Messages.properties

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Merge branch 'develop' into features/JAL-2909_bamImport_2_11_2

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JAL-3616 show name of structure viewer in ‘new view’ button

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JAL-3829 fetch 3D beacons now started by clicking button shown above the drop-down filter/manual input combo box.

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JAL-2909 mininal merge of bam import demo to Jalview 2.11.2 develop Merge remote-tracking branch 'origin/features/JAL-2909_bamImport2_11' into features/JAL-2909_bamImport_2_11_2

Conflicts:

src/jalview/io/AlignmentFileReaderI.java

src/jalview/io/AppletFormatAdapter.java

src/jalview/io/FileFormat.java

src/jalview/io/FileLoader.java

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JAL-3829 report when 3d-beacons doesn’t provide any models

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JAL-3829 alternative UX: need to select 3d-beacons from dropdown if db-refs need to be fetched

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JAL-3829 do better at detecting structure type, prompt to retrieve Uniprot ids for proteins without canonical Ids and show provider in the Structure Chooser’s cache view

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JAL-3774 combined changes from bug/JAL-3774_splitFrameFinder: i) fixed focus Finder from split frame. ii) missing i18n added, overlong translation shortened. iii) better translation.

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JAL-3739 (combined) commits from feature/JAL-3739_useFormFieldText

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JAL-3503 Added a Startup tab in Preferences, with gui for JVMMEMMAX and JVMMEMPC settings. Allowed jalview.bin.Launcher and getdown to read/use these memory settings at launch. Added channel.props to getdown appdir, used to determing correct .jalview_properties file. Refactored MemorySetting a bit, with more helper methods for the Preferences tab.

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Merge branch 'feature/JAL-3692enaEndpoint' into patch/for2.11.2/JAL-3821_ena_rna_moltype

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JAL-3739 catch parameter errors and report to the user

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JAL-3774 missing i18n added, overlong translation shortened

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JAL-3774 fixed focus Finder from split frame

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JAL-3719 Format->Colour Gaps option uses Overview gap colour logic pulled up to alignment viewport sequence renderer

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JAL-3719 Format->Colour Gaps option uses Overview gap colour logic pulled up to alignment viewport sequence renderer Conflicts: resources/lang/Messages.properties resources/lang/Messages_es.properties

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JAL-3490 merged with 2.11.2 develop

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Merge branch 'patch/Release_2_11_1_Branch_patch_JAL-3490' into releases/Release_2_11_1_Branch

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JAL-3676 More explicit tooltip about resetting log level on Console close. Also clarified code to set initial log level and re-set on close to previously set level.

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JAL-3676 More explicit tooltip about resetting log level on Console close. Also clarified code to set initial log level and re-set on close to previously set level.

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Merge branch 'merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch' into releases/Release_2_11_1_Branch

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JAL-3633 Memory only proxy auth password storage. Open Preferences->Connection tab when proxy password needed

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JAL-3633 Memory only proxy auth password storage. Open Preferences->Connection tab when proxy password needed

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JAL-3633 Added Preferences for Proxy Authentication. No jalview_properties yet

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JAL-3633 Added Preferences for Proxy Authentication. No jalview_properties yet

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JAL-3633 label.proxy_server -> label.proxy_servers

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JAL-3633 label.proxy_server -> label.proxy_servers

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JAL-3692 EMBL flatfile fetcher / parser (todo: CDS dbrefs and mappings)

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JAL-3692 EMBL flatfile fetcher / parser (todo: CDS dbrefs and mappings) Conflicts: src/jalview/ws/dbsources/EmblXmlSource.java src/jalview/ws/ebi/EBIFetchClient.java

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JAL-3633 Remember system set proxy properties. Add options in Preferences for No proxy, system proxy, or custom proxy servers.

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