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2023-02-03	Ben Soares	JAL-629 Fasta sequence id reading whitespace fix. Flexioble...	commit \| commitdiff \| tree
2023-02-03	Ben Soares	JAL-629 "updated" json-simple	commit \| commitdiff \| tree
2023-01-26	Ben Soares	JAL-629 example files from nf-core	commit \| commitdiff \| tree
2023-01-26	Ben Soares	JAL-629 helper eclipse CLI run	commit \| commitdiff \| tree
2023-01-26	Ben Soares	JAL-629 adjust arg type for tempfac-shading -- was...	commit \| commitdiff \| tree
2023-01-23	Ben Soares	JAL-629 Attempts to add PAE to structure. --headless...	commit \| commitdiff \| tree
2023-01-18	Ben Soares	JAL-629 make sequence id key 'seqid'	commit \| commitdiff \| tree
2023-01-11	Ben Soares	JAL-629 added Alphafold cif, pdb and PAE json files...	commit \| commitdiff \| tree
2023-01-11	Ben Soares	JAL-629 refactoring TFType. Remove i18n identification...	commit \| commitdiff \| tree
2022-12-19	Ben Soares	JAL-629 Add image output and quit	commit \| commitdiff \| tree
2022-12-15	Ben Soares	JAL-629 move SubId to more logical place. Attempt removal...	commit \| commitdiff \| tree
2022-12-14	Ben Soares	JAL-629 Open Structure Viewer from cmdline	commit \| commitdiff \| tree
2022-12-09	Ben Soares	JAL-629 null check, fixed tests!	commit \| commitdiff \| tree
2022-12-08	Ben Soares	JAL-629 fix opening files	commit \| commitdiff \| tree
2022-12-08	Ben Soares	JAL-629 stray code deleted	commit \| commitdiff \| tree
2022-12-08	Ben Soares	JAL-629 Allow attachment of pAE file to a particular...	commit \| commitdiff \| tree
2022-12-05	Ben Soares	JAL-629 implementation of --tempfac options	commit \| commitdiff \| tree
2022-11-30	Ben Soares	JAL-4101 Updated Rfam* tests	commit \| commitdiff \| tree
2022-11-30	Ben Soares	JAL-4101 Updated DEFAULT_RFAM_BASEURL	commit \| commitdiff \| tree
2022-11-29	Ben Soares	JAL-4101 Updated Rfam* tests	commit \| commitdiff \| tree
2022-11-29	Ben Soares	JAL-4101 Updated DEFAULT_RFAM_BASEURL	commit \| commitdiff \| tree
2022-11-23	Ben Soares	JAL-629 Doing things with the command line arguments	commit \| commitdiff \| tree
2022-10-27	Ben Soares	JAL-4083 don't need globalUseScriptWait after all,...	commit \| commitdiff \| tree
2022-10-27	Ben Soares	JAL-4083 only set globalUseScriptWait if needed	commit \| commitdiff \| tree
2022-10-27	Ben Soares	JAL-4083 Use jmolViewer.scriptWait instead of jmolViewer...	commit \| commitdiff \| tree
2022-10-26	Ben Soares	Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL...	commit \| commitdiff \| tree
2022-10-26	Ben Soares	JAL-3416 (and others) increasing number of STDERR lines...	commit \| commitdiff \| tree
2022-10-25	Ben Soares	JAL-3416 Making FlatLaF default for macs due to a problem...	commit \| commitdiff \| tree
2022-10-11	Ben Soares	JAL-4014 Changed gecos display names to match labels...	commit \| commitdiff \| tree
2022-08-23	Ben Soares	JAL-4014 JAL-4063 Added gecos colourScheme names (INFO...	commit \| commitdiff \| tree
2022-07-26	Ben Soares	JAL-4036 Fixed the virus_host_id query field	commit \| commitdiff \| tree
2022-07-26	Ben Soares	JAL-4036 Added text to help about different number...	commit \| commitdiff \| tree
2022-07-25	Ben Soares	JAL-4036 updated help about new UniProt API	commit \| commitdiff \| tree
2022-07-25	Ben Soares	JAL-4036 moved a comment block	commit \| commitdiff \| tree
2022-07-25	Ben Soares	JAL-4034 button looks better also on other OSes with...	commit \| commitdiff \| tree
2022-07-22	Ben Soares	JAL-4036 Changes made from code review CR-JAL-265	commit \| commitdiff \| tree
2022-07-22	Ben Soares	JAL-4036 Add getDbName to the GFTSPanelI and add an...	commit \| commitdiff \| tree
2022-07-22	Ben Soares	JAL-4036 removing the query field code from the dropdown...	commit \| commitdiff \| tree
2022-07-21	Ben Soares	JAL-4036 Don't autosearch changing index when autosearch...	commit \| commitdiff \| tree
2022-07-21	Ben Soares	JAL-4036 add search fieldname to dropdown list	commit \| commitdiff \| tree
2022-07-21	Ben Soares	JAL-4036 removed often duplicated pluralisation in...	commit \| commitdiff \| tree
2022-07-21	Ben Soares	JAL-4036 New configuration, target and pagination process...	commit \| commitdiff \| tree
2022-07-15	Ben Soares	JAL-4034 Use the new non-modal JDialog for 3DBeacons...	commit \| commitdiff \| tree
2022-07-15	Ben Soares	JAL-4034 Allow request for non-modal JDialog, which...	commit \| commitdiff \| tree
2022-07-12	Ben Soares	JAL-4034 change to jalview property name	commit \| commitdiff \| tree
2022-07-12	Ben Soares	JAL-4034 showConfirmDialog works for both desktop and...	commit \| commitdiff \| tree
2022-07-11	Ben Soares	JAL-4034 Non-blocking 3D Beacons query after warning...	commit \| commitdiff \| tree
2022-07-11	Ben Soares	JAL-4034 allow a jalview_property to set the threshold...	commit \| commitdiff \| tree
2022-06-28	Ben Soares	Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQH...	commit \| commitdiff \| tree
2022-06-28	Ben Soares	JAL-1988 Don't put Quit in the File menu if there's...	commit \| commitdiff \| tree
2022-06-23	Ben Soares	Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQH...	commit \| commitdiff \| tree
2022-06-23	Ben Soares	JAL-1988 Check for setHandler capability to avoid About...	commit \| commitdiff \| tree
2022-06-13	Ben Soares	JAL-1988 Hack to ensure Quit dialog box is moved to...	commit \| commitdiff \| tree
2022-06-13	Ben Soares	JAL-4004 Fix missing whatsNew.html when not building...	commit \| commitdiff \| tree
2022-06-07	Ben Soares	JAL-4020 class formatting	commit \| commitdiff \| tree
2022-06-06	Ben Soares	JAL-4020 updated tests	commit \| commitdiff \| tree
2022-06-06	Ben Soares	JAL-4020 class reformatting	commit \| commitdiff \| tree
2022-05-12	Ben Soares	JAL-4014 4 gecos colour schemes added	commit \| commitdiff \| tree
2022-04-27	Ben Soares	JAL-1544 version number typo, probably copy and paste	commit \| commitdiff \| tree
2022-04-27	Ben Soares	JAL-3989 Populate template files for hugo build: archive...	commit \| commitdiff \| tree
2022-04-25	Ben Soares	JAL-3989 moved getdown build dirs to build/website...	commit \| commitdiff \| tree
2022-04-25	Ben Soares	JAL-3989 Independent creation of JSON installer sections	commit \| commitdiff \| tree
2022-04-21	Ben Soares	Merge branch 'develop' into merge/JAL-3978+JAL-3553...	commit \| commitdiff \| tree
2022-04-21	Ben Soares	Merge branch 'develop' into task/JAL-3991_check_actual_JAVA_...	commit \| commitdiff \| tree
2022-04-06	Ben Soares	JAL-3991 Made info displayed only when needed (Java...	commit \| commitdiff \| tree
2022-04-06	Ben Soares	JAL-3991 Added information output about the slightly...	commit \| commitdiff \| tree
2022-04-06	Ben Soares	JAL-3991 JAVA_COMPILE_VERSION put into build_properties...	commit \| commitdiff \| tree
2022-04-05	Ben Soares	JAL-3989 slight refactor of build.gradle, add more...	commit \| commitdiff \| tree
2022-04-04	Ben Soares	JAL-3989 fix a build date once in build.gradle, not...	commit \| commitdiff \| tree
2022-03-31	Ben Soares	Merge branch 'task/JAL-3553_improved_install4j_output_txt...	commit \| commitdiff \| tree
2022-03-31	Ben Soares	Merge branch 'develop' into improvement/JAL-3978_add_gradle_...	commit \| commitdiff \| tree
2022-03-30	Ben Soares	JAL-360 JAL-3975 make AlignFrame the parent of FeatureEditor...	commit \| commitdiff \| tree
2022-03-21	Ben Soares	JAL-3416 Updated FlatLaF to 2.1	commit \| commitdiff \| tree
2022-03-18	Ben Soares	JAL-3978 Using getdowninstanceappdir and getdowninstanceappb...	commit \| commitdiff \| tree
2022-03-18	Ben Soares	JAL-3978 Getdown add getdownappbase property to launched...	commit \| commitdiff \| tree
2022-03-18	Ben Soares	JAL-3978 New tasks to build archive 'old' dir with...	commit \| commitdiff \| tree
2022-03-16	Ben Soares	JAL-3978 task stub and getdown splash screens	commit \| commitdiff \| tree
2022-03-13	Ben Soares	Append git.hash and git.branch to RELEASE file stored...	commit \| commitdiff \| tree
2022-03-11	Ben Soares	JAL-3973 This fixes the gradle build when not in a...	commit \| commitdiff \| tree
2022-03-08	Ben Soares	JAL-3103 updated help doc to remove default browser...	commit \| commitdiff \| tree
2022-03-08	Ben Soares	JAL-3103 Removed code and unused widgets for defaultBrowser	commit \| commitdiff \| tree
2022-03-08	Ben Soares	JAL-3103 Remove BrowserLauncher2 and use Desktop.browse...	commit \| commitdiff \| tree
2022-03-08	Ben Soares	JAL-3103 add BrowserLauncher2 LGPLv2.1 to THIRDPARTYLIBS	commit \| commitdiff \| tree
2022-03-08	Ben Soares	JAL-3103 Put jalview.jar first in getdown for .properties...	commit \| commitdiff \| tree
2022-03-07	Ben Soares	JAL-3103 Switched to (a wrapper around) BrowserLauncher2	commit \| commitdiff \| tree
2022-03-04	Ben Soares	JAL-3830 added command line to whatsnew and releases	commit \| commitdiff \| tree
2022-03-04	Ben Soares	JAL-3830 Added new command line usage to docs	commit \| commitdiff \| tree
2022-03-04	Ben Soares	JAL-3608 added to LaF documentation	commit \| commitdiff \| tree
2022-03-03	Ben Soares	JAL-3830 fix broken/buggy install4j9 setting of executeSetup...	commit \| commitdiff \| tree
2022-03-02	Ben Soares	JAL-3691 bumped the version to 1.8.3-1.2.12 in source...	commit \| commitdiff \| tree
2022-03-02	Ben Soares	JAL-3962 Added jre/bin and dist folders to the native...	commit \| commitdiff \| tree
2022-03-02	Ben Soares	JAL-3130 updated download_jres.sh	commit \| commitdiff \| tree
2022-02-12	Ben Soares	JAL-3949 fix testProps path and make line count more...	commit \| commitdiff \| tree
2022-02-11	Ben Soares	Merge branch 'update/JAL-3949_jalview_bin_Console_to_cure_sa...	commit \| commitdiff \| tree
2022-02-11	Ben Soares	JLogger loglevel check on whether to call the actual...	commit \| commitdiff \| tree
2022-02-11	Ben Soares	JAL-3949 fixed failing commandlinetests due to more...	commit \| commitdiff \| tree
2022-02-11	Ben Soares	JAL-3949 added Java Console autoscrolling help paragraph	commit \| commitdiff \| tree
2022-02-11	Ben Soares	JAL-3949 read ~/.jalview_properties before initialising...	commit \| commitdiff \| tree
2022-02-11	Ben Soares	Merge branch 'develop' into update/JAL-3949_abstracted_loggi...	commit \| commitdiff \| tree
2022-02-11	Ben Soares	JAL-3949 Complete new abstracted logging framework...	commit \| commitdiff \| tree
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