jalview

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JAL-3349 Remove processed args from list to send to jalview

JAL-3349 Added a prefix for cli args to getdown that get turned into JVM args for Jalview. Also a -jvmmempc lookup

JAL-3348 prepping getdown to pass JVM command line args

JAL-3111 fix broken helpTOC link

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

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

JAL-3111 release date now 4th July 2019 - codename 'bastille'

Merge branch 'documentation/JAL-3111_release_211' into develop

JAL-3111 formatting

JAL-3111 new known defect from JAL-797

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

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    /help/help/html/features/importvcf.html
JAL-3322 increase concurrent downloads in getdown

JAL-3333 removed unused variable

JAL-3322 getdown jars with network timeouts applied

JAL-3332 Sensible default timeout values for network connections (8s connect_timeout, 15s read_timeout)

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JAL-3333 using floats for smoother weighting

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    /src/jalview/gui/WebserviceInfo.java
JAL-3333 Sorry couldn't resist adding a bit of weighting to the rotation

JAL-3333 Title text now appears instantly. Altering speed of rotating logo depending on queuing or running status. Rotating logo now 'parks' rather than jumps at completion.

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    /src/jalview/gui/WebserviceInfo.java
Merge branch 'bug/JAL-3333_Blurry_fonts_in_WebServiceInfo_window_title_in_macOS_mojave' into develop

Merging in simple change from transparent image to white background and removing alpha channel in image model.

JAL-3333 changed RGB model. Tested in mojave and Windows (works)

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    /resources/images/Jalview_Logo_small_with_border.png
JAL-3111 release notes for JAL-3330 JAL-3021 (tweak) and JAL-3333

Merge branch 'bug/JAL-3333_Blurry_fonts_in_WebServiceInfo_window_title_in_macOS_mojave' into develop

JAL-3111 release notes for JAL-2820 JAL-2207

JAL-3111 backed out report of fix to JAL-3178 in release notes - since not fixed for 2.11

JAL-3333 Smooth rotation of image now too

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    /resources/images/Jalview_Logo_small_with_border.png
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    /src/jalview/gui/WebserviceInfo.java
Merge branch 'documentation/JAL-3111_release_211' into develop

JAL-3111 final release date for 2.11.0

JAL-3333 added height to rotating image preferred size