jalview

Conflicts:

resources/lang/Messages.properties

resources/lang/Messages_es.properties

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

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

-- 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.

-- 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

-- 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

- 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.