jalview

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Commits this week: 4
Total Committers: 73
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Commits this week: 4

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Thursday 03 Feb
7:38 pm

Ben Soares

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-2.17.0.jar
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    /j11lib/log4j-api-2.17.0.jar
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    /j11lib/log4j-api-2.17.1.jar
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    /j11lib/log4j-core-2.17.0.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-2.17.0.jar
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    /j8lib/log4j-1.2-api-2.17.1.jar
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    /j8lib/log4j-core-2.17.0.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
2:59 pm

Jim Procter <j.procter@dundee.ac.uk>

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)

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    /src/jalview/util/MappingUtils.java
2:20 pm

Jim Procter <j.procter@dundee.ac.uk>

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
1:41 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3806 todo - problem seems to be Protein:Many CDS are not selected

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    /src/jalview/util/MappingUtils.java
1:18 pm

Jim Procter <j.procter@dundee.ac.uk>

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
Saturday 29 Jan
1:00 am

Ben Soares

JAL-3830 JAL-3420 added new jvl_file to install4j9 template

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    /utils/install4j/install4j9_template.install4j
12:57 am

Ben Soares

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

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    /build.gradle
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    /gradle.properties
Friday 28 Jan
6:22 pm

Ben Soares

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

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6:22 pm

Ben Soares

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

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    /utils/install4j/auto_file_associations-i4j8.pl
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    /utils/install4j/file_associations_auto-Info_plist.xml
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    /utils/install4j/file_associations_auto-install4j8.xml
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    /utils/install4j/install4j8_template.install4j
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    /utils/install4j/jvl_file.svg
5:24 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3137 tests are for linux only

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    /test/jalview/bin/HiDPISettingTest2.java
5:08 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'merge/develop_JAL-3725' into develop

Conflicts:

src/jalview/gui/PopupMenu.java

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    /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
4:57 pm

Ben Soares

Merge branch 'develop' into JAL-3416_different_look_and_feel_on_linux

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    /src/jalview/bin/Jalview.java
Thursday 27 Jan
6:35 pm

Ben Soares

update to flatlaf 2.0.1

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2:21 pm

Jim Procter <j.procter@dundee.ac.uk>

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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    /build.gradle
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    /resources/lang/Messages.properties
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    /src/jalview/bin/Launcher.java
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    /src/jalview/gui/Preferences.java
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    /src/jalview/jbgui/GPreferences.java
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    /src/jalview/util/StringUtils.java
Wednesday 26 Jan
11:41 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'develop' into releases/Release_2_11_2_Branch

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11:41 pm

Jim Procter <j.procter@dundee.ac.uk>

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
11:33 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'develop' into releases/Release_2_11_2_Branch

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11:32 pm

Jim Procter <j.procter@dundee.ac.uk>

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

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    /help/help/html/releases.html
11:26 pm

Jim Procter <j.procter@dundee.ac.uk>

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

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7:54 pm

Jim Procter <j.procter@dundee.ac.uk>

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
7:36 pm

Jim Procter <j.procter@dundee.ac.uk>

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/gui/PopupMenu.java
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    /src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
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    /test/jalview/util/MapListTest.java
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    /test/jalview/util/MappingUtilsTest.java
6:34 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'develop' into releases/Release_2_11_2_Branch

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6:32 pm

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'releases/Release_2_11_1_Branch'

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Wednesday 19 Jan
1:45 pm

Mateusz Warowny

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/slivka/SlivkaWSDiscoverer.java
Tuesday 18 Jan
12:24 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3940 update 2.11.2 release notes for 2.11.1.7 patch release (again)

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    /help/help/html/releases.html
11:44 am

Jim Procter <j.procter@dundee.ac.uk>

JAL-3940 errant heading in release notes..

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    /help/help/html/releases.html
8:14 am

Jim Procter <j.procter@dundee.ac.uk>

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

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Monday 17 Jan
12:50 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3703 patch Windows save file test for 2.11.1 codebase

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    /test/jalview/io/WindowsFileLoadAndSaveTest.java
12:39 pm

Jim Procter <j.procter@dundee.ac.uk>

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

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12:38 pm

Jim Procter <j.procter@dundee.ac.uk>

JAL-3940 fix issues in release notes

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    /help/help/html/releases.html