jalview

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Merge branch 'merge/develop_JAL-1260' into develop

JAL-1260 rudimentary parsing of LOCUS line to at least get accession id

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    /src/jalview/io/GenBankFile.java
JAL-3079 JAL-3055 remember to reset font transform after rendering logo

JAL-3779 Added to documentation

JAL-3774 combined changes from bug/JAL-3774_splitFrameFinder: i) fixed focus Finder from split frame. ii) missing i18n added, overlong translation shortened. iii) better translation.

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    /resources/lang/Messages_es.properties
JAL-3739 (combined) commits from feature/JAL-3739_useFormFieldText

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    /resources/lang/Messages_es.properties
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    /src/jalview/gui/OptsAndParamsPage.java
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    /src/jalview/gui/WsJobParameters.java
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    /src/jalview/ws/jws2/Jws2Client.java
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    /src/jalview/ws/jws2/MsaWSClient.java
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    /src/jalview/ws/jws2/dm/JabaOption.java
JAL-3761 listToArray became rangeListToArray

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    /test/jalview/util/MappingUtilsTest.java
JAL-3761 listToArray became rangeListToArray

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    /src/jalview/io/EmblFlatFile.java
JAL-3818 formatting

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    /src/jalview/ext/jmol/JalviewJmolBinding.java
Merge branch 'develop' into merge/develop_ben2

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

JAL-3829 Fixed Jmol jar -- duplicates of other classes were causing problem with shadow jar

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    /j11lib/Jmol-14.31.53-dedup.jar
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    /j8lib/Jmol-14.31.53-dedup.jar
Merge branch 'Jalview-JS/bug/JAL-3762_URLparamsOverrideInfoArg' into develop

Merge branch 'develop' into merge/develop_ben2

Merge branch 'features/r2_11_2/JAL-3829_3dbeacons' into develop

JAL-3829 parallel not welcome here

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    /test/jalview/gui/StructureChooserTest.java
JAL-3829 test flakiness and human flakiness

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    /test/jalview/gui/StructureChooserTest.java
JAL-3829 more info on test fail - seems to be flaky

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    /test/jalview/gui/StructureChooserTest.java
Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

Merge branch 'features/r2_11_2/JAL-3829_3dbeacons' into develop

JAL-3551 - doc tweak

JAL-3855 JAL-3829 better checks on PDB or mmCIF file based on URL path (though should really determine when processing via jmolData now we have mechanism) - ChimeraX in particular cares about file endings

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    /src/jalview/gui/StructureViewerBase.java
JAL-3829 JAL-3855 moved routing for retrieving structures prior to opening a Jmol view to AppJmolBinding - this could be refactored further

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    /src/jalview/gui/AppJmolBinding.java
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    /src/jalview/gui/StructureViewerBase.java
JAL-3829 JAL-3855 ignore case when detecting alphafold ID

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    /src/jalview/ws/dbsources/EBIAlfaFold.java
JAL-3855 detect an alphafold model and import its temperature factor as reliability

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    /src/jalview/ext/jmol/JmolParser.java
JAL-3829 move mock query and responses to files

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    /src/jalview/fts/service/pdb/PDBFTSRestClient.java
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    /test/jalview/gui/StructureChooserTest.java
JAL-2422 Also look in ~/Applications for ChimeraX on macOS

Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons

Merge branch 'feature/JAL-2422ChimeraX' into develop

JAL-3829 3d-beacons doesn’t work as a sequence source just now