jalview

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JAL-3210 ben testing

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    /swingjs/SwingJS-site.zip-dist
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    /swingjs/net.sf.j2s.core-3.2.4.jar
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    /swingjs/net.sf.j2s.core.jar-dist
JAL-3210 ben testing

JAL-3210 ben testing

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    /.settings/org.eclipse.jdt.core.prefs
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    /j11lib/Jmol-14.29.17-no_netscape.jar
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    /utils/publishHelp.xml
JAL-3402 suppress unmapped chains in View Chain menu

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    /src/jalview/gui/StructureViewerBase.java
JAL-3400 include sequence name in View | Show Chain menu

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/gui/StructureViewerBase.java
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    /src/jalview/jbgui/GStructureViewer.java
JAL-3401 JAL-3253-applet

fixes too-early multiple calls to AlignPanel.repaint() and, via repaint

manager to the desktop, also SeqCanvas.paintComponent. See

Jalview2XML.java

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    /src/jalview/gui/AlignmentPanel.java
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    /src/jalview/project/Jalview2XML.java
Platform.timeCheck - just resetting duration for reset/set-mark..set-mark/get sequence.

JAL-3383 JAL-3253-applet shortcut binary search when position is out of range.

JAL-3390 showSelectedChains pulled up to base class for Jmol/Chimera

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/gui/ChimeraViewFrame.java
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    /src/jalview/gui/StructureViewerBase.java
Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure

Conflicts:

resources/lang/Messages.properties

resources/lang/Messages_es.properties

src/jalview/ext/rbvi/chimera/ChimeraCommands.java

test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java

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    /resources/lang/Messages_es.properties
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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
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    /utils/testnglibs/testng-sources.jar
JAL-3187 (fudge) look in both alignments for stored mappings

Merge branch 'develop' into feature/JAL-3187linkedFeatures

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

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    /src/intervalstore/api/IntervalI.java
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    /src/intervalstore/api/IntervalStoreI.java
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    /src/intervalstore/nonc/IntervalComparator.java
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    /src/intervalstore/nonc/IntervalStore.java
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    /src/jalview/datamodel/features/FeatureStoreJS.java
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    /src/jalview/io/vamsas/Sequencefeature.java
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    /unused/nonc/IntervalI.java
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    /unused/nonc/IntervalStore.java
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    /unused/nonc/IntervalStoreI.java
JAL-3253-applet comments/Overrides only

JAL-3390 first pass refactoring for JalviewJmolBinding.showStructures

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    /src/jalview/appletgui/AppletJmol.java
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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/ext/jmol/JmolCommands.java
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    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
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    /src/jalview/gui/StructureViewerBase.java
JAL-3210 updating gradle files

JAL-3390 pull up of getShownResidues() to AAStructureBindingModel

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    /src/jalview/ext/rbvi/chimera/AtomSpecModel.java
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    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
JAL-3390 redraw structures if alignment only and hidden regions change

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    /src/jalview/gui/StructureViewerBase.java
JAL-3383 JAL-3253-applet

-adds timing test reports.

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    /temp/timing-IntervalStore.txt
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    /temp/timing-noIntervalStore.txt
JAL-3390 new View menu option to hide hidden regions in structure

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    /resources/lang/Messages_es.properties
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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/ext/jmol/JmolCommands.java
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    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
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    /src/jalview/gui/StructureViewerBase.java
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    /src/jalview/jbgui/GStructureViewer.java
JAL-3383 JAL-3253-applet

-adds equivalent of features.contains()

-timing within 0.5 sec for braf.jvp load of human variants.

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    /src/jalview/datamodel/features/FeatureStoreJS.java
JAL-3390 Chimera showStructures() respects visible/chain selections

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    /src/jalview/appletgui/AppletJmol.java
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    /src/jalview/ext/jmol/JalviewJmolBinding.java
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    /src/jalview/gui/ChimeraViewFrame.java
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    /src/jalview/gui/StructureViewerBase.java
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    /src/jalview/jbgui/GStructureViewer.java
JAL-3390 pull-up refactoring towards functional changes...

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    /src/jalview/api/AlignmentViewPanel.java
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    /src/jalview/gui/AppJmolBinding.java
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    /src/jalview/gui/ChimeraViewFrame.java
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    /src/jalview/gui/StructureViewerBase.java
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    /src/jalview/gui/ViewSelectionMenu.java
JAL-3383 JAL-3253-applet

possibly a bit faster as a static reference to the Function.

JAL-3383 JAL-3253-applet

-- Dissociates IntervalStore and BinarySearch from FeatureStoreJS.

-- Adds test FeatureStoreJS

-- cursory timing test in TestNG suggest JS version is 2x faster in

*Java* (TestNG FeatureStoreTest 120 ms vs. FeatueStoreJSTest 66 ms) for

default test.

-- hypothesize that overhead of lambda functions is coming into play

here. Needs a more heavy-duty test.

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    /src/jalview/datamodel/features/FeatureStore.java
JAL-3383 JAL-3253-applet

-- Adds FileStoreI interface

-- Makes FileStore.java abstract superclass for FileStoreImpl (for Java)

and FileStoreJS (for JavaScript)

-- Passing all FeatureStoreJSTest TestNG tests

-- Passing all SequenceFeatureTest TestNG tests

-- About 10% faster for Java on TestNG tests.

-- full rendering in < 250 ms for JavaScript -- this is approximately 15

times faster than before I started this experiment.

Platform: timer mark 13.396 0.209 overviewrender 16000 pixels row:14 redraw:false

Platform: timer mark 14.884 0.186 overviewrender 16000 pixels row:14 redraw:false

Platform: timer mark 15.989 0.185 overviewrender 16000 pixels row:14 redraw:false

Platform: timer mark 17.216 0.229 overviewrender 16000 pixels row:14 redraw:false

Platform: timer mark 18.148 0.239 overviewrender 16000 pixels row:14 redraw:false

Platform: timer mark 18.924 0.198 overviewrender 16000 pixels row:14 redraw:false

Platform: timer mark 21.827 0.233 overviewrender 16000 pixels row:14 redraw:false

JAL-3383 JAL-3253-applet

-- Adds FileStoreI interface

-- Makes FileStore.java abstract superclass for FileStoreImpl (for Java)

and FileStoreJS (for JavaScript)

-- Passing all FeatureStoreJSTest TestNG tests

-- Passing all SequenceFeatureTest TestNG tests

-- About 10% faster for Java on TestNG tests.

-- full rendering in < 250 ms for JavaScript -- this is approximately 15

times faster than before I started this experiment.

Platform: timer mark 13.396 0.209 overviewrender 16000 pixels row:14 redraw:false

Platform: timer mark 14.884 0.186 overviewrender 16000 pixels row:14 redraw:false

Platform: timer mark 15.989 0.185 overviewrender 16000 pixels row:14 redraw:false

Platform: timer mark 17.216 0.229 overviewrender 16000 pixels row:14 redraw:false

Platform: timer mark 18.148 0.239 overviewrender 16000 pixels row:14 redraw:false

Platform: timer mark 18.924 0.198 overviewrender 16000 pixels row:14 redraw:false

Platform: timer mark 21.827 0.233 overviewrender 16000 pixels row:14 redraw:false

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    /src/jalview/datamodel/features/FeatureStore.java
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    /src/jalview/datamodel/features/FeatureStoreI.java
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    /src/jalview/datamodel/features/FeatureStoreImpl.java
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    /src/jalview/datamodel/features/FeatureStoreJS.java
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    /test/jalview/datamodel/features/FeatureStoreJSTest.java
JavaDoc comments; minor code clean-up

adds comments JAL-3383

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    /src/jalview/datamodel/features/FeatureStore.java
JAL-3383 JAL-3253-applet additional efficiencies; FeatureStore alternative to IntervalStore

- implemented for JavaScript only (see SequenceFeatures):

boolean useIntervalStore = /**

* @j2sNative false &&

*/

true;

but can be tested in Java and JavaScript by changing either of those to

true/false.

- only requires storage for one sorted array in FeatureSorter:

private SequenceFeature[] orderedFeatureStarts;

and one additional linked-list field pointer in SequenceFeature:

SequenceFeature containedBy

- when running, the position is looked up in the begin-sorted feature

array, and then the containedBy links are simply traversed using:

SequenceFeature sf = findClosestFeature(orderedFeatureStarts, pos);

while (sf != null) {

if (sf.end >= pos)

{

result.add(sf);

}

sf = sf.containedBy;

}

- my preliminary timing tests suggest this is 2x faster than

IntervalStore in JavaScript.

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    /src/jalview/datamodel/Sequence.java
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    /src/jalview/datamodel/SequenceI.java
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    /src/jalview/datamodel/features/FeatureStore.java