jalview.git
2024-04-18 MorellThomasMerge branch 'test/progressBar' into feature/JAL-4159_p...
2024-04-18 MorellThomasImplemented ProgressBar for PaSiMap
2024-04-12 MorellThomasinlcude progress
2024-03-15 MorellThomasFix output of all dimensions
2024-03-15 MorellThomasAlogirthm working, but still giving slightly off results
2024-03-07 MorellThomasInlcude 8 dimensions
2024-03-06 MorellThomasFix PaSiMap on selected sequences
2024-03-06 MorellThomasTest version to switch branches
2024-01-31 MorellThomasFix output points column labels
2024-01-10 MorellThomasFixed PaSiMap output columns
2023-12-05 MorellThomasCleanup, note: rectangular selection works by holding...
2023-12-05 MorellThomasAdapts PCA points to support rectangular selection
2023-12-05 MorellThomasEnable rectangular selection for PaSiMap
2023-12-04 MorellThomasNew independent jbgui Panel for PaSiMap. Revert the...
2023-12-04 MorellThomasNew GPCAPanel button : output pairwise alignments ...
2023-12-01 MorellThomasApplying adjustablenw_params.patch (JAL-4159)
2023-11-27 MorellThomasCommit before pushing to Jalview remote
2023-10-01 MorellThomasFix Reset Button for PaSiMap and issue with indelfreeAs...
2023-09-18 MorellThomasFix buttons on the PaSiMap plot window
2023-09-16 MorellThomasCorrectly working implementation of the PaSiMap pipeline
2023-09-16 MorellThomasAlmost working
2023-09-08 MorellThomasProperly integrated endGaps option for AlignSeq.traceAl...
2023-09-07 MorellThomasMerge branch 'hardcode'
2023-09-07 MorellThomasMerge remote-tracking branch 'origin/releases/Release_2...
2023-09-07 MorellThomasImplemented least-squares optimisation in ccAnalysis
2023-08-04 MorellThomasFix alignment and score calculation for cc_analysis
2023-07-23 James ProcterMerge branch 'develop' into releases/Release_2_11_3_Branch
2023-07-23 James ProcterJAL-4090 JAL-4243 bio.tools json file release notes
2023-07-22 MorellThomasImplement MSA, scoring and counting the connections
2023-07-22 James ProcterJAL-4243 Jalview 2.11.2.7’s biotool record as JSON...
2023-07-20 James ProcterJAL-3855 tree title for PAE matrix tree is PAE Matrix... patch/JAL-3855_fixup_pae
2023-07-20 James ProcterJAL-3855 auto select clusters and fix up colouring...
2023-07-19 James ProcterMerge branch 'develop' into releases/Release_2_11_3_Branch
2023-07-19 James ProcterMerge branch 'patch/JAL-3855_fixup_pae' into develop
2023-07-18 James ProcterMerge branch 'develop' into patch/JAL-3855_fixup_pae
2023-07-18 James ProcterJAL-4153 comments re patch incorrectly committed under...
2023-07-18 Ben SoaresJAL-4513 move comments
2023-07-18 Ben SoaresJAL-4513 now re-add the SwingUtilities.invokeAndWait... bug/JAL-4513_JvCacheableInputBoxTest_flaky_on_build_server
2023-07-18 James ProcterJAL-3855 PAE matrices are transposed on import from...
2023-07-18 James ProcterJAL-3855 JAL-4124 test checks asymmetric matrices are...
2023-07-18 James ProcterJAL-3858 fix off-by-one in matrix visualisation and...
2023-07-18 James ProcterJAL-3858 flip diagonal so matrix visualisation is top...
2023-07-18 James ProcterJAL-3858 annotation .height is bigger than graphHeight...
2023-07-18 Ben SoaresJAL-4513 reduce wait to invoke fail
2023-07-18 Ben SoaresJAL-4513 add a SwingUtilities.invokeAndWait() to see...
2023-07-18 James ProcterMerge branch 'develop' into releases/Release_2_11_3_Branch
2023-07-17 Ben SoaresJAL-3599 Updated default eclipse to 'latest' and made...
2023-07-17 James ProcterJAL-4119 TRACE level console message reporting download...
2023-07-17 James ProcterJAL-4090 JAL-4165 known issue
2023-07-17 James ProcterJAL-4090 JAL-4165 known issue
2023-07-17 James ProcterJAL-4223 add testdata for test
2023-07-17 James ProcterJAL-4090 mark JAL-4178 and JAL-4142 as known issues
2023-07-17 James ProcterJAL-4217 move Commands.structureImageTest to testTask1
2023-07-12 James ProcterJAL-4223 - test and patch to ensure numbering matches...
2023-07-11 James ProcterMerge branch 'develop' into releases/Release_2_11_3_Branch
2023-07-09 MorellThomasCopied PCA files to PaSiMap analogues and changed all...
2023-07-08 MorellThomasIncludes the PaSiMap button in the CalculationChooser
2023-07-07 James ProcterMerge branch 'patch/JAL-4195_cli_eps_export_npe' into...
2023-07-07 James ProcterJAL-4217 JAL-629 built in 25s time out waiting for...
2023-07-07 James ProcterJAL-4090 update 2.11.3.0 release notes (with in-progres...
2023-07-07 James ProcterMerge branch 'patch/JAL-4119_sifts_ftp_split' into...
2023-07-07 James ProcterMerge branch 'develop' into patch/JAL-4195_cli_eps_expo... patch/JAL-4195_cli_eps_export_npe
2023-07-07 James ProcterJAL-4195 add exception handling for all other CommandsT...
2023-07-07 James ProcterJAL-4221 update description when transferring annotatio...
2023-07-07 James ProcterJAL-629 even more console debug for --structureviewer...
2023-07-06 James ProcterJAL-629 liberal defensive coding, comments about refact...
2023-07-06 James ProcterJAL-629 make —structure image work again after threadin...
2023-07-06 James ProcterJAL-4217 catch case when the structure viewer doesn...
2023-07-06 James ProcterJAL-4217 interruptedExceptions should also break any...
2023-07-06 James ProcterJAL-2292 verify mixed case alignment actually aligns
2023-07-06 James ProcterJAL-4217 wrap imageExport CLI method's call to imageExp...
2023-07-06 James ProcterJAL-4217 wrap imageExport CLI method's call to imageExp...
2023-07-05 James ProcterMerge branch 'patch/JAL-2292_caseSensitivePAE' into...
2023-07-05 James ProcterMerge branch 'patch/JAL-4213_addref_with_selection...
2023-07-04 James ProcterMerge branch 'develop' into releases/Release_2_11_3_Branch
2023-07-04 James ProcterMerge branch 'merge/from_2_11_2_7_to_2_11_3_0' into...
2023-07-04 James ProcterJAL-4117 JAL-1551 source licensing
2023-07-04 James ProcterJAL-4117 Fri June 30th release of 2.11.2.7 with Jalview...
2023-07-02 MorellThomasFixed build.gradle, provide diff
2023-06-30 James ProcterJAL-4217 try really hard to shut down and dispose of...
2023-06-30 James ProcterJAL-4216 release notes
2023-06-30 James ProcterJAL-4216 compute size of annotation using start/end...
2023-06-30 James ProcterMerge branch 'task/JAL-4001_Plausible_API' into develop
2023-06-30 Ben SoaresJAL-4001 Added a random id to User-Agent to ensure... task/JAL-4001_Plausible_API
2023-06-29 James ProcterMerge branch 'task/JAL-4001_Plausible_API' into develop
2023-06-29 James ProcterJAL-4117 JAL-4001 plausible analytics release notes...
2023-06-29 James ProcterJAL-4090 update from 2.11.2.7 JAL-4117 - version bump...
2023-06-29 James ProcterJAL-4001 analytics url provided by https://jalview...
2023-06-28 Ben SoaresJAL-4001 change Plausible discovery URL
2023-06-28 Ben SoaresJAL-4001 remove headless code from analytics
2023-06-28 Ben SoaresJAL-4001 Remove analytics for --headless mode
2023-06-27 Ben SoaresJAL-4001 Added useful props information
2023-06-22 Ben SoaresMerge branch 'develop' into task/JAL-4001_Plausible_API
2023-06-22 Ben SoaresJAL-4001 Fix default API url
2023-06-22 James ProcterJAL-4213 don’t pass active selection when actioning... patch/JAL-4213_addref_with_selection
2023-06-22 James ProcterJAL-4213 - document the addReferenceAnnotations method...
2023-06-22 Ben SoaresJAL-4001 Added 'installation' property.
2023-06-22 James ProcterJAL-2292 - ensure mapping is built for equal symbols... patch/JAL-2292_caseSensitivePAE
2023-06-22 Ben SoaresJAL-4001 Added lookup to https://jalview.org/config...
2023-06-22 Ben SoaresJAL-4019 corrected to '>' to '>=' for percentage compar... bug/JAL-4125_flatlaf_quithandler_external_structureviewers_not_closed
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