help.jhm

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JAL-4014 4 gecos colour schemes added to help documentation

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JAL-3608 JAL-3830 tweaked the what’s new text and updated helpTOC

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JAL-3746 more what’s new and release notes

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JAL-3503 2.11.2.0 release notes and docs

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JAL-3551 pymol docs - work in progress

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JAL-3741 http to https (and jar to jvp for exampleFile defaults!) Conflicts: src/jalview/bin/Jalview.java src/jalview/gui/Desktop.java

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JAL-3676 Documentation in Help for Java Console, Logging and Reporting Bugs

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Merge branch 'develop' into alpha/JAL-3362_Jalview_212_alpha update for 2.11.1 release

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JAL-3567 JAL-3407 document sequence features report and the additional info provided for virtual features. Also bumped release date to 22st April

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JAL-3407 JAL-3187 help documentation for virtual features and tabbed feature settings for linked cds/protein views

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JAL-3376 documentation for standard attributes for variants from VCF

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Merge branch 'merge/JAL-3285_mchmmer_with_211_develop' into alpha/JAL-3362_Jalview_212_alpha

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JAL-3111 JAL-3348 JVL file documentation

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Merge branch 'develop' into tasks/JAL-3311_removeVamsasMenu

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JAL-3111 whats new and JAL-2738 JAL-2743 expanded help documentation for VCF

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JAL-3311 remove menus and documentation relating to VAMSAS - dead code will be backed out in later jalview releases.

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Merge branch 'develop' into developtomchmmer JAL-3285 merged 2.11 develop into the features/mchmmer branch - need to fix code for migration from Castor to JAXB - need to check Stockholm file IO and tests Good luck !

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JAL-3224 JAL-3225 Fixed help image mangling, moved help to help/help and added this in to eclipse classpath generation

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