JAL-4241 Create sequence mapping before adjusting annotations
[jalview.git] / src /
2023-07-28 Mateusz WarownyJAL-4241 Create sequence mapping before adjusting annot... mmw/bug/JAL-4241-annotation-alignment-fix
2023-07-28 Mateusz Warowny --- Adding issue comments
2023-04-24 Mateusz WarownyJAL-4155 Replace unsafe casting to AlignmentPanel with...
2023-04-24 James ProcterJAL-4155 Viewport holds a reference to its AlignmentVie...
2023-03-28 Mateusz WarownyJAL-4154 Add Platform.forArch method.
2023-03-28 Mateusz WarownyMerge branch 'JAL-4152-typed-singleton-provider' into...
2023-03-28 Mateusz WarownyMerge branch 'development/Release_2_12_Branch' into...
2023-03-24 Mateusz WarownyJAL-4152 Remove redundant casts from getInstance usages. JAL-4152-typed-singleton-provider
2023-03-22 Mateusz WarownyJAL-4152 Make return type of getInstance a generic...
2023-03-15 Mateusz WarownyJAL-4146 Change occurrences of <br/> to <br>
2023-03-01 Mateusz WarownyJAL-4136 Replace uses of isBlank with isEmpty
2023-02-24 Mateusz WarownyJAL-4135 replace stream.toString(Charset) calls with...
2023-02-22 Mateusz WarownyJAL-4130 Replace Collection#forEach call with for loop
2023-02-22 Mateusz WarownyJAL-4130 Avoid using thenComparing of the Comparator...
2023-02-17 Mateusz WarownyJAL-4131 Replace usages of requireNonNullElse
2023-02-16 Mateusz WarownyJAL-4130 Workaround the j2s issue with final variables...
2023-02-06 Mateusz WarownyJAL-3878 Change Cache.log calls to Console
2023-02-06 Mateusz WarownyMerge branch 'JAL-3878_ws-overhaul-3' into mmw/Release_...
2023-01-20 Jim ProcterMerge branch 'develop' into development/Release_2_12_Br...
2023-01-20 Jim ProcterMerge branch 'patch/JAL-4114_updated_3dbeacons_api...
2023-01-20 Jim ProcterJAL-4114 model_page_url not required in v2.0 response patch/JAL-4114_updated_3dbeacons_api
2023-01-20 Jim ProcterJAL-4102 update 2.12 from 2.11.2.6 patch release -...
2023-01-20 Jim ProcterMerge branch 'patch/JAL-4114_updated_3dbeacons_api...
2023-01-20 Jim ProcterMerge branch 'patch/Release_2_11_2_6_Branch' into develop
2023-01-20 Jim ProcterJAL-2353 primary ref candidates that should be promoted... patch/Release_2_11_2_6_Branch
2023-01-20 Jim ProcterJAL-4114 only rank model qualities that are computed...
2023-01-20 Jim ProcterJAL-4114 alphafold now marked as AB-INITIO so adjust...
2023-01-20 Jim ProcterJAL-4114 additional warnings when PDBe doesn’t return...
2023-01-20 Jim ProcterJAL-4114 patch REST client for changed JSON schema...
2023-01-20 Jim ProcterJAL-4114 formatting
2023-01-06 Jim ProcterMerge branch 'improvement/JAL-4111_suffixed_DEVELOP_cha...
2022-12-16 Jim ProcterJAL-4109 examine -Djalview.loglevel on startup to decid...
2022-12-16 Jim ProcterJAL-4107 fix merge and avoid NPE
2022-12-14 Jim ProcterMerge branch 'develop' into update_212_Dec_merge_with_2...
2022-12-13 Jim ProcterMerge branch 'alpha/origin_2022_JAL-3066_Jalview_212_sl...
2022-11-30 Ben SoaresJAL-4101 Updated DEFAULT_RFAM_BASEURL
2022-11-30 Jim ProcterJAL-2353 patch for Ensembl refs from uniprot - needs...
2022-11-29 Ben SoaresJAL-4101 Updated DEFAULT_RFAM_BASEURL
2022-11-21 Jim ProcterMerge commit 'alpha/update_2_12_for_2_11_2_series_merge...
2022-10-25 Ben SoaresJAL-3416 Making FlatLaF default for macs due to a probl...
2022-10-11 Jim ProcterJAL-4073 fix PEBCAK failure
2022-10-06 Jim Procterstable url for PFAM retrieval via interpro api :) JAL...
2022-10-06 Jim ProcterJAL-1551 formatting
2022-10-06 Jim ProcterJAL-4073 Pfam retrieval now works via a template includ...
2022-10-06 Jim ProcterPatch for JAL-4074 - any content ending in ‘gzip’ recog...
2022-09-14 Jim ProcterMerge branch 'bug/JAL-3612_overviewFeatureOrdering...
2022-08-08 Jim ProcterJAL-4046 JAL-3993 imports reformatting
2022-08-08 Jim ProcterJAL-4046 JAL-3993 patch for 2.11.2.4 release
2022-08-08 Jim ProcterMerge branch 'task/JAL-3991_check_actual_JAVA_VERSION_a...
2022-08-08 Jim ProcterMerge branch 'improvement/JAL-4014_gecos_colour_schemes...
2022-08-08 Jim ProcterMerge branch 'patch/JAL-4036_uniprot_fts_legacy_endpoin...
2022-08-08 Jim ProcterJAL-4034 show the loading spinner when switching betwee...
2022-08-08 Jim ProcterMerge branch 'features/JAL-4034_improve_3dbeacons_butto...
2022-07-25 Ben SoaresJAL-4036 moved a comment block
2022-07-25 Ben SoaresJAL-4034 button looks better also on other OSes with...
2022-07-24 Ben SoaresJAL-4034 add round corners to 3DB confirmation button...
2022-07-22 Ben SoaresJAL-4036 Changes made from code review CR-JAL-265
2022-07-22 Ben SoaresJAL-4036 Add getDbName to the GFTSPanelI and add an...
2022-07-22 Ben SoaresJAL-4036 removing the query field code from the dropdow...
2022-07-21 Ben SoaresJAL-4036 Don't autosearch changing index when autosearc...
2022-07-21 Ben SoaresJAL-4036 add search fieldname to dropdown list
2022-07-21 Ben SoaresJAL-4036 New configuration, target and pagination proce...
2022-07-20 Jim ProcterJAL-4045 - don't apply distribution dependent scale...
2022-07-15 Ben SoaresJAL-4034 Use the new non-modal JDialog for 3DBeacons...
2022-07-15 Ben SoaresJAL-4034 Allow request for non-modal JDialog, which...
2022-07-12 Ben SoaresJAL-4034 change to jalview property name
2022-07-12 Ben SoaresJAL-4034 showConfirmDialog works for both desktop and...
2022-07-11 Ben SoaresJAL-4034 Non-blocking 3D Beacons query after warning...
2022-07-11 Ben SoaresJAL-4034 allow a jalview_property to set the threshold...
2022-07-04 Jim ProcterJAL-4034 fix #3 change uniprot ref fetch dialog to...
2022-07-04 Jim ProcterJAL-4034 Fix #2 show an icon and a button to press...
2022-06-30 Jim ProcterJAL-4036 use the legacy endpoint (and report the FTS...
2022-06-28 Ben SoaresMerge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS...
2022-06-28 Ben SoaresJAL-1988 Don't put Quit in the File menu if there's...
2022-06-23 Ben SoaresMerge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS...
2022-06-23 Ben SoaresJAL-1988 Check for setHandler capability to avoid About...
2022-06-17 Ben SoaresJAL-3027 Avoid FlatLAF Desktop class is JalviewJS
2022-06-15 Jim ProcterJAL-1988 JAL-3416 avoid unnecessary static flag
2022-06-15 Jim ProcterJAL-3418 JAL-1988 don’t need java version check anymore
2022-06-13 Ben SoaresJAL-1988 Hack to ensure Quit dialog box is moved to...
2022-06-13 Ben SoaresJAL-1988 Moved APQHandlers to jalview.jbgui and called...
2022-06-13 Jim ProcterMerge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS...
2022-06-13 Ben SoaresJAL-3416 remove flat as default for linux
2022-06-13 Ben SoaresJAL-1988 JAL-3416 Using the flatlaf-extras About, Prefe...
2022-06-13 Ben SoaresJAL-3416 Added some mac specific FlatLAF settings....
2022-06-09 Jim ProcterMerge branch 'bug/JAL-4020_add_pymolwin_paths' into...
2022-06-09 Jim ProcterJAL-4026 ignore StructureSelectionManager events if...
2022-06-09 Jim ProcterJAL-4026 update the viewport’s wrapped width after...
2022-06-08 Jim ProcterMerge branch 'improvement/JAL-4023_snotation_for_trees...
2022-06-08 Jim ProcterMerge branch 'patch/JAL-4024_jumpScrollHang' into develop
2022-06-08 Jim ProcterJAL-4024 only render partially when new view overlaps... patch/JAL-4024_jumpScrollHang
2022-06-07 Ben SoaresJAL-4020 class formatting
2022-06-07 Ben SoaresJAL-4020 added the \Scripts\pymol.exe. to the pathList
2022-06-06 Ben SoaresJAL-4020 Added the +2 arg for PyMOLWin.exe allowing...
2022-06-06 Ben SoaresJAL-4020 class reformatting
2022-06-06 Ben SoaresJAL-4020 Added path search for global installation...
2022-06-06 Jim ProcterJAL-4023 use %g for distances (scientific notation... improvement/JAL-4023_snotation_for_trees
2022-06-06 Ben SoaresJAL-4020 Added search for PyMOLWinWithConsole.bat ...
2022-06-06 Jim ProcterJAL-4023 store distances as doubles
2022-05-12 Ben SoaresJAL-4014 4 gecos colour schemes added
next