jalview

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JAL-2424 final contig now an inclusive range

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    /src/jalview/datamodel/AlignmentView.java
JAL-2295 Spanish translations for superposition / errors

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    /resources/lang/Messages_es.properties
JAL-2295 Spanish translations added

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    /resources/lang/Messages_es.properties
JAL-2361 Spanish text added

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    /resources/lang/Messages_es.properties
JAL-2485 Bug fix to filter out uniprot response header row by excluding the first row

JAL-2482 added null check

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    /src/jalview/ws/sifts/SiftsClient.java
JAL-2482 Bugfix

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    /src/jalview/ws/sifts/SiftsClient.java
JAL-2361 tweak layout of warning message

Merge branch 'bug/JAL-2255_seq-fetcher-broken-on-linux' into develop

JAL-2255 Bug fix

Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

JAL-2361 option to save on OK of changed named colour scheme

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    /src/jalview/gui/UserDefinedColours.java
JAL-2361 make a modified saved scheme the backout checkpoint for Cancel

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    /src/jalview/gui/UserDefinedColours.java
JAL-2384 JAL-2371 update ResidueShader on change of colour by conservation / pid

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    /src/jalview/appletgui/AlignFrame.java
JAL-2361 simplify constructors, select unsaved but applied user defined colour scheme in menu

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    /src/jalview/gui/ColourMenuHelper.java
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    /src/jalview/gui/UserDefinedColours.java
JAL-2361 apply any saved changes to current colour scheme

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    /src/jalview/gui/ColourMenuHelper.java
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    /src/jalview/gui/UserDefinedColours.java
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    /src/jalview/jbgui/GUserDefinedColours.java
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    /src/jalview/schemes/ColourSchemes.java
JAL-2314 made non-test method non-public

Merge branch 'develop' into bug/JAL-2314

Merge branch 'develop' into bug/JAL-2461

JAL-2405 additional checks for circular reference in context or dataset

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    /src/jalview/datamodel/SequenceGroup.java
JAL-2472 PrivilegedAccessor added

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    /test/junit/extensions/PA.java
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    /test/junit/extensions/PrivilegedAccessor.java
Merge branch 'develop' into bug/JAL-2431splitFrameNewView

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/AlignmentPanel.java
JAL-2430 code tidy, unit test for Jmol hidden column colours

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    /src/jalview/ext/jmol/JmolCommands.java
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    /test/jalview/ext/jmol/JmolCommandsTest.java
Merge branch 'develop' into bug/JAL-1608createGroups

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    /resources/lang/Messages_es.properties
JAL-1608 leave Create Group, Remove Group menu items enabled

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    /src/jalview/jbgui/GAlignFrame.java
JAL-2401 code and help tidy for review comments

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    /src/jalview/gui/UserDefinedColours.java
JAL-2401 don't apply lower case colour to upper case

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    /src/jalview/gui/UserDefinedColours.java
Merge branch 'develop' into bug/JAL-2399textColour

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
JAL-2346 JAL-1933 test updated to include Occupancy

JAL-2346 always run setup!