THIRDPARTYLIBS

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JAL-3874 - replace Jmol with custom build of 14.31.53 from Jmol-SwingJS GitHub repo

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THIRDPARTYLIBS referred to intervalstore-v1.0 still

JAL-3252 tgz unpacking no longer needed by getdown. Unfinished code and dependency on apache-commons-compress removed. Documentation mentioning common-compress updated.

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JAL-3210 Barebones gradle/buildship/eclipse. See README

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JAL-3337 Tidied up j8libs in THIRDPARTYLIBS. Replaced jersey-*-1.19.jar with jersey-*-1.19.4.jar in j8lib. Removed lib/ folder from sourceDist. Added instructions for running testNG with a specific group of tests to building.md

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JAL-3337 Updated the j11lib jars (don't need to be converted to modules) that aren't in j8libs. Added licensing information for these jars to THIRDPARTYLIBS.

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JAL-3337 starting to add to THIRDPARTYLIBS

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Can remove class Jalview$FeatureFetcher.

Can remove class Jalview$FeatureFetcher.

JAL-3035 removed spring libraries as only used for jdas

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Were added 2012 commit 3d37b44 "jdas runtime dependencies". All classes in jars are org.springframework.*, no longer referenced in any source code in Jalview. I will remove from classpath and THIRD...

Were added 2012 commit 3d37b44 "jdas runtime dependencies".
All classes in jars are org.springframework.*, no longer referenced in any source code in Jalview.
I will remove from classpath and THIRDPARTYLIBS.

yeah. probably.

yeah. probably.

I tried removing these (Spring jars) and Jalview seemed to function ok. Can they go?

I tried removing these (Spring jars) and Jalview seemed to function ok. Can they go?

promote classgraph to desktop dependency

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JAL-3112 Use classgraph to reconstruct the classpath for launching Jalview

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JAL-3111 drop hts-1.33 as a dependency (in favour of htsjdk-2.12)

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Merge branch 'develop' into releases/Release_2_11_Branch JAL-3091 bring 2.11 onto release 2.10.5 to simplify merge

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JAL-2988 JAL-2968 renamed patched VAqua5 to VAqua5-patch.jar and documented patch along with instructions for rebuilding the jar

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JAL-2988 JAL-2976 update to latest VAqua release: VAqua5

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update spikes/mungo from JAL-3076 patch branch

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

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

could remove above comment

could remove above comment

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

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

Also remove GDasSourceBrowser

Also remove GDasSourceBrowser

remove above 3 fields

remove above 3 fields

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).

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).

remove -dasserver line

remove -dasserver line

remove variable

remove variable

remove the above block and methods checkDasArguments, startFeatureFetching.

remove the above block and methods checkDasArguments, startFeatureFetching.

remove DAS constants

remove DAS constants

can remove DAS_REGISTRY_URL and DAS_ACTIVE_SOURCE

can remove DAS_REGISTRY_URL and DAS_ACTIVE_SOURCE