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JAL-3438 spotless for 2.11.2.0

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JAL-3438 - all src and test run through spotless..

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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

  1. … 6 more files in changeset.
JAL-3763 refactored getCoveringMapping for virtual feature discovery

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JAL-3763 refactored getCoveringMapping for virtual feature discovery

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Merge branch 'releases/Release_2_11_1_Branch' into bug/JAL-3509hideResnum

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I suggest we close this. It's all ancient history now.

I suggest we close this. It's all ancient history now.

Merge branch 'Jalview-JS/develop' into develop

Conflicts:

build.gradle

src/jalview/gui/PopupMenu.java

src/jalview/io/SequenceAnnotationReport.java

src/jalview/io/StockholmFile.java

src/jalview/util/DBRefUtils.java

src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java

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changeset discussion

  1. Jim Procter: relevant issue is JAL-3626
JAL-367 code tidy

"Translated by Jalview"

"Translated by Jalview"

duplicate code here - will delete

duplicate code here - will delete

Not really imputation - suggest 'Translated by Jalview'

Not really imputation - suggest 'Translated by Jalview'

this is a little costly - could do it in one call ?

this is a little costly - could do it in one call ?

JAL-3567: Genomic position shown in virtual feature tooltip
JAL-3567: Genomic position shown in virtual feature tooltip
JAL-3567 report mapped location for virtual features in tooltip etc

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temp push

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3253-omnibus save

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JAL-3210 fudge for JalviewJS to avoid IntervalStore incompatibility

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Merge branch 'develop' into Jalview-JS/develop

Conflicts:

.gitignore

build.gradle

gradle.properties

src/jalview/gui/AlignFrame.java

src/jalview/gui/Desktop.java

src/jalview/gui/FeatureSettings.java

src/jalview/gui/JvSwingUtils.java

src/jalview/util/MessageManager.java

test/jalview/gui/AlignmentPanelTest.java

test/jalview/gui/JvSwingUtilsTest.java

test/jalview/gui/PopupMenuTest.java

utils/eclipse/org.eclipse.jdt.core.jalview.prefs

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JAL-3253 temporary branch SwingJS upgrade with testNG fixes Java 8

  1. … 51 more files in changeset.
JAL-3560 tweak to force use of standard Java HashSet

adds Platform.getOrderedHashSet()

adds Platform.setJavaScriptMapObjectEnabled(boolean enabled)

sets the results from SequenceFeatures.getFeatureTypesForGroups(...) to

be a standard Java HashSet, not using the JavaScript Map object.

  1. … 11 more files in changeset.
JAL-3187 unit test for findComplementFeaturesAtResidue

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Couldn't you just move fr.featuresAdded() to here ?

Couldn't you just move fr.featuresAdded() to here ?

if this is public, there's a risk of recursive notifications. Probably want the 'firing' state conditional moved to here.

if this is public, there's a risk of recursive notifications. Probably want the 'firing' state conditional moved to here.

The semantics are unclear for isFeatureDisplayed .. e.g. if isFeatureDisplayed==false then does the caller then have to call isFeatureHidden to check visiblity ?

The semantics are unclear for isFeatureDisplayed .. e.g. if isFeatureDisplayed==false then does the caller then have to call isFeatureHidden to check visiblity ?