Platform.isJS(), DBRefEntry[] -...
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2019-01-25
hansonr
JSON refactoring
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2019-01-21
gmungoc
JAL-3187 (hacked up) show complement features on struct...
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2019-01-18
gmungoc
JAL-3143 'id' not 'ID' attribute drives generation...
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2018-06-20
hansonr
JAL-3032 for (var var
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2018-03-07
Jim Procter
Merge branch 'releases/Release_2_10_4_Branch' into...
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2018-02-09
gmungoc
JAL-2789 avoid using transcript (with no UTR) as CDS...
bug/JAL-2666
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2018-02-09
gmungoc
JAL-2789 code format changes only (before functional...
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2018-02-05
gmungoc
JAL-2897 more informative description on synonymous...
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2018-02-05
gmungoc
Merge branch 'spikes/mungo' into trialMerge
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diff to current
2018-02-05
gmungoc
JAL-2897 more informative description on synonymous...
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2018-01-30
gmungoc
JAL-1793 update spike build to latest incl stop and...
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2018-01-30
gmungoc
JAL-2898 show 'stop_gained' variants on peptide sequences
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2018-01-30
gmungoc
JAL-2897 generate peptide variants for synonymous codon...
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2018-01-30
gmungoc
JAL-2897 formatting change only prior to functional...
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2017-10-27
gmungoc
JAL-1793 spike branch updated to latest
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2017-10-26
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
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2017-10-05
gmungoc
JAL-2738 update spikes/mungo
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2017-10-05
gmungoc
JAL-2755 transfer chromosomal reference from transcript...
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2017-10-04
gmungoc
JAL-2738 match consequence "Allele" to VCF allele;...
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2017-10-03
gmungoc
JAL-2738 copy to spikes/mungo
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2017-09-26
gmungoc
JAL-2738 JAL-2154 add DBRef from transcript to synthesi...
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2017-09-25
gmungoc
JAL-2738 one constant in codebase for "alleles" attribu...
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2017-09-21
gmungoc
JAL-2738 compute VCF on peptide, extract AF (allele...
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2017-09-04
gmungoc
JAL-2617 unit tests for CDS + stop codon, CDS with...
bug/JAL-2617mappedStopCodon
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2017-09-01
gmungoc
JAL-2617 omit stop codon from synthesized CDS sequence
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2017-08-21
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
features/JAL-2446NCList
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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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2017-06-09
gmungoc
JAL-2446 merged to spike branch
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2017-05-25
gmungoc
JAL-2050 make SequenceFeature.score final, adjust const...
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2017-05-15
gmungoc
JAL-2480 redundant code removed
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diff to current
2017-05-12
gmungoc
JAL-2525 get sequence features for Ontology term(s...
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diff to current
2017-05-09
gmungoc
JAL-2505 use constructors to set (what will be) final...
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diff to current
2017-03-01
gmungoc
Merge branch 'features/JAL-2295setChimeraAttributes...
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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
2016-11-08
gmungoc
JAL-2295 make RangeComparator a top level class for...
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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
2016-10-06
Jim Procter
JAL-2089 Merge branch releases/Release_2_10_Branch...
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commitdiff
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diff to current
2016-10-05
Jim Procter
JAL-2189 source formatting
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commitdiff
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diff to current
2016-09-27
gmungoc
JAL-2230 use correct mapping to transfer features to...
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diff to current
2016-08-30
Jim Procter
Merge branch 'develop' into merge/develop_bug/JAL-2154p...
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2016-08-29
Jim Procter
JAL-2154 don’t synthesise multiple CDS|<Acc> sequences...
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diff to current
2016-08-26
Jim Procter
JAL-2154 don’t add any remaining xrefed sequences of...
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commitdiff
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diff to current
2016-08-26
gmungoc
JAL-2049 set Ensembl variant source to ENSEMBL if ...
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diff to current
2016-08-25
Jim Procter
JAL-2154 JAL-2106 transfer primary refs to CDS for...
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diff to current
2016-08-25
Jim Procter
Merge branch 'trailm' into trial_fixMakeCDSDBRefPropagation
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2016-08-25
Jim Procter
Merge branch 'develop' into refactor/JAL-2106_sourceDbR...
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2016-08-24
Jim Procter
JAL-2106 removed setSourceDBRef, refactor getSourceDBRe...
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2016-08-23
Jim Procter
JAL-2154 propagate from contig to CDS after constructin...
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diff to current
2016-08-23
Jim Procter
JAL-2154 should only add mappings between dataset sequences
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diff to current
2016-08-23
Jim Procter
JAL-2154 - only copy DBRef from contig to new CDS seque...
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diff to current
2016-08-22
gmungoc
JAL-2011 adjust method to fix failing unit test
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commitdiff
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diff to current
2016-07-14
Jim Procter
JAL-2110 JAL-2147 JAL-2145 - pad CDS alignment reconstr...
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diff to current
2016-07-12
Jim Procter
JAL-2110 test demonstrating limitation of current imple...
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diff to current
2016-07-12
Jim Procter
JAL-2110 javadoc
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diff to current
2016-07-12
Jim Procter
JAL-2110 scalability todo
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diff to current
2016-07-12
Jim Procter
JAL-1381 JAL-2110 efficiency TODO
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diff to current
2016-07-07
gmungoc
JAL-2110 added alignAsSameSequences to handle 'direct...
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commitdiff
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diff to current
2016-07-06
gmungoc
JAL-2110 AlignmentUtils.alignCdsAsProtein implemented
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commitdiff
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diff to current
2016-07-06
gmungoc
JAL-2110 ensuring mapped dbrefs between protein and cds
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diff to current
2016-07-04
gmungoc
JAL-2110 use shared dataset when copying alignment...
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diff to current
2016-07-04
gmungoc
Revert "JAL-2110 use shared alignment dataset when...
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diff to current
2016-07-04
gmungoc
JAL-2110 use shared alignment dataset when copying...
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commitdiff
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diff to current
2016-07-01
gmungoc
JAL-2110 bug fixing and tidying for get cross-refs
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commitdiff
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diff to current
2016-07-01
gmungoc
JAL-2110 add 'products' parameter to filter results...
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