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JAL-345 add to AlignViewController API and define a keystroke listener following same modifiers as select highlighted columns

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JAL-345 invert logic is not quite right - REVISE THIS!

JAL-345 also include any sequences that have highlighted regions

JAL-345 view controller method to select highlighted sequences (note - doesn’t select sequences which contain search results, just ID highlights)

JAL-345 refactor list of sequences that are highlighted from Id Canvas to Alignment Viewport

Merge branch 'merge/JAL-3091_JAL-3111_develop_211' into develop

JAL-3112 increased TEST_TIMEOUT to 9000ms - needed after inclusion discovered class path entries

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JAL-3112 Use classgraph to reconstruct the classpath for launching Jalview

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    • binary
Merge branch 'merge/JAL-3091_JAL-3111_develop_211' into develop

JAL-3111 drop hts-1.33 as a dependency (in favour of htsjdk-2.12)

Merge branch 'merge/JAL-3091_JAL-3111_develop_211' into develop

Merge branch 'releases/Release_2_11_Branch' into merge/JAL-3091_develop_211

Merge branch 'develop' into releases/Release_2_11_Branch JAL-3091 bring 2.11 onto release 2.10.5 to simplify merge

JAL-3091 changed release date to 10th September - tweaked release notes.

JAL-3106 normalise extension before checking if it is '.jar' when constructing fileformat/extension name index

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JAL-3107 update any group associated annotation rows when a new group is created

JAL-2988 JAL-2968 renamed patched VAqua5 to VAqua5-patch.jar and documented patch along with instructions for rebuilding the jar

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    • binary
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JAL-2988 if selected file is null (On Java 10/OSX - happens if user has entered text after selecting a file), try and get the filename from the UI. If no file can be gotten, cancel the save operation

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JAL-2988 workaround: overload getSelectedFile() because calling setSelectedFile(..) results in getSelectedFile()==null on OSX/Java 10/VAqua4/5.

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JAL-3106 use .jvp as default

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JAL-3105 fix for focus transfer after window closed on OSX

JAL-3091 code committed in error (failed patch for JAL-2854)

JAL-3091 release notes for JAL-3104

JAL-3105 reallocate quality and consensus annotation rows so old values aren’t rendered when alignments become shorter

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JAL-2854 compute visible annotation panel height and provide it directly to via Scrollable interface

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JAL-3065 don’t quote class path args for Runtime.exec java launch command (needs to be ported to 2.11)

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JAL-3091 update whats new!

JAL-3091 update Java 10 known issues/workarounds in whats new

JAL-3091 known defect in whats new for Java 10 issues: JAL-3103 JAL-3102

JAL-3091 add Ben Soares to authors list and switch ordering of Toch and Kira (since Kira left after Toch).