jalview

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JAL-3521 working minimal build.gradle for debian and 2.11.2. Flexmark plugin might be a problem

JAL-3521 not quite working minimal build.gradle for debian and 2.11.2

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    /utils/debian/debian_build.gradle
JAL-3829 do better at detecting structure type, prompt to retrieve Uniprot ids for proteins without canonical Ids and show provider in the Structure Chooser’s cache view

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    /resources/fts/tdbeacons_data_columns.txt
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    /src/jalview/gui/StructureChooser.java
JAL-3829 make sure structure data type reflects actual format identified

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    /src/jalview/ext/jmol/JmolParser.java
JAL-3829 store 3db metadata on PDBEntry so it can be shown in Cache/etc

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    /src/jalview/datamodel/PDBEntry.java
JAL-3829 allow PDBEntry with file and ID with mismatching case to override one without a file

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    /src/jalview/datamodel/PDBEntry.java
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    /test/jalview/datamodel/PDBEntryTest.java
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-1260 rudimentary parsing of LOCUS line to at least get accession id

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    /src/jalview/io/GenBankFile.java
Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons

JAL-3079 JAL-3055 remember to reset font transform after rendering logo

JAL-3874 - replace Jmol with custom build of 14.31.53 from Jmol-SwingJS GitHub repo

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    /j11lib/Jmol-14.31.53-dedup.jar
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    /j11lib/Jmol-14.31.53.jar
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    /j8lib/Jmol-14.31.53-dedup.jar
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    /j8lib/Jmol-14.31.53.jar
JAL-2226 transfer chain annotation when calcId, label and description are distinct - so annotations from multiple chains and structures are all shown.

JAL-2226 new method to search for annotation matching particular description as well as calcId and label

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    /src/jalview/datamodel/Sequence.java
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    /src/jalview/datamodel/SequenceI.java
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    /test/jalview/datamodel/SequenceTest.java
JAL-3874 attempt to add source jars to eclipse through buildship

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    /j11sources/Jmol-14.31.53-sources.jar
JAL-3829 belt and braces check to make sure there is a pdbe response available to join records from

JAL-3779 Added to documentation

JAL-3871 replaced Jmol with zip -F version fo Jmol and added excludeDuplicates flags to build.gradle

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    /j11lib/Jmol-14.31.53-dedup.jar
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    /j11lib/Jmol-14.31.53.jar
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    /j8lib/Jmol-14.31.53-dedup.jar
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    /j8lib/Jmol-14.31.53.jar
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
Merge branch 'develop' into doc/JAL-3746_Release_2_11_2

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

JAL-3746 fix bad merge from 2.11.1.4/5 branch cherrypick

JAL-3842 fix automatic what's new link for custom version builds