JAL-3035: Remove dependency on jdas client library

Activity

CR-JAL-166 17

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    Participant Role Time Spent Comments Latest Comment
    Author 26m 1 yeah. probably.
    Reviewer - 100% reviewed 31m 16 Can remove class Jalview$FeatureFetcher.
    Total   57m 17  
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    Objectives

    the protocol formerly known as BioDAS is no more.

    Branches in review

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    Issues Raised From Comments

    Key Summary State Assignee
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    General Comments

    Mungo Carstairs

    Are we ok with also removing the capability of hosting a local DAS source wit...

    Are we ok with also removing the capability of hosting a local DAS source with this change?

    Mungo Carstairs

    AlignFrame.build_fetchdbmenu has a branch of code which I think is no longer ...

    AlignFrame.build_fetchdbmenu has a branch of code which I think is no longer hit and could be removed?
    Lines 5115 - 5243 (case otherdb.size() > 1).

    Mungo Carstairs

    Run MessageBundleChecker to show 25 entries that can now be removed from Mess...

    Run MessageBundleChecker to show 25 entries that can now be removed from Messages(_es).properties.

    Mungo Carstairs

    jalview.util.DBRefUtils - can remove dasCoordinateSystemsLookup and (unused) ...

    jalview.util.DBRefUtils - can remove dasCoordinateSystemsLookup and (unused) isDasCoordinateSystem

    Mungo Carstairs

    Can remove class Jalview$FeatureFetcher.

    Can remove class Jalview$FeatureFetcher.

    /help/html/features/clarguments.html Changed
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    /help/html/features/dasfeatures.html Deleted
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    /help/html/features/dassettings.html Deleted
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    /help/html/features/preferences.html Changed
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    /help/html/features/seqfeatures.html Changed
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    /help/html/features/seqfetch.html Changed
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    /help/html/menus/alignmentMenu.html Changed
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    /help/html/menus/alwview.html Changed
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    /help/html/menus/wsmenu.html Changed
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    /help/html/webServices/dbreffetcher.html Changed
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    /help/html/webServices/index.html Changed
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    /help/html/releases.html Changed
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    /help/help.jhm Changed
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    /help/helpTOC.xml Changed
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    /lib/jdas-1.0.4.jar Deleted
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    /src/jalview/bin/Cache.java Changed 3
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    /src/jalview/bin/Cache.java Changed
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    /src/jalview/bin/Jalview.java Changed 3
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    /src/jalview/bin/Jalview.java Changed
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    /src/jalview/gui/DasSourceBrowser.java Deleted 1
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    /src/jalview/gui/FeatureSettings.java Changed 1
    /src/jalview/gui/JDatabaseTree.java Changed
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    /src/jalview/gui/Preferences.java Changed
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    /src/jalview/gui/SequenceFetcher.java Changed
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    /src/jalview/gui/SequenceFetcher.java Changed
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    /src/jalview/jbgui/GPreferences.java Changed
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    /src/jalview/.../api/DasSourceRegistryI.java Deleted
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    /src/jalview/.../das/api/jalviewSourceI.java Deleted
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    /src/.../datamodel/DasSequenceSource.java Deleted
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    /src/.../datamodel/DasSourceRegistry.java Deleted
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    /src/jalview/.../datamodel/JalviewSource.java Deleted
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    /src/jalview/ws/DBRefFetcher.java Changed 1
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    /src/.../ws/DasSequenceFeatureFetcher.java Deleted
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    /src/jalview/ws/SequenceFetcher.java Changed
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    /test/jalview/analysis/CrossRefTest.java Changed
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    /test/.../dbsources/RemoteFormatTest.java Changed
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    /test/.../seqfetcher/DasSequenceFetcher.java Deleted
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    /test/.../ws/PDBSequenceFetcherTest.java Changed
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    /test/jalview/ws/SequenceFetcherTest.java Changed
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    /.classpath Changed
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    /.classpath.js Changed
    /RELEASE Changed
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    /THIRDPARTYLIBS Changed 3
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    /nbbuild.xml Changed
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