help.jhm

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

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Can remove class Jalview$FeatureFetcher.

Can remove class Jalview$FeatureFetcher.

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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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?

Merge remote-tracking branch 'origin/features/JAL-2814ftsHelp' into merge/JAL-2814

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update spikes/mungo from JAL-3076 patch branch

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Merge branch 'features/mchmmer' into merge/wsinterfaces_mchmmer_JAL-3070_JAL-1950 merging refactored wsui with mchmmer to get latest service parameters goodness.

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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

can remove this

can remove this

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

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

JAL-3035: Remove dependency on jdas client library
JAL-3035: Remove dependency on jdas client library
JAL-3032 just the changes pulled already

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JAL-3035 remove DAS UI documentation

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Update spike branch to latest (HMMSearch file chooser arg)

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Merge branch 'develop' into features/mchmmer

Conflicts:

src/jalview/bin/Jalview.java

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JAL-2895 replace $$Jalview-Version$$ in help.jhm with build version when indexing built in help pages

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JAL-2814 help links from PDB and Uniprot FTS panels

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JAL-2629 update spike branch to latest

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