jalview

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JAL-3210 improved gradle jalviewjsServerStart

JAL-3210 gradle jalviewjsServer now working. Up to date src and swingjs from Jalview-JS/...applet branch. Transpiles and launches.

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    /resources/lang/Messages.properties
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JAL-3210 cleaning up dependencies in build.gradle and added a [not currently working] HTTP server for localhost

JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from the applet branch. AND IT WORKS (sometimes)

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    /src/com/stevesoft/pat/RegexReader.java
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    /src/ext/vamsas/JpredSoapBindingStub.java
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JAL-3210 create a site.tar.gz. Some improvement to eclipse-workspace handling

JAL-3210 Now includes creating the .project, .classpath and .settings as a depenedency

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

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    /.externalToolBuilders/Jalview Release 2.7 build.xml [Builder].launch
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    /.externalToolBuilders/Jalview Release indices [Builder].launch
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Merge branch 'Jalview-JS/jim/JAL-3253-JAL-3418' into Jalview-JS/JAL-3253-applet

JAL-3235 -Dtestng-verbosity=10 to trace execution of TestNG tests

JAL-3253 fix scrollTo termination check.

JAL-3418 debug testng execution - verbosity=10

Merge branch 'Jalview-JS/JAL-3253-applet' of https://source.jalview.org/git/jalview.git into Jalview-JS/JAL-3253-applet

JAL-3253-applet JAL-3414 Display Settings dialog slow to open

SwingJS-site.zip

corrects code in JSDialog that called parent.addNotify() every time, not

just before it has been connected.

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    /swingjs/ver/3.2.4/SwingJS-site.zip
JAL-3253-applet JAL-3397 delete fix

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JAL-3253-applet JAL-3397 JAL-3383 fast IntervalStore for JavaScript

fully commented and cleaned code

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    /src/jalview/datamodel/features/FeatureStoreJS.java
JAL-3253-applet JAL-3397 JAL-3383 fast IntervalStore for JavaScript

needs testing in JavaScript

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    /src/intervalstore/api/IntervalI.java
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    /src/jalview/datamodel/features/FeatureStoreJS.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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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-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/jalview/datamodel/features/FeatureStoreJS.java
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JAL-3253-applet comments/Overrides only

JAL-3383 JAL-3253-applet

-adds timing test reports.

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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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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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JavaDoc comments; minor code clean-up

adds comments JAL-3383

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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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