jalview

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

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Friday 04 Feb
2:34 pm

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

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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    • -12
    • +64
    /src/jalview/datamodel/AlignedCodonFrame.java
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    /src/jalview/util/MappingUtils.java
    • -10
    • +0
    /test/jalview/util/MappingUtilsTest.java
1:19 pm

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

JAL-3806 JAL-3725 update tests since CDS mappings now exclude the stop codon

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    • -5
    • +5
    /test/jalview/io/EmblFlatFileTest.java
    • -1
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    /test/jalview/io/GenBankFileTest.java
1:13 pm

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

JAL-3806 require mapping extent covers both sequence’s dataset sequence to avoid spurious mappings from overlapping CDS

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    • -3
    • +5
    /src/jalview/datamodel/AlignedCodonFrame.java
    • -0
    • +2
    /src/jalview/util/MappingUtils.java
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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    • binary
    /j11lib/log4j-1.2-api-2.17.0.jar
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    /j11lib/log4j-1.2-api-2.17.1.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
    • binary
    /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-api-2.17.0.jar
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    /j8lib/log4j-api-2.17.1.jar
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    /j8lib/log4j-core-2.17.0.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
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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    • -4
    • +5
    /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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    • -44
    • +39
    /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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    • +1
    /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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    • +6
    /test/jalview/analysis/CrossRefTest.java
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-install4j8.xml
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    /utils/install4j/install4j8_template.install4j
    • binary
    /utils/install4j/jvl_file.icns
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    /utils/install4j/jvl_file.png
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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
    • -25
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    /test/jalview/util/MappingUtilsTest.java
Thursday 27 Jan
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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    /gradle.properties
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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/bin/Launcher.java
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    /src/jalview/bin/MemorySetting.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>

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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    • -1
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    /test/jalview/bin/CommandLineOperations.java
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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    • +1
    /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/util/MappingUtils.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
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
Monday 17 Jan
12:36 pm

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

JAL-3940 update 2.11.2 release notes for 2.11.1.7 patch release

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    /help/help/html/releases.html
11:54 am

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

JAL-3746 possible release date 1st Feb 2022

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    /help/help/html/releases.html
11:54 am

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

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

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    /help/help/html/releases.html
11:45 am

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

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

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Wednesday 12 Jan
12:32 pm

Ben Soares

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

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    /test/jalview/io/BackupFilesTest.java
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    /test/jalview/io/WindowsFileLoadAndSaveTest.java
Tuesday 11 Jan
8:13 pm

Ben Soares

JAL-3703 fix Gff3 shared InputStream with embedded FASTA data

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    /src/jalview/io/AlignFile.java
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    /src/jalview/io/FastaFile.java
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    /src/jalview/io/FeaturesFile.java
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    /src/jalview/io/FileParse.java
4:04 pm

Ben Soares

close filehandles straight after parse, without setting an error

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    /src/jalview/io/AlignFile.java
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    /src/jalview/project/Jalview2XML.java
Monday 10 Jan
8:31 pm

Ben Soares

JAL-3937 enable AIA download of intermediate certificates when needed

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    /src/jalview/bin/Jalview.java
Thursday 06 Jan
12:29 pm

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

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

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    /src/jalview/io/EMBLLikeFlatFile.java
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    /test/jalview/io/EmblFlatFileTest.java
9:58 am

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

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

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    /help/help/html/releases.html
9:47 am

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

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

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