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Merge branch 'bug/JAL-3806_mappingCoversSequence_for2112' into develop Combines patches for JAL-3806 prior to redaction of shared CDS dataset sequences with patches for JAL-3673 Conflicts: src/jalview/datamodel/AlignedCodonFrame.java src/jalview/util/MappingUtils.java test/jalview/util/MappingUtilsTest.java

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    /test/jalview/util/MappingUtilsTest.java
JAL-3806 JAL-3725 update tests since CDS mappings now exclude the stop codon

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    /test/jalview/io/EmblFlatFileTest.java
JAL-3806 require mapping extent covers both sequence’s dataset sequence to avoid spurious mappings from overlapping CDS

JAL-3949 upgraded log4j to 2.17.1 (no actual known vulnerabilities\!), though this doesn't fix the issue

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    /j11lib/log4j-1.2-api-2.17.1.jar
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    /j11lib/log4j-api-2.17.1.jar
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    /j11lib/log4j-core-2.17.1.jar
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    /j11lib/log4j-slf4j18-impl-2.17.0.jar
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    /j11lib/log4j-slf4j18-impl-2.17.1.jar
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    /j8lib/log4j-1.2-api-2.17.1.jar
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    /j8lib/log4j-api-2.17.1.jar
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    /j8lib/log4j-core-2.17.1.jar
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    /j8lib/log4j-slf4j18-impl-2.17.0.jar
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    /j8lib/log4j-slf4j18-impl-2.17.1.jar
JAL-3806 use the covers() test for each selected sequence and the complementary alignment’s sequence as a filter for direct CDS-Protein mappings (ensures overlapping CDS coding for distinct proteins do not all get selected)

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
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

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    /utils/install4j/jvl_file.icns
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    /utils/install4j/jvl_file.ico
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    /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 '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
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
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
JAL-3940 update 2.11.2 release notes for 2.11.1.7 patch release (again)

JAL-3940 update 2.11.2 release notes for 2.11.1.7 patch release

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 fix Gff3 shared InputStream with embedded FASTA data

close filehandles straight after parse, without setting an error

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

Merge branch 'critical/JAL-3933_log4j_update_for_develop_branch' into develop