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JAL-3383 JAL-3397 JAL-3253-applet IntervalStore options
authorhansonr <hansonr@STO24954W.ad.stolaf.edu>
Tue, 6 Aug 2019 21:25:13 +0000 (16:25 -0500)
committerhansonr <hansonr@STO24954W.ad.stolaf.edu>
Tue, 6 Aug 2019 21:25:13 +0000 (16:25 -0500)
commit0031ee4b6a42ad328e417cb65c7a840183e62e87
tree6e2e0c754fc31c48c2dd4c3e0d4e7888c59c2b29tree | snapshot
parente6b6f08502b7a31b22ae18e31c4ada1dba58be54commit | diff
JAL-3383 JAL-3397 JAL-3253-applet IntervalStore options

In SequenceFeatures:

INTERVAL_STORE_NCLIST  (default for Java)
 - no changes from previous

 INTERVAL_STORE_NONCLIST (Java option)
 - uses intervalstore.nonc.IntervalStore
 - optional "lazy" just-in-time sorting
 - passes the following TestNG tests:

IntervalStoreJ.test.intervalstore.nonc...
NoNCListBuilderTest.java
NoNCListIntervalIteratorTest.java
NoNCListIntervalStoreTest.java
NoNCListIntervalTest.java
NoNCListLoadTest.java
NoNCListRandomisedTest.java
NoNCListTimingTests.java

test.jalview.datamodel.features...
FeatureStoreNoNCTest.java
FeatureStoreJSTest.java
SequenceFeaturesTest.java
17 files changed:
src/intervalstore/api/IntervalI.java [new file with mode: 0644] blob
src/intervalstore/api/IntervalStoreI.java [new file with mode: 0644] blob
src/intervalstore/nonc/IntervalComparator.java [new file with mode: 0644] blob
src/intervalstore/nonc/IntervalStore.java [new file with mode: 0644] blob
src/jalview/datamodel/Sequence.java diff | blob | history
src/jalview/datamodel/SequenceFeature.java diff | blob | history
src/jalview/datamodel/features/FeatureStore.java diff | blob | history
src/jalview/datamodel/features/FeatureStoreImpl.java diff | blob | history
src/jalview/datamodel/features/FeatureStoreJS.java diff | blob | history
src/jalview/datamodel/features/SequenceFeatures.java diff | blob | history
src/jalview/io/FileLoader.java diff | blob | history
src/jalview/io/vamsas/Sequencefeature.java diff | blob | history
src/jalview/project/Jalview2XML.java diff | blob | history
test/jalview/datamodel/features/FeatureStoreNoNCTest.java [new file with mode: 0644] blob
unused/nonc/IntervalI.java [new file with mode: 0644] blob
unused/nonc/IntervalStore.java [new file with mode: 0644] blob
unused/nonc/IntervalStoreI.java [new file with mode: 0644] blob