jalview

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JAL-3210 testing

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JAL-3362 keep Java 1.8 build happy by specifying generic type arguments

Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into merge-212

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JAL-3210 test commit

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JAL-3210 updating. no test

JAL-3210 updating. no test

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JAL-3235 isolated the 'unsafe' override of entrySet to the saveProperties method, since we only need ordered output on save

JAL-2987 release notes

JAL-3407 update RELEASE and cut new release notes in releaseHistory.html

JAL-3407 JAL-3406 update credits in Jalview 2.11.1

JAL-3404 fix up test compilation errors

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
JAL-3404 explicit getModelForPdbFile lookup

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JAL-3990 fix typo in showStructures command for Chimera

JAL-3390 refactoring tidy of colourBySequence call stack

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JAL-3187 removal of variant feature (non-virtual) transfer to protein

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JAL-3390 move StructureCommands to utils package

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JAL-3390 improved Jmol colour by sequence command + tests + deprecations

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JAL-3210 ben testing

JAL-3210 ben testing

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JAL-3210 ben testing

JAL-3210 ben testing

JAL-3403 Fit To Window menu item for Jmol

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JAL-3390 StructureCommands atomspec helper, corrected Jmol atomspec/test

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JAL-3210 ben testing

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JAL-3210 ben testing

JAL-3210 ben testing

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JAL-3210 ben testing

JAL-3210 ben testing

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JAL-3402 suppress unmapped chains in View Chain menu

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JAL-3400 include sequence name in View | Show Chain menu

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