jalview

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JAL-2309 Adjusted timeout on headless tests

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    /test/jalview/bin/CommandLineOperations.java
JAL-2295 extracted AtomSpecModel for reuse in Chimera commands

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    /src/jalview/ext/rbvi/chimera/AtomSpecModel.java
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    /src/jalview/ext/rbvi/chimera/ChimeraCommands.java
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    /test/jalview/ext/rbvi/chimera/AtomSpecModelTest.java
JAL-2295 make RangeComparator a top level class for reuse

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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/ext/ensembl/EnsemblSeqProxy.java
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    /src/jalview/util/RangeComparator.java
JAL-2280 Updated spanish translation as recommended by Juan

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    /resources/lang/Messages_es.properties
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
Merge branch 'develop' into features/JAL-2295setChimeraAttributes

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

JAL-2295 handle no progress bar message properly

JAL-2295 small tidy of javadoc only

JAL-2295 (unoptimised) write Jalview features as Chimera attributes

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    /src/jalview/gui/ChimeraViewFrame.java
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