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JAL-3070 JAL-3066 fix initialisation of slivka ServiceWithParameters
[jalview.git]
/
src
/
jalview
/
datamodel
/
2019-09-26
Jim Procter
JAL-3070 allow SequenceI.findPositions(0,column+1)...
tree
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commitdiff
2019-09-26
Jim Procter
JAL-3070 JAL-3066 AlignmentI.findOrAddAnnotation(Alignm...
tree
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commitdiff
2019-08-13
Jim Procter
Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into...
tree
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commitdiff
2019-08-07
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
tree
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commitdiff
2019-07-30
gmungoc
JAL-3198 more efficient Sequence.getDisplayId()
tree
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commitdiff
2019-07-26
gmungoc
Merge branch 'features/JAL-3375vcfValidation' into
tree
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commitdiff
2019-07-25
gmungoc
JAL-3375 ignore '.' values for VCF data
tree
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commitdiff
2019-07-10
Jim Procter
Merge branch 'merge/JAL-3285_mchmmer_with_211_develop...
tree
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commitdiff
2019-07-08
gmungoc
JAL-3187 derived peptide variants tweaks and tests
tree
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commitdiff
2019-07-05
gmungoc
JAL-3187 initial refactoring towards peptide variant...
tree
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commitdiff
2019-07-03
tva
JAL-2629 evalues and bit scores now conserved after...
tree
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commitdiff
2019-07-03
tva
JAL-2629 can now filter by sequence e-value or bit...
tree
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commitdiff
2019-07-02
tva
JAL-2629 add simple jackhmmer functionality
tree
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commitdiff
2019-06-28
tva
JAL-2629 add HMM Match Score colour scheme
tree
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commitdiff
2019-06-17
gmungoc
JAL-2792 JAL-3187 linked features (if shown) in Feature...
tree
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commitdiff
2019-06-17
gmungoc
JAL-3187 add sequence to feature details table (and...
tree
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commitdiff
2019-06-13
gmungoc
JAL-3303 ignore deletions when computing peptide variants
tree
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commitdiff
2019-06-11
gmungoc
JAL-3187 CDS has same dataset sequence as transcript
tree
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commitdiff
2019-06-10
tva
JAL-3297 pad gaps in alignment to ensure hmmalign runs
tree
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commitdiff
2019-06-07
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
tree
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commitdiff
2019-06-07
tva
JAL-3291 issue fixed, passing tests added
tree
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commitdiff
2019-06-07
gmungoc
JAL-2738 use GeneLocus extends DBRefEntry to hold chrom...
tree
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commitdiff
2019-06-06
gmungoc
Merge branch 'develop' into trialMerge
tree
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commitdiff
2019-06-05
tva
JAL-3285 add unmerged code to AlignmentAnnotation
tree
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commitdiff
2019-06-05
tva
JAL-3285 add unmerged code to SequenceGroup
tree
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commitdiff
2019-06-04
Jim Procter
Merge branch 'develop' into developtomchmmer
tree
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commitdiff
2019-03-21
Ben Soares
JAL-3130 Replaced deprecated Class.newInstance() with...
tree
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commitdiff
2019-03-20
Ben Soares
JAL-3130 Lots of deprecation fixes. See utils/deprecat...
tree
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commitdiff
2019-03-11
gmungoc
Merge branch 'feature/JAL-3127_seqidChainshading' into...
tree
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commitdiff
2019-03-05
gmungoc
Merge remote-tracking branch 'origin/bug/JAL-2839findWi...
tree
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commitdiff
2019-03-04
gmungoc
Merge branch 'bug/JAL-3072scrollThread' into merge...
tree
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commitdiff
2019-03-04
gmungoc
Merge remote-tracking branch 'origin/bug/JAL-3082select...
tree
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commitdiff
2019-03-04
gmungoc
Merge branch 'bug/JAL-3099alignmentVisibleWidth' into...
tree
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commitdiff
2019-03-01
gmungoc
Merge branch 'bug/JAL-3164complementOverview' into...
tree
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commitdiff
2019-03-01
gmungoc
Merge branch 'feature/intervalStoreJ' into merge/JAL...
tree
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commitdiff
2019-03-01
gmungoc
JAL-3140 reduced coupling to intervalstore.jar
feature/intervalStoreJ
tree
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commitdiff
2019-02-28
gmungoc
JAL-3140 confine intervalstore imports to jalview.datam...
tree
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commitdiff
2019-02-24
gmungoc
JAL-3198 SequenceGroup 'bulk constructor' without dupli...
tree
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commitdiff
2019-02-21
gmungoc
JAL-3187 handle no mapping / complement features withou...
tree
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commitdiff
2019-02-20
gmungoc
JAL-3187 read peptide variant from CSQ:HGVSp if present...
tree
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commitdiff
2019-02-19
gmungoc
JAL-3187 hacks to get peptide variant in to Jmol hover...
tree
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commitdiff
2019-01-21
gmungoc
JAL-3187 unit tests updated and errors caught
tree
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commitdiff
2019-01-21
gmungoc
JAL-3187 findFeaturesAtResidue answer in render order...
tree
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commitdiff
2019-01-21
gmungoc
JAL-3187 (hacked up) show complement features on struct...
tree
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commitdiff
2019-01-16
Jim Procter
Merge branch 'features/pca_jaxb_datasetrefs_JAL-3171_JA...
tree
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commitdiff
2018-12-19
Jim Procter
Merge branch 'features/JAL-1767pcaInProject' into bug...
tree
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commitdiff
2018-12-17
Jim Procter
Merge branch 'bug/JAL-2750' into develop
tree
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commitdiff
2018-12-17
Jim Procter
Merge branch 'develop' into bug/JAL-2541cutRelocateFeatures
tree
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commitdiff
2018-12-06
Ben Soares
JAL-3130 incorporating feature/JAL-3063jaxbNoCastor...
tree
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commitdiff
2018-11-29
gmungoc
JAL-3140 NCList now via IntervalStore library
tree
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commitdiff
2018-11-28
gmungoc
JAL-3164 redraw complement overview on hide columns
bug/JAL-3164complementOverview
tree
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commitdiff
2018-11-19
Jim Procter
JAL-3156 JAL-3127 code tidy
tree
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commitdiff
2018-11-19
Jim Procter
JAL-3156 javadoc re JAL-3127 and FIXME to make Alignmen...
tree
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commitdiff
2018-09-14
gmungoc
JAL-3116 parse EMBL XML with JAXB (todo: update unit...
tree
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commitdiff
2018-09-13
gmungoc
JAL-3116 Uniprot XML unmarshalled using JAXB not Castor
tree
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commitdiff
2018-09-11
Jim Procter
Merge branch 'develop' into releases/Release_2_11_Branch
tree
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commitdiff
2018-09-10
gmungoc
JAL-3099 new method AlignmentI.getVisibleWidth()
tree
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commitdiff
2018-08-27
Ben Soares
JAL-3061 / JAL-3053
tree
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commitdiff
2018-08-16
gmungoc
JAL-3082 handle regex error, exclusive threshold, unit...
tree
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commitdiff
2018-08-10
gmungoc
JAL-3076 refactor for more efficient scan of 'gene...
tree
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commitdiff
2018-08-02
Ben Soares
JAL-3053
tree
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commitdiff
2018-07-30
bsoares
Fixed bug ignoring "alpha" extended braces in RNA SS...
tree
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commitdiff
2018-07-25
gmungoc
JAL-3074 don't scroll up/down on drag out of scale...
tree
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commitdiff
2018-07-18
Jim Procter
Merge branch 'features/mchmmer' into features/mchmmer_m...
features/mchmmer_merge_JAL-1950
tree
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commitdiff
2018-06-05
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-06-04
Jim Procter
JAL-3017 parse multiple variant elements for uniprot...
tree
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commitdiff
2018-06-02
Jim Procter
JAL-3017 parse multiple variant elements for uniprot...
tree
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commitdiff
2018-06-01
Jim Procter
JAL-1950 JAL-2937 allow individual groups to be remater...
tree
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commitdiff
2018-06-01
Jim Procter
JAL-1551 formatting
tree
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commitdiff
2018-06-01
Jim Procter
JAL-1950 JAL-2937 allow copy of group without sequences...
tree
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commitdiff
2018-06-01
Jim Procter
JAL-1950 JAL-2937 allow copy of sequences from group...
tree
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commitdiff
2018-05-31
gmungoc
JAL-2808 don't capture or report min-max for mixed...
tree
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commitdiff
2018-05-31
Jim Procter
Merge branch 'spike/JAL-1950_hmmer3client' into feature...
tree
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commitdiff
2018-05-31
Jim Procter
Merge branch 'develop' into spike/JAL-1950_hmmer3client
tree
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commitdiff
2018-05-28
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-05-28
gmungoc
Merge remote-tracking branch 'origin/releases/Release_2...
tree
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commitdiff
2018-05-21
gmungoc
JAL-2920 use HGVS notation for protein variant feature
tree
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commitdiff
2018-05-11
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-05-11
gmungoc
JAL-2986 corrected findIndex for out of range residue...
tree
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commitdiff
2018-05-10
Jim Procter
Merge branch 'bug/JAL-2920_uniprotvariantfeature' into...
tree
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commitdiff
2018-05-10
Jim Procter
JAL-2920 simplified logic and added corner cases for...
tree
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commitdiff
2018-05-08
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-05-07
gmungoc
Merge branch 'releases/Release_2_10_4_Branch' into...
tree
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commitdiff
2018-05-07
gmungoc
JAL-1767 unit test for save and restore PCA
features/JAL-1767pcaInProject
tree
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commitdiff
2018-05-07
Jim Procter
JAL-2906 apply GPLv3 license source
tree
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commitdiff
2018-05-04
gmungoc
JAL-1767 refactorings to enable faithful restore of...
tree
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commitdiff
2018-04-27
gmungoc
JAL-1767 refactoring and tidying of RotatableCanvas...
tree
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commitdiff
2018-04-26
gmungoc
JAL-2962 code tidying/documentation (non-functional...
tree
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commitdiff
2018-04-23
gmungoc
JAL-2956 save/restore HMMER profile to/from Jalview...
tree
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commitdiff
2018-04-23
gmungoc
JAL-2954 more efficient SearchResults.markColumns
tree
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commitdiff
2018-04-17
gmungoc
JAL-2629 choice of hmm profile now a parameter not...
tree
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commitdiff
2018-04-16
gmungoc
JAL-2629 JAL-2937 remove redundant is/setHMMConsensusSe...
tree
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commitdiff
2018-04-09
Mungo Carstairs
JAL-2629 more error checking
tree
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commitdiff
2018-03-30
gmungoc
JAL-2599 MapList from HMM nodes to consensus dataset...
tree
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commitdiff
2018-03-30
gmungoc
JAL-2939 field/method naming more consistent
tree
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commitdiff
2018-03-30
gmungoc
JAL-2941 'map hmm to RF' removed pending clarifications
tree
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commitdiff
2018-03-26
gmungoc
JAL-2939 always store Information profile
tree
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commitdiff
2018-03-20
gmungoc
JAL-2629 InformationThread.findOrCreateAnnotation and...
tree
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commitdiff
2018-03-20
gmungoc
Merge branch 'develop' into features/mchmmer
tree
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commitdiff
2018-03-16
gmungoc
Merge remote-tracking branch 'origin/releases/Release_2...
tree
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commitdiff
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