jalview

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JAL-3763 (for whatever reason) need to increase timeout for command line ops to 10.5s (OSX Monterey, MBP late 2018)

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    /test/jalview/bin/CommandLineOperations.java
Merge branch 'task/JAL-3763_newDatasetForCds' into merge/develop_task/JAL-3763_newDatasetForCds

Conflicts:

src/jalview/analysis/AlignmentUtils.java

src/jalview/util/MapList.java

test/jalview/util/MapListTest.java

test/jalview/util/MappingUtilsTest.java

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    /src/jalview/analysis/AlignmentUtils.java
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    /src/jalview/datamodel/SearchResults.java
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    /src/jalview/util/MappingUtils.java
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    /test/jalview/util/MappingUtilsTest.java
Merge branch 'develop' into releases/Release_2_11_2_Branch

Merge branch 'releases/Release_2_11_1_Branch'

JAL-3878 Move listeners list from the WebServiceDiscoverer interface.

Listeners list defined in the interface was globally shared

among all discoverer instances. Listeners should be kept by

the discoverer instance instead.

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    /src/jalview/ws2/OperationsChangeListenerList.java
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    /src/jalview/ws2/WebServiceDiscovererI.java
JAL-3940 update 2.11.2 release notes for 2.11.1.7 patch release (again)

JAL-3940 errant heading in release notes..

Merge branch 'patch/r2_11_1_branch_JAL-3703_closing_files' into releases/Release_2_11_1_Branch

JAL-3703 patch Windows save file test for 2.11.1 codebase

Merge branch 'patch/r2_11_1_branch_JAL-3703_closing_files' into releases/Release_2_11_1_Branch

JAL-3940 fix issues in release notes

JAL-3940 update 2.11.2 release notes for 2.11.1.7 patch release

JAL-3940 bump version and update release notes - release set for Tuesday 18th January 2022

JAL-3940 update release notes for JAL-3702,JAL-3935 in 2.11.1.7 release

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3746 possible release date 1st Feb 2022

JAL-3746 Release notes for patch JAL-3702 JAL-3915

Merge branch 'bug/JAL-3703_saving_a_file_in_Windows_10_fails' into develop

JAL-3703 Test that fails in Windows only, and only when the file handle isn't relinquished

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    /test/jalview/io/WindowsFileLoadAndSaveTest.java
JAL-3703 Test that fails in Windows only, and only when the file handle isn't relinquished

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    /test/jalview/io/WindowsFileLoadAndSaveTest.java
JAL-3703 fix Gff3 shared InputStream with embedded FASTA data

JAL-3703 fix Gff3 shared InputStream with embedded FASTA data

close filehandles straight after parse, without setting an error

Conflicts:

src/jalview/project/Jalview2XML.java

(locale aware PDBID string compare)

close filehandles straight after parse, without setting an error

JAL-3937 update releases.html

JAL-3937 enable AIA download of intermediate certificates when needed

JAL-3937 enable AIA download of intermediate certificates when needed

JAL-3806 JAL-3725 propagate relaxed criteria for stop codon truncation from EMBLXmlSource to EMBLFlatFile parser

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    /test/jalview/io/EmblFlatFileTest.java
Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3746 update release history for 2.11.1.5 and 2.11.1.6 patch releases