jalview

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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-966 JAL-1854 removed redundant methods / modifiers from search result interface, corrected faulty toString

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    /src/jalview/datamodel/SearchResults.java
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    /test/jalview/analysis/FinderTest.java
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    /test/jalview/datamodel/MatchTest.java
JAL-2302 unit tests added for Finder

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    /test/jalview/analysis/FinderTest.java
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
JAL-2308 Fixed hiddenColsTest

JAL-2312 unit test for bug fix - repeated mapping generated from SIFTS when heuristic identification fails for some SIFTS entities

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    /test/jalview/io/3ucu.cif
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    /test/jalview/ws/sifts/SiftsClientTest.java
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

JAL-2312 Bug fix for repeated mapping generation from SIFTS when heuristic identification fails for some SIFTS entities

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    /src/jalview/ws/sifts/SiftsClient.java
JAL-2310 don't double-count sequence matches; code tidying

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    /src/jalview/analysis/Finder.java
JAL-2281 test added to show searchRefs is now not case sensitive

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    /test/jalview/util/DBRefUtilsTest.java
JAL-2281 Minor unit test addition

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    /test/jalview/util/DBRefUtilsTest.java
JAL-2295 step 1 new menu item to transfer Jalview attributes (no action yet)

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    /src/jalview/gui/ChimeraViewFrame.java
Merge remote-tracking branch 'origin/bug/JAL-2282' into develop

JAL-2281 Unit test updates

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    /test/jalview/util/DBRefUtilsTest.java
JAL-345 JAL-1738 menu item, AlignFrame action listener and documentation for Select->Select Highlighted Regions.

Accelerator key (CMD-L) doesn’t seem to work right now.

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    /src/jalview/jbgui/GAlignFrame.java
Merge remote-tracking branch 'origin/bug/JAL-2282' into develop

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    /src/jalview/appletgui/APopupMenu.java
JAL-1738 JAL-345 fix test - method appears to work

JAL-2301 table formatted, and corrected to match the diagram and code

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    /help/html/misc/aaproperties.html
JAL-1738 JAL-345 fix for JAL-2302 only report Matches that are not contained by the previous match.

JAL-1738 JAL-345 switch expected/observed in test

JAL-2281 Use DBRefs.selectRefs to uppercase URL link target

JAL-345 JAL-1738 fix test (still passes)