Fix buttons on the PaSiMap plot window
[jalview.git] / src /
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 MorellThomasImplemented least-squares optimisation in ccAnalysis
2023-08-04 MorellThomasFix alignment and score calculation for cc_analysis
2023-07-22 MorellThomasImplement MSA, scoring and counting the connections
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...
2023-07-18 James ProcterJAL-3855 PAE matrices are transposed on import from...
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...
2023-07-17 James ProcterJAL-4119 TRACE level console message reporting download...
2023-07-12 James ProcterJAL-4223 - test and patch to ensure numbering matches...
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 ProcterJAL-4217 JAL-629 built in 25s time out waiting for...
2023-07-07 James ProcterMerge branch 'patch/JAL-4119_sifts_ftp_split' into...
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-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 ProcterJAL-4117 JAL-1551 source licensing
2023-06-30 James ProcterJAL-4217 try really hard to shut down and dispose of...
2023-06-30 James ProcterJAL-4216 compute size of annotation using start/end...
2023-06-30 Ben SoaresJAL-4001 Added a random id to User-Agent to ensure... task/JAL-4001_Plausible_API
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
2023-06-21 James ProcterMerge branch 'patch/JAL-4196_structure_viewer_synchroni... patch/JAL-4196_structure_viewer_synchronising
2023-06-21 Ben SoaresJAL-4001 Rationalise user-agent string into HttpUtils
2023-06-21 Ben SoaresJAL-4001 Change wording from google to plausible or...
2023-06-20 Ben SoaresJAL-4001 rename the init method
2023-06-20 Ben SoaresJAL-4001 Working Plausible analytics
2023-06-20 Ben SoaresJAL-4001 Plausible class
2023-06-20 Ben SoaresJAL-4001 Added a genuine client_id (from gtag). Added... task/JAL-4001_migrate_googleanalytics_to_GA4
2023-06-17 Ben SoaresJAL-4001 Check --nousagestats before doing analytics...
2023-06-16 Ben SoaresJAL-4001 Add a _geo=1 to query string and JSON. Add...
2023-06-16 Ben SoaresJAL-4001 Remove jgoogleanalytics code and jar
2023-06-16 Ben SoaresJAL-4001 make page_location the same encoding as the...
2023-06-15 Ben SoaresJAL-4001 Changed for Java 8 compatibility
2023-06-14 Ben SoaresJAL-4001 Trying to see extra information in GA dashboard
2023-06-14 Ben SoaresMerge branch 'develop' into task/JAL-4001_migrate_googl...
2023-06-09 Ben SoaresJAL-3599 Make jalviewjs dependOn jalviewjsLaunchTest...
2023-06-09 Ben SoaresJAL-3599 Deliberate NPE to see if build plan fails
2023-06-08 Ben SoaresJAL-3599 gradle tasks to test JalviewJS launches in...
2023-06-08 Ben SoaresJAL-4001 Only send defaultParams for application_launch...
2023-06-08 Ben SoaresMerge branch 'develop' into task/JAL-4001_migrate_googl...
2023-06-08 James ProcterMerge branch 'develop' into patch/JAL-4196_structure_vi...
2023-06-08 James ProcterJAL-4196 make very sure we avoid CME by defensively...
2023-06-08 James ProcterJAL-4196 report an error if structure view doesn’t...
2023-06-08 James ProcterJAL-4196 structure view cli tests wait using new jalvie...
2023-06-08 Ben SoaresJAL-3416 FlatLaf SystemInfo failing in JalviewJS. ...
2023-06-08 Ben SoaresMerge branch 'develop' into task/JAL-4001_migrate_googl...
2023-06-07 Ben SoaresJAL-4001 Javadoc for the method to use
2023-06-07 James ProcterJAL-4195 add exception handling for all image output...
2023-06-07 James ProcterMerge branch 'patch/JAL-4195_cli_eps_export_npe' into...
2023-06-07 James ProcterJAL-4195 catch thrown exceptions (if any) during image...
2023-06-07 Ben SoaresMerge branch 'develop' into task/JAL-4001_migrate_googl...
2023-06-07 Ben SoaresJAL-4001 Added more params for application_launch
2023-06-07 Ben SoaresJAL-4001 removed a test param
2023-06-07 Ben SoaresJAL-4001 GA4 tracking is now ENABLED. Currently loggin...
2023-06-07 James ProcterJAL-4195 tidy up desktop instances after creating them
2023-06-06 James ProcterJAL-4195 report full stack trace for exceptions raised...
2023-06-06 James ProcterJAL-4160 --colour can now take user defined scheme...
2023-06-06 James ProcterJAL-4160 JAL-4195 wait around until alignFrame calculat...
2023-06-06 James ProcterJAL-1551 formatting and javadoc for ArgParser rather...
2023-06-06 James ProcterJAL-629 - remove TODO from jalview.bin.Jalview since...
2023-06-06 James ProcterJAL-4195 Debug message indicating creation of an image...
2023-06-06 James ProcterJAL-1551 a bit of javadoc for Jalview.testoutput methods
2023-06-05 Ben SoaresJAL-4001 debugging statements
2023-06-05 Ben SoaresJAL-4001 untested GA4 client code
2023-06-05 Ben SoaresJAL-4001 most of google analytics client
2023-06-05 Ben SoaresJAL-4001 start of GA4 client class
2023-06-02 Ben SoaresMerge branch 'develop' into task/JAL-4001_migrate_googl...
2023-06-01 Ben SoaresMerge branch 'develop' into improvement/JAL-4193_cl_arg...
2023-06-01 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold...
2023-06-01 Ben SoaresJAL-629 fixing test EBIAlphaFoldTest.checkImportPAEToSt...
2023-06-01 Ben SoaresJAL-4001 Changed title+message to MessageManager
2023-06-01 Ben SoaresJAL-4193 JAL-4194 sessionProperties layer in Cache...
2023-06-01 James ProcterMerge branch 'develop' into features/JAL-4134_use_annot...
2023-06-01 James ProcterJAL-4134 properly resolve positions in associated align... features/JAL-4134_use_annotation_row_for_colours_and_groups
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