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Applying adjustablenw_params.patch (JAL-4159)
[jalview.git]
/
src
/
jalview
/
analysis
/
2023-12-01
MorellThomas
Applying adjustablenw_params.patch (JAL-4159)
tree
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commitdiff
2023-10-01
MorellThomas
Fix Reset Button for PaSiMap and issue with indelfreeAs...
tree
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commitdiff
2023-09-18
MorellThomas
Fix buttons on the PaSiMap plot window
tree
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commitdiff
2023-09-16
MorellThomas
Correctly working implementation of the PaSiMap pipeline
tree
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commitdiff
2023-09-16
MorellThomas
Almost working
tree
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commitdiff
2023-09-08
MorellThomas
Properly integrated endGaps option for AlignSeq.traceAl...
tree
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commitdiff
2023-09-07
MorellThomas
Merge branch 'hardcode'
tree
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commitdiff
2023-09-07
MorellThomas
Implemented least-squares optimisation in ccAnalysis
tree
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commitdiff
2023-08-04
MorellThomas
Fix alignment and score calculation for cc_analysis
tree
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commitdiff
2023-07-22
MorellThomas
Implement MSA, scoring and counting the connections
tree
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commitdiff
2023-07-20
James Procter
JAL-3855 auto select clusters and fix up colouring...
tree
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commitdiff
2023-07-09
MorellThomas
Copied PCA files to PaSiMap analogues and changed all...
tree
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commitdiff
2023-07-05
James Procter
Merge branch 'patch/JAL-2292_caseSensitivePAE' into...
tree
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commitdiff
2023-06-22
James Procter
JAL-4213 - document the addReferenceAnnotations method...
tree
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commitdiff
2023-06-22
James Procter
JAL-2292 - ensure mapping is built for equal symbols...
patch/JAL-2292_caseSensitivePAE
tree
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commitdiff
2023-05-22
James Procter
JAL-4134 catch NPE - though in principle this should...
tree
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commitdiff
2023-05-22
James Procter
JAL-1551 spotless
tree
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commitdiff
2023-05-19
James Procter
JAL-1551 spotlessApply
tree
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commitdiff
2023-05-19
James Procter
JAL-1551 spotlessApply
tree
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commitdiff
2023-05-18
James Procter
JAL-4134 properly specify BinaryNode as a typed generic...
tree
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commitdiff
2023-05-15
James Procter
JAL-4182 patch - map selection group onto sequence...
tree
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commitdiff
2023-05-13
James Procter
JAL-2349 JAL-3855 helper method to make it easy to...
tree
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commitdiff
2023-05-12
James Procter
JAL-2349 allow PAE or other contact matrices to hold...
tree
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commitdiff
2023-03-15
James Procter
JAL-4091 JAL-4147 - revised annotation label display...
tree
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commitdiff
2023-03-15
James Procter
JAL-4091 JAL-629 ‘Add Reference Annotations’ takes...
tree
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commitdiff
2023-02-27
James Procter
JAL-4134 fix more of the egregious SeqNode/BinaryNode...
tree
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commitdiff
2023-02-27
James Procter
JAL-4134 use average distance between PAE elements...
tree
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commitdiff
2023-02-27
James Procter
JAL-4134 compute normalised dot product for contact...
tree
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commitdiff
2023-02-23
James Procter
JAL-4134 group columns using a tree cut - seems to...
tree
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commitdiff
2023-02-23
James Procter
JAL-4134 - brutal hack to build a tree clustering colum...
tree
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commitdiff
2023-02-23
James Procter
JAL-4134 - refactor tree calculation code to work with...
tree
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commitdiff
2022-12-05
Ben Soares
JAL-629 implementation of --tempfac options
tree
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commitdiff
2022-10-29
Jim Procter
Merge branch 'features/JAL-4061_and_JAL-4062_findselect...
tree
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commitdiff
2022-10-17
Jim Procter
JAL-2349 JAL-3855 Integrate pAE retrieval in StructureF...
tree
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commitdiff
2022-09-15
Jim Procter
JAL-4061 use alignment panel’s feature renderer to...
tree
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commitdiff
2022-09-15
Jim Procter
JAL-4061 support incremental search of features
tree
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commitdiff
2022-09-15
Jim Procter
JAL-4061 tests, bugfixes and TODOs for matching feature...
tree
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commitdiff
2022-09-14
Jim Procter
JAL-4061 JAL-4062 Find can now search features
tree
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commitdiff
2022-03-08
Jim Procter
JAL-3438 spotless for 2.11.2.0
tree
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commitdiff
2022-02-11
Jim Procter
JAL-3949 - refactor logging from jalview.bin.Cache...
tree
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commitdiff
2022-02-11
Ben Soares
Merge branch 'develop' into update/JAL-3949_abstracted_...
tree
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commitdiff
2022-02-11
Ben Soares
JAL-3949 Complete new abstracted logging framework...
tree
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commitdiff
2022-02-04
Jim Procter
Merge branch 'bug/JAL-3806_mappingCoversSequence_for211...
bug/JAL-3806_without_shared_DS_for_2_11_2
tree
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commitdiff
2022-02-03
Jim Procter
JAL-2305 comments re testFindXrefSequences_withFetch...
tree
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commitdiff
2022-01-26
Jim Procter
Merge branch 'task/JAL-3763_newDatasetForCds' into...
tree
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commitdiff
2021-09-21
Ben Soares
JAL-3691 automatic insertion of Locale.ROOT to toUpperC...
tree
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commitdiff
2020-10-29
Jim Procter
JAL-3759 exclude hidden columns when processing...
tree
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commitdiff
2020-10-29
Jim Procter
Merge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11...
tree
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commitdiff
2020-10-28
Jim Procter
fix for JAL-3765
tree
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commitdiff
2020-10-27
Jim Procter
JAL-3700 JAL-3748 JAL-3763 don’t add stop codon via...
tree
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commitdiff
2020-10-22
gmungoc
JAL-3763 always make a new dataset sequence for CDS...
tree
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commitdiff
2020-10-20
Jim Procter
fix for JAL-3765
tree
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commitdiff
2020-10-08
gmungoc
JAL-3763 always make a new dataset sequence for CDS...
tree
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commitdiff
2020-09-22
Jim Procter
JAL-3748 don’t trash start/end on SequenceI reconstruct...
tree
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commitdiff
2020-09-16
Jim Procter
JAL-3748 pass a list to findAlignedSequence to return...
tree
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commitdiff
2020-08-17
Jim Procter
JAL-3490 merged with 2.11.2 develop
tree
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commitdiff
2020-08-10
gmungoc
JAL-3490 match count independent of contiguous matches...
patch/Release_2_11_1_Branch_patch_JAL-3490
tree
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commitdiff
2020-06-29
Jim Procter
Merge branch 'bug/JAL-3490findSpanHiddenGaps' into...
tree
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commitdiff
2020-05-18
gmungoc
Merge branch 'Jalview-JS/develop' into develop
tree
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commitdiff
2020-04-21
Jim Procter
JAL-3407 add GPL license to Jalview source files
tree
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commitdiff
2020-03-30
gmungoc
Merge branch 'develop' into Jalview-JS/develop
tree
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commitdiff
2020-02-18
Mungo Carstairs
JAL-3536 JAL-3187 don't create duplicate CDS-to-protein...
bug/JAL-3536getCrossrefTwice
tree
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commitdiff
2020-01-28
gmungoc
JAL-3187 one more obsolete method removed
tree
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commitdiff
2019-12-12
gmungoc
JAL-3490 unit test for ignore hidden regions with selec...
tree
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commitdiff
2019-12-11
gmungoc
JAL-3490 tests for skip hidden regions (and a bug fix)
tree
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commitdiff
2019-12-11
gmungoc
JAL-3490 revised layout and search algorithm (more...
tree
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commitdiff
2019-11-29
gmungoc
JAL-3490 Finder match across entirely gapped hidden...
tree
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commitdiff
2019-11-01
Ben Soares
JAL-3474 removed all .cvsignore files stored in the...
improvement/JAL-3474_lots_of_.cvsignore_files
tree
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commitdiff
2019-10-08
gmungoc
Merge branch 'develop' into Jalview-JS/develop
tree
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commitdiff
2019-08-22
gmungoc
JAL-3187 one more obsolete method removed
tree
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commitdiff
2019-08-09
gmungoc
JAL-3187 removal of variant feature (non-virtual) trans...
tree
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commitdiff
2019-07-16
gmungoc
JAL-3210 Merge branch 'develop' into trialMerge
tree
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commitdiff
2019-07-10
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
tree
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commitdiff
2019-06-18
gmungoc
JAL-3313 don't double count mapped codons
tree
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commitdiff
2019-06-17
gmungoc
JAL-3187 update alignAs code and unit tests for 'shared...
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
2019-06-07
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
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
2019-04-18
hansonr
explicit Hashtable objects
tree
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commitdiff
2019-04-11
Jim Procter
Merge branch 'develop' into task/JAL-3130_Java_11_inves...
tree
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commitdiff
2019-04-04
gmungoc
JAL-3220 unneeded main methods removed
tree
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commitdiff
2019-03-27
gmungoc
Merge branch 'develop' into Jalview-JS/develop
tree
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commitdiff
2019-03-27
gmungoc
JAL-2620 improved error reporting on failure to load...
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
2019-03-13
gmungoc
Merge branch 'develop' into trialMerge
tree
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commitdiff
2019-03-11
gmungoc
JAL-1270 JAL-2416 JAL-2839 set alwaysRun=true in test...
tree
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commitdiff
2019-03-07
gmungoc
Merge branch 'feature/JAL-3205symmetricCalc' into develop
tree
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commitdiff
2019-03-05
gmungoc
Merge remote-tracking branch 'origin/features/JAL-2620a...
tree
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commitdiff
2019-03-05
gmungoc
Merge remote-tracking branch 'origin/bug/JAL-2839findWi...
tree
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commitdiff
2019-03-03
gmungoc
JAL-3205 faster calculation with symmetric score matrix
tree
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commitdiff
2019-02-28
gmungoc
Merge branch 'feature/JAL-3143ensemblJSON' into merge...
tree
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commitdiff
2019-02-27
gmungoc
JAL-3202 discard zero percentages in extracted profile
tree
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commitdiff
2019-02-20
gmungoc
Merge branch 'feature/JAL-3143ensemblJSON' into feature...
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
2019-02-04
hansonr
refactoring for DBMODList
tree
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commitdiff
2019-01-29
gmungoc
Merge branch 'feature/JAL-3143ensemblJSON' into trialMerge
tree
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commitdiff
2019-01-26
hansonr
Jalview.isJS() --> Platform.isJS(), DBRefEntry[] -...
tree
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commitdiff
2019-01-25
hansonr
JSON refactoring
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commitdiff
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