jalview

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Merge branch 'develop' into task/JAL-3991_check_actual_JAVA_VERSION_against_build_properties_in_application_startup

JAL-3992 bump version and report updates in 2.11.2.2 release notes

Merge branch 'bug/JAL-3997_NPE_in_wrapped_mode' into develop

Merge branch 'bug/JAL-3365_extendedDSSP_via_stockholm' into develop

JAL-3997 check for tooltip being null before checking equivalence to last tooltip string

Merge branch 'task/JAL-3992_update_docs' into bug/JAL-3365_extendedDSSP_via_stockholm

JAL-3992 fix path

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    /help/help/html/features/cursorMode.html
JAL-3365 expand range of allowed DSSP secondary structure symbols in Stockholm files

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    • +12
    /test/jalview/io/StockholmFileTest.java
JAL-3992 shift+arrow to jump to next gap/residue in cursor/keyboard editing mode

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    /help/help/html/features/cursorMode.html
JAL-3991 Made info displayed only when needed (Java 11+)

JAL-3991 Added information output about the slightly alarming 'WARNING: An illegal reflective access operation has occurred' error that occurs for linux users. It can't be avoided so informing the user should help with alarm levels.

JAL-3991 JAVA_COMPILE_VERSION put into build_properties. Check for possible JVM mismatch in jalview.bin.LaunchUtils. STDERR warning from jalview.bin.Launcher. Console and optional popup warning in jalview.bin.Jalview.

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    • +4
    /resources/lang/Messages_es.properties
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    • +113
    /src/jalview/util/LaunchUtils.java
Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3990 release notes and what’s new

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3981 patch tests and remove errant imports

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3990 gradle spotlessApply

JAL-3990 release notes for 2.11.2.1 patch release

Merge branch 'bug/JAL-3980_JAL-3981_tooltips_sequence_details' into develop

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3983 release note for JAL-3985

Merge branch 'bug/JAL-3085_avoid_414_error_for_PDBFTS' into develop

JAL-3085 update tests and mock responses, new P0dtd1 testcase

JAL-3985 formatting

JAL-3985 split PDB id queries into multiple queries so server doesn’t 414

Merge branch 'patch/JAL-3976_3dbeaconsnull' into develop

JAL-3976 fix mock PDBFTS query & responses

JAL-3983 known issue note for JAL-3984

JAL-3983 release notes for JAL-3975 and known issue note for JAL-3984