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Merge branch 'merge/develop_JAL-3725' into develop

Conflicts:

src/jalview/gui/PopupMenu.java

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Merge branch 'bug/JAL-3633_read_proxy_settings_from_jalview_properties_in_getdown' into develop

Conflicts:

src/jalview/bin/MemorySetting.java

  1. … 8 more files in changeset.
Merge branch 'task/JAL-3763_newDatasetForCds' into merge/develop_task/JAL-3763_newDatasetForCds

Conflicts:

src/jalview/analysis/AlignmentUtils.java

src/jalview/util/MapList.java

test/jalview/util/MapListTest.java

test/jalview/util/MappingUtilsTest.java

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JAL-3878 Create backbone for new web services

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JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and added import java.util.Locale appropriately

  1. … 96 more files in changeset.
Merge branch 'Jalview-JS/bug/JAL-3762_URLparamsOverrideInfoArg' into develop

JAL-3829 JalviewJS workarounds/patches

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patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

patch needed for 2.11.2 - JAL-3518 - catch case when no replies are available

semantics for determining if a PDB file has a SIFTs mapping - could be absorbed into the PDB metadata object

semantics for determining if a PDB file has a SIFTs mapping - could be absorbed into the PDB metadata object

magic logic to recognise which structure database provider client to use - PDB or AlphaFold - ensures metadata and annotation rows are propagates

magic logic to recognise which structure database provider client to use - PDB or AlphaFold - ensures metadata and annotation rows are propagates

Reviewing the alphafold + contact matrix patch for 2.11.2
Reviewing the alphafold + contact matrix patch for 2.11.2
JAL-3855 convenience method to check a URL will return a 200

JAL-3633 refactored/simplified LaunchUtils code

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JAL-3503 Added a Startup tab in Preferences, with gui for JVMMEMMAX and JVMMEMPC settings. Allowed jalview.bin.Launcher and getdown to read/use these memory settings at launch. Added channel.props to getdown appdir, used to determing correct .jalview_properties file. Refactored MemorySetting a bit, with more helper methods for the Preferences tab.

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JAL-3594 Allow a channel to use a different preferences file than .jalview_properties, with initial read from .jalview_properties

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Revert "Merge branch 'bug/JAL-3806_mappingCoversSequence' into releases/Release_2_11_1_Branch"

This reverts commit cb628aab46f9027e71b71203b322f96710e09990, reversing

changes made to a40669b2eeb34a6c760b63c172a31a194b456f24.

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JAL-3806 fix and test for one-to-many sequence mapping case

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JAL-3878 Initial preparation.

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JAL-3794 X and N are counted as DNA characters, but we also check how many Ns - if there were no real nucleotide characters we always return protein for poly-asparagine

JAL-3794 X and N are counted as DNA characters, but we also check how many Ns - if there were no real nucleotide characters we always return protein for poly-asparagine

JAL-3761 more consistent parameter naming

JAL-3761 more consistent parameter naming

Merge branch 'Jalview-JS/develop' into merge_js_develop also patched new code from JAL-3690 refactorings

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JAL-3594 Adjustments to allow JalviewJS to use ChannelProperties, and new utils/channels dir for jalviewjs and jalviewjs-release

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JAL-3594 Images for splash screen

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JAL-3594 JAL-3728 Added taskbar icons to desktop and Java console. Changed "Jalview" to "app_name" in various appropriate places

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JAL-3594 added BG logo. Changed some named Jalviews to app_name property. Added test-release and default channels.

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JAL-3594 Default values for channel properties defined in code as fallback

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Agreed. I seem to remember (this was a while ago now) that I found isAMacAndNotJS() and thought it might be an important distinction. Sounds like it's just redundant? Can tidy this another time then.

Agreed. I seem to remember (this was a while ago now) that I found isAMacAndNotJS() and thought it might be an important distinction. Sounds like it's just redundant? Can tidy this another time then.