jalview

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JAL-3806 use same logic as for mouse over highlighting to work out extent of selected region in complement alignment

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    /src/jalview/util/MappingUtils.java
JAL-3806 todo - problem seems to be Protein:Many CDS are not selected

JAL-2305 comments re testFindXrefSequences_withFetch is failing - looks like test data needs to be revised for assumptions made by CrossRef about sequences retrieved from dbsources

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    /src/jalview/analysis/CrossRef.java
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    /test/jalview/analysis/CrossRefTest.java
JAL-3830 JAL-3420 added new jvl_file to install4j9 template

Merge branch 'develop' into improvement/JAL-3830_install4j9_macos_setup_application

Merge branch 'develop' into improvement/JAL-3420_match_jvl_icon_with_new_website_jvl_icon

new jvl_file svg, png, ico and icns files, and changed references to Jalview-Launch to jvl_file

    • binary
    /utils/install4j/jvl_file.icns
    • binary
    /utils/install4j/jvl_file.ico
    • binary
    /utils/install4j/jvl_file.png
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    /utils/install4j/jvl_file.svg
JAL-3137 tests are for linux only

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    /test/jalview/bin/HiDPISettingTest2.java
Merge branch 'merge/develop_JAL-3725' into develop

Conflicts:

src/jalview/gui/PopupMenu.java

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    /src/jalview/util/MappingUtils.java
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    /test/jalview/util/MapListTest.java
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    /test/jalview/util/MappingUtilsTest.java
Merge branch 'develop' into JAL-3416_different_look_and_feel_on_linux

update to flatlaf 2.0.1

    • binary
    /j11lib/flatlaf-2.0.1.jar
    • binary
    /j8lib/flatlaf-2.0.1.jar
Merge branch 'bug/JAL-3633_read_proxy_settings_from_jalview_properties_in_getdown' into develop

Conflicts:

src/jalview/bin/MemorySetting.java

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/bin/MemorySetting.java
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    /src/jalview/jbgui/GPreferences.java
Merge branch 'develop' into releases/Release_2_11_2_Branch

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 'develop' into releases/Release_2_11_2_Branch

JAL-3746 note about adding JAL-3700,JAL-3751,JAL-3763 release notes

Merge branch 'merge/develop_task/JAL-3763_newDatasetForCds' into develop

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