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jalview.git
2023-12-05 MorellThomasEnable rectangular selection for PaSiMap commit | commitdiff | tree | snapshot
2023-12-04 MorellThomasNew independent jbgui Panel for PaSiMap. Revert the... commit | commitdiff | tree | snapshot
2023-12-04 MorellThomasNew GPCAPanel button : output pairwise alignments ... commit | commitdiff | tree | snapshot
2023-12-01 MorellThomasApplying adjustablenw_params.patch (JAL-4159) commit | commitdiff | tree | snapshot
2023-11-27 MorellThomasCommit before pushing to Jalview remote commit | commitdiff | tree | snapshot
2023-10-01 MorellThomasFix Reset Button for PaSiMap and issue with indelfreeAs... commit | commitdiff | tree | snapshot
2023-09-18 MorellThomasFix buttons on the PaSiMap plot window commit | commitdiff | tree | snapshot
2023-09-16 MorellThomasCorrectly working implementation of the PaSiMap pipeline commit | commitdiff | tree | snapshot
2023-09-16 MorellThomasAlmost working commit | commitdiff | tree | snapshot
2023-09-08 MorellThomasProperly integrated endGaps option for AlignSeq.traceAl... commit | commitdiff | tree | snapshot
2023-09-07 MorellThomasMerge branch 'hardcode' commit | commitdiff | tree | snapshot
2023-09-07 MorellThomasMerge remote-tracking branch 'origin/releases/Release_2... commit | commitdiff | tree | snapshot
2023-09-07 MorellThomasImplemented least-squares optimisation in ccAnalysis commit | commitdiff | tree | snapshot
2023-08-04 MorellThomasFix alignment and score calculation for cc_analysis commit | commitdiff | tree | snapshot
2023-07-23 James ProcterMerge branch 'develop' into releases/Release_2_11_3_Branch commit | commitdiff | tree | snapshot
2023-07-23 James ProcterJAL-4090 JAL-4243 bio.tools json file release notes commit | commitdiff | tree | snapshot
2023-07-22 MorellThomasImplement MSA, scoring and counting the connections commit | commitdiff | tree | snapshot
2023-07-22 James ProcterJAL-4243 Jalview 2.11.2.7’s biotool record as JSON... commit | commitdiff | tree | snapshot
2023-07-20 James ProcterJAL-3855 tree title for PAE matrix tree is PAE Matrix... patch/JAL-3855_fixup_pae commit | commitdiff | tree | snapshot
2023-07-20 James ProcterJAL-3855 auto select clusters and fix up colouring... commit | commitdiff | tree | snapshot
2023-07-19 James ProcterMerge branch 'develop' into releases/Release_2_11_3_Branch commit | commitdiff | tree | snapshot
2023-07-19 James ProcterMerge branch 'patch/JAL-3855_fixup_pae' into develop commit | commitdiff | tree | snapshot
2023-07-18 James ProcterMerge branch 'develop' into patch/JAL-3855_fixup_pae commit | commitdiff | tree | snapshot
2023-07-18 James ProcterJAL-4153 comments re patch incorrectly committed under... commit | commitdiff | tree | snapshot
2023-07-18 Ben SoaresJAL-4513 move comments commit | commitdiff | tree | snapshot
2023-07-18 Ben SoaresJAL-4513 now re-add the SwingUtilities.invokeAndWait... bug/JAL-4513_JvCacheableInputBoxTest_flaky_on_build_server commit | commitdiff | tree | snapshot
2023-07-18 James ProcterJAL-3855 PAE matrices are transposed on import from... commit | commitdiff | tree | snapshot
2023-07-18 James ProcterJAL-3855 JAL-4124 test checks asymmetric matrices are... commit | commitdiff | tree | snapshot
2023-07-18 James ProcterJAL-3858 fix off-by-one in matrix visualisation and... commit | commitdiff | tree | snapshot
2023-07-18 James ProcterJAL-3858 flip diagonal so matrix visualisation is top... commit | commitdiff | tree | snapshot
2023-07-18 James ProcterJAL-3858 annotation .height is bigger than graphHeight... commit | commitdiff | tree | snapshot
2023-07-18 Ben SoaresJAL-4513 reduce wait to invoke fail commit | commitdiff | tree | snapshot
2023-07-18 Ben SoaresJAL-4513 add a SwingUtilities.invokeAndWait() to see... commit | commitdiff | tree | snapshot
2023-07-18 James ProcterMerge branch 'develop' into releases/Release_2_11_3_Branch commit | commitdiff | tree | snapshot
2023-07-17 Ben SoaresJAL-3599 Updated default eclipse to 'latest' and made... commit | commitdiff | tree | snapshot
2023-07-17 James ProcterJAL-4119 TRACE level console message reporting download... commit | commitdiff | tree | snapshot
2023-07-17 James ProcterJAL-4090 JAL-4165 known issue commit | commitdiff | tree | snapshot
2023-07-17 James ProcterJAL-4090 JAL-4165 known issue commit | commitdiff | tree | snapshot
2023-07-17 James ProcterJAL-4223 add testdata for test commit | commitdiff | tree | snapshot
2023-07-17 James ProcterJAL-4090 mark JAL-4178 and JAL-4142 as known issues commit | commitdiff | tree | snapshot
2023-07-17 James ProcterJAL-4217 move Commands.structureImageTest to testTask1 commit | commitdiff | tree | snapshot
2023-07-12 James ProcterJAL-4223 - test and patch to ensure numbering matches... commit | commitdiff | tree | snapshot
2023-07-11 James ProcterMerge branch 'develop' into releases/Release_2_11_3_Branch commit | commitdiff | tree | snapshot
2023-07-09 MorellThomasCopied PCA files to PaSiMap analogues and changed all... commit | commitdiff | tree | snapshot
2023-07-08 MorellThomasIncludes the PaSiMap button in the CalculationChooser commit | commitdiff | tree | snapshot
2023-07-07 James ProcterMerge branch 'patch/JAL-4195_cli_eps_export_npe' into... commit | commitdiff | tree | snapshot
2023-07-07 James ProcterJAL-4217 JAL-629 built in 25s time out waiting for... commit | commitdiff | tree | snapshot
2023-07-07 James ProcterJAL-4090 update 2.11.3.0 release notes (with in-progres... commit | commitdiff | tree | snapshot
2023-07-07 James ProcterMerge branch 'patch/JAL-4119_sifts_ftp_split' into... commit | commitdiff | tree | snapshot
2023-07-07 James ProcterMerge branch 'develop' into patch/JAL-4195_cli_eps_expo... patch/JAL-4195_cli_eps_export_npe commit | commitdiff | tree | snapshot
2023-07-07 James ProcterJAL-4195 add exception handling for all other CommandsT... commit | commitdiff | tree | snapshot
2023-07-07 James ProcterJAL-4221 update description when transferring annotatio... commit | commitdiff | tree | snapshot
2023-07-07 James ProcterJAL-629 even more console debug for --structureviewer... commit | commitdiff | tree | snapshot
2023-07-06 James ProcterJAL-629 liberal defensive coding, comments about refact... commit | commitdiff | tree | snapshot
2023-07-06 James ProcterJAL-629 make —structure image work again after threadin... commit | commitdiff | tree | snapshot
2023-07-06 James ProcterJAL-4217 catch case when the structure viewer doesn... commit | commitdiff | tree | snapshot
2023-07-06 James ProcterJAL-4217 interruptedExceptions should also break any... commit | commitdiff | tree | snapshot
2023-07-06 James ProcterJAL-2292 verify mixed case alignment actually aligns commit | commitdiff | tree | snapshot
2023-07-06 James ProcterJAL-4217 wrap imageExport CLI method's call to imageExp... commit | commitdiff | tree | snapshot
2023-07-06 James ProcterJAL-4217 wrap imageExport CLI method's call to imageExp... commit | commitdiff | tree | snapshot
2023-07-05 James ProcterMerge branch 'patch/JAL-2292_caseSensitivePAE' into... commit | commitdiff | tree | snapshot
2023-07-05 James ProcterMerge branch 'patch/JAL-4213_addref_with_selection... commit | commitdiff | tree | snapshot
2023-07-04 James ProcterMerge branch 'develop' into releases/Release_2_11_3_Branch commit | commitdiff | tree | snapshot
2023-07-04 James ProcterMerge branch 'merge/from_2_11_2_7_to_2_11_3_0' into... commit | commitdiff | tree | snapshot
2023-07-04 James ProcterJAL-4117 JAL-1551 source licensing commit | commitdiff | tree | snapshot
2023-07-04 James ProcterJAL-4117 Fri June 30th release of 2.11.2.7 with Jalview... commit | commitdiff | tree | snapshot
2023-07-02 MorellThomasFixed build.gradle, provide diff commit | commitdiff | tree | snapshot
2023-06-30 James ProcterJAL-4217 try really hard to shut down and dispose of... commit | commitdiff | tree | snapshot
2023-06-30 James ProcterJAL-4216 release notes commit | commitdiff | tree | snapshot
2023-06-30 James ProcterJAL-4216 compute size of annotation using start/end... commit | commitdiff | tree | snapshot
2023-06-30 James ProcterMerge branch 'task/JAL-4001_Plausible_API' into develop commit | commitdiff | tree | snapshot
2023-06-30 Ben SoaresJAL-4001 Added a random id to User-Agent to ensure... task/JAL-4001_Plausible_API commit | commitdiff | tree | snapshot
2023-06-29 James ProcterMerge branch 'task/JAL-4001_Plausible_API' into develop commit | commitdiff | tree | snapshot
2023-06-29 James ProcterJAL-4117 JAL-4001 plausible analytics release notes... commit | commitdiff | tree | snapshot
2023-06-29 James ProcterJAL-4090 update from 2.11.2.7 JAL-4117 - version bump... commit | commitdiff | tree | snapshot
2023-06-29 James ProcterJAL-4001 analytics url provided by https://jalview... commit | commitdiff | tree | snapshot
2023-06-28 Ben SoaresJAL-4001 change Plausible discovery URL commit | commitdiff | tree | snapshot
2023-06-28 Ben SoaresJAL-4001 remove headless code from analytics commit | commitdiff | tree | snapshot
2023-06-28 Ben SoaresJAL-4001 Remove analytics for --headless mode commit | commitdiff | tree | snapshot
2023-06-27 Ben SoaresJAL-4001 Added useful props information commit | commitdiff | tree | snapshot
2023-06-22 Ben SoaresMerge branch 'develop' into task/JAL-4001_Plausible_API commit | commitdiff | tree | snapshot
2023-06-22 Ben SoaresJAL-4001 Fix default API url commit | commitdiff | tree | snapshot
2023-06-22 James ProcterJAL-4213 don’t pass active selection when actioning... patch/JAL-4213_addref_with_selection commit | commitdiff | tree | snapshot
2023-06-22 James ProcterJAL-4213 - document the addReferenceAnnotations method... commit | commitdiff | tree | snapshot
2023-06-22 Ben SoaresJAL-4001 Added 'installation' property. commit | commitdiff | tree | snapshot
2023-06-22 James ProcterJAL-2292 - ensure mapping is built for equal symbols... patch/JAL-2292_caseSensitivePAE commit | commitdiff | tree | snapshot
2023-06-22 Ben SoaresJAL-4001 Added lookup to https://jalview.org/config... commit | commitdiff | tree | snapshot
2023-06-22 Ben SoaresJAL-4019 corrected to '>' to '>=' for percentage compar... bug/JAL-4125_flatlaf_quithandler_external_structureviewers_not_closed commit | commitdiff | tree | snapshot
2023-06-21 James ProcterMerge branch 'patch/JAL-4196_structure_viewer_synchroni... patch/JAL-4196_structure_viewer_synchronising commit | commitdiff | tree | snapshot
2023-06-21 Ben SoaresJAL-4001 Rationalise user-agent string into HttpUtils commit | commitdiff | tree | snapshot
2023-06-21 Ben SoaresJAL-4001 Change wording from google to plausible or... commit | commitdiff | tree | snapshot
2023-06-20 Ben SoaresJAL-4001 rename the init method commit | commitdiff | tree | snapshot
2023-06-20 Ben SoaresJAL-4001 Working Plausible analytics commit | commitdiff | tree | snapshot
2023-06-20 Ben SoaresJAL-4001 Plausible class commit | commitdiff | tree | snapshot
2023-06-20 Ben SoaresJAL-4001 Added a genuine client_id (from gtag). Added... task/JAL-4001_migrate_googleanalytics_to_GA4 commit | commitdiff | tree | snapshot
2023-06-17 Ben SoaresJAL-4001 Check --nousagestats before doing analytics... commit | commitdiff | tree | snapshot
2023-06-16 Ben SoaresJAL-4001 Add a _geo=1 to query string and JSON. Add... commit | commitdiff | tree | snapshot
2023-06-16 Ben SoaresJAL-4001 Remove jgoogleanalytics code and jar commit | commitdiff | tree | snapshot
2023-06-16 Ben SoaresJAL-4001 make page_location the same encoding as the... commit | commitdiff | tree | snapshot
2023-06-15 Ben SoaresJAL-4001 Changed for Java 8 compatibility commit | commitdiff | tree | snapshot
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