jalview

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JAL-2309 Made test timeout slightly longer

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    /test/jalview/bin/CommandLineOperations.java
JAL-2309 Adjusted timeout on headless tests

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    /test/jalview/bin/CommandLineOperations.java
JAL-2292 updated method calls

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    /src/jalview/ws/sifts/SiftsClient.java
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

JAL-2292 renamed method and improved implementation as suggested by Kira

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    /test/jalview/util/ComparisonTest.java
JAL-1270 renamed helper method so it is not run as a test

JAL-2272 another test case

JAL-1805 groups=Functional added where missing

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    /test/jalview/ext/htsjdk/TestHtsContigDb.java
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    /test/jalview/io/PfamFormatInputTest.java
JAL-2272 unit tests added for Platform.isControlDown

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    /test/jalview/util/PlatformTest.java
JAL-2318 updated help text

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    /help/html/colourSchemes/abovePID.html
JAL-2282 show url links that need checked; remove 'www' from default

Merge remote-tracking branch 'origin/bug/JAL-2282' into develop

JAL-2315 Clear sequenceURLLinks if all sequence links are removed.

JAL-2292 squashed bug that breaks feature mapping for different cased residues

JAL-2292 added javadoc for compareChar(..) utility method

Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

JAL-2195 JAL-2262 house keeping

JAL-2292 fix for wrong mapping output in sequence mapping output window where sequence residue has different case with structure residue

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    /src/jalview/ws/sifts/SiftsClient.java
JAL-2292 Wrote utility method for comparing two char either case sensitively or insensitively

JAL-2292 Unit test for utility method for comparing two chars

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    /test/jalview/util/ComparisonTest.java
Merge remote-tracking branch 'origin/bug/JAL-2282' into develop

JAL-2282 Better check for existing url links

JAL-2272 right mouse button on Mac is not Cmd equivalent!

JAL-2282 Remove Cache dependency from applet

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    /src/jalview/appletgui/APopupMenu.java
JAL-2282 Message box stays on top at Jalview open; checks for links before deciding whether to display.

JAL-2282 Link menu disabled if there are no valid links

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    /src/jalview/appletgui/APopupMenu.java
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    /test/jalview/gui/PopupMenuTest.java
JAL-2282 Updated warn.url_must_contain

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    /resources/lang/Messages_es.properties
JAL-2282 If checkbox on warning dialog is unclicked, reset cache settings for checking url links.

JAL-2281 Back out unit test update, as Mungo already added.

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    /test/jalview/util/DBRefUtilsTest.java
Merge remote-tracking branch 'origin/develop' into bug/JAL-2282

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    /test/jalview/util/DBRefUtilsTest.java