Messages.properties

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

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JAL-3685 Fixed single quotes in formatMessage messages

JAL-3628 Fixed oddly worded and non-formatted error popups when saving fails

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JAL-3628 Fixed oddly worded and non-formatted error popups when saving fails

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JAL-3311 JAL-3141 JAL-3144 tidying obsolete message bundle entries

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JAL-3676 Added Log Level ComboBox and Copy to Clipboard button in Java Console

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JAL-3676 Added Log Level ComboBox and Copy to Clipboard button in Java Console

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Merge branch 'bug/JAL-3490findSpanHiddenGaps' into patch/Release_2_11_1_Branch_patch_JAL-3490

Conflicts:

resources/lang/Messages.properties

resources/lang/Messages_es.properties

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Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure

Conflicts:

gradle.properties

resources/lang/Messages.properties

resources/lang/Messages_es.properties

src/jalview/api/structures/JalviewStructureDisplayI.java

src/jalview/appletgui/AppletJmol.java

src/jalview/ext/jmol/JalviewJmolBinding.java

src/jalview/ext/jmol/JmolCommands.java

src/jalview/ext/rbvi/chimera/AtomSpecModel.java

src/jalview/ext/rbvi/chimera/ChimeraCommands.java

src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java

src/jalview/gui/AlignFrame.java

src/jalview/gui/AlignmentPanel.java

src/jalview/gui/AppJmol.java

src/jalview/gui/ChimeraViewFrame.java

src/jalview/gui/JalviewChimeraBindingModel.java

src/jalview/gui/StructureViewerBase.java

src/jalview/structures/models/AAStructureBindingModel.java

test/jalview/ext/jmol/JmolCommandsTest.java

test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java

test/jalview/structures/models/AAStructureBindingModelTest.java

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JAL-3551 copy Jalview features to Pymol 'p' (with pull refactoring)

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Merge branch 'develop' into feature/JAL-3551Pymol

Conflicts:

src/jalview/ext/jmol/JalviewJmolBinding.java

src/jalview/ext/jmol/JmolCommands.java

src/jalview/gui/AppJmol.java

src/jalview/gui/AppJmolBinding.java

src/jalview/gui/ChimeraViewFrame.java

src/jalview/gui/StructureViewerBase.java

src/jalview/jbgui/GPreferences.java

src/jalview/jbgui/GStructureViewer.java

src/jalview/project/Jalview2XML.java

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